Bio


Dr. Witte joined the Stanford community in July 2021. In addition to serving as Vice Chair and professor in the Department of Epidemiology & Population Health, and as a professor of Biomedical Data Science and, by courtesy, of Genetics, he will also serve as a member of the Stanford Cancer Institute.

Dr. Witte is an internationally recognized expert in genetic epidemiology. His scholarly contributions include deciphering the genetic and environmental basis of prostate cancer and developing widely used methods for the genetic epidemiologic study of disease. His prostate cancer work has used comprehensive genome-wide studies of germline genetics, transcriptomics, and somatic genomics to successfully detect novel variants underlying the risk and aggressiveness of this common disease. A key aspect of this work has been distinguishing genetic factors that may drive increased prostate cancer risk and mortality among African American men. Providing an avenue to determine which men are more likely to be diagnosed with clinically relevant prostate cancer and require additional screening or specific treatment can help reduce disparities in disease prevalence and outcomes across populations. Dr. Witte has also developed novel hierarchical and polygenic risk score modeling for undertaking genetic epidemiology studies. These advances significantly improve our ability to detect disease-causing genes and to translate genetic epidemiologic findings into medical practice.

Dr. Witte has received the Leadership Award from the International Genetic Epidemiology Society (highest award), and the Stephen B. Hulley Award for Excellence in Teaching. His extensive teaching portfolio includes a series of courses in genetic and molecular epidemiology. He has mentored over 50 graduate students and postdoctoral fellows, serves on the executive committees of multiple graduate programs, and has directed a National Institutes of Health funded post-doctoral training program in genetic epidemiology for over 20 years. Recently appointed to the National Cancer Institute Board of Scientific Counselors, Dr. Witte has been continuously supported by the National Institutes of Health.

Academic Appointments


Honors & Awards


  • Undergraduate Honors, University of California, Santa Barbara (1986)
  • Ruth F. Richards Outstanding Student Award, University of California, Los Angeles (1994)
  • Glennan Fellow Award for Innovative Teaching, CWRU Center for Innovation in Teaching and Education (2000)
  • Visiting Scientist Award, International Agency for Research on Cancer, Lyon, France (2003)
  • Directors Invited Lecture, NHGRI / NIH (2010)
  • Stephen B. Hulley Award for Excellence in Teaching, University of California, San Francisco (2011)
  • Up for a Challenge Grand Prize, National Cancer Institute (2016)
  • Robert Millikan Symposium Memorial Lecture, University of North Carolina Lineberger Comprehensive Cancer Center (2017)
  • Leadership Award, International Genetic Epidemiology Society (2018)

Boards, Advisory Committees, Professional Organizations


  • Reviewer, Promotion and Tenure reviews external Institutions (2004 - Present)
  • Member, External Advisory Board, Post-GWA, Studies in Testicular Germ Cell Tumors (2013 - Present)
  • Member, NIH Board of Scientific Counselors – Clinical Sciences and Epidemiology (2020 - Present)
  • Member, Data Science and Population Research Cores, Norris Comprehensive Cancer Center, USC, External Advisory Committee (2020 - Present)

Professional Education


  • PhD, University of California, Los Angeles, Epidemiology (1994)
  • MS, University of California, Berkeley, Industrial Engineering & Operations Research (1988)
  • BS, University of California, Santa Barbara, Mathematical Sciences (1986)

Patents


  • John Witte. "United States Patent 62/896,457 METHODS, COMPOSITIONS, AND SYSTEMS FOR PROFILING OR PREDICTING IMMUNE RESPONSE"

2021-22 Courses


Stanford Advisees


All Publications


  • Discovery and fine-mapping of height loci via high-density imputation of GWASs in individuals of African ancestry. American journal of human genetics Graff, M., Justice, A. E., Young, K. L., Marouli, E., Zhang, X., Fine, R. S., Lim, E., Buchanan, V., Rand, K., Feitosa, M. F., Wojczynski, M. K., Yanek, L. R., Shao, Y., Rohde, R., Adeyemo, A. A., Aldrich, M. C., Allison, M. A., Ambrosone, C. B., Ambs, S., Amos, C., Arnett, D. K., Atwood, L., Bandera, E. V., Bartz, T., Becker, D. M., Berndt, S. I., Bernstein, L., Bielak, L. F., Blot, W. J., Bottinger, E. P., Bowden, D. W., Bradfield, J. P., Brody, J. A., Broeckel, U., Burke, G., Cade, B. E., Cai, Q., Caporaso, N., Carlson, C., Carpten, J., Casey, G., Chanock, S. J., Chen, G., Chen, M., Chen, Y. I., Chen, W., Chesi, A., Chiang, C. W., Chu, L., Coetzee, G. A., Conti, D. V., Cooper, R. S., Cushman, M., Demerath, E., Deming, S. L., Dimitrov, L., Ding, J., Diver, W. R., Duan, Q., Evans, M. K., Falusi, A. G., Faul, J. D., Fornage, M., Fox, C., Freedman, B. I., Garcia, M., Gillanders, E. M., Goodman, P., Gottesman, O., Grant, S. F., Guo, X., Hakonarson, H., Haritunians, T., Harris, T. B., Harris, C. C., Henderson, B. E., Hennis, A., Hernandez, D. G., Hirschhorn, J. N., McNeill, L. H., Howard, T. D., Howard, B., Hsing, A. W., Hsu, Y. H., Hu, J. J., Huff, C. D., Huo, D., Ingles, S. A., Irvin, M. R., John, E. M., Johnson, K. C., Jordan, J. M., Kabagambe, E. K., Kang, S. J., Kardia, S. L., Keating, B. J., Kittles, R. A., Klein, E. A., Kolb, S., Kolonel, L. N., Kooperberg, C., Kuller, L., Kutlar, A., Lange, L., Langefeld, C. D., Le Marchand, L., Leonard, H., Lettre, G., Levin, A. M., Li, Y., Li, J., Liu, Y., Liu, Y., Liu, S., Lohman, K., Lotay, V., Lu, Y., Maixner, W., Manson, J. E., McKnight, B., Meng, Y., Monda, K. L., Monroe, K., Moore, J. H., Mosley, T. H., Mudgal, P., Murphy, A. B., Nadukuru, R., Nalls, M. A., Nathanson, K. L., Nayak, U., N'Diaye, A., Nemesure, B., Neslund-Dudas, C., Neuhouser, M. L., Nyante, S., Ochs-Balcom, H., Ogundiran, T. O., Ogunniyi, A., Ojengbede, O., Okut, H., Olopade, O. I., Olshan, A., Padhukasahasram, B., Palmer, J., Palmer, C. D., Palmer, N. D., Papanicolaou, G., Patel, S. R., Pettaway, C. A., Peyser, P. A., Press, M. F., Rao, D. C., Rasmussen-Torvik, L. J., Redline, S., Reiner, A. P., Rhie, S. K., Rodriguez-Gil, J. L., Rotimi, C. N., Rotter, J. I., Ruiz-Narvaez, E. A., Rybicki, B. A., Salako, B., Sale, M. M., Sanderson, M., Schadt, E., Schreiner, P. J., Schurmann, C., Schwartz, A. G., Shriner, D. A., Signorello, L. B., Singleton, A. B., Siscovick, D. S., Smith, J. A., Smith, S., Speliotes, E., Spitz, M., Stanford, J. L., Stevens, V. L., Stram, A., Strom, S. S., Sucheston, L., Sun, Y. V., Tajuddin, S. M., Taylor, H., Taylor, K., Tayo, B. O., Thun, M. J., Tucker, M. A., Vaidya, D., Van Den Berg, D. J., Vedantam, S., Vitolins, M., Wang, Z., Ware, E. B., Wassertheil-Smoller, S., Weir, D. R., Wiencke, J. K., Williams, S. M., Williams, L. K., Wilson, J. G., Witte, J. S., Wrensch, M., Wu, X., Yao, J., Zakai, N., Zanetti, K., Zemel, B. S., Zhao, W., Zhao, J. H., Zheng, W., Zhi, D., Zhou, J., Zhu, X., Ziegler, R. G., Zmuda, J., Zonderman, A. B., Psaty, B. M., Borecki, I. B., Cupples, L. A., Liu, C., Haiman, C. A., Loos, R., Ng, M. C., North, K. E. 2021

    Abstract

    Although many loci have been associated with height in European ancestry populations, very few have been identified in African ancestry individuals. Furthermore, many of the known loci have yet to be generalized to and fine-mapped within a large-scale African ancestry sample. We performed sex-combined and sex-stratified meta-analyses in up to 52,764 individuals with height and genome-wide genotyping data from the African Ancestry Anthropometry Genetics Consortium (AAAGC). We additionally combined our African ancestry meta-analysis results with published European genome-wide association study (GWAS) data. In the African ancestry analyses, we identified three novel loci (SLC4A3, NCOA2, ECD/FAM149B1) in sex-combined results and two loci (CRB1, KLF6) in women only. In the African plus European sex-combined GWAS, we identified an additional three novel loci (RCCD1, G6PC3, CEP95) which were equally driven by AAAGC and European results. Among 39 genome-wide significant signals at known loci, conditioning index SNPs from European studies identified 20 secondary signals. Two of the 20 new secondary signals and none of the 8 novel loci had minor allele frequencies (MAF) < 5%. Of 802 known European height signals, 643 displayed directionally consistent associations with height, of which 205 were nominally significant (p < 0.05) in the African ancestry sex-combined sample. Furthermore, 148 of 241 loci contained ≤20 variants in the credible sets that jointly account for 99% of the posterior probability of driving the associations. In summary, trans-ethnic meta-analyses revealed novel signals and further improved fine-mapping of putative causal variants in loci shared between African and European ancestry populations.

    View details for DOI 10.1016/j.ajhg.2021.02.011

    View details for PubMedID 33713608

  • Cell-free DNA concentration and fragment size as a biomarker for prostate cancer. Scientific reports Chen, E., Cario, C. L., Leong, L., Lopez, K., Marquez, C. P., Chu, C., Li, P. S., Oropeza, E., Tenggara, I., Cowan, J., Simko, J. P., Chan, J. M., Friedlander, T., Wyatt, A. W., Aggarwal, R., Paris, P. L., Carroll, P. R., Feng, F., Witte, J. S. 2021; 11 (1): 5040

    Abstract

    Prostate cancer is the most commonly diagnosed neoplasm in American men. Although existing biomarkers may detect localized prostate cancer, additional strategies are necessary for improving detection and identifying aggressive disease that may require further intervention. One promising, minimally invasive biomarker is cell-free DNA (cfDNA), which consist of short DNA fragments released into circulation by dying or lysed cells that may reflect underlying cancer. Here we investigated whether differences in cfDNA concentration and cfDNA fragment size could improve the sensitivity for detecting more advanced and aggressive prostate cancer. This study included 268 individuals: 34 healthy controls, 112 men with localized prostate cancer who underwent radical prostatectomy (RP), and 122 men with metastatic castration-resistant prostate cancer (mCRPC). Plasma cfDNA concentration and fragment size were quantified with the Qubit 3.0 and the 2100 Bioanalyzer. The potential relationship between cfDNA concentration or fragment size and localized or mCRPC prostate cancer was evaluated with descriptive statistics, logistic regression, and area under the curve analysis with cross-validation. Plasma cfDNA concentrations were elevated in mCRPC patients in comparison to localized disease (OR5ng/mL=1.34, P=0.027) or to being a control (OR5ng/mL=1.69, P=0.034). Decreased average fragment size was associated with an increased risk of localized disease compared to controls (OR5bp=0.77, P=0.0008). This study suggests that while cfDNA concentration can identify mCRPC patients, it is unable to distinguish between healthy individuals and patients with localized prostate cancer. In addition to PSA, average cfDNA fragment size may be an alternative that can differentiate between healthy individuals and those with localized disease, but the low sensitivity and specificity results in an imperfect diagnostic marker. While quantification of cfDNA may provide a quick, cost-effective approach to help guide treatment decisions in advanced disease, its use is limited in the setting of localized prostate cancer.

    View details for DOI 10.1038/s41598-021-84507-z

    View details for PubMedID 33658587

  • Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction. Nature genetics Conti, D. V., Darst, B. F., Moss, L. C., Saunders, E. J., Sheng, X., Chou, A., Schumacher, F. R., Olama, A. A., Benlloch, S., Dadaev, T., Brook, M. N., Sahimi, A., Hoffmann, T. J., Takahashi, A., Matsuda, K., Momozawa, Y., Fujita, M., Muir, K., Lophatananon, A., Wan, P., Le Marchand, L., Wilkens, L. R., Stevens, V. L., Gapstur, S. M., Carter, B. D., Schleutker, J., Tammela, T. L., Sipeky, C., Auvinen, A., Giles, G. G., Southey, M. C., MacInnis, R. J., Cybulski, C., Wokolorczyk, D., Lubinski, J., Neal, D. E., Donovan, J. L., Hamdy, F. C., Martin, R. M., Nordestgaard, B. G., Nielsen, S. F., Weischer, M., Bojesen, S. E., Roder, M. A., Iversen, P., Batra, J., Chambers, S., Moya, L., Horvath, L., Clements, J. A., Tilley, W., Risbridger, G. P., Gronberg, H., Aly, M., Szulkin, R., Eklund, M., Nordstrom, T., Pashayan, N., Dunning, A. M., Ghoussaini, M., Travis, R. C., Key, T. J., Riboli, E., Park, J. Y., Sellers, T. A., Lin, H., Albanes, D., Weinstein, S. J., Mucci, L. A., Giovannucci, E., Lindstrom, S., Kraft, P., Hunter, D. J., Penney, K. L., Turman, C., Tangen, C. M., Goodman, P. J., Thompson, I. M., Hamilton, R. J., Fleshner, N. E., Finelli, A., Parent, M., Stanford, J. L., Ostrander, E. A., Geybels, M. S., Koutros, S., Freeman, L. E., Stampfer, M., Wolk, A., Hakansson, N., Andriole, G. L., Hoover, R. N., Machiela, M. J., Sorensen, K. D., Borre, M., Blot, W. J., Zheng, W., Yeboah, E. D., Mensah, J. E., Lu, Y., Zhang, H., Feng, N., Mao, X., Wu, Y., Zhao, S., Sun, Z., Thibodeau, S. N., McDonnell, S. K., Schaid, D. J., West, C. M., Burnet, N., Barnett, G., Maier, C., Schnoeller, T., Luedeke, M., Kibel, A. S., Drake, B. F., Cussenot, O., Cancel-Tassin, G., Menegaux, F., Truong, T., Koudou, Y. A., John, E. M., Grindedal, E. M., Maehle, L., Khaw, K., Ingles, S. A., Stern, M. C., Vega, A., Gomez-Caamano, A., Fachal, L., Rosenstein, B. S., Kerns, S. L., Ostrer, H., Teixeira, M. R., Paulo, P., Brandao, A., Watya, S., Lubwama, A., Bensen, J. T., Fontham, E. T., Mohler, J., Taylor, J. A., Kogevinas, M., Llorca, J., Castano-Vinyals, G., Cannon-Albright, L., Teerlink, C. C., Huff, C. D., Strom, S. S., Multigner, L., Blanchet, P., Brureau, L., Kaneva, R., Slavov, C., Mitev, V., Leach, R. J., Weaver, B., Brenner, H., Cuk, K., Holleczek, B., Saum, K., Klein, E. A., Hsing, A. W., Kittles, R. A., Murphy, A. B., Logothetis, C. J., Kim, J., Neuhausen, S. L., Steele, L., Ding, Y. C., Isaacs, W. B., Nemesure, B., Hennis, A. J., Carpten, J., Pandha, H., Michael, A., De Ruyck, K., De Meerleer, G., Ost, P., Xu, J., Razack, A., Lim, J., Teo, S., Newcomb, L. F., Lin, D. W., Fowke, J. H., Neslund-Dudas, C., Rybicki, B. A., Gamulin, M., Lessel, D., Kulis, T., Usmani, N., Singhal, S., Parliament, M., Claessens, F., Joniau, S., Van den Broeck, T., Gago-Dominguez, M., Castelao, J. E., Martinez, M. E., Larkin, S., Townsend, P. A., Aukim-Hastie, C., Bush, W. S., Aldrich, M. C., Crawford, D. C., Srivastava, S., Cullen, J. C., Petrovics, G., Casey, G., Roobol, M. J., Jenster, G., van Schaik, R. H., Hu, J. J., Sanderson, M., Varma, R., McKean-Cowdin, R., Torres, M., Mancuso, N., Berndt, S. I., Van Den Eeden, S. K., Easton, D. F., Chanock, S. J., Cook, M. B., Wiklund, F., Nakagawa, H., Witte, J. S., Eeles, R. A., Kote-Jarai, Z., Haiman, C. A. 2021

    Abstract

    Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction.

    View details for DOI 10.1038/s41588-020-00748-0

    View details for PubMedID 33398198

  • Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer Via Targeted, Multiregion Sequencing. JCO precision oncology Chen, E., Cario, C. L., Leong, L., Lopez, K., Marquez, C. P., Li, P. S., Oropeza, E., Tenggara, I., Cowan, J., Simko, J. P., Kageyama, R., Wells, D. K., Chan, J. M., Friedlander, T., Aggarwal, R., Paris, P. L., Feng, F., Carroll, P. R., Witte, J. S. 2021; 5

    Abstract

    Cell-free DNA (cfDNA) may allow for minimally invasive identification of biologically relevant genomic alterations and genetically distinct tumor subclones. Although existing biomarkers may detect localized prostate cancer, additional strategies interrogating genomic heterogeneity are necessary for identifying and monitoring aggressive disease. In this study, we aimed to evaluate whether circulating tumor DNA can detect genomic alterations present in multiple regions of localized prostate tumor tissue.METHODS: Low-pass whole-genome and targeted sequencing with a machine-learning guided 2.5-Mb targeted panel were used to identify single nucleotide variants, small insertions and deletions (indels), and copy-number alterations in cfDNA. The majority of this study focuses on the subset of 21 patients with localized disease, although 45 total individuals were evaluated, including 15 healthy controls and nine men with metastatic castration-resistant prostate cancer. Plasma cfDNA was barcoded with duplex unique molecular identifiers. For localized cases, matched tumor tissue was collected from multiple regions (one to nine samples per patient) for comparison.RESULTS: Somatic tumor variants present in heterogeneous tumor foci from patients with localized disease were detected in cfDNA, and cfDNA mutational burden was found to track with disease severity. Somatic tissue alterations were identified in cfDNA, including nonsynonymous variants in FOXA1, PTEN, MED12, and ATM. Detection of these overlapping variants was associated with seminal vesicle invasion (P = .019) and with the number of variants initially found in the matched tumor tissue samples (P = .0005).CONCLUSION: Our findings demonstrate the potential of targeted cfDNA sequencing to detect somatic tissue alterations in heterogeneous, localized prostate cancer, especially in a setting where matched tumor tissue may be unavailable (ie, active surveillance or treatment monitoring).

    View details for DOI 10.1200/PO.20.00428

    View details for PubMedID 34250416

  • The landscape of host genetic factors involved in immune response to common viral infections. Genome medicine Kachuri, L., Francis, S. S., Morrison, M. L., Wendt, G. A., Bosse, Y., Cavazos, T. B., Rashkin, S. R., Ziv, E., Witte, J. S. 2020; 12 (1): 93

    Abstract

    BACKGROUND: Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and therapeutic opportunities.METHODS: We conducted a comprehensive study including genome-wide and transcriptome-wide association analyses to identify genetic loci associated with immunoglobulin G antibody response to 28 antigens for 16 viruses using serological data from 7924 European ancestry participants in the UK Biobank cohort.RESULTS: Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. We identified specific amino acid (AA) residues that are associated with seroreactivity, the strongest associations presented in a range of AA positions within DRbeta1 at positions 11, 13, 71, and 74 for Epstein-Barr virus (EBV), Varicella zoster virus (VZV), human herpesvirus 7, (HHV7), and Merkel cell polyomavirus (MCV). Genome-wide association analyses discovered 7 novel genetic loci outside the HLA associated with viral antibody response (P<5.0*10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for MCV, and CXCR5 (11q23.3) and TBKBP1 (17q21.32) for HHV7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P=5.0*10-15 (MCV), NTN5: P=1.1*10-9 (BKV), and P2RY13: P=1.1*10-8 EBV nuclear antigen. We also demonstrated pleiotropy between viral response genes and complex diseases, from autoimmune disorders to cancer to neurodegenerative and psychiatric conditions.CONCLUSIONS: Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants beyond the HLA that contribute to host-virus interaction.

    View details for DOI 10.1186/s13073-020-00790-x

    View details for PubMedID 33109261

  • Congenital diaphragmatic hernia and maternal dietary nutrient pathways and diet quality. Birth defects research Carmichael, S. L., Ma, C., Witte, J. S., Yang, W., Rasmussen, S. A., Brunelli, L., Nestoridi, E., Shaw, G. M., Feldkamp, M. L., National Birth Defects Prevention Study 2020

    Abstract

    INTRODUCTION: We examined the association of congenital diaphragmatic hernia (CDH) with maternal dietary intake, using semi-Bayes hierarchical models and principal components analysis to consider intake of nutrients that contribute to one-carbon metabolism and oxidative stress pathways, and a diet quality index.METHODS: We included data on 825 cases and 11,108 nonmalformed controls born from 1997-2011 whose mother participated in the National Birth Defects Prevention Study (NBDPS), a multisite, population-based case-control study. Exposure data were from maternal telephone interviews, which included a food frequency questionnaire. Adjusted odds ratios (aOR) and 95% confidence intervals (CI) were generated from logistic regression models that included nutritional factors as continuous variables and were adjusted for maternal energy intake, race-ethnicity, parity, and vitamin supplement intake.RESULTS: In the semi-Bayes hierarchical model that included all nutrients and confounders, riboflavin was the only nutrient for which the 95% CI excluded 1.0; the aOR for a 1SD increase was 0.83. The aORs were 0.79 (95% CI 0.69-0.91) for the one-carbon metabolism pathway score, 0.90 (95% CI 0.80-1.01) for oxidative stress, and 0.85 (95% CI 0.77-0.93) for diet quality (the aORs correspond to a 1 SD increase).CONCLUSIONS: The findings from this study provide some support for the hypothesis that better prepregnancy nutrition is associated with reduced risk for CDH. These results provide etiologic clues but should be interpreted with caution given the novelty of the investigation.

    View details for DOI 10.1002/bdr2.1770

    View details for PubMedID 32744808

  • A meta-analysis of genome-wide association study and eQTL analysis of multiple myeloma among African Americans Du, Z., Weinhold, N., Song, G., Rand, K. A., Van den Berg, D. J., Hwang, A. E., Sheng, X., Hom, V., Ailawadhi, S., Nooka, A. K., Singhal, S., Pawlish, K., Peters, E., Bock, C., Mohrbacher, A., Stram, A., Berndt, S., Blot, W. J., Casey, G., Stevens, V. L., Kittles, R., Goodman, P. J., Diver, W., Hennis, A., Nemesure, B., Klein, E. A., Rybicki, B. A., Stanford, J. L., Witte, J. S., Signorello, L., John, E. M., Bernstein, L., Stroup, A., Stephens, O. W., Zangari, M., Van Rhee, F., Olshan, A., Zheng, W., Hu, J. J., Ziegler, R., Nyante, S. J., Ingles, S., Press, M., Carpten, J., Chanock, S., Mehta, J., Colditz, G. A., Wolf, J., Martin, T. G., Tomasson, M., Fiala, M. A., Terebelo, H., Janakiraman, N., Kolonel, L., Anderson, K. C., Le Marchand, L., Auclair, D., Chiu, B., Ziv, E., Stram, D., Vij, R., Bernal-Mizrachi, L., Morgan, G. J., Zonder, J. A., Huff, C., Lonial, S., Orlowski, R. Z., Conti, D., Haiman, C. A. AMER ASSOC CANCER RESEARCH. 2020
  • A meta-analysis of genome-wide association studies of multiple myeloma among men and women of African ancestry. Blood advances Du, Z., Weinhold, N., Song, G. C., Rand, K. A., Van Den Berg, D. J., Hwang, A. E., Sheng, X., Hom, V., Ailawadhi, S., Nooka, A. K., Singhal, S., Pawlish, K., Peters, E. S., Bock, C., Mohrbacher, A., Stram, A., Berndt, S. I., Blot, W. J., Casey, G., Stevens, V. L., Kittles, R., Goodman, P. J., Diver, W. R., Hennis, A., Nemesure, B., Klein, E. A., Rybicki, B. A., Stanford, J. L., Witte, J. S., Signorello, L., John, E. M., Bernstein, L., Stroup, A. M., Stephens, O. W., Zangari, M., Van Rhee, F., Olshan, A., Zheng, W., Hu, J. J., Ziegler, R., Nyante, S. J., Ingles, S. A., Press, M. F., Carpten, J. D., Chanock, S. J., Mehta, J., Colditz, G. A., Wolf, J., Martin, T. G., Tomasson, M., Fiala, M. A., Terebelo, H., Janakiraman, N., Kolonel, L., Anderson, K. C., Le Marchand, L., Auclair, D., Chiu, B. C., Ziv, E., Stram, D., Vij, R., Bernal-Mizrachi, L., Morgan, G. J., Zonder, J. A., Huff, C. A., Lonial, S., Orlowski, R. Z., Conti, D. V., Haiman, C. A., Cozen, W. 2020; 4 (1): 181–90

    Abstract

    Persons of African ancestry (AA) have a twofold higher risk for multiple myeloma (MM) compared with persons of European ancestry (EA). Genome-wide association studies (GWASs) support a genetic contribution to MM etiology in individuals of EA. Little is known about genetic risk factors for MM in individuals of AA. We performed a meta-analysis of 2 GWASs of MM in 1813 cases and 8871 controls and conducted an admixture mapping scan to identify risk alleles. We fine-mapped the 23 known susceptibility loci to find markers that could better capture MM risk in individuals of AA and constructed a polygenic risk score (PRS) to assess the aggregated effect of known MM risk alleles. In GWAS meta-analysis, we identified 2 suggestive novel loci located at 9p24.3 and 9p13.1 at P < 1 * 10-6; however, no genome-wide significant association was noted. In admixture mapping, we observed a genome-wide significant inverse association between local AA at 2p24.1-23.1 and MM risk in AA individuals. Of the 23 known EA risk variants, 20 showed directional consistency, and 9 replicated at P < .05 in AA individuals. In 8 regions, we identified markers that better capture MM risk in persons with AA. AA individuals with a PRS in the top 10% had a 1.82-fold (95% confidence interval, 1.56-2.11) increased MM risk compared with those with average risk (25%-75%). The strongest functional association was between the risk allele for variant rs56219066 at 5q15 and lower ELL2 expression (P = 5.1 * 10-12). Our study shows that common genetic variation contributes to MM risk in individuals with AA.

    View details for DOI 10.1182/bloodadvances.2019000491

    View details for PubMedID 31935283

  • The landscape of host genetic factors involved in infection to common viruses and SARS-CoV-2. medRxiv : the preprint server for health sciences Kachuri, L. n., Francis, S. S., Morrison, M. n., Bossé, Y. n., Cavazos, T. B., Rashkin, S. R., Ziv, E. n., Witte, J. S. 2020

    Abstract

    Humans and viruses have co-evolved for millennia resulting in a complex host genetic architecture. Understanding the genetic mechanisms of immune response to viral infection provides insight into disease etiology and informs public health interventions.We conducted a comprehensive study linking germline genetic variation and gene expression with antibody response to 28 antigens for 16 viruses using serological data from 7924 participants in the UK Biobank cohort. Using test results from 2010 UK Biobank subjects, we also investigated genetic determinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.Signals in human leukocyte antigen (HLA) class II region dominated the landscape of viral antibody response, with 40 independent loci and 14 independent classical alleles, 7 of which exhibited pleiotropic effects across viral families. Genome-wide association analyses discovered 7 novel genetic loci associated with viral antibody response (P<5.0×10-8), including FUT2 (19q13.33) for human polyomavirus BK (BKV), STING1 (5q31.2) for Merkel cell polyomavirus (MCV), as well as CXCR5 (11q23.3) and TBKBP1 (17q21.32) for human herpesvirus 7. Transcriptome-wide association analyses identified 114 genes associated with response to viral infection, 12 outside of the HLA region, including ECSCR: P=5.0×10-15 (MCV), NTN5: P=1.1×10-9 (BKV), and P2RY13: P=1.1×10-8 (Epstein-Barr virus nuclear antigen). We also demonstrated pleiotropy between viral response genes and complex diseases, such as C4A expression in varicella zoster virus and schizophrenia. Finally, our analyses of SARS-CoV-2 revealed the first genome-wide significant infection susceptibility signal in EHF, an epithelial-specific transcriptional repressor implicated in airway disease. Targeted analyses of expression quantitative trait loci suggest a possible role for tissue-specific ACE2 expression in modifying SARS-CoV-2 susceptibility.Our study confirms the importance of the HLA region in host response to viral infection and elucidates novel genetic determinants of host-virus interaction. Our results may have implications for complex disease etiology and COVID-19.

    View details for DOI 10.1101/2020.05.01.20088054

    View details for PubMedID 32511533

    View details for PubMedCentralID PMC7273301

  • Comprehensive Investigation of White Blood Cell and Gene Expression Profiles As Risk Factors for Multiple Myeloma in African Americans Kachuri, L., Du, Z., Weinhold, N., Song, G., Rand, K., Van den Berg, D., Hwang, A., Sheng, X., Hom, V., Ailawadhi, S., Nooka, A. K., Singhal, S., Peters, E. S., Bock, C., Mohrbacher, A., Stram, A., Berndt, S. I., Blot, W. J., John, E. M., Bernstein, L., Stroup, A., Zangari, M., van Rhee, F., Olshan, A., Zheng, W., Ingles, S., Press, M., Carpten, J., Chanock, S. J., Mehta, J., Colditz, G. A., Wolf, J., Martin, T. G., Fiala, M. A., Terebelo, H. R., Janakiraman, N., Kolonel, L., Anderson, K. C., Le Marchand, L., Auclair, D., Chiu, B., Stram, D., Vij, R., Bernal-Mizrachi, L., Morgan, G., Zonder, J. A., Huff, C., Lonial, S., Orlowski, R. Z., Conti, D., Haiman, C. A., Ziv, E., Witte, J. S., Cozen, W. AMER SOC HEMATOLOGY. 2019
  • A Genome-wide Association Study of Prostate Cancer in Latinos. International journal of cancer Du, Z., Hopp, H., Ingles, S. A., Huff, C., Sheng, X., Weaver, B., Stern, M., Hoffmann, T. J., John, E. M., Van Den Eeden, S. K., Strom, S., Leach, R. J., Thompson, I. M., Witte, J. S., Conti, D. V., Haiman, C. A. 2019

    Abstract

    Latinos represent less than 1% of samples analyzed to date in genome-wide association studies of cancer. The clinical value of genetic information in guiding personalized medicine in populations of non-European ancestry will require additional discovery and risk locus characterization efforts across populations. In the present study, we performed a GWAS of PrCa in 2,820 Latino PrCa cases and 5,293 controls to search for novel PrCa risk loci and to examine the generalizability of known PrCa risk loci in Latino men. We also conducted a genetic admixture mapping scan to identify PrCa risk alleles associated with local ancestry. Genome-wide significant associations were observed with 84 variants all located at the known PrCa risk regions at 8q24 (128.484-128.548) and 10q11.22 (MSMB gene). In admixture mapping, we observed genome-wide significant associations with local African ancestry at 8q24. Of the 162 established PrCa risk variants that are common in Latino men, 135 (83.3%) had effects that were directionally consistent as previously reported, among which 55 (34.0%) were statistically significant with P<0.05. A polygenic risk model of the known PrCa risk variants showed that, compared to men with average risk (25th -75th percentile of the polygenic risk score distribution), men in the top 10% had a 3.19-fold (95% CI: 2.65, 3.84) increased PrCa risk. In conclusion, we found that the known PrCa risk variants can effectively stratify PrCa risk in Latino men. Larger studies in Latino populations will be required to discover and characterize genetic risk variants for PrCa and improve risk stratification for this population. This article is protected by copyright. All rights reserved.

    View details for DOI 10.1002/ijc.32525

    View details for PubMedID 31226226

  • Identification of novel susceptibility loci and genes for prostate cancer risk: A transcriptome-wide association study in over 140,000 European descendants. Cancer research Wu, L. n., Wang, J. n., Cai, Q. n., Cavazos, T. B., Emami, N. C., Long, J. n., Shu, X. O., Lu, Y. n., Guo, X. n., Bauer, J. A., Pasaniuc, B. n., Penney, K. L., Freedman, M. L., Kote-Jarai, Z. n., Witte, J. S., Haiman, C. A., Eeles, R. A., Zheng, W. n. 2019

    Abstract

    Genome-wide association studies have identified genetic variants associated with prostate cancer risk. However, these variants explain only a small fraction of the heritable component of prostate cancer risk, and the genes responsible for many of the identified associations remain unknown. To discover novel prostate cancer genetic loci and possible causal genes at previously identified risk loci, we performed a transcriptome-wide association study in 79,194 cases and 61,112 controls of European ancestry. Using data from the Genotype-Tissue Expression Project, we established genetic models to predict gene expression across the transcriptome for both prostate models and cross-tissue models and evaluated model performance using two independent datasets. We identified significant associations for 137 genes at P < 2.61×10-6, a Bonferroni-corrected threshold, including nine genes that remained significant at P < 2.61×10-6 after adjusting for all known prostate cancer risk variants in nearby regions. Of the 128 remaining associated genes, 94 have not yet been reported as potential target genes at known loci. We silenced 14 genes and many showed a consistent effect on viability and colony-forming efficiency in three cell lines. Our study provides substantial new information to advance our understanding of prostate cancer genetics and biology.

    View details for DOI 10.1158/0008-5472.CAN-18-3536

    View details for PubMedID 31101764

  • Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology NATURE GENETICS Ferreira, M. A., Vonk, J. M., Baurecht, H., Marenholz, I., Tian, C., Hoffman, J. D., Helmer, Q., Tillander, A., Ullemar, V., van Dongen, J., Lu, Y., Rueschendorf, F., Esparza-Gordillo, J., Medway, C. W., Mountjoy, E., Burrows, K., Hummel, O., Grosche, S., Brumpton, B. M., Witte, J. S., Hottenga, J., Willemsen, G., Zheng, J., Rodriguez, E., Hotze, M., Franke, A., Revez, J. A., Beesley, J., Matheson, M. C., Dharmage, S. C., Bain, L. M., Fritsche, L. G., Gabrielsen, M. E., Balliu, B., Nielsen, J. B., Zhou, W., Hveem, K., Langhammer, A., Holmen, O. L., Loset, M., Abecasis, G. R., Willer, C. J., Arnold, A., Homuth, G., Schmidt, C. O., Thompson, P. J., Martin, N. G., Duffy, D. L., Novak, N., Schulz, H., Karrasch, S., Gieger, C., Strauch, K., Melles, R. B., Hinds, D. A., Huebner, N., Weidinger, S., Magnusson, P. E., Jansen, R., Jorgenson, E., Lee, Y., Boomsma, D. I., Almqvist, C., Karlsson, R., Koppelman, G. H., Paternoster, L., 23andMe Res Team, AAGC collaborators, BIOS consortium, LifeLines Cohort Study 2017; 49 (12): 1752-+

    Abstract

    Asthma, hay fever (or allergic rhinitis) and eczema (or atopic dermatitis) often coexist in the same individuals, partly because of a shared genetic origin. To identify shared risk variants, we performed a genome-wide association study (GWAS; n = 360,838) of a broad allergic disease phenotype that considers the presence of any one of these three diseases. We identified 136 independent risk variants (P < 3 × 10-8), including 73 not previously reported, which implicate 132 nearby genes in allergic disease pathophysiology. Disease-specific effects were detected for only six variants, confirming that most represent shared risk factors. Tissue-specific heritability and biological process enrichment analyses suggest that shared risk variants influence lymphocyte-mediated immunity. Six target genes provide an opportunity for drug repositioning, while for 36 genes CpG methylation was found to influence transcription independently of genetic effects. Asthma, hay fever and eczema partly coexist because they share many genetic risk variants that dysregulate the expression of immune-related genes.

    View details for PubMedID 29083406

  • Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology PLOS GENETICS Mechanic, L. E., Lindstrom, S., Daily, K. M., Sieberts, S. K., Amos, C. I., Chen, H., Cox, N. J., Dathe, M., Feuer, E. J., Guertin, M. J., Hoffman, J., Liu, Y., Moore, J. H., Myers, C. L., Ritchie, M. D., Schildkraut, J., Schumacher, F., Witte, J. S., Wang, W., Williams, S. M., Gillanders, E. M., U4C Challenge Participants, U4C Challenge Data Contributors 2017; 13 (9): e1006945

    View details for DOI 10.1371/journal.pgen.1006945

    View details for Web of Science ID 000411976100005

    View details for PubMedID 28957327

    View details for PubMedCentralID PMC5619686

  • Two Novel Susceptibility Loci for Prostate Cancer in Men of African Ancestry JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE Conti, D. V., Wang, K., Sheng, X., Bensen, J. T., Hazelett, D. J., Cook, M. B., Ingles, S. A., Kittles, R. A., Strom, S. S., Rybicki, B. A., Nemesure, B., Isaacs, W. B., Stanford, J. L., Zheng, W., Sanderson, M., John, E. M., Park, J. Y., Xu, J., Stevens, V. L., Berndt, S. I., Haiman, C. A., PRACTICAL ELLIPSE Consortium 2017; 109 (8)

    Abstract

    Prostate cancer incidence is 1.6-fold higher in African Americans than in other populations. The risk factors that drive this disparity are unknown and potentially consist of social, environmental, and genetic influences. To investigate the genetic basis of prostate cancer in men of African ancestry, we performed a genome-wide association meta-analysis using two-sided statistical tests in 10 202 case subjects and 10 810 control subjects. We identified novel signals on chromosomes 13q34 and 22q12, with the risk-associated alleles found only in men of African ancestry (13q34: rs75823044, risk allele frequency = 2.2%, odds ratio [OR] = 1.55, 95% confidence interval [CI] = 1.37 to 1.76, P = 6.10 × 10-12; 22q12.1: rs78554043, risk allele frequency = 1.5%, OR = 1.62, 95% CI = 1.39 to 1.89, P = 7.50 × 10-10). At 13q34, the signal is located 5' of the gene IRS2 and 3' of a long noncoding RNA, while at 22q12 the candidate functional allele is a missense variant in the CHEK2 gene. These findings provide further support for the role of ancestry-specific germline variation in contributing to population differences in prostate cancer risk.

    View details for PubMedID 29117387

    View details for PubMedCentralID PMC5448553

  • Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium PLOS GENETICS Ng, M. Y., Graff, M., Lu, Y., Justice, A. E., Mudgal, P., Liu, C., Young, K., Yanek, L. R., Feitosa, M. F., Wojczynski, M. K., Rand, K., Brody, J. A., Cade, B. E., Dimitrov, L., Duan, Q., Guo, X., Lange, L. A., Nalls, M. A., Okut, H., Tajuddin, S. M., Tayo, B. O., Vedantam, S., Bradfield, J. P., Chen, G., Chen, W., Chesi, A., Irvin, M. R., Padhukasahasram, B., Smith, J. A., Zheng, W., Allison, M. A., Ambrosone, C. B., Bandera, E. V., Bartz, T. M., Berndt, S. I., Bernstein, L., Blot, W. J., Bottinger, E. P., Carpten, J., Chanock, S. J., Chen, Y., Conti, D. V., Cooper, R. S., Fornage, M., Freedman, B. I., Garcia, M., Goodman, P. J., Hsu, Y. H., Hu, J., Huff, C. D., Ingles, S. A., John, E. M., Kittles, R., Klein, E., Li, J., McKnight, B., Nayak, U., Nemesure, B., Ogunniyi, A., Olshan, A., Press, M. F., Rohde, R., Rybicki, B. A., Salako, B., Sanderson, M., Shao, Y., Siscovick, D. S., Stanford, J. L., Stevens, V. L., Stram, A., Strom, S. S., Vaidya, D., Witte, J. S., Yao, J., Zhu, X., Ziegler, R. G., Zonderman, A. B., Adeyemo, A., Ambs, S., Cushman, M., Faul, J. D., Hakonarson, H., Levin, A. M., Nathanson, K. L., Ware, E. B., Weir, D. R., Zhao, W., Zhi, D., Arnett, D. K., Grant, S. A., Kardia, S. R., Oloapde, O. I., Rao, D. C., Rotimi, C. N., Sale, M. M., Williams, L., Zemel, B. S., Becker, D. M., Borecki, I. B., Evans, M. K., Harris, T. B., Hirschhorn, J. N., Li, Y., Patel, S. R., Psaty, B. M., Rotter, J. I., Wilson, J. G., Bowden, D. W., Cupples, L., Haiman, C. A., Loos, R. F., North, K. E., Bone Mineral Density Childhood Stu 2017; 13 (4): e1006719

    Abstract

    Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes. In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHRadjBMI and eight previously established loci at P < 5×10-8: seven for BMI, and one for WHRadjBMI in African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHRadjBMI when combined with European GWAS. In the sex-stratified analyses, we identified three novel loci for BMI (INTS10/LPL and MLC1 in men, IRX4/IRX2 in women) and four for WHRadjBMI (SSX2IP, CASC8, PDE3B and ZDHHC1/HSD11B2 in women) in individuals of African ancestry or both African and European ancestry. For four of the novel variants, the minor allele frequency was low (<5%). In the trans-ethnic fine mapping of 47 BMI loci and 27 WHRadjBMI loci that were locus-wide significant (P < 0.05 adjusted for effective number of variants per locus) from the African ancestry sex-combined and sex-stratified analyses, 26 BMI loci and 17 WHRadjBMI loci contained ≤ 20 variants in the credible sets that jointly account for 99% posterior probability of driving the associations. The lead variants in 13 of these loci had a high probability of being causal. As compared to our previous HapMap imputed GWAS for BMI and WHRadjBMI including up to 71,412 and 27,350 African ancestry individuals, respectively, our results suggest that 1000 Genomes imputation showed modest improvement in identifying GWAS loci including low frequency variants. Trans-ethnic meta-analyses further improved fine mapping of putative causal variants in loci shared between the African and European ancestry populations.

    View details for PubMedID 28430825

  • Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. American journal of epidemiology McAllister, K. n., Mechanic, L. E., Amos, C. n., Aschard, H. n., Blair, I. A., Chatterjee, N. n., Conti, D. n., Gauderman, W. J., Hsu, L. n., Hutter, C. M., Jankowska, M. M., Kerr, J. n., Kraft, P. n., Montgomery, S. B., Mukherjee, B. n., Papanicolaou, G. J., Patel, C. J., Ritchie, M. D., Ritz, B. R., Thomas, D. C., Wei, P. n., Witte, J. S. 2017; 186 (7): 753–61

    Abstract

    Recently, many new approaches, study designs, and statistical and analytical methods have emerged for studying gene-environment interactions (G×Es) in large-scale studies of human populations. There are opportunities in this field, particularly with respect to the incorporation of -omics and next-generation sequencing data and continual improvement in measures of environmental exposures implicated in complex disease outcomes. In a workshop called "Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases," held October 17-18, 2014, by the National Institute of Environmental Health Sciences and the National Cancer Institute in conjunction with the annual American Society of Human Genetics meeting, participants explored new approaches and tools that have been developed in recent years for G×E discovery. This paper highlights current and critical issues and themes in G×E research that need additional consideration, including the improved data analytical methods, environmental exposure assessment, and incorporation of functional data and annotations.

    View details for DOI 10.1093/aje/kwx227

    View details for PubMedID 28978193

  • Telomere structure and maintenance gene variants and risk of five cancer types INTERNATIONAL JOURNAL OF CANCER Karami, S., Han, Y., Pande, M., Cheng, I., Rudd, J., Pierce, B. L., Nutter, E. L., Schumacher, F. R., Kote-Jarai, Z., Lindstrom, S., Witte, J. S., Fang, S., Han, J., Kraft, P., Hunter, D. J., Song, F., Hung, R. J., McKay, J., Gruber, S. B., Chanock, S. J., Risch, A., Shen, H., Haiman, C. A., Boardman, L., Ulrich, C. M., Casey, G., Peters, U., Al Olama, A. A., Berchuck, A., Berndt, S. I., Bezieau, S., Brennan, P., Brenner, H., Brinton, L., Caporaso, N., Chan, A. T., Chang-Claude, J., Christiani, D. C., Cunningham, J. M., Easton, D., Eeles, R. A., Eisen, T., Gala, M., Gallinger, S. J., Gayther, S. A., Goode, E. L., Gronberg, H., Henderson, B. E., Houlston, R., Joshi, A. D., Kury, S., Landi, M. T., Le Marchand, L., Muir, K., Newcomb, P. A., Permuth-Wey, J., Pharoah, P., Phelan, C., Potter, J. D., Ramus, S. J., Risch, H., Schildkraut, J., Slattery, M. L., Song, H., Wentzensen, N., White, E., Wiklund, F., Zanke, B. W., Sellers, T. A., Zheng, W., Chatterjee, N., Amos, C. I., Doherty, J. A. 2016; 139 (12): 2655-2670

    Abstract

    Telomeres cap chromosome ends, protecting them from degradation, double-strand breaks, and end-to-end fusions. Telomeres are maintained by telomerase, a reverse transcriptase encoded by TERT, and an RNA template encoded by TERC. Loci in the TERT and adjoining CLPTM1L region are associated with risk of multiple cancers. We therefore investigated associations between variants in 22 telomere structure and maintenance gene regions and colorectal, breast, prostate, ovarian, and lung cancer risk. We performed subset-based meta-analyses of 204,993 directly-measured and imputed SNPs among 61,851 cancer cases and 74,457 controls of European descent. Independent associations for SNP minor alleles were identified using sequential conditional analysis (with gene-level p value cutoffs ≤3.08 × 10(-5) ). Of the thirteen independent SNPs observed to be associated with cancer risk, novel findings were observed for seven loci. Across the DCLRE1B region, rs974494 and rs12144215 were inversely associated with prostate and lung cancers, and colorectal, breast, and prostate cancers, respectively. Across the TERC region, rs75316749 was positively associated with colorectal, breast, ovarian, and lung cancers. Across the DCLRE1B region, rs974404 and rs12144215 were inversely associated with prostate and lung cancers, and colorectal, breast, and prostate cancers, respectively. Near POT1, rs116895242 was inversely associated with colorectal, ovarian, and lung cancers, and RTEL1 rs34978822 was inversely associated with prostate and lung cancers. The complex association patterns in telomere-related genes across cancer types may provide insight into mechanisms through which telomere dysfunction in different tissues influences cancer risk.

    View details for DOI 10.1002/ijc.30288

    View details for Web of Science ID 000387619400003

    View details for PubMedCentralID PMC5198774

  • A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Rand, K. A., Song, C., Dean, E., Serie, D. J., Curtin, K., Sheng, X., Hu, D., Huff, C. A., Bernal-Mizrachi, L., Tomasson, M. H., Ailawadhi, S., Singhal, S., Pawlish, K., Peters, E. S., Bock, C. H., Stram, A., Van den Berg, D. J., Edlund, C. K., Conti, D. V., Zimmerman, T., Hwang, A. E., Huntsman, S., Graff, J., Nooka, A., Kong, Y., Pregja, S. L., Berndt, S. I., Blot, W. J., Carpten, J., Casey, G., Chu, L., Diver, W. R., Stevens, V. L., Lieber, M. R., Goodman, P. J., Hennis, A. J., Hsing, A. W., Mehta, J., Kittles, R. A., Kolb, S., Klein, E. A., Leske, C., Murphy, A. B., Nemesure, B., Neslund-Dudas, C., Strom, S. S., Vij, R., Rybicki, B. A., Stanford, J. L., Signorello, L. B., Witte, J. S., Ambrosone, C. B., Bhatti, P., John, E. M., Bernstein, L., Zheng, W., Olshan, A. F., Hu, J. J., Ziegler, R. G., Nyante, S. J., Bandera, E. V., Birmann, B. M., Ingles, S. A., Press, M. F., Atanackovic, D., Glenn, M. J., Cannon-Albright, L. A., Jones, B., Tricot, G., Martin, T. G., Kumar, S. K., Wolf, J. L., Halverson, S. L., Rothman, N., Brooks-Wilson, A. R., Rajkumar, S. V., Kolonel, L. N., Chanock, S. J., Slager, S. L., Severson, R. K., Janakiraman, N., Terebelo, H. R., Brown, E. E., De Roos, A. J., Mohrbacher, A. F., Colditz, G. A., Giles, G. G., Spinelli, J. J., Chiu, B. C., Munshi, N. C., Anderson, K. C., Levy, J., Zonder, J. A., Orlowski, R. Z., Lonial, S., Camp, N. J., Vachon, C. M., Ziv, E., Stram, D. O., Hazelett, D. J., Haiman, C. A., Cozen, W. 2016; 25 (12): 1609-1618

    Abstract

    Genome-wide association studies (GWAS) in European populations have identified genetic risk variants associated with multiple myeloma.We performed association testing of common variation in eight regions in 1,318 patients with multiple myeloma and 1,480 controls of European ancestry and 1,305 patients with multiple myeloma and 7,078 controls of African ancestry and conducted a meta-analysis to localize the signals, with epigenetic annotation used to predict functionality.We found that variants in 7p15.3, 17p11.2, 22q13.1 were statistically significantly (P < 0.05) associated with multiple myeloma risk in persons of African ancestry and persons of European ancestry, and the variant in 3p22.1 was associated in European ancestry only. In a combined African ancestry-European ancestry meta-analysis, variation in five regions (2p23.3, 3p22.1, 7p15.3, 17p11.2, 22q13.1) was statistically significantly associated with multiple myeloma risk. In 3p22.1, the correlated variants clustered within the gene body of ULK4 Correlated variants in 7p15.3 clustered around an enhancer at the 3' end of the CDCA7L transcription termination site. A missense variant at 17p11.2 (rs34562254, Pro251Leu, OR, 1.32; P = 2.93 × 10(-7)) in TNFRSF13B encodes a lymphocyte-specific protein in the TNF receptor family that interacts with the NF-κB pathway. SNPs correlated with the index signal in 22q13.1 cluster around the promoter and enhancer regions of CBX7 CONCLUSIONS: We found that reported multiple myeloma susceptibility regions contain risk variants important across populations, supporting the use of multiple racial/ethnic groups with different underlying genetic architecture to enhance the localization and identification of putatively functional alleles.A subset of reported risk loci for multiple myeloma has consistent effects across populations and is likely to be functional. Cancer Epidemiol Biomarkers Prev; 25(12); 1609-18. ©2016 AACR.

    View details for PubMedID 27587788

  • Sequence variation in folate pathway genes and risks of human cleft lip with or without cleft palate. American journal of medical genetics. Part A Marini, N. J., Yang, W., Asrani, K., Witte, J. S., Rine, J., Lammer, E. J., Shaw, G. M. 2016; 170 (11): 2777-2787

    Abstract

    In an effort to comprehensively interrogate genetic variation in the folate pathway for risk of cleft lip with or without cleft palate (CLP), we evaluated 504 common and rare variants in 35 folate-related genes in a panel of 330 infants with CLP and 367 non-malformed controls. Odds ratios (OR) with 95% confidence intervals were computed for common genotypes. A Case-Control Difference metric was calculated for rare variants to highlight differentially occurring alleles. Interactions between variants and a maternal folate intake variable were also evaluated. In gene-only results, significant odds ratios were observed for multiple variants in the BHMT/BHMT2/DMGDH gene cluster, particularly in Hispanic infants. Also in this cluster, rare variant analysis highlighted a substantial case-control difference in BHMT rs60340837 (synonymous Y284Y). In Hispanics, the ALDH1L1 I812V variant (rs4646750) was the most significant risk allele: OR = 3.8 (95%CI = 1.6-9.2) when heterozygous. In non-Hispanic white infants, we observed significant risk for AHCYL2 rs1095423 (homozygous OR = 3.0, 95%CI 1.1-7.8) and the 68 bp CBS insertion (c.844ins68; heterozygous OR = 2.4, 95%CI = 1.1-5.3). Rare variant analysis in this group revealed case-control differences in MTRR and several other methionine cycle genes, a process implicated previously in clefting risk. In women with low folate intake specifically, increased risks were observed for CBS rs2851391 (OR = 3.6, 95%CI = 1.3-9.6) and the R259P nonsynonymous variant of TCN2 (rs1801198; OR = 2.8, 95%CI = 1.2-6.3). This comprehensive study provides further direction on candidate loci to help disentangle the folate-related developmental phenomena in human clefting risk. © 2016 Wiley Periodicals, Inc.

    View details for DOI 10.1002/ajmg.a.37874

    View details for PubMedID 27604992

  • Joint effects of genetic variants and residential proximity to pesticide applications on hypospadias risk. Birth defects research. Part A, Clinical and molecular teratology Carmichael, S. L., Yang, W., Ma, C., Roberts, E., Kegley, S., English, P., Lammer, E. J., Witte, J. S., Shaw, G. M. 2016; 106 (8): 653-658

    Abstract

    We examined risks associated with joint exposure of gene variants and pesticides.Analyses included 189 cases and 390 male controls born from 1991 to 2003 in California's San Joaquin Valley. We used logistic regression to examine risks associated with joint exposures of gene variants and pesticides that our previous work identified as associated with hypospadias. Genetic variables were based on variants in DGKK, genes involved in sex steroid synthesis/metabolism, and genes involved in genital tubercle development. Pesticide exposure was based on residential proximity to commercial agricultural pesticide applications.Odds ratios (ORs) were highest among babies with joint exposures, who had two- to fourfold increased risks; for example, the OR was 3.7 (95% confidence interval [CI], 0.8-16.5) among subjects with the risk-associated DGKK haplotype and pesticide exposure; OR, 1.5 (95% CI, 0.7-3.1) among subjects with the haplotype and no pesticide exposure; and OR, 0.9 (95% CI, 0.5-1.6) among subjects without the haplotype but with pesticide exposure, relative to subjects with neither. However, results did not provide statistical evidence that these risks were significantly greater than expected on an additive scale, relative to risks associated with one exposure at a time.We observed elevated risks associated with joint exposures to selected pesticides and genetic variants but no statistical evidence for interaction. Birth Defects Research (Part A) 106:653-658, 2016. © 2016 Wiley Periodicals, Inc.

    View details for DOI 10.1002/bdra.23508

    View details for PubMedID 27098078

    View details for PubMedCentralID PMC4983249

  • Prostate Cancer Susceptibility in Men of African Ancestry at 8q24. Journal of the National Cancer Institute Han, Y., Rand, K. A., Hazelett, D. J., Ingles, S. A., Kittles, R. A., Strom, S. S., Rybicki, B. A., Nemesure, B., Isaacs, W. B., Stanford, J. L., Zheng, W., Schumacher, F. R., Berndt, S. I., Wang, Z., Xu, J., Rohland, N., Reich, D., Tandon, A., Pasaniuc, B., Allen, A., Quinque, D., Mallick, S., Notani, D., Rosenfeld, M. G., Jayani, R. S., Kolb, S., Gapstur, S. M., Stevens, V. L., Pettaway, C. A., Yeboah, E. D., Tettey, Y., Biritwum, R. B., Adjei, A. A., Tay, E., Truelove, A., Niwa, S., Chokkalingam, A. P., John, E. M., Murphy, A. B., Signorello, L. B., Carpten, J., Leske, M. C., Wu, S., Hennis, A. J., Neslund-Dudas, C., Hsing, A. W., Chu, L., Goodman, P. J., Klein, E. A., Zheng, S. L., Witte, J. S., Casey, G., Lubwama, A., Pooler, L. C., Sheng, X., Coetzee, G. A., Cook, M. B., Chanock, S. J., Stram, D. O., Watya, S., Blot, W. J., Conti, D. V., Henderson, B. E., Haiman, C. A. 2016; 108 (7)

    Abstract

    The 8q24 region harbors multiple risk variants for distinct cancers, including >8 for prostate cancer. In this study, we conducted fine mapping of the 8q24 risk region (127.8-128.8Mb) in search of novel associations with common and rare variation in 4853 prostate cancer case patients and 4678 control subjects of African ancestry. All statistical tests were two-sided. We identified three independent associations at P values of less than 5.00×10(-8), all of which were replicated in studies from Ghana and Uganda (combined sample = 5869 case patients, 5615 control subjects; rs114798100: risk allele frequency [RAF] = 0.04, per-allele odds ratio [OR] = 2.31, 95% confidence interval [CI] = 2.04 to 2.61, P = 2.38×10(-40); rs72725879: RAF = 0.33, OR = 1.37, 95% CI = 1.30 to 1.45, P = 3.04×10(-27); and rs111906932: RAF = 0.03, OR = 1.79, 95% CI = 1.53 to 2.08, P = 1.39×10(-13)). Risk variants rs114798100 and rs111906923 are only found in men of African ancestry, with rs111906923 representing a novel association signal. The three variants are located within or near a number of prostate cancer-associated long noncoding RNAs (lncRNAs), including PRNCR1, PCAT1, and PCAT2. These findings highlight ancestry-specific risk variation and implicate prostate-specific lncRNAs at the 8q24 prostate cancer susceptibility region.

    View details for DOI 10.1093/jnci/djv431

    View details for PubMedID 26823525

  • Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants GENOME RESEARCH Uricchio, L. H., Zaitlen, N. A., Ye, C. J., Witte, J. S., Hernandez, R. D. 2016; 26 (7): 863-873

    Abstract

    The role of rare alleles in complex phenotypes has been hotly debated, but most rare variant association tests (RVATs) do not account for the evolutionary forces that affect genetic architecture. Here, we use simulation and numerical algorithms to show that explosive population growth, as experienced by human populations, can dramatically increase the impact of very rare alleles on trait variance. We then assess the ability of RVATs to detect causal loci using simulations and human RNA-seq data. Surprisingly, we find that statistical performance is worst for phenotypes in which genetic variance is due mainly to rare alleles, and explosive population growth decreases power. Although many studies have attempted to identify causal rare variants, few have reported novel associations. This has sometimes been interpreted to mean that rare variants make negligible contributions to complex trait heritability. Our work shows that RVATs are not robust to realistic human evolutionary forces, so general conclusions about the impact of rare variants on complex traits may be premature.

    View details for DOI 10.1101/gr.202440.115

    View details for Web of Science ID 000378986000001

    View details for PubMedID 27197206

  • Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation NATURE COMMUNICATIONS Gusev, A., Shi, H., Kichaev, G., Pomerantz, M., Li, F., Long, H. W., Ingles, S. A., Kittles, R. A., Strom, S. S., Rybicki, B. A., Nemesure, B., Isaacs, W. B., Zheng, W., Pettaway, C. A., Yeboah, E. D., Tettey, Y., Biritwum, R. B., Adjei, A. A., Tay, E., Truelove, A., Niwa, S., Chokkalingam, A. P., John, E. M., Murphy, A. B., Signorello, L. B., Carpten, J., Leske, M. C., Wu, S., Hennis, A. J., Neslund-Dudas, C., Hsing, A. W., Chu, L., Goodman, P. J., Klein, E. A., Witte, J. S., Casey, G., Kaggwa, S., Cook, M. B., Stram, D. O., Blot, W. J., Eeles, R. A., Easton, D., Kote-Jarai, Z., Al Olama, A. A., Benlloch, S., Muir, K., Giles, G. G., Southey, M. C., FitzGerald, L. M., Gronberg, H., Wiklund, F., Aly, M., Henderson, B. E., Schleutker, J., Wahlfors, T., Tammela, T. L., Nordestgaard, B. G., Key, T. J., Travis, R. C., Neal, D. E., Donovan, J. L., Hamdy, F. C., Pharoah, P., Pashayan, N., Khaw, K., Stanford, J. L., Thibodeau, S. N., McDonnell, S. K., Schaid, D. J., Maier, C., Vogel, W., Luedeke, M., Herkommer, K., Kibel, A. S., Cybulski, C., Wokolorczyk, D., Kluzniak, W., Cannon-Albright, L., Teerlink, C., Brenner, H., Dieffenbach, A. K., Arndt, V., Park, J. Y., Sellers, T. A., Lin, H., Slavov, C., Kaneva, R., Mitev, V., Batra, J., Spurdle, A., Clements, J. A., Teixeira, M. R., Pandha, H., Michael, A., Paulo, P., Maia, S., Kierzek, A., Conti, D. V., Albanes, D., Berg, C., Berndt, S. I., Campa, D., Crawford, E. D., Diver, W. R., Gapstur, S. M., Gaziano, J. M., Giovannucci, E., Hoover, R., Hunter, D. J., Johansson, M., Kraft, P., Le Marchand, L., Lindstrom, S., Navarro, C., Overvad, K., Riboli, E., Siddiq, A., Stevens, V. L., Trichopoulos, D., Vineis, P., Yeager, M., Trynka, G., Raychaudhuri, S., Schumacher, F. R., Price, A. L., Freedman, M. L., Haiman, C. A., Pasaniuc, B., Cook, M., Guy, M., Govindasami, K., Leongamornlert, D., Sawyer, E. J., Wilkinson, R., Saunders, E. J., Tymrakiewicz, M., Dadaev, T., Morgan, A., Fisher, C., Hazel, S., Livni, N., Lophatananon, A., Pedersen, J., Hopper, J. L., Adolfson, J., Stattin, P., Johansson, J., Cavalli-Bjoerkman, C., Karlsson, A., Broms, M., Auvinen, A., Kujala, P., Maeaettaenen, L., Murtola, T., Taari, K., Weischer, M., Nielsen, S. F., Klarskov, P., Roder, A., Iversen, P., Wallinder, H., Gustafsson, S., Cox, A., Brown, P., George, A., Marsden, G., Lane, A., Davis, M., Zheng, W., Signorello, L. B., Blot, W. J., Tillmans, L., Riska, S., Wang, L., Rinckleb, A., Lubiski, J., Stegmaier, C., Pow-Sang, J., Park, H., Radlein, S., Rincon, M., Haley, J., Zachariah, B., Kachakova, D., Popov, E., Mitkova, A., Vlahova, A., Dikov, T., Christova, S., Heathcote, P., Wood, G., Malone, G., Saunders, P., Eckert, A., Yeadon, T., Kerr, K., Collins, A., Turner, M., Srinivasan, S., Kedda, M., Alexander, K., Omara, T., Wu, H., Henrique, R., Pinto, P., Santos, J., Barros-Silva, J. 2016; 7

    Abstract

    Although genome-wide association studies have identified over 100 risk loci that explain ∼33% of familial risk for prostate cancer (PrCa), their functional effects on risk remain largely unknown. Here we use genotype data from 59,089 men of European and African American ancestries combined with cell-type-specific epigenetic data to build a genomic atlas of single-nucleotide polymorphism (SNP) heritability in PrCa. We find significant differences in heritability between variants in prostate-relevant epigenetic marks defined in normal versus tumour tissue as well as between tissue and cell lines. The majority of SNP heritability lies in regions marked by H3k27 acetylation in prostate adenoc7arcinoma cell line (LNCaP) or by DNaseI hypersensitive sites in cancer cell lines. We find a high degree of similarity between European and African American ancestries suggesting a similar genetic architecture from common variation underlying PrCa risk. Our findings showcase the power of integrating functional annotation with genetic data to understand the genetic basis of PrCa.

    View details for DOI 10.1038/ncomms10979

    View details for PubMedID 27052111

  • Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions. Human molecular genetics Han, Y., Hazelett, D. J., Wiklund, F., Schumacher, F. R., Stram, D. O., Berndt, S. I., Wang, Z., Rand, K. A., Hoover, R. N., Machiela, M. J., Yeager, M., Burdette, L., Chung, C. C., Hutchinson, A., Yu, K., Xu, J., Travis, R. C., Key, T. J., Siddiq, A., Canzian, F., Takahashi, A., Kubo, M., Stanford, J. L., Kolb, S., Gapstur, S. M., Diver, W. R., Stevens, V. L., Strom, S. S., Pettaway, C. A., Al Olama, A. A., Kote-Jarai, Z., Eeles, R. A., Yeboah, E. D., Tettey, Y., Biritwum, R. B., Adjei, A. A., Tay, E., Truelove, A., Niwa, S., Chokkalingam, A. P., Isaacs, W. B., Chen, C., Lindstrom, S., Le Marchand, L., Giovannucci, E. L., Pomerantz, M., Long, H., Li, F., Ma, J., Stampfer, M., John, E. M., Ingles, S. A., Kittles, R. A., Murphy, A. B., Blot, W. J., Signorello, L. B., Zheng, W., Albanes, D., Virtamo, J., Weinstein, S., Nemesure, B., Carpten, J., Leske, M. C., Wu, S., Hennis, A. J., Rybicki, B. A., Neslund-Dudas, C., Hsing, A. W., Chu, L., Goodman, P. J., Klein, E. A., Zheng, S. L., Witte, J. S., Casey, G., Riboli, E., Li, Q., Freedman, M. L., Hunter, D. J., Gronberg, H., Cook, M. B., Nakagawa, H., Kraft, P., Chanock, S. J., Easton, D. F., Henderson, B. E., Coetzee, G. A., Conti, D. V., Haiman, C. A. 2015; 24 (19): 5603-5618

    Abstract

    Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation.

    View details for DOI 10.1093/hmg/ddv269

    View details for PubMedID 26162851

  • Detecting gene-environment interactions in human birth defects: Study designs and statistical methods BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY Tai, C. G., Graff, R. E., Liu, J., Passarelli, M. N., Mefford, J. A., Shaw, G. M., Hoffmann, T. J., Witte, J. S. 2015; 103 (8): 692-702

    Abstract

    The National Birth Defects Prevention Study (NBDPS) contains a wealth of information on affected and unaffected family triads, and thus provides numerous opportunities to study gene-environment interactions (G×E) in the etiology of birth defect outcomes. Depending on the research objective, several analytic options exist to estimate G×E effects that use varying combinations of individuals drawn from available triads.In this study, we discuss important considerations in the collection of genetic data and environmental exposures.We will also present several population- and family-based approaches that can be applied to data from the NBDPS including case-control, case-only, family-based trio, and maternal versus fetal effects. For each, we describe the data requirements, applicable statistical methods, advantages, and disadvantages.A range of approaches can be used to evaluate potentially important G×E effects in the NBDPS. Investigators should be aware of the limitations inherent to each approach when choosing a study design and interpreting results. Birth Defects Research (Part A) 103:692-702, 2015. © 2015 Wiley Periodicals, Inc.

    View details for DOI 10.1002/bdra.23382

    View details for Web of Science ID 000359740800006

    View details for PubMedID 26010994

    View details for PubMedCentralID PMC4537677

  • Developments in our understanding of the genetic basis of birth defects BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY Webber, D. M., MacLeod, S. L., Bamshad, M. J., Shaw, G. M., Finnell, R. H., Shete, S. S., Witte, J. S., Erickson, S. W., Murphy, L. D., Hobbs, C. 2015; 103 (8): 680-691

    Abstract

    Birth defects are a major cause of morbidity and mortality worldwide. There has been much progress in understanding the genetic basis of familial and syndromic forms of birth defects. However, the etiology of nonsydromic birth defects is not well-understood. Although there is still much work to be done, we have many of the tools needed to accomplish the task. Advances in next-generation sequencing have introduced a sea of possibilities, from disease-gene discovery to clinical screening and diagnosis. These advances have been fruitful in identifying a host of candidate disease genes, spanning the spectrum of birth defects. With the advent of CRISPR-Cas9 gene editing, researchers now have a precise tool for characterizing this genetic variation in model systems. Work in model organisms has also illustrated the importance of epigenetics in human development and birth defects etiology. Here we review past and current knowledge in birth defects genetics. We describe genotyping and sequencing methods for the detection and analysis of rare and common variants. We remark on the utility of model organisms and explore epigenetics in the context of structural malformation. We conclude by highlighting approaches that may provide insight into the complex genetics of birth defects. Birth Defects Research (Part A) 103:680-691, 2015. © 2015 Wiley Periodicals, Inc.

    View details for DOI 10.1002/bdra.23385

    View details for Web of Science ID 000359740800005

    View details for PubMedID 26033863

    View details for PubMedCentralID PMC4537658

  • Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults PLOS ONE Chen, F., He, J., Zhang, J., Chen, G. K., Thomas, V., Ambrosone, C. B., Bandera, E. V., Berndt, S. I., Bernstein, L., Blot, W. J., Cai, Q., Carpten, J., Casey, G., Chanock, S. J., Cheng, I., Chu, L., Deming, S. L., Driver, W. R., Goodman, P., Hayes, R. B., Hennis, A. J., Hsing, A. W., Hu, J. J., Ingles, S. A., John, E. M., Kittles, R. A., Kolb, S., Leske, M. C., Millikan, R. C., Monroe, K. R., Murphy, A., Nemesure, B., Neslund-Dudas, C., Nyante, S., Ostrander, E. A., Press, M. F., Rodriguez-Gil, J. L., Rybicki, B. A., Schumacher, F., Stanford, J. L., Signorello, L. B., Strom, S. S., Stevens, V., Van Den Berg, D., Wang, Z., Witte, J. S., Wu, S., Yamamura, Y., Zheng, W., Ziegler, R. G., Stram, A. H., Kolonel, L. N., Le Marchand, L., Henderson, B. E., Haiman, C. A., Stram, D. O. 2015; 10 (6)

    Abstract

    Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that today's GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious.

    View details for DOI 10.1371/journal.pone.0131106

    View details for Web of Science ID 000358151300033

    View details for PubMedCentralID PMC4488332

  • Genetic Polymorphisms in ESR1 and ESR2 Genes, and Risk of Hypospadias in a Multiethnic Study Population JOURNAL OF UROLOGY Choudhry, S., Baskin, L. S., Lammer, E. J., Witte, J. S., Dasgupta, S., Ma, C., Surampalli, A., Shen, J., Shaw, G. M., Carmichael, S. L. 2015; 193 (5): 1625-1631

    Abstract

    Estrogenic endocrine disruptors acting via estrogen receptors α (ESR1) and β (ESR2) have been implicated in the etiology of hypospadias, a common congenital malformation of the male external genitalia. We determined the association of single nucleotide polymorphisms in ESR1 and ESR2 genes with hypospadias in a racially/ethnically diverse study population of California births.We investigated the relationship between hypospadias and 108 ESR1 and 36 ESR2 single nucleotide polymorphisms in 647 cases and 877 population based nonmalformed controls among infants born in selected California counties from 1990 to 2003. Subgroup analyses were performed by race/ethnicity (nonHispanic white and Hispanic subjects) and by hypospadias severity (mild to moderate and severe).Odds ratios for 33 of the 108 ESR1 single nucleotide polymorphisms had p values less than 0.05 (p = 0.05 to 0.007) for risk of hypospadias. However, none of the 36 ESR2 single nucleotide polymorphisms was significantly associated. In stratified analyses the association results were consistent by disease severity but different sets of single nucleotide polymorphisms were significantly associated with hypospadias in nonHispanic white and Hispanic subjects. Due to high linkage disequilibrium across the single nucleotide polymorphisms, haplotype analyses were conducted and identified 6 haplotype blocks in ESR1 gene that had haplotypes significantly associated with an increased risk of hypospadias (OR 1.3 to 1.8, p = 0.04 to 0.00001). Similar to single nucleotide polymorphism analysis, different ESR1 haplotypes were associated with risk of hypospadias in nonHispanic white and Hispanic subjects. No significant haplotype association was observed for ESR2.The data provide evidence that ESR1 single nucleotide polymorphisms and haplotypes influence the risk of hypospadias in white and Hispanic subjects, and warrant further examination in other study populations.

    View details for DOI 10.1016/j.juro.2014.11.087

    View details for Web of Science ID 000353113200073

    View details for PubMedID 25463985

  • Generalizability of established prostate cancer risk variants in men of African ancestry INTERNATIONAL JOURNAL OF CANCER Han, Y., Signorello, L. B., Strom, S. S., Kittles, R. A., Rybicki, B. A., Stanford, J. L., Goodman, P. J., Berndt, S. I., Carpten, J., Casey, G., Chu, L., Conti, D. V., Rand, K. A., Diver, W. R., Hennis, A. J., John, E. M., Kibel, A. S., Klein, E. A., Kolb, S., Le Marchand, L., Leske, M. C., Murphy, A. B., Neslund-Dudas, C., Park, J. Y., Pettaway, C., Rebbeck, T. R., Gapstur, S. M., Zheng, S. L., Wu, S., Witte, J. S., Xu, J., Isaacs, W., Ingles, S. A., Hsing, A., Easton, D. F., Eeles, R. A., Schumacher, F. R., Chanock, S., Nemesure, B., Blot, W. J., Stram, D. O., Henderson, B. E., Haiman, C. A. 2015; 136 (5): 1210-1217

    Abstract

    Genome-wide association studies have identified more than 80 risk variants for prostate cancer, mainly in European or Asian populations. The generalizability of these variants in other racial/ethnic populations needs to be understood before the loci can be used widely in risk modeling. In our study, we examined 82 previously reported risk variants in 4,853 prostate cancer cases and 4,678 controls of African ancestry. We performed association testing for each variant using logistic regression adjusted for age, study and global ancestry. Of the 82 known risk variants, 68 (83%) had effects that were directionally consistent in their association with prostate cancer risk and 30 (37%) were significantly associated with risk at p < 0.05, with the most statistically significant variants being rs116041037 (p = 3.7 × 10(-26) ) and rs6983561 (p = 1.1 × 10(-16) ) at 8q24, as well as rs7210100 (p = 5.4 × 10(-8) ) at 17q21. By exploring each locus in search of better markers, the number of variants that captured risk in men of African ancestry (p < 0.05) increased from 30 (37%) to 44 (54%). An aggregate score comprised of these 44 markers was strongly associated with prostate cancer risk [per-allele odds ratio (OR) = 1.12, p = 7.3 × 10(-98) ]. In summary, the consistent directions of effects for the vast majority of variants in men of African ancestry indicate common functional alleles that are shared across populations. Further exploration of these susceptibility loci is needed to identify the underlying biologically relevant variants to improve prostate cancer risk modeling in populations of African ancestry.

    View details for DOI 10.1002/ijc.29066

    View details for Web of Science ID 000346350500046

    View details for PubMedCentralID PMC4268262

  • Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways NATURE NEUROSCIENCE O'Dushlaine, C., Rossin, L., Lee, P. H., Duncan, L., Parikshak, N. N., Newhouse, S., Ripke, S., Neale, B. M., Purcell, S. M., Posthuma, D., Nurnberger, J. I., Lee, S. H., Faraone, S. V., Perlis, R. H., Mowry, B. J., Thapar, A., Goddard, M. E., Witte, J. S., Absher, D., Agartz, I., Akil, H., Amin, F., Andreassen, O. A., Anjorin, A., Anney, R., Anttila, V., Arking, D. E., Asherson, P., Azevedo, M. H., Backlund, L., Badner, J. A., Bailey, A. J., Banaschewski, T., Barchas, J. D., Barnes, M. R., Barrett, T. B., Bass, N., Battaglia, A., Bauer, M., Bayes, M., Bellivier, F., Bergen, S. E., Berrettini, W., Betancur, C., Bettecken, T., Biederman, J., Binder, E. B., Black, D. W., Blackwood, D. H., Bloss, C. S., Boehnke, M., Boomsma, D. I., Breuer, R., Bruggeman, R., Cormican, P., Buccola, N. G., Buitelaar, J. K., Bunney, W. E., Buxbaum, J. D., Byerley, W. F., Byrne, E. M., Caesar, S., Cahn, W., Cantor, R. M., Casas, M., Chakravarti, A., Chambert, K., Choudhury, K., Cichon, S., Mattheisen, M., Cloninger, C. R., Collier, D. A., Cook, E. H., Coon, H., Cormand, B., Corvin, A., Coryell, W. H., Craig, D. W., Craig, I. W., Crosbie, J., Cuccaro, M. L., Curtis, D., Czamara, D., Datta, S., Dawson, G., Day, R., de Geus, E. J., Degenhardt, F., Djurovic, S., Donohoe, G. J., Doyle, A. E., Duan, J., Dudbridge, F., Duketis, E., Ebstein, R. P., Edenberg, H. J., Elia, J., Ennis, S., Etain, B., Fanous, A., Farmer, A. E., Ferrier, I. N., Flicldnger, M., Fombonne, E., Foroud, T., Frank, J., Franke, B., Fraser, C., Freedman, R., Freimer, N. B., Freitag, C. M., Friedl, M., Frisen, L., Gailagher, L., Gejman, P. V., Georgieva, L., Gershon, E. S., Giegling, I., Gill, M., Gordon, S. D., Gordon-Smith, K., Green, E. K., Greenwood, T. A., Grice, D. E., Gross, M., Grozeva, D., Guan, W., Gurling, H., de Haan, L., Haines, J. L., Hakonarson, H., Hallmayer, J., Hamilton, S. P., Hamshere, M. L., Hansen, T. F., Hartmann, A. M., Hautzinger, M., Heath, A. C., Henders, A. K., Herms, S., Hickie, I. B., Hipolito, M., Hoefels, S., Holsboer, F., Hoogendijk, W. J., Hottenga, J., Hultman, C. M., Hus, V., Ingason, A., Ising, M., Jamain, S., Jones, E. G., Jones, I., Jones, L., Tzeng, J., Kaehler, A. K., Kahn, R. S., Kandaswamy, R., Keller, M. C., Kennedy, J. L., Kenny, E., Kent, L., Kim, Y., Kirov, G. K., Klauck, S. M., Klei, L., Knowles, J. A., Kohli, M. A., Koller, D. L., Konte, B., Korszun, A., Krabbendam, L., Krasucki, R., Kuntsi, J., Kwan, P., Landen, M., Laengstroem, N., Lathrop, M., Lawrence, J., Lawson, W. B., Leboyer, M., Ledbetter, D. H., Lencz, T., Lesch, K., Levinson, D. F., Lewis, C. M., Li, J., Lichtenstein, P., Lieberman, J. A., Lin, D., Linszen, D. H., Liu, C., Lohoff, F. W., Loo, S. K., Lord, C., Lowe, J. K., Lucae, S., MacIntyre, D. J., Madden, P. A., Maestrini, E., Magnusson, P. K., Mahon, P. B., Maier, W., Malhotra, A. K., Mane, S. M., Martin, C. L., Martin, N. G., Matthews, K., Mattingsdal, M., McCarroll, S. A., McGhee, K. A., McGough, J. J., McGrath, P. J., McGuffin, P., McInnis, M. G., McIntosh, A., McKinney, R., McLean, A. W., McMahon, F. J., McMahon, W. M., McQuillin, A., Medeiros, H., Medland, S. E., Meier, S., Melle, I., Meng, F., Meyer, J., Middeldorp, C. M., Middleton, L., Milanova, V., Miranda, A., Monaco, A. P., Montgomery, G. W., Moran, J. L., Moreno-De-Luca, D., Morken, G., Morris, D. W., Morrow, E. M., Moskvina, V., Muglia, P., Muehleisen, T. W., Muir, W. J., Mueller-Myhsok, B., Murtha, M., Myers, R. M., Myin-Germeys, I., Neale, M. C., Nelson, S. F., Nievergelt, C. M., Nikolov, I., Nimgaonkar, V., Nolen, W. A., Noethen, M. M., Nwulia, E. A., Nyholt, D. R., Oades, R. D., Olincy, A., Oliveira, G., Olsen, L., Ophoff, R. A., Osby, U., Owen, M. J., Palotie, A., Parr, J. R., Paterson, A. D., Pato, C. N., Pato, M. T., Penninx, B. W., Pergadia, M. L., Pericak-Vance, M. A., Pickard, B. S., Pimm, J., Piven, J., Potash, J. B., Poustka, F., Propping, P., Puri, V., Quested, D. J., Quinn, E. M., Ramos-Quiroga, J. A., Rasmussen, H. B., Raychaudhuri, S., Rehnstroem, K., Reif, A., Ribases, M., Rice, J. P., Rietschel, M., Roeder, K., Roeyers, H., Rothenberger, A., Rouleau, G., Ruderfer, D., Rujescu, D., Sanders, A. R., Sanders, S. J., Santangelo, S. L., Sergeant, J. A., Schachar, R., Schalling, M., Schatzberg, A. F., Scheftner, W. A., Schellenberg, G. D., Scherer, S. W., Schork, N. J., Schulze, T. G., Schumacher, J., Schwarz, M., Scolnick, E., Scott, L. J., Shi, J., Shilling, P. D., Shyn, S. I., Silverman, J. M., Slager, S. L., Smalley, S. L., Smit, J. H., Smith, E. N., Sonuga-Barke, E. J., Cair, D. S., State, M., Steffens, M., Steinhausen, H., Strauss, J. S., Strohmaier, J., Stroup, T. S., Sutdiffe, J. S., Szatmari, P., Szelinger, S., Thirumalai, S., Thompson, R. C., Todorov, A. A., Tozzi, F., Treutlein, J., Uhr, M., van den Oord, E. J., Van Grootheest, G., van Os, J., Vicente, A. M., Vieland, V. J., Vincent, J. B., Visscher, P. M., Walsh, C. A., Wassink, T. H., Watson, S. J., Weissman, M. M., Werge, T., Wienker, T. F., Wijsman, E. M., Willemsen, G., Williams, N., Willsey, A. J., Witt, S. H., Xu, W., Young, A. H., Yu, T. W., Zammit, S., Zandi, P. P., Zhang, P., Zitman, F. G., Zoellner, S., Devlin, B., Kelsoe, J. R., Sklar, P., Daly, M. J., O'Donovan, M. C., Craddock, N., Kendler, K. S., Weiss, L. A., Wray, N. R., Zhao, Z., Geschwind, D. H., Sullivan, P. F., Smoller, J. W., Holmans, P. A., Breen, G. 2015; 18 (2): 199-209

    Abstract

    Genome-wide association studies (GWAS) of psychiatric disorders have identified multiple genetic associations with such disorders, but better methods are needed to derive the underlying biological mechanisms that these signals indicate. We sought to identify biological pathways in GWAS data from over 60,000 participants from the Psychiatric Genomics Consortium. We developed an analysis framework to rank pathways that requires only summary statistics. We combined this score across disorders to find common pathways across three adult psychiatric disorders: schizophrenia, major depression and bipolar disorder. Histone methylation processes showed the strongest association, and we also found statistically significant evidence for associations with multiple immune and neuronal signaling pathways and with the postsynaptic density. Our study indicates that risk variants for psychiatric disorders aggregate in particular biological pathways and that these pathways are frequently shared between disorders. Our results confirm known mechanisms and suggest several novel insights into the etiology of psychiatric disorders.

    View details for DOI 10.1038/nn.3922

    View details for Web of Science ID 000348631800010

    View details for PubMedID 25599223

    View details for PubMedCentralID PMC4378867

  • Methodological Considerations in Estimation of Phenotype Heritability Using Genome-Wide SNP Data, Illustrated by an Analysis of the Heritability of Height in a Large Sample of African Ancestry Adults. PloS one Chen, F., He, J., Zhang, J., Chen, G. K., Thomas, V., Ambrosone, C. B., Bandera, E. V., Berndt, S. I., Bernstein, L., Blot, W. J., Cai, Q., Carpten, J., Casey, G., Chanock, S. J., Cheng, I., Chu, L., Deming, S. L., Driver, W. R., Goodman, P., Hayes, R. B., Hennis, A. J., Hsing, A. W., Hu, J. J., Ingles, S. A., John, E. M., Kittles, R. A., Kolb, S., Leske, M. C., Millikan, R. C., Monroe, K. R., Murphy, A., Nemesure, B., Neslund-Dudas, C., Nyante, S., Ostrander, E. A., Press, M. F., Rodriguez-Gil, J. L., Rybicki, B. A., Schumacher, F., Stanford, J. L., Signorello, L. B., Strom, S. S., Stevens, V., Van Den Berg, D., Wang, Z., Witte, J. S., Wu, S., Yamamura, Y., Zheng, W., Ziegler, R. G., Stram, A. H., Kolonel, L. N., Le Marchand, L., Henderson, B. E., Haiman, C. A., Stram, D. O. 2015; 10 (6)

    Abstract

    Height has an extremely polygenic pattern of inheritance. Genome-wide association studies (GWAS) have revealed hundreds of common variants that are associated with human height at genome-wide levels of significance. However, only a small fraction of phenotypic variation can be explained by the aggregate of these common variants. In a large study of African-American men and women (n = 14,419), we genotyped and analyzed 966,578 autosomal SNPs across the entire genome using a linear mixed model variance components approach implemented in the program GCTA (Yang et al Nat Genet 2010), and estimated an additive heritability of 44.7% (se: 3.7%) for this phenotype in a sample of evidently unrelated individuals. While this estimated value is similar to that given by Yang et al in their analyses, we remain concerned about two related issues: (1) whether in the complete absence of hidden relatedness, variance components methods have adequate power to estimate heritability when a very large number of SNPs are used in the analysis; and (2) whether estimation of heritability may be biased, in real studies, by low levels of residual hidden relatedness. We addressed the first question in a semi-analytic fashion by directly simulating the distribution of the score statistic for a test of zero heritability with and without low levels of relatedness. The second question was addressed by a very careful comparison of the behavior of estimated heritability for both observed (self-reported) height and simulated phenotypes compared to imputation R2 as a function of the number of SNPs used in the analysis. These simulations help to address the important question about whether today's GWAS SNPs will remain useful for imputing causal variants that are discovered using very large sample sizes in future studies of height, or whether the causal variants themselves will need to be genotyped de novo in order to build a prediction model that ultimately captures a large fraction of the variability of height, and by implication other complex phenotypes. Our overall conclusions are that when study sizes are quite large (5,000 or so) the additive heritability estimate for height is not apparently biased upwards using the linear mixed model; however there is evidence in our simulation that a very large number of causal variants (many thousands) each with very small effect on phenotypic variance will need to be discovered to fill the gap between the heritability explained by known versus unknown causal variants. We conclude that today's GWAS data will remain useful in the future for causal variant prediction, but that finding the causal variants that need to be predicted may be extremely laborious.

    View details for DOI 10.1371/journal.pone.0131106

    View details for PubMedID 26125186

  • Leveraging population admixture to characterize the heritability of complex traits NATURE GENETICS Zaitlen, N., Pasaniuc, B., Sankararaman, S., Bhatia, G., Zhang, J., Gusev, A., Young, T., Tandon, A., Pollack, S., Vilhjalmsson, B. J., Assimes, T. L., Berndt, S. I., Blot, W. J., Chanock, S., Franceschini, N., Goodman, P. G., He, J., Hennis, A. J., Hsing, A., Ingles, S. A., Isaacs, W., Kittles, R. A., Klein, E. A., Lange, L. A., Nemesure, B., Patterson, N., Reich, D., Rybicki, B. A., Stanford, J. L., Stevens, V. L., Strom, S. S., Whitse, E. A., Witte, J. S., Xu, J., Haiman, C., Wilson, J. G., Kooperberg, C., Stram, D., Reiner, A. P., Tang, H., Price, A. L. 2014; 46 (12): 1356-1362

    Abstract

    Despite recent progress on estimating the heritability explained by genotyped SNPs (h(2)g), a large gap between h(2)g and estimates of total narrow-sense heritability (h(2)) remains. Explanations for this gap include rare variants or upward bias in family-based estimates of h(2) due to shared environment or epistasis. We estimate h(2) from unrelated individuals in admixed populations by first estimating the heritability explained by local ancestry (h(2)γ). We show that h(2)γ = 2FSTCθ(1 - θ)h(2), where FSTC measures frequency differences between populations at causal loci and θ is the genome-wide ancestry proportion. Our approach is not susceptible to biases caused by epistasis or shared environment. We applied this approach to the analysis of 13 phenotypes in 21,497 African-American individuals from 3 cohorts. For height and body mass index (BMI), we obtained h(2) estimates of 0.55 ± 0.09 and 0.23 ± 0.06, respectively, which are larger than estimates of h(2)g in these and other data but smaller than family-based estimates of h(2).

    View details for DOI 10.1038/ng.3139

    View details for Web of Science ID 000345547300019

    View details for PubMedCentralID PMC4244251

  • Genome-wide Scan of 29,141 African Americans Finds No Evidence of Directional Selection since Admixture AMERICAN JOURNAL OF HUMAN GENETICS Bhatia, G., Tandon, A., Patterson, N., Aldrich, M. C., Ambrosone, C. B., Amos, C., Bandera, E. V., Berndt, S. I., Bernstein, L., Blot, W. J., Bock, C. H., Caporaso, N., Casey, G., Deming, S. L., Diver, W. R., Gapstur, S. M., Gillanders, E. M., Harris, C. C., Henderson, B. E., Ingles, S. A., Isaacs, W., De Jager, P. L., John, E. M., Kittles, R. A., Larkin, E., McNeill, L. H., Millikan, R. C., Murphy, A., Neslund-Dudas, C., Nyante, S., Press, M. F., Rodriguez-Gil, J. L., Rybicki, B. A., Schwartz, A. G., Signorello, L. B., Spitz, M., Strom, S. S., Tucker, M. A., Wiencke, J. K., Witte, J. S., Wu, X., Yamamura, Y., Zanetti, K. A., Zheng, W., Ziegler, R. G., Chanock, S. J., Haiman, C. A., Reich, D., Price, A. L. 2014; 95 (4): 437-444

    Abstract

    The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study's conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas.

    View details for DOI 10.1016/j.ajhg.2014.08.011

    View details for Web of Science ID 000342654300008

    View details for PubMedCentralID PMC4185117

  • A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer NATURE GENETICS Al Olama, A. A., Kote-Jarai, Z., Berndt, S. I., Conti, D. V., Schumacher, F., Han, Y., Benlloch, S., Hazelett, D. J., Wang, Z., Saunders, E., Leongamornlert, D., Lindstrom, S., Jugurnauth-Little, S., Dadaev, T., Tymrakiewicz, M., Stram, D. O., Rand, K., Wan, P., Stram, A., Sheng, X., Pooler, L. C., Park, K., Xia, L., Tyrer, J., Kolonel, L. N., Le Marchand, L., Hoover, R. N., Machiela, M. J., Yeager, M., Burdette, L., Chung, C. C., Hutchinson, A., Yu, K., Goh, C., Ahmed, M., Govindasami, K., Guy, M., Tammela, T. L., Auvinen, A., Wahlfors, T., Schleutker, J., Visakorpi, T., Leinonen, K. A., Xu, J., Aly, M., Donovan, J., Travis, R. C., Key, T. J., Siddiq, A., Canzian, F., Khaw, K., Takahashi, A., Kubo, M., Pharoah, P., Pashayan, N., Weischer, M., Nordestgaard, B. G., Nielsen, S. F., Klarskov, P., Roder, M. A., Iversen, P., Thibodeau, S. N., McDonnell, S. K., Schaid, D. J., Stanford, J. L., Kolb, S., Holt, S., Knudsen, B., Coll, A. H., Gapstur, S. M., Diver, W. R., Stevens, V. L., Maier, C., Luedeke, M., Herkommer, K., Rinckleb, A. E., Strom, S. S., Pettaway, C., Yeboah, E. D., Tettey, Y., Biritwum, R. B., Adjei, A. A., Tay, E., Truelove, A., Niwa, S., Choklcalingam, A. P., Cannon-Albright, L., Cybulski, C., Wokolorczyk, D., Kluzniak, W., Park, J., Sellers, T., Lin, H., Isaacs, W. B., Partin, A. W., Brenner, H., Dieffenbach, A. K., Stegmaier, C., Chen, C., Giovannucci, E. L., Ma, J., Stampfer, M., Penney, K. L., Mucci, L., John, E. M., Ingles, S. A., Kittles, R. A., Murphy, A. B., Pandha, H., Michael, A., Kierzek, A. M., Blot, W., Signorello, L. B., Zheng, W., Albanes, D., Virtamo, J., Weinstein, S., Nemesure, B., Carpten, J., Leske, C., Wu, S., Hennis, A., Kibel, A. S., Rybicki, B. A., Neslund-Dudas, C., Hsing, A. W., Chu, L., Goodman, P. J., Klein, E. A., Zheng, S. L., Batra, J., Clements, J., Spurdle, A., Teixeira, M. R., Paulo, P., Maia, S., Slavov, C., Kaneva, R., Mitev, V., Witte, J. S., Casey, G., Gillanders, E. M., Seminara, D., Riboli, E., Hamdy, F. C., Coetzee, G. A., Li, Q., Freedman, M. L., Hunter, D. J., Muir, K., Gronberg, H., Nea, D. E., Southey, M., Giles, G. G., Severi, G., Cook, M. B., Nakagawa, H., Wiklund, F., Kraft, P., Chanock, S. J., Henderson, B. E., Easton, D. F., Eeles, R. A., Haiman, C. A. 2014; 46 (10): 1103-1109

    Abstract

    Genome-wide association studies (GWAS) have identified 76 variants associated with prostate cancer risk predominantly in populations of European ancestry. To identify additional susceptibility loci for this common cancer, we conducted a meta-analysis of > 10 million SNPs in 43,303 prostate cancer cases and 43,737 controls from studies in populations of European, African, Japanese and Latino ancestry. Twenty-three new susceptibility loci were identified at association P < 5 × 10(-8); 15 variants were identified among men of European ancestry, 7 were identified in multi-ancestry analyses and 1 was associated with early-onset prostate cancer. These 23 variants, in combination with known prostate cancer risk variants, explain 33% of the familial risk for this disease in European-ancestry populations. These findings provide new regions for investigation into the pathogenesis of prostate cancer and demonstrate the usefulness of combining ancestrally diverse populations to discover risk loci for disease.

    View details for DOI 10.1038/ng.3094

    View details for Web of Science ID 000342554100013

  • Copy Number Variation in Bronchopulmonary Dysplasia AMERICAN JOURNAL OF MEDICAL GENETICS PART A Hoffmann, T. J., Shaw, G. M., Stevenson, D. K., Wang, H., Quaintance, C. C., Oehlert, J., Jelliffe-Pawlowski, L. L., Gould, J. B., Witte, J. S., O'Brodovich, H. M. 2014; 164 (10): 2672–75

    View details for DOI 10.1002/ajmg.a.36659

    View details for Web of Science ID 000342279600041

    View details for PubMedID 24975634

    View details for PubMedCentralID PMC4167221

  • Genetic Epidemiology and Nonsyndromic Structural Birth Defects From Candidate Genes to Epigenetics JAMA PEDIATRICS Hobbs, C. A., Chowdhury, S., Cleves, M. A., Erickson, S., MacLeod, S. L., Shaw, G. M., Shete, S., Witte, J. S., Tycko, B. 2014; 168 (4): 371-377

    Abstract

    Birth defects are a leading cause of infant morbidity and mortality worldwide. The vast majority of birth defects are nonsyndromic, and although their etiologies remain mostly unknown, evidence supports the hypothesis that they result from the complex interaction of genetic, epigenetic, environmental, and lifestyle factors. Since our last review published in 2002 describing the basic tools of genetic epidemiology used to study nonsyndromic structural birth defects, many new approaches have become available and have been used with varying success. Through rapid advances in genomic technologies, investigators are now able to investigate large portions of the genome at a fraction of previous costs. With next-generation sequencing, research has progressed from assessing a small percentage of single-nucleotide polymorphisms to assessing the entire human protein-coding repertoire (exome)-an approach that is starting to uncover rare but informative mutations associated with nonsyndromic birth defects. Herein, we report on the current state of the genetic epidemiology of birth defects and comment on future challenges and opportunities. We consider issues of study design, and we discuss common variant approaches, including candidate gene studies and genome-wide association studies. We also discuss the complexities embedded in exploring interactions between genes and the environment. We complete our review by describing new and promising next-generation sequencing technologies and examining how the study of epigenetic mechanisms could become the key to unraveling the complex etiologies of nonsyndromic structural birth defects.

    View details for DOI 10.1001/jamapediatrics.2013.4858

    View details for Web of Science ID 000336839200014

    View details for PubMedID 24515445

    View details for PubMedCentralID PMC3981910

  • Hypospadias and Genes Related to Genital Tubercle and Early Urethral Development JOURNAL OF UROLOGY Carmichael, S. L., Ma, C., Choudhry, S., Lammer, E. J., Witte, J. S., Shaw, G. M. 2013; 190 (5): 1884-1892

    Abstract

    PURPOSE: We determined whether variants in genes associated with genital tubercle (the anlage for the penis) and early urethral development were associated with hypospadias in humans. MATERIALS AND METHODS: We examined 293 relatively common tagSNPs in BMP4, BMP7, FGF8, FGF10, FGFR2, HOXA13, HOXD13, HOXA4, HOXB6, SRY, WT1, WTAP, SHH, GLI1, GLI2, and GLI3. The analysis included 624 cases (81 mild, 319 moderate, 209 severe, 15 undetermined severity) and 844 population-based non-malformed male controls born in California from 1990-2003. RESULTS: There were 28 SNPs for which any of the comparisons (i.e., overall or for a specific severity) had a p-value <0.01. The homozygous variant genotypes for four SNPs in BMP7were associated with at least 2-fold increased risk of hypospadias, regardless of severity. Five SNPs for FGF10were associated with 3- to 4-fold increased risks, regardless of severity; for four of them, results were restricted to whites. For GLI1, GLI2and GLI3, there were 12 associated SNPs but results were inconsistent by severity and race-ethnicity. For SHH, one SNP was associated with 2.4-fold increased risk of moderate hypospadias. For WT1, six SNPs were associated with approximately 2-fold increased risks, primarily for severe hypospadias. CONCLUSIONS: This study provides evidence that SNPs in several genes that contribute to genital tubercle and early urethral development are associated with hypospadias risk.

    View details for DOI 10.1016/j.juro.2013.05.061

    View details for Web of Science ID 000325471400089

    View details for PubMedID 23727413

  • Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs NATURE GENETICS Lee, S. H., Ripke, S., Neale, B. M., Faraone, S. V., Purcell, S. M., Perlis, R. H., Mowry, B. J., Thapar, A., Goddard, M. E., Witte, J. S., Absher, D., Agartz, I., Akil, H., Amin, F., Andreassen, O. A., Anjorin, A., Anney, R., Anttila, V., Arking, D. E., Asherson, P., Azevedo, M. H., Backlund, L., Badner, J. A., Bailey, A. J., Banaschewski, T., Barchas, J. D., Barnes, M. R., Barrett, T. B., Bass, N., Battaglia, A., Bauer, M., Bayes, M., Bellivier, F., Bergen, S. E., Berrettini, W., Betancur, C., Bettecken, T., Biederman, J., Binder, E. B., Black, D. W., Blackwood, D. H., Bloss, C. S., Boehnke, M., Boomsma, D. I., Breen, G., Breuer, R., Bruggeman, R., Cormican, P., Buccola, N. G., Buitelaar, J. K., Bunney, W. E., Buxbaum, J. D., Byerley, W. F., Byrne, E. M., Caesar, S., Cahn, W., Cantor, R. M., Casas, M., Chakravarti, A., Chambert, K., Choudhury, K., Cichon, S., Cloninger, C. R., Collier, D. A., Cook, E. H., Coon, H., Cormand, B., Corvin, A., Coryell, W. H., Craig, D. W., Craig, I. W., Crosbie, J., Cuccaro, M. L., Curtis, D., Czamara, D., Datta, S., Dawson, G., Day, R., de Geus, E. J., Degenhardt, F., Djurovic, S., Donohoe, G. J., Doyle, A. E., Duan, J., Dudbridge, F., Duketis, E., Ebstein, R. P., Edenberg, H. J., Elia, J., Ennis, S., Etain, B., Fanous, A., Farmer, A. E., Ferrier, I. N., Flickinger, M., Fombonne, E., Foroud, T., Frank, J., Franke, B., Fraser, C., Freedman, R., Freimer, N. B., Freitag, C. M., Friedl, M., Frisen, L., Gallagher, L., Gejman, P. V., Georgieva, L., Gershon, E. S., Geschwind, D. H., Giegling, I., Gill, M., Gordon, S. D., Gordon-Smith, K., Green, E. K., Greenwood, T. A., Grice, D. E., Gross, M., Grozeva, D., Guan, W., Gurling, H., de Haan, L., Haines, J. L., Hakonarson, H., Hallmayer, J., Hamilton, S. P., Hamshere, M. L., Hansen, T. F., Hartmann, A. M., Hautzinger, M., Heath, A. C., Henders, A. K., Herms, S., Hickie, I. B., Hipolito, M., Hoefels, S., Holmans, P. A., Holsboer, F., Hoogendijk, W. J., Hottenga, J., Hultman, C. M., Hus, V., Ingason, A., Ising, M., Jamain, S., Jones, E. G., Jones, I., Jones, L., Tzeng, J., Kaehler, A. K., Kahn, R. S., Kandaswamy, R., Keller, M. C., Kennedy, J. L., Kenny, E., Kent, L., Kim, Y., Kirov, G. K., Klauck, S. M., Klei, L., Knowles, J. A., Kohli, M. A., Koller, D. L., Konte, B., Korszun, A., Krabbendam, L., Krasucki, R., Kuntsi, J., Kwan, P., Landen, M., Langstrom, N., Lathrop, M., Lawrence, J., Lawson, W. B., Leboyer, M., Ledbetter, D. H., Lee, P. H., Lencz, T., Lesch, K., Levinson, D. F., Lewis, C. M., Li, J., Lichtenstein, P., Lieberman, J. A., Lin, D., Linszen, D. H., Liu, C., Lohoff, F. W., Loo, S. K., Lord, C., Lowe, J. K., Lucae, S., MacIntyre, D. J., Madden, P. A., Maestrini, E., Magnusson, P. K., Mahon, P. B., Maier, W., Malhotra, A. K., Mane, S. M., Martin, C. L., Martin, N. G., Mattheisen, M., Matthews, K., Mattingsdal, M., McCarroll, S. A., McGhee, K. A., McGough, J. J., McGrath, P. J., McGuffin, P., McInnis, M. G., McIntosh, A., McKinney, R., McLean, A. W., McMahon, F. J., McMahon, W. M., McQuillin, A., Medeiros, H., Medland, S. E., Meier, S., Melle, I., Meng, F., Meyer, J., Middeldorp, C. M., Middleton, L., Milanova, V., Miranda, A., Monaco, A. P., Montgomery, G. W., Moran, J. L., Moreno-De-Luca, D., Morken, G., Morris, D. W., Morrow, E. M., Moskvina, V., Muglia, P., Muehleisen, T. W., Muir, W. J., Mueller-Myhsok, B., Murtha, M., Myers, R. M., Myin-Germeys, I., Neale, M. C., Nelson, S. F., Nievergelt, C. M., Nikolov, I., Nimgaonkar, V., Nolen, W. A., Noethen, M. M., Nurnberger, J. I., Nwulia, E. A., Nyholt, D. R., O'Dushlaine, C., Oades, R. D., Olincy, A., Oliveira, G., Olsen, L., Ophoff, R. A., Osby, U., Owen, M. J., Palotie, A., Parr, J. R., Paterson, A. D., Pato, C. N., Pato, M. T., Penninx, B. W., Pergadia, M. L., Pericak-Vance, M. A., Pickard, B. S., Pimm, J., Piven, J., Posthuma, D., Potash, J. B., Poustka, F., Propping, P., Puri, V., Quested, D. J., Quinn, E. M., Antoni Ramos-Quiroga, J., Rasmussen, H. B., Raychaudhuri, S., Rehnstroem, K., Reif, A., Ribases, M., Rice, J. P., Rietschel, M., Roeder, K., Roeyers, H., Rossin, L., Rothenberger, A., Rouleau, G., Ruderfer, D., Rujescu, D., Sanders, A. R., Sanders, S. J., Santangelo, S. L., Sergeant, J. A., Schachar, R., Schalling, M., Schatzberg, A. F., Scheftner, W. A., Schellenberg, G. D., Scherer, S. W., Schork, N. J., Schulze, T. G., Schumacher, J., Schwarz, M., Scolnick, E., Scott, L. J., Shi, J., Shilling, P. D., Shyn, S. I., Silverman, J. M., Slager, S. L., Smalley, S. L., Smit, J. H., Smith, E. N., Sonuga-Barke, E. J., St Clair, D., State, M., Steffens, M., Steinhausen, H., Strauss, J. S., Strohmaier, J., Stroup, T. S., Sutcliffe, J. S., Szatmari, P., Szelinger, S., Thirumalai, S., Thompson, R. C., Todorov, A. A., Tozzi, F., Treutlein, J., Uhr, M., van den Oord, E. J., Van Grootheest, G., van Os, J., Vicente, A. M., Vieland, V. J., Vincent, J. B., Visscher, P. M., Walsh, C. A., Wassink, T. H., Watson, S. J., Weissman, M. M., Werge, T., Wienker, T. F., Wijsman, E. M., Willemsen, G., Williams, N., Willsey, A. J., Witt, S. H., Xu, W., Young, A. H., Yu, T. W., Zammit, S., Zandi, P. P., Zhang, P., Zitman, F. G., Zoellner, S., Devlin, B., Kelsoe, J. R., Sklar, P., Daly, M. J., O'Donovan, M. C., Craddock, N., Sullivan, P. F., Smoller, J. W., Kendler, K. S., Wray, N. R. 2013; 45 (9): 984-?

    Abstract

    Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17-29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD and major depressive disorder (0.32 ± 0.07 s.e.), low between schizophrenia and ASD (0.16 ± 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn's disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders.

    View details for DOI 10.1038/ng.2711

    View details for Web of Science ID 000323748200007

    View details for PubMedID 23933821

    View details for PubMedCentralID PMC3800159

  • A Genome-Wide Association Study (GWAS) for Bronchopulmonary Dysplasia. Pediatrics Wang, H., St Julien, K. R., Stevenson, D. K., Hoffmann, T. J., Witte, J. S., Lazzeroni, L. C., Krasnow, M. A., Quaintance, C. C., Oehlert, J. W., Jelliffe-Pawlowski, L. L., Gould, J. B., Shaw, G. M., O'Brodovich, H. M. 2013; 132 (2): 290-297

    Abstract

    Twin studies suggest that heritability of moderate-severe bronchopulmonary dysplasia (BPD) is 53% to 79%, we conducted a genome-wide association study (GWAS) to identify genetic variants associated with the risk for BPD.The discovery GWAS was completed on 1726 very low birth weight infants (gestational age = 25(0)-29(6/7) weeks) who had a minimum of 3 days of intermittent positive pressure ventilation and were in the hospital at 36 weeks' postmenstrual age. At 36 weeks' postmenstrual age, moderate-severe BPD cases (n = 899) were defined as requiring continuous supplemental oxygen, whereas controls (n = 827) inhaled room air. An additional 795 comparable infants (371 cases, 424 controls) were a replication population. Genomic DNA from case and control newborn screening bloodspots was used for the GWAS. The replication study interrogated single-nucleotide polymorphisms (SNPs) identified in the discovery GWAS and those within the HumanExome beadchip.Genotyping using genomic DNA was successful. We did not identify SNPs associated with BPD at the genome-wide significance level (5 × 10(-8)) and no SNP identified in previous studies reached statistical significance (Bonferroni-corrected P value threshold .0018). Pathway analyses were not informative.We did not identify genomic loci or pathways that account for the previously described heritability for BPD. Potential explanations include causal mutations that are genetic variants and were not assayed or are mapped to many distributed loci, inadequate sample size, race ethnicity of our study population, or case-control differences investigated are not attributable to underlying common genetic variation.

    View details for DOI 10.1542/peds.2013-0533

    View details for PubMedID 23897914

  • A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry. Nature genetics Monda, K. L., Chen, G. K., Taylor, K. C., Palmer, C., Edwards, T. L., Lange, L. A., Ng, M. C., Adeyemo, A. A., Allison, M. A., Bielak, L. F., Chen, G., Graff, M., Irvin, M. R., Rhie, S. K., Li, G., Liu, Y., Liu, Y., Lu, Y., Nalls, M. A., Sun, Y. V., Wojczynski, M. K., Yanek, L. R., Aldrich, M. C., Ademola, A., Amos, C. I., Bandera, E. V., Bock, C. H., Britton, A., Broeckel, U., Cai, Q., Caporaso, N. E., Carlson, C. S., Carpten, J., Casey, G., Chen, W., Chen, F., Chen, Y. I., Chiang, C. W., Coetzee, G. A., Demerath, E., Deming-Halverson, S. L., Driver, R. W., Dubbert, P., Feitosa, M. F., Feng, Y., Freedman, B. I., Gillanders, E. M., Gottesman, O., Guo, X., Haritunians, T., Harris, T., Harris, C. C., Hennis, A. J., Hernandez, D. G., McNeill, L. H., Howard, T. D., Howard, B. V., Howard, V. J., Johnson, K. C., Kang, S. J., Keating, B. J., Kolb, S., Kuller, L. H., Kutlar, A., Langefeld, C. D., Lettre, G., Lohman, K., Lotay, V., Lyon, H., Manson, J. E., Maixner, W., Meng, Y. A., Monroe, K. R., Morhason-Bello, I., Murphy, A. B., Mychaleckyj, J. C., Nadukuru, R., Nathanson, K. L., Nayak, U., N'Diaye, A., Nemesure, B., Wu, S., Leske, M. C., Neslund-Dudas, C., Neuhouser, M., Nyante, S., Ochs-Balcom, H., Ogunniyi, A., Ogundiran, T. O., Ojengbede, O., Olopade, O. I., Palmer, J. R., Ruiz-Narvaez, E. A., Palmer, N. D., Press, M. F., Rampersaud, E., Rasmussen-Torvik, L. J., Rodriguez-Gil, J. L., Salako, B., Schadt, E. E., Schwartz, A. G., Shriner, D. A., Siscovick, D., Smith, S. B., Wassertheil-Smoller, S., Speliotes, E. K., Spitz, M. R., Sucheston, L., Taylor, H., Tayo, B. O., Tucker, M. A., Van den Berg, D. J., Edwards, D. R., Wang, Z., Wiencke, J. K., Winkler, T. W., Witte, J. S., Wrensch, M., Wu, X., Yang, J. J., Levin, A. M., Young, T. R., Zakai, N. A., Cushman, M., Zanetti, K. A., Zhao, J. H., Zhao, W., Zheng, Y., Zhou, J., Ziegler, R. G., Zmuda, J. M., Fernandes, J. K., Gilkeson, G. S., Kamen, D. L., Hunt, K. J., Spruill, I. J., Ambrosone, C. B., Ambs, S., Arnett, D. K., Atwood, L., Becker, D. M., Berndt, S. I., Bernstein, L., Blot, W. J., Borecki, I. B., Bottinger, E. P., Bowden, D. W., Burke, G., Chanock, S. J., Cooper, R. S., Ding, J., Duggan, D., Evans, M. K., Fox, C., Garvey, W. T., Bradfield, J. P., Hakonarson, H., Grant, S. F., Hsing, A., Chu, L., Hu, J. J., Huo, D., Ingles, S. A., John, E. M., Jordan, J. M., Kabagambe, E. K., Kardia, S. L., Kittles, R. A., Goodman, P. J., Klein, E. A., Kolonel, L. N., Le Marchand, L., Liu, S., McKnight, B., Millikan, R. C., Mosley, T. H., Padhukasahasram, B., Williams, L. K., Patel, S. R., Peters, U., Pettaway, C. A., Peyser, P. A., Psaty, B. M., Redline, S., Rotimi, C. N., Rybicki, B. A., Sale, M. M., Schreiner, P. J., Signorello, L. B., Singleton, A. B., Stanford, J. L., Strom, S. S., Thun, M. J., Vitolins, M., Zheng, W., Moore, J. H., Williams, S. M., Ketkar, S., Zhu, X., Zonderman, A. B., Kooperberg, C., Papanicolaou, G. J., Henderson, B. E., Reiner, A. P., Hirschhorn, J. N., Loos, R. J., North, K. E., Haiman, C. A. 2013; 45 (6): 690-696

    Abstract

    Genome-wide association studies (GWAS) have identified 36 loci associated with body mass index (BMI), predominantly in populations of European ancestry. We conducted a meta-analysis to examine the association of >3.2 million SNPs with BMI in 39,144 men and women of African ancestry and followed up the most significant associations in an additional 32,268 individuals of African ancestry. We identified one new locus at 5q33 (GALNT10, rs7708584, P = 3.4 × 10(-11)) and another at 7p15 when we included data from the GIANT consortium (MIR148A-NFE2L3, rs10261878, P = 1.2 × 10(-10)). We also found suggestive evidence of an association at a third locus at 6q16 in the African-ancestry sample (KLHL32, rs974417, P = 6.9 × 10(-8)). Thirty-two of the 36 previously established BMI variants showed directionally consistent effect estimates in our GWAS (binomial P = 9.7 × 10(-7)), five of which reached genome-wide significance. These findings provide strong support for shared BMI loci across populations, as well as for the utility of studying ancestrally diverse populations.

    View details for DOI 10.1038/ng.2608

    View details for PubMedID 23583978

  • Diacylglycerol Kinase K Variants Impact Hypospadias in a California Study Population JOURNAL OF UROLOGY Carmichael, S. L., Mohammed, N., Ma, C., Iovannisci, D., Choudhry, S., Baskin, L. S., Witte, J. S., Shaw, G. M., Lammer, E. J. 2013; 189 (1): 305-311

    Abstract

    A recent genome wide association study demonstrated the novel finding that variants in DGKK are associated with hypospadias. Our objectives were to determine whether this finding could be replicated in a more racially/ethnically diverse study population of California births and to provide a more comprehensive investigation of variants.We examined the association of 27 DGKK single nucleotide polymorphisms with hypospadias relative to population based nonmalformed controls born in selected California counties from 1990 to 2003. Analyses included a maximum of 928 controls and 665 cases (mild in 91, moderate in 336, severe in 221 and undetermined in 17). Results for mild and moderate cases were similar, so they were grouped together.For mild and moderate cases OR for 15 of the 27 single nucleotide polymorphisms had p values less than 0.05, with 2 less than 1 and the others ranging from 1.3 to 1.8. Among severe cases ORs tended to be closer to 1, and none of the p values were less than 0.05. Due to high linkage disequilibrium across the single nucleotide polymorphisms, haplotype analyses were conducted and 2 blocks were generated. These analyses identified a set of 8 variants associated with a threefold to fourfold increased risk relative to the most common haplotype, regardless of severity of the phenotype (OR 4.1, p <10(-4) for mild to moderate cases and 3.3, p = 0.001 for severe cases).This study confirms that DGKK variants are associated with hypospadias. Additional studies are needed to allow a more thorough investigation of DGKK variability and to delineate the mechanism by which DGKK contributes to urethral development.

    View details for DOI 10.1016/j.juro.2012.09.002

    View details for Web of Science ID 000312604800107

    View details for PubMedID 23177175

  • High Quality Genome-Wide Genotyping from Archived Dried Blood Spots without DNA Amplification. PloS one St Julien, K. R., Jelliffe-Pawlowski, L. L., Shaw, G. M., Stevenson, D. K., O'Brodovich, H. M., Krasnow, M. A. 2013; 8 (5): e64710

    Abstract

    Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.

    View details for DOI 10.1371/journal.pone.0064710

    View details for PubMedID 23737996

    View details for PubMedCentralID PMC3667813

  • Global patterns of prostate cancer incidence, aggressiveness, and mortality in men of african descent. Prostate cancer Rebbeck, T. R., Devesa, S. S., Chang, B., Bunker, C. H., Cheng, I., Cooney, K., Eeles, R., Fernandez, P., Giri, V. N., Gueye, S. M., Haiman, C. A., Henderson, B. E., Heyns, C. F., Hu, J. J., Ingles, S. A., Isaacs, W., Jalloh, M., John, E. M., Kibel, A. S., Kidd, L. R., Layne, P., Leach, R. J., Neslund-Dudas, C., Okobia, M. N., Ostrander, E. A., Park, J. Y., Patrick, A. L., Phelan, C. M., Ragin, C., Roberts, R. A., Rybicki, B. A., Stanford, J. L., Strom, S., Thompson, I. M., Witte, J., Xu, J., Yeboah, E., Hsing, A. W., Zeigler-Johnson, C. M. 2013; 2013: 560857-?

    Abstract

    Prostate cancer (CaP) is the leading cancer among men of African descent in the USA, Caribbean, and Sub-Saharan Africa (SSA). The estimated number of CaP deaths in SSA during 2008 was more than five times that among African Americans and is expected to double in Africa by 2030. We summarize publicly available CaP data and collected data from the men of African descent and Carcinoma of the Prostate (MADCaP) Consortium and the African Caribbean Cancer Consortium (AC3) to evaluate CaP incidence and mortality in men of African descent worldwide. CaP incidence and mortality are highest in men of African descent in the USA and the Caribbean. Tumor stage and grade were highest in SSA. We report a higher proportion of T1 stage prostate tumors in countries with greater percent gross domestic product spent on health care and physicians per 100,000 persons. We also observed that regions with a higher proportion of advanced tumors reported lower mortality rates. This finding suggests that CaP is underdiagnosed and/or underreported in SSA men. Nonetheless, CaP incidence and mortality represent a significant public health problem in men of African descent around the world.

    View details for DOI 10.1155/2013/560857

    View details for PubMedID 23476788

    View details for PubMedCentralID PMC3583061

  • A Genetic Signature of Spina Bifida Risk from Pathway-Informed Comprehensive Gene-Variant Analysis PLOS ONE Marini, N. J., Hoffmann, T. J., Lammer, E. J., Hardin, J., Lazaruk, K., Stein, J. B., Gilbert, D. A., Wright, C., Lipzen, A., Pennacchio, L. A., Carmichael, S. L., Witte, J. S., Shaw, G. M., Rine, J. 2011; 6 (11)

    Abstract

    Despite compelling epidemiological evidence that folic acid supplements reduce the frequency of neural tube defects (NTDs) in newborns, common variant association studies with folate metabolism genes have failed to explain the majority of NTD risk. The contribution of rare alleles as well as genetic interactions within the folate pathway have not been extensively studied in the context of NTDs. Thus, we sequenced the exons in 31 folate-related genes in a 480-member NTD case-control population to identify the full spectrum of allelic variation and determine whether rare alleles or obvious genetic interactions within this pathway affect NTD risk. We constructed a pathway model, predetermined independent of the data, which grouped genes into coherent sets reflecting the distinct metabolic compartments in the folate/one-carbon pathway (purine synthesis, pyrimidine synthesis, and homocysteine recycling to methionine). By integrating multiple variants based on these groupings, we uncovered two provocative, complex genetic risk signatures. Interestingly, these signatures differed by race/ethnicity: a Hispanic risk profile pointed to alterations in purine biosynthesis, whereas that in non-Hispanic whites implicated homocysteine metabolism. In contrast, parallel analyses that focused on individual alleles, or individual genes, as the units by which to assign risk revealed no compelling associations. These results suggest that the ability to layer pathway relationships onto clinical variant data can be uniquely informative for identifying genetic risk as well as for generating mechanistic hypotheses. Furthermore, the identification of ethnic-specific risk signatures for spina bifida resonated with epidemiological data suggesting that the underlying pathogenesis may differ between Hispanic and non-Hispanic groups.

    View details for DOI 10.1371/journal.pone.0028408

    View details for Web of Science ID 000298168100069

    View details for PubMedID 22140583

    View details for PubMedCentralID PMC3227667

  • Identification, Replication, and Fine-Mapping of Loci Associated with Adult Height in Individuals of African Ancestry PLOS GENETICS N'Diaye, A., Chen, G. K., Palmer, C. D., Ge, B., Tayo, B., Mathias, R. A., Ding, J., Nalls, M. A., Adeyemo, A., Adoue, V., Ambrosone, C. B., Atwood, L., Bandera, E. V., Becker, L. C., Berndt, S. I., Bernstein, L., Blot, W. J., Boerwinkle, E., Britton, A., Casey, G., Chanock, S. J., Demerath, E., Deming, S. L., Diver, W. R., Fox, C., Harris, T. B., Hernandez, D. G., Hu, J. J., Ingles, S. A., John, E. M., Johnson, C., Keating, B., Kittles, R. A., Kolonel, L. N., Kritchevsky, S. B., Le Marchand, L., Lohman, K., Liu, J., Millikan, R. C., Murphy, A., Musani, S., Neslund-Dudas, C., North, K. E., Nyante, S., Ogunniyi, A., Ostrander, E. A., Papanicolaou, G., Patel, S., Pettaway, C. A., Press, M. F., Redline, S., Rodriguez-Gil, J. L., Rotimi, C., Rybicki, B. A., Salako, B., Schreiner, P. J., Signorello, L. B., Singleton, A. B., Stanford, J. L., Stram, A. H., Stram, D. O., Strom, S. S., Suktitipat, B., Thun, M. J., Witte, J. S., Yanek, L. R., Ziegler, R. G., Zheng, W., Zhu, X., Zmuda, J. M., Zonderman, A. B., Evans, M. K., Liu, Y., Becker, D. M., Cooper, R. S., Pastinen, T., Henderson, B. E., Hirschhorn, J. N., Lettre, G., Haiman, C. A. 2011; 7 (10)

    Abstract

    Adult height is a classic polygenic trait of high heritability (h(2) approximately 0.8). More than 180 single nucleotide polymorphisms (SNPs), identified mostly in populations of European descent, are associated with height. These variants convey modest effects and explain approximately10% of the variance in height. Discovery efforts in other populations, while limited, have revealed loci for height not previously implicated in individuals of European ancestry. Here, we performed a meta-analysis of genome-wide association (GWA) results for adult height in 20,427 individuals of African ancestry with replication in up to 16,436 African Americans. We found two novel height loci (Xp22-rs12393627, P = 3.4×10(-12) and 2p14-rs4315565, P = 1.2×10(-8)). As a group, height associations discovered in European-ancestry samples replicate in individuals of African ancestry (P = 1.7×10(-4) for overall replication). Fine-mapping of the European height loci in African-ancestry individuals showed an enrichment of SNPs that are associated with expression of nearby genes when compared to the index European height SNPs (P<0.01). Our results highlight the utility of genetic studies in non-European populations to understand the etiology of complex human diseases and traits.

    View details for DOI 10.1371/journal.pgen.1002298

    View details for Web of Science ID 000296665400007

    View details for PubMedID 21998595

    View details for PubMedCentralID PMC3188544

  • The landscape of recombination in African Americans NATURE Hinch, A. G., Tandon, A., Patterson, N., Song, Y., Rohland, N., Palmer, C. D., Chen, G. K., Wang, K., Buxbaum, S. G., Akylbekova, E. L., Aldrich, M. C., Ambrosone, C. B., Amos, C., Bandera, E. V., Berndt, S. I., Bernstein, L., Blot, W. J., Bock, C. H., Boerwinkle, E., Cai, Q., Caporaso, N., Casey, G., Cupples, L. A., Deming, S. L., Diver, W. R., Divers, J., Fornage, M., Gillanders, E. M., Glessner, J., Harris, C. C., Hu, J. J., Ingles, S. A., Isaacs, W., John, E. M., Kao, W. H., Keating, B., Kittles, R. A., Kolonel, L. N., Larkin, E., Le Marchand, L., McNeill, L. H., Millikan, R. C., Murphy, A., Musani, S., Neslund-Dudas, C., Nyante, S., Papanicolaou, G. J., Press, M. F., Psaty, B. M., Reiner, A. P., Rich, S. S., Rodriguez-Gil, J. L., Rotter, J. I., Rybicki, B. A., Schwartz, A. G., Signorello, L. B., Spitz, M., Strom, S. S., Thun, M. J., Tucker, M. A., Wang, Z., Wiencke, J. K., Witte, J. S., Wrensch, M., Wu, X., Yamamura, Y., Zanetti, K. A., Zheng, W., Ziegler, R. G., Zhu, X., Redline, S., Hirschhorn, J. N., Henderson, B. E., Taylor, H. A., Price, A. L., Hakonarson, H., Chanock, S. J., Haiman, C. A., Wilson, J. G., Reich, D., Myers, S. R. 2011; 476 (7359): 170-U67

    Abstract

    Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P value < 10(-245)). We identify a 17-base-pair DNA sequence motif that is enriched in these hotspots, and is an excellent match to the predicted binding target of PRDM9 alleles common in West Africans and rare in Europeans. Sites of this motif are predicted to be risk loci for disease-causing genomic rearrangements in individuals carrying these alleles. More generally, this map provides a resource for research in human genetic variation and evolution.

    View details for DOI 10.1038/nature10336

    View details for Web of Science ID 000293731900028

    View details for PubMedID 21775986

    View details for PubMedCentralID PMC3154982

  • Socioeconomic status and prostate cancer incidence and mortality rates among the diverse population of California CANCER CAUSES & CONTROL Cheng, I., Witte, J. S., McClure, L. A., Shema, S. J., Cockburn, M. G., John, E. M., Clarke, C. A. 2009; 20 (8): 1431-1440

    Abstract

    The racial/ethnic disparities in prostate cancer rates are well documented, with the highest incidence and mortality rates observed among African-Americans followed by non-Hispanic Whites, Hispanics, and Asian/Pacific Islanders. Whether socioeconomic status (SES) can account for these differences in risk has been investigated in previous studies, but with conflicting results. Furthermore, previous studies have focused primarily on the differences between African-Americans and non-Hispanic Whites, and little is known for Hispanics and Asian/Pacific Islanders.To further investigate the relationship between SES and prostate cancer among African-Americans, non-Hispanic Whites, Hispanics, and Asian/Pacific Islanders, we conducted a large population-based cross-sectional study of 98,484 incident prostate cancer cases and 8,997 prostate cancer deaths from California.Data were abstracted from the California Cancer Registry, a population-based surveillance, epidemiology, and end results (SEER) registry. Each prostate cancer case and death was assigned a multidimensional neighborhood-SES index using the 2000 US Census data. SES quintile-specific prostate cancer incidence and mortality rates and rate ratios were estimated using SEER*Stat for each race/ethnicity categorized into 10-year age groups.For prostate cancer incidence, we observed higher levels of SES to be significantly associated with increased risk of disease [SES Q1 vs. Q5: relative risk (RR) = 1.28; 95% confidence interval (CI): 1.25-1.30]. Among younger men (45-64 years), African-Americans had the highest incidence rates followed by non-Hispanic Whites, Hispanics, and Asian/Pacific Islanders for all SES levels. Yet, among older men (75-84 years) Hispanics, following African-Americans, displayed the second highest incidence rates of prostate cancer. For prostate cancer deaths, higher levels of SES were associated with lower mortality rates of prostate cancer deaths (SES Q1 vs. Q5: RR = 0.88; 95% CI: 0.92-0.94). African-Americans had a twofold to fivefold increased risk of prostate cancer deaths in comparison to non-Hispanic Whites across all levels of SES.Our findings suggest that SES alone cannot account for the greater burden of prostate cancer among African-American men. In addition, incidence and mortality rates of prostate cancer display different age and racial/ethnic patterns across gradients of SES.

    View details for DOI 10.1007/s10552-009-9369-0

    View details for Web of Science ID 000270737900020

    View details for PubMedID 19526319

    View details for PubMedCentralID PMC2746891

  • Nonsteroidal antiinflammatory drugs and decreased risk of advanced prostate cancer: Modification by lymphotoxin alpha AMERICAN JOURNAL OF EPIDEMIOLOGY Liu, X., Plummer, S. J., Nock, N. L., Casey, G., Witte, J. S. 2006; 164 (10): 984-989

    Abstract

    The potentially protective effect of nonsteroidal antiinflammatory drugs (NSAIDs) on prostate cancer may only exist among certain subgroups of men, such as those with particular variants in inflammatory response genes. To investigate this, the authors undertook a case-control study (n = 1,012) of the association between NSAIDs and more advanced prostate cancer in Ohio men recruited between 2001 and 2004 and evaluated whether this association was modified by a functional polymorphism in the lymphotoxin alpha (LTA) gene (LTA C+80A, where the CC genotype results in higher LTA production). The authors observed an inverse association between aspirin or ibuprofen use and disease (odds ratio = 0.67, 95% confidence interval: 0.52, 0.87). This was modified by the LTA C+80A variant (p for interaction = 0.03): Among men with the CC genotype, the inverse association between NSAIDs and prostate cancer was substantially stronger (odds ratio = 0.43, 95% confidence interval: 0.28, 0.67). For men without the CC genotype, NSAID use was not associated with disease (p = 0.30). The authors observed similar associations when examining dose/duration of NSAID use. This suggests that any potential chemoprevention of prostate cancer by NSAIDs may be most appropriate for men with the LTA +80CC genotype.

    View details for DOI 10.1093/aje/kwj294

    View details for Web of Science ID 000241958900009

    View details for PubMedID 16931544

  • Polymorphisms in estrogen bioactivation, detoxification and oxidative DNA base excision repair genes and prostate cancer risk CARCINOGENESIS Nock, N. L., Cicek, M. S., Li, L., Liu, X., Rybicki, B. A., Moreira, A., Plummer, S. J., Casey, G., Witte, J. S. 2006; 27 (9): 1842-1848

    Abstract

    To date, the potential impact of hormones on prostate cancer has predominantly focused on receptor-mediated events. However, catechol estrogens, if not inactivated by catechol-O-methyltransferase (COMT), can generate large quantities of reactive oxygen species (ROS). ROS may cause a spectrum of damage including oxidative DNA base lesions, which can lead to irreversible mutation(s) if they are not repaired by base excision repair (BER) systems. hOGG1 is a key enzyme in short patch BER because it recognizes and performs initial excision of the most common form of oxidative DNA base damage, 8-hydroxyguanine (8-oxo-dG). To investigate potential non-receptor-mediated estrogen effects, we evaluated the association between COMT Val158Met and hOGG1 Ser326Cys polymorphisms and prostate cancer in a family-based case-control study (439 prostate cancer cases, 479 brother controls). We observed no noteworthy associations between these polymorphisms and prostate cancer risk in the total study population. However, among men with more aggressive prostate cancer, the hOGG1 326 Cys/Cys genotype was inversely associated with disease (OR=0.30; 95% CI=0.09-0.98). Combining the lower activity CYP1B1 432 Leu/Leu or Leu/Val genotypes (which may decrease the level of catechol estrogens and ROS generated) with the hOGG1 326 Cys/Cys genotype and the XRCC1 399 Arg/Arg or Arg/Gln genotypes (which may enhance BER) resulted in an even further reduced risk in Caucasians with more aggressive disease (OR=0.09; 95% CI=0.01-0.56). Including the high-activity COMT 158Val allele to this combination also lowered aggressive prostate cancer risk but the effect was not as strong (OR=0.20; 95% CI=0.05-0.88). The decreased risk we observed with the hOGG1 326 Cys/Cys genotype confirms an earlier report and the further reduced risk found with the CYP1B1 (432 Leu/Leu or Leu/Val)-hOGG1 (326 Cys/Cys)-XRCC1 (Arg/Arg or Arg/Gln) genotype combination may lend new insights to the importance of ROS generated from non-receptor-mediated estrogenic mechanisms in more aggressive prostate cancer.

    View details for DOI 10.1093/carcin/bgl022

    View details for Web of Science ID 000239901000013

    View details for PubMedID 16569655

  • Novel missense mutations of the Deleted-in-AZoospermia-Like (DAZL) gene in infertile women and men REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY Tung, J. Y., Rosen, M. P., Nelson, L. M., Turek, P. J., Witte, J. S., Cramer, D. W., Cedars, M. I., Reijo-Pera, R. A. 2006; 4

    Abstract

    The Deleted-in-AZoospermia-Like (DAZL) gene has homologs required for germ cell development in many organisms. Recently, we showed that there are several common polymorphisms within the DAZL gene that are associated with age at ovarian failure/menopause and sperm count.Here we sought to identify rare mutations in DAZL and examine their phenotypes in men and women. We sequenced the DAZL gene in 519 individuals; sequences spanned the entire coding region of the gene.We report the identification of four putative missense mutations in DAZL. Three individuals that were heterozygous for a DAZL mutation reported having children, while two individuals that were homozygous reported no children. These mutations were found only in infertile men and women.Given the strong data associating DAZL polymorphisms and deletions with fertility in humans and model organisms, we suggest that these mutations may be associated with age at menopause and/or sperm count and warrant further biochemical and genetic investigation.

    View details for DOI 10.1186/1477-7827-4-40

    View details for Web of Science ID 000240146900001

    View details for PubMedID 16884537

    View details for PubMedCentralID PMC1557510

  • Polymorphisms in polycyclic aromatic hydrocarbon metabolism and conjugation genes, interactions with smoking and prostate cancer risk CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Nock, N. L., Liu, Cicek, M. S., Li, L., Macarie, F., Rybicki, B. A., Plummer, S. J., MacLennan, G. T., Casey, G., Witte, J. S. 2006; 15 (4): 756-761

    Abstract

    The relationship between cigarette smoking and prostate cancer remains unclear. Any potential association may depend on the individuals' ability to metabolize and detoxify cigarette carcinogens--such as polycyclic aromatic hydrocarbons. To investigate this, we studied the association between prostate cancer and smoking, as well as the main and modifying effects of functional polymorphisms in genes that metabolize polycyclic aromatic hydrocarbons (CYP1A1 Ile(462)Val, microsomal epoxide hydrolase His(139)Arg) and detoxify reactive derivatives (GSTM1 null deletion, GSTT1 null deletion, GSTP1 Ile(105)Val and Ala(114)Val) using a family-based case-control design (439 prostate cancer cases and 479 brother controls). Within the entire study population, there were no main effects for smoking or any of the polymorphisms. However, the nondeleted GSTM1 allele was inversely associated with prostate cancer [odds ratio (OR), 0.50; 95% confidence interval (95% CI), 0.26-0.94] among men with less aggressive disease (Gleason score < 7 and clinical tumor stage < T2c) and positively associated (OR, 1.68; 95% CI, 1.01-2.79) with prostate cancer in men with more aggressive disease (Gleason score > or = 7 or clinical tumor stage > or = T2c). We also found a statistically significant negative multiplicative interaction between the GSTM1 nondeleted allele and heavy smoking (> 20 pack-years) in the total study population (P = 0.01) and in Caucasians (P = 0.01). Among Caucasians, heavy smoking increased prostate cancer risk nearly 2-fold in those with the GSTM1 null genotype (OR, 1.73; 95% CI, 0.99-3.05) but this increased risk was not observed in heavy smokers who carried the GSTM1 nondeleted allele (OR, 0.95; 95% CI, 0.53-1.71). Our results highlight the importance of considering genetic modifiers of carcinogens when evaluating smoking in prostate cancer.

    View details for DOI 10.1158/1055-9965.EPI-05-0826

    View details for Web of Science ID 000237045100025

    View details for PubMedID 16614120

  • No association between genetic polymorphisms in insulin and insulin receptor substrate-1 and prostate cancer CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Li, L., Cicek, M. S., Casey, G., Witte, J. S. 2005; 14 (10): 2462-2463
  • No association between a tetranucleotide repeat polymorphism of CYP19 and prostate cancer CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Li, L., Cicek, M. S., Casey, G., Witte, J. S. 2004; 13 (12): 2280-2281

    View details for Web of Science ID 000226077100045

    View details for PubMedID 15598794

  • Relationship between methylenetetrahydrofolate reductase C677T and A1298C genotypes and haplotypes and prostate cancer risk and aggressiveness CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Cicek, M. S., Nock, N. L., Li, L., Conti, D. V., Casey, G., Witte, J. S. 2004; 13 (8): 1331-1336

    Abstract

    Previous reports indicate that polymorphisms in the MTHFR gene play a role in cancer development, but their potential impact on prostate cancer has not been well studied. Here, we evaluate the association between two MTHFR polymorphisms, C677T and A1298C, and prostate cancer risk and aggressiveness in a moderately large family-based case-control study (439 cases and 479 sibling controls). Among all study subjects, we observed no association between the C677T variant and prostate cancer but a slight positive association between the A1298C variant and risk of this disease [odds ratio (OR) 1.41, 95% confidence interval (CI) 0.96-2.06; P = 0.08]. When stratifying the study population by disease aggressiveness at diagnosis, the C677T variant was positively associated with risk among men with less advanced disease (OR 1.86, 95% CI 1.00-3.46; P = 0.05). In contrast, when looking at men with more advanced disease, the C677T variant was inversely associated with risk (OR 0.51, 95% CI 0.32-0.82; P = 0.01), whereas the A1298C variant was positively associated with risk (OR 1.79, 95% CI 1.06-3.02; P = 0.03). Furthermore, the 677T-1298A haplotype was positively associated with prostate cancer among men with less advanced disease (OR 1.84, 95% CI 1.07-3.16; P = 0.03) and inversely associated with risk of more advanced disease (OR 0.47, 95% CI 0.29-0.76; P = 0.002). Our findings suggest that 677T and 1298A, or another variant on their haplotype, may be associated with a reduced risk of progression to more advanced prostate cancer.

    View details for Web of Science ID 000223155500011

    View details for PubMedID 15298954

  • Genetic dissection of complex traits with chromosome substitution strains of mice SCIENCE Singer, J. B., Hill, A. E., Burrage, L., Olszens, K. R., Song, J. H., Justice, M., O'Brien, W. E., Conti, D. V., Witte, J. S., Lander, E. S., Nadeau, J. H. 2004; 304 (5669): 445-448

    Abstract

    Chromosome substitution strains (CSSs) have been proposed as a simple and powerful way to identify quantitative trait loci (QTLs) affecting developmental, physiological, and behavioral processes. Here, we report the construction of a complete CSS panel for a vertebrate species. The CSS panel consists of 22 mouse strains, each of which carries a single chromosome substituted from a donor strain (A/J) onto a common host background (C57BL/6J). A survey of 53 traits revealed evidence for 150 QTLs affecting serum levels of sterols and amino acids, diet-induced obesity, and anxiety. These results demonstrate that CSSs greatly facilitate the detection and identification of genes that control the wide diversity of naturally occurring phenotypic variation in the A/J and C57BL/6J inbred strains.

    View details for DOI 10.1126/science.1093139

    View details for Web of Science ID 000220845400050

    View details for PubMedID 15031436

  • Comprehensive evaluation of the association between prostate cancer and genotypes/haplotypes in CYP17A1, CYP3A4, and SRD5A2 EUROPEAN JOURNAL OF HUMAN GENETICS Loukola, A., Chadha, M., Penn, S. G., Rank, D., Conti, D. V., Thompson, D., Cicek, M., Love, B., Bivolarevic, Yang, Q., Jiang, Y. L., Hanzel, D. K., Dains, K., Paris, P. L., Casey, G., Witte, J. S. 2004; 12 (4): 321-332

    Abstract

    Genes involved in the testosterone biosynthetic pathway - such as CYP17A1, CYP3A4, and SRD5A2 - represent strong candidates for affecting prostate cancer. Previous work has detected associations between individual variants in these three genes and prostate cancer risk and aggressiveness. To more comprehensively evaluate CYP17A1, CYP3A4, and SRD5A2, we undertook a two-phase study of the relationship between their genotypes/haplotypes and prostate cancer. Phase I of the study first searched for single-nucleotide polymorphisms (SNPs) in these genes by resequencing 24 individuals from the Coriell Polymorphism Discovery Resource, 92-110 men from prostate cancer case-control sibships, and by leveraging public databases. In all, 87 SNPs were discovered and genotyped in 276 men from case-control sibships. Those SNPs exhibiting preliminary case-control allele frequency differences, or distinguishing (ie, 'tagging') common haplotypes across the genes, were identified for further study (24 SNPs in total). In Phase II of the study, the 24 SNPs were genotyped in an additional 841 men from case-control sibships. Finally, associations between genotypes/haplotypes in CYP17A1, CYP3A4, and SRD5A2 and prostate cancer were evaluated in the total case-control sample of 1117 brothers from 506 sibships. Family-based analyses detected associations between prostate cancer risk or aggressiveness and a number of CYP3A4 SNPs (P-values between 0.006 and 0.05), a CYP3A4 haplotype (P-values 0.05 and 0.009 in nonstratified and stratified analysis, respectively), and two SRD5A2 SNPs in strong linkage disequilibrium (P=0.02). Undertaking a two-phase study comprising SNP discovery, haplotype tagging, and association analyses allowed us to more fully decipher the relation between CYP17A1, CYP3A4, and SRD5A2 and prostate cancer.

    View details for DOI 10.1038/sj.ejhg.5201101

    View details for Web of Science ID 000220879300010

    View details for PubMedID 14560315

  • No association between genetic Polymorphisms in 1GF-1 and IGFBP-3 and prostate cancer CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Li, L., Cicek, M. S., Casey, G., Witte, J. S. 2004; 13 (3): 497-498

    View details for Web of Science ID 000220081000026

    View details for PubMedID 15006930

  • DNA repair gene XRCC1 and XPD polymorphisms and risk of prostate cancer CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Rybicki, B. A., Conti, D. V., Moreira, A., Cicek, M., Casey, G., Witte, J. S. 2004; 13 (1): 23-29

    Abstract

    The X-ray repair cross-complementing group 1 (XRCC1) and xeroderma pigmentosum group D (XPD) genes are involved in base excision repair and nucleotide excision repair of DNA repair pathways, respectively. A growing body of evidence suggests that XRCC1 and XPD are important in environmentally induced cancers, and polymorphisms in both genes have been identified. To determine whether the XRCC1 (codon Arg399Gln) and XPD (codon Asp312Asn and codon Lys751Gln) polymorphisms are associated with prostate cancer susceptibility, we genotyped these polymorphisms in a primarily Caucasian sample of 506 sibships (n = 1,117) ascertained through a brother with prostate cancer. Sibships were analyzed with a Cox proportional hazards model with age at prostate cancer diagnosis as the outcome. Of the three polymorphisms investigated, only the XPD codon 312 Asn/Asn genotype had an odds ratio (OR) significantly different from one (OR, 1.61; 95% CI, 1.03-2.53). Analyses stratified by the clinical characteristics of affected brothers in the sibship did not reveal any significant heterogeneity in risk. In exploring two-way gene interactions, we found a markedly elevated risk for the combination of the XPD codon 312 Asn/Asn and XRCC1 codon 399 Gln/Gln genotypes (OR, 4.81; 95% CI, 1.66-13.97). In summary, our results suggest that the XPD codon 312 Asn allele may exert a modest positive effect on prostate cancer risk when two copies of the allele are present, and this effect is enhanced by the XRCC codon 399 Gln allele in its recessive state.

    View details for DOI 10.1158/1055-9965.EPI-03-0053

    View details for Web of Science ID 000188438300006

    View details for PubMedID 14744728

  • Comparison of missing data approaches in linkage analysis Xing, C., Schumacher, F. R., Conti, D. V., Witte, J. S. BIOMED CENTRAL LTD. 2003: S44

    Abstract

    Observational cohort studies have been little used in linkage analyses due to their general lack of large, disease-specific pedigrees. Nevertheless, the longitudinal nature of such studies makes them potentially valuable for assessing the linkage between genotypes and temporal trends in phenotypes. The repeated phenotype measures in cohort studies (i.e., across time), however, can have extensive missing information. Existing methods for handling missing data in observational studies may decrease efficiency, introduce biases, and give spurious results. The impact of such methods when undertaking linkage analysis of cohort studies is unclear. Therefore, we compare here six methods of imputing missing repeated phenotypes on results from genome-wide linkage analyses of four quantitative traits from the Framingham Heart Study cohort.We found that simply deleting observations with missing values gave many more nominally statistically significant linkages than the other five approaches. Among the latter, those with similar underlying methodology (i.e., imputation- versus model-based) gave the most consistent results, although some discrepancies remained.Different methods for addressing missing values in linkage analyses of cohort studies can give substantially diverse results, and must be carefully considered to protect against biases and spurious findings.

    View details for DOI 10.1186/1471-2156-4-S1-S44

    View details for Web of Science ID 000188320900044

    View details for PubMedID 14975112

    View details for PubMedCentralID PMC1866480

  • Genome-wide scan of brothers: Replication and fine mapping of prostate cancer susceptibility and aggressiveness loci PROSTATE Witte, J. S., Suarez, B. K., Thiel, B., Lin, J., Yu, A., Banerjee, T. K., Burmester, J. K., Casey, G., Catalona, W. J. 2003; 57 (4): 298-308

    Abstract

    Substantial evidence suggests that genetic factors play an important role in both the risk of prostate cancer and its biologic aggressiveness. Here we investigate prostate cancer susceptibility and aggressiveness with genome-wide linkage analyses of affected brothers.We first undertook a new genome-wide linkage study of 259 brothers with prostate cancer. Our analyses tested whether the proportion of marker alleles shared by brothers was correlated with disease status or Gleason score. To further clarify 11 linkage regions observed here or previously, we genotyped and analyzed an additional 101 finely spaced markers in the 259 men, and in 594 previously studied brothers, allowing for a pooled genome-wide analysis of 853 affected brothers.In the new study, we detected linkage to prostate cancer on chromosome 16q23 (P = 0.009), replicating previous results, and to chromosome 11q24 (P = 0.001). In the pooled analysis, the 16q23 linkage was strengthened (P = 0.0005), as was our previous linkage to chromosome 16p (P = 0.0001), and we detected linkage to chromosome 2q32 (P = 0.009). When evaluating Gleason score, our new study detected linkage to chromosome 7q32 (P = 0.0009), again replicating previous results, and to chromosomes 5p15 (P = 0.003), 9q34 (P = 0.009), 10q26 (P = 0.03), and 18p11 (P = 0.02). In the pooled analysis of Gleason score, we observed stronger linkage to chromosome 7q32 (P = 0.0002), but slightly weaker linkage to chromosomes 5q33 (P = 0.005) and 19q13 (P = 0.009) than previously reported. In addition, the new linkages to chromosomes 10q26 and 18p11 were strengthened (P = 0.0002 and P = 0.002, respectively).Our results provide compelling evidence for loci harboring prostate cancer susceptibility and tumor aggressiveness genes, especially on chromosomes 16q23 and 7q32.

    View details for DOI 10.1002/pros.10304

    View details for Web of Science ID 000186871700006

    View details for PubMedID 14601026

  • Relation of serum insulin-like growth factor-I (IGF-I) and IGF binding protein-3 to risk of prostate cancer (United States) CANCER CAUSES & CONTROL Li, L., Yu, H., Schumacher, F., Casey, G., Witte, J. S. 2003; 14 (8): 721-726

    Abstract

    Insulin-like growth factor I (IGF-I) exerts potent mitogenic and antiapoptotic effects on prostatic epithelial cells. Insulin-like growth factor binding protein-3 (IGFBP-3) modulates the effects of IGF-I, and independently induces apoptosis and inhibits cell growth. Previous studies have inconsistently associated IGF-I and IGFBP-3 with prostate cancer. To try and further clarify these potential associations, we undertook a sibling-matched case-control study.Serum IGF-I and IGFBP-3 were determined for 845 men (408 cases and 437 sibling controls). Conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the association between the serum IGF levels and prostate cancer.Among all study subjects, only the molar ratio of IGF-I to IGFBP-3 was associated with prostate cancer: comparing those in the highest to lowest quartiles gave an OR = 1.62 (95% CI = 1.02-2.57, trend-p = 0.04). Among men with clinically less aggressive disease, we observed positive associations between prostate cancer and high levels of IGF-I (OR = 2.78, 95% CI = 1.06-6.80, trend-p = 0.03), and IGFBP-3 (OR = 2.68, 95% CI = 1.08-6.80, trend-p = 0.04). Simultaneously modeling both left the IGF-I result essentially unchanged, while substantially weakening the IGFBP-3 association.We found that a high IGF-I to IGFBP-3 molar ratio was associated with an increased risk of prostate cancer. Furthermore, high IGF-I was associated with increased risk of prostate cancer among men with less advanced disease at diagnosis. These results lend support to the hypothesis that IGF-I, or the IGF-I to IGFBP-3 molar ratio, is an important risk factor for prostate cancer.

    View details for DOI 10.1023/A:1026383824791

    View details for Web of Science ID 000186272300004

    View details for PubMedID 14674736

  • CYP3A4 and CYP3A5 genotypes, haplotypes, and risk of prostate cancer CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Plummer, S. J., Conti, D. V., Paris, P. L., Curran, A. P., Casey, G., Witte, J. S. 2003; 12 (9): 928-932

    Abstract

    Previous case-only studies have shown that men with the CYP3A4*1B promoter variant are at an increased risk of developing more aggressive forms of prostate cancer. However, no changes in CYP3A4 activity have been found in CYP3A4*1B carriers, suggesting that its association with disease may simply reflect linkage disequilibrium with another functional variant. CYP3A5 is located within 200 kb of CYP3A4, and a variant in CYP3A5 (*1/*3) correlates with function of the CYP3A5 enzyme. In this study, the potential effect of CYP3A4*1B and CYP3A5*1 on prostate cancer risk and aggressiveness were evaluated in a family-based case-control population. The CYP3A4*1B variant was positively associated with prostate cancer among Caucasians with more aggressive disease [odds ratio (OR), 1.91; 95% confidence interval (CI), 1.02-3.57; P=0.04], and inversely associated with risk among Caucasians with less aggressive disease (OR, 0.08; 95% CI, 0.01-0.49; P=0.006) and men with an age of diagnosis <63 (OR, 0.51; 95% CI, 0.26-1.00; P=0.05). The CYP3A5*1 variant was inversely associated with prostate cancer, especially among Caucasians with less aggressive disease (OR, 0.42; 95% CI, 0.22-0.78; P=0.006). As expected based on these genotype-level results, the CYP3A4*1B/CYP3A5*3 haplotype was positively associated with disease (OR, 2.91; 95% CI, 1.36-6.23; P=0.006), and the CYP3A4*1B/CYP3A5*1 haplotype was inversely associated with risk among Caucasians with less aggressive disease (OR, 0.07; 95% CI, 0.01-0.51; P=0.009). These findings suggest that the CYP3A4 and CYP3A5 variants, or other alleles on the haplotypes they help distinguish, are associated with prostate cancer risk and aggressiveness.

    View details for Web of Science ID 000185467900019

    View details for PubMedID 14504207

  • Prostate cancer aggressiveness locus on chromosome segment 19q12-q13.1 identified by linkage and allelic imbalance studies GENES CHROMOSOMES & CANCER Neville, P. J., Conti, D. V., Krumroy, L. M., Catalona, W. J., Suarez, B. K., Witte, J. S., Casey, G. 2003; 36 (4): 332-339

    Abstract

    Whole-genome scan studies recently identified a locus on chromosome segments 19q12-q13.11 linked to prostate tumor aggressiveness by use of the Gleason score as a quantitative trait. We have now completed finer-scale linkage mapping across this region that confirmed and narrowed the candidate region to 2 cM, with a peak between markers D19S875 and D19S433. We also performed allelic imbalance (AI) studies across this region in primary prostate tumors from 52 patients unselected for family history or disease status. A high level of AI was observed, with the highest rates at markers D19S875 (56%) and D19S433 (60%). Furthermore, these two markers defined a smallest common region of AI of 0.8 Mb, with 15 (29%) prostate tumors displaying interstitial AI involving one or both markers. In addition, we noted a positive association between AI at marker D19S875 and extension of tumor beyond the margin (P = 0.02) as well as a higher Gleason score (P = 0.06). These data provide strong evidence that we have mapped a prostate tumor aggressiveness locus to chromosome segments 19q12-q13.11 that may play a role in both familial and non-familial forms of prostate cancer.

    View details for DOI 10.1002/gcc.10165

    View details for Web of Science ID 000181479000002

    View details for PubMedID 12619157

  • Hierarchical modeling of linkage disequilibrum: Genetic structure and spatial relations AMERICAN JOURNAL OF HUMAN GENETICS Conti, D. V., Witte, J. S. 2003; 72 (2): 351-363

    Abstract

    Linkage disequilibrium (LD) mapping offers much promise for the positional cloning of disease-causing genes. However, conventional estimates of LD may fluctuate substantially across contiguous genomic regions, because of population-specific phenomena such as mutation, genetic drift, population structure, and variations in allele frequencies. This fluctuation makes it difficult to interpret patterns of LD and distinguish where a causal gene is located. To address this issue, we propose hierarchical modeling of LD (HLD) for fine-scale mapping. This approach incorporates information on haplotype block structure and chromosomal spatial relations to refine the pattern of LD, increasing the ability to localize disease genes. Here, we present a framework for HLD, a simulation study assessing the performance of HLD under various scenarios, and an application of HLD to existing data. This work demonstrates that hierarchical modeling of linkage disequilibrium is a valuable and flexible approach for fine-scale mapping.

    View details for DOI 10.1086/346117

    View details for Web of Science ID 000180680000015

    View details for PubMedID 12525994

    View details for PubMedCentralID PMC379228

  • Prostate cancer aggressiveness locus on chromosome 7q32-q33 identified by linkage and allelic imbalance studies NEOPLASIA Neville, P. J., Conti, D. V., Paris, P. L., Levin, H., Catalona, W. J., Suarez, B. K., Witte, J. S., Casey, G. 2002; 4 (5): 424-431

    Abstract

    The biologic aggressiveness of prostate tumors is an important indicator of prognosis. Chromosome 7q32-q33 was recently reported to show linkage to more aggressive prostate cancer, based on Gleason score, in a large sibling pair study. We report confirmation and narrowing of the linked region using finer-scale genotyping. We also report a high frequency of allelic imbalance (AI) defined within this locus in a series of 48 primary prostate tumors from men unselected for family history or disease status. The highest frequency of AI was observed with adjacent markers D7S2531 (52%) and D7S1804 (36%). These two markers delineated a common region of AI, with 24 tumors exhibiting interstitial AI involving one or both markers. The 1.1-Mb candidate region contains relatively few transcripts. Additionally, we observed positive associations between interstitial AI at D7S1804 and early age at diagnosis (P=.03) as well as a high combined Gleason score and tumor stage (P=.06). Interstitial AI at D7S2531 was associated with a positive family history of prostate cancer (P=.05). These data imply that we have localized a prostate cancer tumor aggressiveness loci to chromosome 7q32-q33 that is involved in familial and nonfamilial forms of prostate cancer.

    View details for DOI 10.1038/sj.neo.7900254

    View details for Web of Science ID 000177749500007

    View details for PubMedID 12192601

    View details for PubMedCentralID PMC1564121

  • Analysis of mutational spectra: locating hotspots and clusters of mutations using recursive segmentation STATISTICS IN MEDICINE Fijal, B. A., Idury, R. M., Witte, J. S. 2002; 21 (13): 1867-1885

    Abstract

    Mutations within different regions of disease-causing genes can vary in their impact on disease initiation and progression. Determining how individual mutations within such genes affect disease risk and progression can improve the accuracy of prognoses and help guide treatment selection. Estimates of mutation-specific risks can be poor, however, when genes have a large number of distinct mutations, and data for any given mutation is sparse. To address this problem, we present here a method of analysing the spectrum of mutations observed across a gene that pools together mutations that appear to have similar effects on disease. One of the assumptions underlying the analysis of mutational spectra created in this manner is that the frequency of the mutation in the sample reflects the degree of its effect on disease development. Additionally, mutations that disrupt the same functionally important region of the gene are expected to have a similar impact on disease development. These mutations tend to form a cluster within the spectrum. Therefore, we developed an algorithm that segments a spectrum into regions containing sites with similar mutational frequencies, and have derived by simulation equations that allow one to evaluate whether segmentation is needed. We used this approach to investigate the spectrum of mutations observed in the p53 tumour suppressor gene in colorectal cancer tumours. Here, recursive segmentation identified the boundaries of apparent clusters better than did other methods, and this approach could identify clusters of mutations which corresponded to biologically important regions of the p53 protein.

    View details for DOI 10.1002/sim.1145

    View details for Web of Science ID 000176642000004

    View details for PubMedID 12111894

  • Point: Population stratification: A problem for case-control studies of candidate-gene associations? CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Thomas, D. C., Witte, J. S. 2002; 11 (6): 505-512

    View details for Web of Science ID 000176142600001

    View details for PubMedID 12050090

  • Androgen receptor CAG repeats and prostate cancer AMERICAN JOURNAL OF EPIDEMIOLOGY Nelson, K. A., Witte, J. S. 2002; 155 (10): 883-890

    Abstract

    Prostate cancer is the most common nonskin malignancy and the second leading cause of cancer deaths among men in the United States. Prostate cancer ([Mendelian Inheritance in Man 176807]) has a complex etiology; presently, age, ethnicity, and family history are the most consistently reported risk factors associated with disease. Other potential risk and protective factors have also been suggested. Androgen, acting through the androgen receptor (AR) is helpful in preserving the normal function and structure of the prostate. The AR ([Mendelian Inheritance in Man 313700]) is a structurally conserved member of the nuclear receptor superfamily of ligand-activated transcription factors. Androgens, such as testosterone, are strong tumor promoters, and work with the AR to augment the effect of any carcinogens present and stimulate cell division. The CAG repeats encode long glutamine homopolymeric amino acid chains in the amino-terminal domain of the AR gene. The authors focus on CAG repeat length because recent research suggests that men with shorter AR CAG lengths (e.g., < or =22 repeats) are at a greater risk of developing prostate cancer than are those with longer variants. Among populations studied to date, African Americans appear to have the highest frequency of short CAG repeats. Several potential interactions have also been explored, including molecular interactions, androgen deprivation therapy, and prostate-specific antigen expression. CAG repeat length can be determined with high sensitivity and specificity. Presently, there is no recommended population screening for AR CAG repeat length.

    View details for DOI 10.1093/aje/155.10.883

    View details for Web of Science ID 000175628800001

    View details for PubMedID 11994226

  • Relation between tumour necrosis factor polymorphism TNF alpha-308 and risk of asthma EUROPEAN JOURNAL OF HUMAN GENETICS Witte, J. S., Palmer, L. J., O'Connor, R. D., Hopkins, P. J., Hall, J. M. 2002; 10 (1): 82-85

    Abstract

    Tumour necrosis factor (TNF) alpha affects immune response and airway inflammation, which are characteristics of asthma. Genetic factors may impact TNFalpha levels, and several polymorphisms in the TNF gene cluster on chromosome 6p21 have been associated with TNFalpha production and potential increased risk of asthma. The present paper evaluates the relation between two single nucleotide polymorphisms (SNPs) in the TNF gene cluster and asthma risk. The SNPs investigated here are guanine (G) to adenosine (A) substitutions in the TNFalpha and lymphotoxin alpha (LTalpha) genes. The TNFalpha SNP is at position -308 in the promoter region (TNFalpha-308), while the LTalpha SNP is in the first intron NcoI recognition sequence (LTalpha-NcoI). (For both SNPs the G allele is denoted as 1, and the A allele 2.) We determined TNFalpha-308 and LTalpha-NcoI genotypes in 511 individuals: 236 asthma cases and 275 non-asthmatic controls. Data were analysed by logistic regression of asthma status on the genotypes and potential confounders. TNFalpha-308*2 was positively associated with asthma, and this relation was strengthened when restricting cases to individuals reporting acute asthma: the adjusted odds ratio (OR) comparing carriers of one or two TNFalpha-308*2 alleles versus none was 1.86 (95% confidence interval (CI)=1.03-3.34, P=0.04). Further restricting the subjects to those with a family history of asthma, and those of European-American ancestry strengthened the association even more: adjusted OR=3.16 (95% CI=1.04-9.66; P=0.04). LTalpha-NcoI*1 was weakly associated with asthma, and analysis of both genes suggests that only the TNFalpha-308*2 allele increases risk of asthma.

    View details for DOI 10.1038/sj.ejhg.5200746

    View details for Web of Science ID 000174655700012

    View details for PubMedID 11896460

  • Model-free linkage analysis with covariates confirms linkage of prostate cancer to chromosomes 1 and 4 AMERICAN JOURNAL OF HUMAN GENETICS Goddard, K. A., Witte, J. S., Suarez, B. K., Catalona, W. J., Olson, J. M. 2001; 68 (5): 1197-1206

    Abstract

    As with many complex genetic diseases, genome scans for prostate cancer have given conflicting results, often failing to provide replication of previous findings. One factor contributing to the lack of consistency across studies is locus heterogeneity, which can weaken or even eliminate evidence for linkage that is present only in a subset of families. Currently, most analyses either fail to account for locus heterogeneity or attempt to account for it only by partitioning data sets into smaller and smaller portions. In the present study, we model locus heterogeneity among affected sib pairs with prostate cancer by including covariates in the linkage analysis that serve as surrogate measures of between-family linkage differences. The model is a modification of the Olson conditional logistic model for affected relative pairs. By including Gleason score, age at onset, male-to-male transmission, and/or number of affected first-degree family members as covariates, we detected linkage near three locations that were previously identified by linkage (1q24-25 [HPC1; LOD score 3.25, P=.00012], 1q42.2-43 [PCAP; LOD score 2.84, P=.0030], and 4q [LOD score 2.80, P=.00038]), near the androgen-receptor locus on Xq12-13 (AR; LOD score 3.06, P=.00053), and at five new locations (LOD score > 2.5). Without covariates, only a few weak-to-moderate linkage signals were found, none of which replicate findings of previous genome scans. We conclude that covariate-based linkage analysis greatly improves the likelihood that linked regions will be found by incorporation of information about heterogeneity within the sample.

    View details for DOI 10.1086/320103

    View details for Web of Science ID 000168171200013

    View details for PubMedID 11309685

    View details for PubMedCentralID PMC1226100

  • Impact of preadjusting a quantitative phenotype prior to sib-pair linkage analysis when gene(x)environment interaction exists Mosley, J., Conti, D. V., Elston, R. C., Witte, J. S. WILEY-LISS. 2001: S837-S842

    Abstract

    The investigation of potential gene x environment (G x E) interactions is an important facet in the study of complex diseases. When G x E interaction exists, linkage analyses of the interacting gene must treat the environmental factor appropriately. Specifically, the common approach of regressing out an environmental factor prior to linkage analysis may be inappropriate if that factor has an interaction with the gene. This is explored here in the Genetic Analysis Workshop 12 simulated data set using the G x E interaction between major gene four (MG4) and environmental factor two (E2). The analysis shows that preadjusting the quantitative trait three (Q3) phenotype for the main effects of several environmental variables, including one (E2) that interacts with MG4, affects the results of a Haseman-Elston linkage analysis. In particular, the agreement in detecting linkage between preadjusting versus not preadjusting was only 78% and 66% using alpha levels of 0.05 and 0.10, respectively. For both approaches, incorporating an interaction term in the regression models enabled linkage to be detected where the evidence was either minimal or not present in an identical-by-descent main effects-only model. Furthermore, preadjustment for E2 did not appear to account for the major discrepancies between the approaches.

    View details for DOI 10.1002/gepi.2001.21.s1.s837

    View details for Web of Science ID 000171462700155

    View details for PubMedID 11793789

  • Introduction: Analysis of sequence data and population structure GENETIC EPIDEMIOLOGY Witte, J. S., Fijal, B. A. 2001; 21: S600-S601

    View details for DOI 10.1002/gepi.2001.21.s1.s600

    View details for Web of Science ID 000171462700111

    View details for PubMedID 11793745

  • Predicting quantitative trait levels by modeling SNP interaction Fijal, B. A., Kim, L. L., Buxbaum, S. G., Witte, J. S. WILEY-LISS. 2001: S608-S613

    Abstract

    Predicting phenotype from genotype is difficult when the phenotype is affected by a gene with numerous weakly penetrant alleles that differ only in the pattern of their single nucleotide polymorphisms (SNPs). While it is probable that SNP interactions affect phenotype, to our knowledge no one has determined the most effective way of evaluating whether SNPs interact and of modeling the interaction. Therefore, to explore this issue, we investigate here three methods of modeling SNP interaction using data from Genetic Analysis Workshop 12. Since major gene 5 (MG5) has sequence information and explains 37% of the variation in quantitative trait 5 (Q5), we focus on using SNPs within MG5 to predict Q5 among individuals who married into the pedigree. As a preliminary screening step, we reduced the number of SNPs from 269 to 34 based on their association with Q5. In our first models we assumed that SNPs affected Q5 in a simple additive manner. These models explained 34% and 15% of the variation in Q5 in women and men, respectively. Our second model was a linear model, which used individual SNPs and simple interaction terms as predictors. These models explained 36% and 16% of the variation in Q5 levels for women and men, respectively. Our last model was a "hit"-based model which was motivated by the hypothesis that disequilibrium between SNPs may reflect the fact that SNPs affect phenotype by acting in concert with other SNPs within their "disequilibrium set." Thus, the number of hits within the disequilibrium sets were used as predictors. These models explained 35% and 19% of the variation in Q5 for women and men, respectively. Our results suggest that phenotype can be predicted from complex patterns of weakly penetrant SNPs using relatively simple models. We concluded that SNP interaction either was not included in the simulation model, or had only a weak impact on Q5 levels.

    View details for DOI 10.1002/gepi.2001.21.s1.s608

    View details for Web of Science ID 000171462700113

    View details for PubMedID 11793747

  • Hierarchical modeling of the relation between sequence variants and a quantitative trait: Addressing multiple comparison and population stratification issues Kim, L. L., Fijal, B. A., Witte, J. S. WILEY-LISS. 2001: S668-S673

    Abstract

    When analyzing the relation between genetic sequence information and disease traits, false-positive associations can arise due to multiple comparisons and population stratification. In an attempt to address these issues, we incorporate into a conventional analytic model higher-level--or "prior"--models that use additional information to improve estimates while allowing for differing population structures. We apply this hierarchical model to simulated data from the Genetic Analysis Workshop 12. We focus on the effects of common candidate gene sequence variants on quantitative risk factor 5 (Q5) levels. In particular, we compare the regression coefficients (and 95% confidence intervals) obtained from conventional (one-stage) analyses versus the corresponding results from the hierarchical analyses. When examining either the marry-ins or all subjects in the general and isolate populations, the conventional model detected numerous sites in candidate genes 1-5 and 7 that had statistically significant regression coefficients (alpha level = 0.05). In contrast, our hierarchical model primarily only detected associations for variants in candidate gene 2, which is the casual gene for Q5.

    View details for DOI 10.1002/gepi.2001.21.s1.s668

    View details for Web of Science ID 000171462700124

    View details for PubMedID 11793759

  • Replication linkage study for prostate cancer susceptibility genes PROSTATE Suarez, B. K., Lin, J., Witte, J. S., Conti, D. V., Resnick, M. I., Klein, E. A., Burmester, J. K., Vaske, D. A., Banerjee, T. K., Catalona, W. J. 2000; 45 (2): 106-114

    Abstract

    Since the publication of the first genome screen for prostate cancer (CaP) 5 years ago, over a dozen linkage studies have appeared. Most attention has been directed to chromosome 1, where two separate regions have been identified as harboring a prostate cancer susceptibility locus: HPC1 in the 1q24-25 interval and PCaP in the 1q42.2-43 interval. Linkage analysis of chromosome 16 has also provided evidence of harboring two loci predisposing to CaP.We report on a replication linkage study of chromosomes 1 and 16 in 45 new and 4 expanded multiplex CaP families. Multipoint Z-scores were obtained for 30 highly polymorphic short-sequence tandem repeat markers spanning chromosome 1, and 22 markers spanning chromosome 16.The replication sample gave no evidence for a CaP susceptibility locus in the 1q24-25 interval and equivocal evidence for such a locus at 1q42.2-43. With respect to chromosome 16, positive Z-scores were obtained over a contiguous interval covering the entire p arm and the proximal half of the q arm.The linkage analysis of our replication sample does not support the existence of HPC1, and the evidence for the existence of PCaP remains equivocal. Evidence of a susceptibility locus on 16p remains strong, but the evidence for a susceptibility locus on 16q is weakened.

    View details for DOI 10.1002/1097-0045(20001001)45:2<106::AID-PROS4>3.0.CO;2-H

    View details for Web of Science ID 000089614600004

    View details for PubMedID 11027409

  • Re: "Asymptotic bias and efficiency in case-control studies of candidate genes and gene-environment interactions: Basic family designs" - Reply AMERICAN JOURNAL OF EPIDEMIOLOGY Witte, J. S., Gauderman, W. J., Thomas, D. C. 2000; 152 (7): 690-691
  • Testing drug response in the presence of genetic information: sampling issues for clinical trials PHARMACOGENETICS Cardon, L. R., Idury, R. M., Harris, T. J., Witte, J. S., Elston, R. C. 2000; 10 (6): 503-510

    Abstract

    Progress towards construction of a dense map of di-allelic markers across the human genome has generated considerable enthusiasm for pharmacogenomic applications. To date, however, nearly all of the effort on single nucleotide polymorphism (SNP) projects has been focused on marker identification and screening, not on how the SNP genotype data actually can be used in clinical trials to advance medical practice. Here, we explore how different properties of SNPs impact the size, scope and design of clinical trials using a simple trial design. We evaluate the clinical trial sampling requirements under different allele frequencies, gene action, gene effect size and number of markers in a genome screen. Power and sample size calculations suggest that allele frequency and type of gene action can have a dramatic impact on trial sample sizes, in that under some conditions the required sample sizes are too large to be applicable in a costly clinical trial setting. In other situations, however, pharmacogenomic clinical trials can yield significant sampling/cost savings over traditional trials. These properties are discussed with regard to the general usage of genetic information in clinical trial settings.

    View details for DOI 10.1097/00008571-200008000-00003

    View details for Web of Science ID 000088986400003

    View details for PubMedID 10975604

  • Genomewide scan for prostate cancer-aggressiveness loci AMERICAN JOURNAL OF HUMAN GENETICS Witte, J. S., Goddard, K. A., Conti, D. V., Elston, R. C., Lin, J., Suarez, B. K., Broman, K. W., Burmester, J. K., Weber, J. L., Catalona, W. J. 2000; 67 (1): 92-99

    Abstract

    The aggressiveness of prostate cancer (PCa) varies widely: some tumors progress to invasive, potentially life-threatening disease, whereas others stay latent for the remainder of an individual's lifetime. The mechanisms resulting in this variability are not yet understood, but they are likely to involve both genetic and environmental influences. To investigate genetic factors, we conducted a genomewide linkage analysis of 513 brothers with PCa, using the Gleason score, which reflects tumor histology, as a quantitative measure of PCa aggressiveness. To our knowledge, this is the first time that a measure of PCa aggressiveness has been directly investigated as a quantitative trait in a genomewide scan. We employed a generalized multipoint Haseman-Elston linkage-analysis approach that regresses the mean-corrected cross product between the brothers' Gleason scores on the estimated proportion of alleles shared by brothers identical by descent at each marker location. Our results suggest that candidate regions on chromosomes 5q, 7q, and 19q give evidence for linkage to PCa-aggressiveness genes. In particular, the strongest signals detected in these regions were at the following markers (with corresponding P values): for chromosome 5q31-33, between markers D5S1480 and D5S820 (P=.0002); for chromosome 7q32, between markers D7S3061 and D7S1804 (P=.0007); and, for chromosome 19q12, at D19S433 (P=.0004). This indicates that one or more of these candidate regions may contain genes that influence the progression of PCa from latent to invasive disease. Identification of such genes would be extremely valuable for elucidation of the mechanism underlying PCa progression and for determination of treatment in men in whom this disease has been diagnosed.

    View details for DOI 10.1086/302960

    View details for Web of Science ID 000088926900012

    View details for PubMedID 10825281

    View details for PubMedCentralID PMC1287106

  • Identification and pine mapping of a region showing a high frequency of allelic imbalance on chromosome 16q23.2 that corresponds to a prostate cancer susceptibility locus CANCER RESEARCH Paris, P. L., Witte, J. S., Kupelian, P. A., Levin, H., Klein, E. A., Catalona, W. J., Casey, G. 2000; 60 (13): 3645-3649

    Abstract

    Linkage to a prostate cancer susceptibility locus was recently reported on chromosome 16q23. We now report a region exhibiting a high frequency of allelic imbalance (AI) corresponding to this locus in tumors from 51 men diagnosed with prostate cancer using the same linked markers. The highest frequency of AI was found at markers D16S3096 (45%) and D16S516 (53%) that map to chromosome 16q23.2. In addition, 19 of the 51 (37%) prostate tumors showed interstitial AI involving one or both of these markers. This result strongly suggests that a candidate prostate cancer tumor suppressor gene maps between markers D16S3096 and D16S516. We estimate that the distance between these markers is approximately 118 kb using a Stanford radiation hybrid panel. We observed a positive association with family history (P = 0.048) when comparing those men showing interstitial AI at markers D16S3096 and/or D16S516 with those without any imbalance at these two markers. Taken together, these data suggest that we have precisely localized a region of chromosome 16q23.2 that may harbor a prostate cancer tumor suppressor gene implicated in the development of non-familial and possibly familial forms of prostate cancer.

    View details for Web of Science ID 000088162400051

    View details for PubMedID 10910080

  • Correlations of individual plasma carotenoid concentrations in free-living older adults NUTRITION RESEARCH Shikany, J. M., Witte, J. S. 2000; 20 (7): 955-965
  • CYP3A activity in African American and European American men: Population differences and functional effect of the CYP3A4*1B 5 '-promoter region polymorphism CLINICAL PHARMACOLOGY & THERAPEUTICS Wandel, C., Witte, J. S., Hall, J. M., Stein, C. M., Wood, A. J., Wilkinson, G. R. 2000; 68 (1): 82-+

    Abstract

    Cytochrome P4503A (CYP3A) activity exhibits considerable interindividual variability. Possible differences in CYP3A activity were investigated in European American and African American men with the use of midazolam as an in vivo probe.Midazolam was simultaneously administered intravenously (1 mg, [15N3]-labeled) and orally (2 mg, unlabeled in capsule form) to 15 young healthy European American men and a similar group of men of African American descent. Plasma concentration-time curves were measured. The subjects were subsequently genotyped with respect to the CYP3A4*B1 polymorphism (A-290G) in the 5'-promoter (nifedipine-specific element) region.The oral bioavailability of midazolam was about equally determined by intestinal and hepatic extraction with CYP3A activity at the former site exhibiting greater variability. Oral bioavailability was related to intestinal metabolism (r = 0.98), whereas hepatic CYP3A activity contributed little to the interindividual variability (r = 0.03). A lower systemic clearance (265+/-54 versus 310+/-56 mL/min; P = .04), but not oral clearance, was observed in African Americans. With one exception, the African Americans possessed a variant CYP3A4*1B allele (4 heterozygotes A/G and 10 homozygote G/G), whereas all of the European Americans were wild-type homozygotes (A/A). Hepatic CYP3A activity and the systemic clearance of midazolam were about 30% lower in G/G homozygotes than in A/A homozygotes (252+/-53 versus 310+/-54 mL/min; P = .02), and a gene-dose effect was present (P = .01). There was no genotype/phenotype relationship with respect to the oral clearance of midazolam.Comparison of CYP3A activity between populations is complicated by frequency distribution differences in the regulatory CYP3A4*1B polymorphism and lower hepatic CYP3A activity associated with the variant allele. However, this reduction is modest; therefore no major and clinically important difference in CYP3A activity is present between Americans of African or European descent.

    View details for DOI 10.1067/mcp.2000.108506

    View details for Web of Science ID 000088387100012

    View details for PubMedID 10945319

  • A genome screen of multiplex sibships with prostate cancer AMERICAN JOURNAL OF HUMAN GENETICS Suarez, B. K., Lin, J., Burmester, J. K., Broman, K. W., Weber, J. L., Banerjee, T. K., Goddard, K. A., Witte, J. S., Elston, R. C., Catalona, W. J. 2000; 66 (3): 933-944

    Abstract

    Analysis of a genome screen of 504 brothers with prostate cancer (CaP) who were from 230 multiplex sibships identified five regions with nominally positive linkage signals, on chromosomes 2q, 12p, 15q, 16p, and 16q. The strongest signal in these data is found on chromosome 16q, between markers D16S515 and D16S3040, a region suspected to contain a tumor-suppressor gene. On the basis of findings from previous genome screens of families with CaP, three preplanned subanalyses were carried out, in the hope of increasing the subgroup homogeneity. Subgroups were formed by dividing the sibships into a group with a positive family history (FH+) that met criteria for "hereditary" CaP (n=111) versus those which did not meet the criteria (n=119) and by dividing the families into those with a mean onset age below the median (n=115) versus those with a mean onset age above the median (n=115). A separate subanalysis was carried out for families with a history of breast cancer (CaB+ [n=53]). Analyses of these subgroups revealed a number of potentially important differences in regions that were nonsignificant when all the families were analyzed together. In particular, the subgroup without a positive family history (FH-) had a signal in a region that is proximal to the putative site of the HPC1 locus on chromosome 1, whereas the late-age-at-onset group had a signal on 4q. The CaB+ subgroup revealed a strong linkage signal at 1p35.1.

    View details for DOI 10.1086/302818

    View details for Web of Science ID 000088373200016

    View details for PubMedID 10712208

    View details for PubMedCentralID PMC1288174

  • On the relative sample size required for multiple comparisons STATISTICS IN MEDICINE Witte, J. S., Elston, R. C., Cardon, L. R. 2000; 19 (3): 369-372

    Abstract

    Multiple comparisons are commonly made in epidemiologic and genetic research. How to appropriately adjust for multiple comparisons remains a controversial issue. This note demonstrates, however, that large increases in the number of comparisons has a limited effect on the sample size required to maintain an experimentwise alpha-level. In particular, the relative sample size required increases only linearly with the logarithm of the number of comparisons made.

    View details for DOI 10.1002/(SICI)1097-0258(20000215)19:3<369::AID-SIM335>3.0.CO;2-N

    View details for Web of Science ID 000084997000007

    View details for PubMedID 10649302

  • Clinical trials in the genomic era: Effects of protective genotypes on sample size and duration of trial CONTROLLED CLINICAL TRIALS Fijal, B. A., Hall, J. M., Witte, J. S. 2000; 21 (1): 7-20

    Abstract

    It is well known that individuals can vary widely in their disease susceptibilities. One potential source of this variation is the genetic makeup of individuals, which can confer either protection or susceptibility to disease. Here we examine the effects of protective genotypes on the sample sizes and time required to detect differences between clinical trial arms. We show that including individuals with protective genotypes in a clinical trial can increase required sample sizes and trial duration. One can deal with this issue by pregenotyping subjects and selectively enrolling them based on their genotype. Thus we also calculate the number of individuals that must be recruited and pregenotyped to fulfill sample size requirements. The benefits of genotypically screening study subjects will depend on numerous factors, including ease of patient recruitment, cost of genotyping, long-term costs of study (or long-term cost per subject), and the strength of the protective effect. We present several examples that show the potential value of incorporating information about protective genotypes into a clinical trial.

    View details for DOI 10.1016/S0197-2456(99)00039-2

    View details for Web of Science ID 000084911500002

    View details for PubMedID 10660000

  • Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations AMERICAN JOURNAL OF HUMAN GENETICS Goddard, K. A., Hopkins, P. J., Hall, J. M., Witte, J. S. 2000; 66 (1): 216-234

    Abstract

    Single-nucleotide polymorphisms (SNPs) may be extremely important for deciphering the impact of genetic variation on complex human diseases. The ultimate value of SNPs for linkage and association mapping studies depends in part on the distribution of SNP allele frequencies and intermarker linkage disequilibrium (LD) across populations. Limited information is available about these distributions on a genomewide scale, particularly for LD. Using 114 SNPs from 33 genes, we compared these distributions in five American populations (727 individuals) of African, European, Chinese, Hispanic, and Japanese descent. The allele frequencies were highly correlated across populations but differed by >20% for at least one pair of populations in 35% of SNPs. The correlation in LD was high for some pairs of populations but not for others (e.g., Chinese American or Japanese American vs. any other population). Regardless of population, average minor-allele frequencies were significantly higher for SNPs in noncoding regions (20%-25%) than for SNPs in coding regions (12%-16%). Interestingly, we found that intermarker LD may be strongest with pairs of SNPs in which both markers are nonconservative substitutions, compared to pairs of SNPs where at least one marker is a conservative substitution. These results suggest that population differences and marker location within the gene may be important factors in the selection of SNPs for use in the study of complex disease with linkage or association mapping methods.

    View details for DOI 10.1086/302727

    View details for Web of Science ID 000085033600024

    View details for PubMedID 10631153

    View details for PubMedCentralID PMC1288328

  • Tutorial in biostatistics genetic mapping of complex traits STATISTICS IN MEDICINE Olson, J. M., Witte, J. S., Elston, R. C. 1999; 18 (21): 2961-2981

    Abstract

    Statistical genetic mapping methods are powerful tools for finding genes that contribute to complex human traits. Mapping methods combine knowledge of the biological mechanisms of inheritance and the randomness inherent in those mechanisms to locate, with increasing precision, trait genes on the human genome. We provide an overview of the two major classes of mapping methods, genetic linkage analysis and linkage disequilibrium analysis, and related concepts of genetic inheritance.

    View details for DOI 10.1002/(SICI)1097-0258(19991115)18:21<2961::AID-SIM206>3.3.CO;2-L

    View details for Web of Science ID 000083386700010

    View details for PubMedID 10523753

  • Association between a CYP3A4 genetic variant and clinical presentation in African-American prostate cancer patients CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Paris, P. L., Kupelian, P. A., Hall, J. M., Williams, T. L., Levin, H., Klein, E. A., Casey, G., Witte, J. S. 1999; 8 (10): 901-905

    Abstract

    Prostate cancer incidence, clinical presentation, and mortality rates vary among different ethnic groups. A genetic variant of CYP3A4, a gene involved in the oxidative deactivation of testosterone, has been associated recently with prostate cancer development in Caucasians. To further investigate this variant, we evaluated its genotype frequencies in different ethnic groups and its association with clinical presentation of prostate cancer in African Americans. CYP3A4 genotypes were assayed in healthy male Caucasian (n = 117), Hispanic (n = 121), African-American (n = 116), Chinese (n = 46), and Japanese (n = 34) volunteers using the TaqMan assay. The association between CYP3A4 genotype and prostate cancer presentation was determined in 174 affected African-American men. Genotype frequency of the CYP3A4 variant differed substantially across ethnic groups, with African Americans much more likely to carry one or two copies than any other group (two-sided P < 0.0001). Among African Americans, 46% (80 of 174) of men with prostate cancer were homozygous for the CYP3A4 variant, whereas only 28% (32 of 116) of African-American healthy volunteers were homozygous (two-sided P < 0.005). A consistent positive association was observed between being homozygous for the CYP3A4 variant in African-American prostate cancer patients and clinical characteristics. Men homozygous for the CYP3A4 variant were more likely to present with higher grade and stage of prostate cancer in a recessive model [odds ratio (OR), 1.7; 95% confidence interval (CI), 0.9-3.4]. This association was even stronger for men who were >65 years of age at diagnosis (n = 103; OR, 2.4; 95% CI, 1.1-5.4). In summary, the CYP3A4 genotype frequency in different ethnic groups broadly followed trends in prostate cancer incidence, presentation, and mortality in the United States. African-American prostate cancer patients had a higher frequency of being homozygous for the CYP3A4 variant than healthy African-American volunteers who were matched solely based on ethnicity. Among the patients, those who were homozygous for the CYP3A4 variant were more likely to present with clinically more advanced prostate cancer.

    View details for Web of Science ID 000083352400009

    View details for PubMedID 10548319

  • Asymptotic bias and efficiency in case-control studies of candidate genes and gene-environment interactions: Basic family designs AMERICAN JOURNAL OF EPIDEMIOLOGY Witte, J. S., Gauderman, W. J., Thomas, D. C. 1999; 149 (8): 693-705

    Abstract

    Case-control designs that use population controls are compared with those that use controls selected from their relatives (i.e., siblings, cousins, or "pseudosibs" based on parental alleles) for estimating the effect of candidate genes and gene-environment interactions. The authors first evaluate the asymptotic bias in relative risk estimates resulting from using population controls when there is confounding due to population stratification. Using siblings or pseudosibs as controls completely addresses this issue, whereas cousins provide only partial protection from population stratification. Next, they show that the conventional conditional likelihood for matched case-control studies can give asymptotically biased effect estimates when applied to the pseudosib approach; the asymptotic bias is toward the null and disappears with disease rarity. They show how to reparameterize the pseudosib likelihood so this approach gives consistent effect estimates. They then show that the designs using population or pseudosib controls are generally the most efficient for estimating the main effect of a candidate gene, followed in efficiency by the design using cousins. Finally, they show that the design using sibling controls can be quite efficient when studying gene-environment interactions. In addition to asymptotic bias and efficiency issues, family-based designs might benefit from a higher motivation to participate among cases' relatives, but these designs have the disadvantage that many potential cases will be excluded from study by having no available controls.

    View details for Web of Science ID 000079671500002

    View details for PubMedID 10206618

  • Likelihood-based approach to estimating twin concordance for dichotomous traits GENETIC EPIDEMIOLOGY Witte, J. S., Carlin, J. B., Hopper, J. L. 1999; 16 (3): 290-304

    Abstract

    Genetic epidemiologists are well aware that the casewise and pairwise twin concordances are two different measures. In determining appropriate estimators for each of these measures, the method of ascertainment must be considered. Here, we derive expressions for the concordance estimators and their asymptotic variances appropriate to different twin ascertainment schemes using a likelihood framework, and apply these formulas to existing data. We emphasize the distinction between concordance measures (i.e., the parameters of interest) and the concordance estimators based on the number of pairs observed. Under random or complete ascertainment the casewise estimator is asymptotically unbiased for the casewise concordance, and the pairwise estimator is asymptotically unbiased for the pairwise concordance. Under incomplete ascertainment, the casewise estimator is biased for the casewise concordance, the pairwise estimator is biased for the pairwise concordance, but the probandwise estimator is asymptotically unbiased for the casewise concordance. One can extend the likelihood equations presented here to allow the concordance parameter of interest to depend on zygosity and, if measured, other factors such as cohabitation status and similarity for genetic markers, while concurrently allowing the disease prevalence to depend on measured covariates.

    View details for DOI 10.1002/(SICI)1098-2272(1999)16:3<290::AID-GEPI5>3.0.CO;2-8

    View details for Web of Science ID 000078966600005

    View details for PubMedID 10096691

  • Model-based and model-free multipoint genome-wide linkage analysis of alcoholism Jacobs, K. B., Wedig, G. C., Schnell, A. H., Witte, J. S., Elston, R. C. WILEY-LISS. 1999: S175-S180

    Abstract

    We analyzed a subset of the Collaborative Study on the Genetics of Alcoholism (COGA) data set as provided by the 11th Genetic Analysis Workshop (GAW11). Linkage analyses were performed using each of the diagnostic criteria for alcoholism included in the data: the COGA criteria (DSM-III-R plus the Feighner criteria) and the narrower World Health Organization diagnosis ICD-10 criteria. Formal segregation analysis using these data was not attempted because only a subset of all the originally ascertained families was made available. Nevertheless, an attempt was made to estimate the best one-locus two-allele genetic model for these data. Model-based multipoint linkage analysis was performed using the results of our trait model fitting, and model-free multipoint linkage analysis was performed with an improved version of the Haseman and Elston linkage method for sib pairs.

    View details for Web of Science ID 000083945800028

    View details for PubMedID 10597432

  • Glutathione transferase null genotype, broccoli, and lower prevalence of colorectal adenomas CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Lin, H. J., Probst-Hensch, N. M., Louie, A., Kau, I. H., Witte, J. S., Ingles, S. A., Frankl, H. D., Lee, E. R., Haile, R. W. 1998; 7 (8): 647-652

    Abstract

    Cruciferous vegetables, especially broccoli, may prevent cancer through anticarcinogenic compounds. For example, broccoli contains isothiocyanates that induce carcinogen-detoxifying enzymes. Glutathione transferase enzymes conjugate isothiocyanates, leading to excretion. We hypothesized that broccoli consumption in combination with the glutathione transferase M1 (GSTM1) null genotype would be associated with a lower prevalence of colorectal adenomas because of higher isothiocyanate levels. We used a case-control study of mainly asymptomatic subjects aged 50-74 years who underwent a screening sigmoidoscopy at either of two Southern California Kaiser Permanente Medical Centers during 1991-1993. Cases (n = 459) had a first-time diagnosis of histologically confirmed adenomas detected by flexible sigmoidoscopy. Controls (n = 507) had no polyp detected. Subjects had a 45-min in-person interview for information on various risk factors and basic demographic data and completed a 126-item, semiquantitative food frequency questionnaire. Blood samples were used for GSTM1 genotyping. Subjects with the highest quartile of broccoli intake (an average of 3.7 servings per week) had an odds ratio of 0.47 (95% confidence interval, 0.30-0.73) for colorectal adenomas, compared with subjects who reportedly never ate broccoli. When stratified by GSTM1 genotype, a protective effect of broccoli was observed only among subjects with the GSTM1 null genotype (P for trend, 0.001; P for interaction, 0.01). The observed broccoli-GSTM1 interaction is compatible with an isothiocyanate mechanism.

    View details for Web of Science ID 000075283700002

    View details for PubMedID 9718215

  • Familial prostate cancer: A different disease? JOURNAL OF UROLOGY Kupelian, P. A., Klein, E. A., Witte, J. S., Kupelian, V. A., Suh, J. H. 1997; 158 (6): 2197-2201

    Abstract

    We analyzed the outcome after radical prostatectomy of patients with familial prostate cancer versus patients with sporadic prostate cancer.The study included 720 patients with prostate carcinoma who were treated with prostatectomy between 1987 and 1996. Patients were excluded from the study if they had received adjuvant or neoadjuvant treatment, or had no available pretreatment prostatic specific antigen (PSA) level, no available biopsy Gleason score, incomplete pathological information or no available followup PSA levels. The analysis was performed on 529 cases. Patients were considered to have a positive family history for prostate cancer when the index patient confirmed the diagnosis of prostate cancer in a first degree relative (brother or father). The outcomes of interest were biochemical relapse-free survival, local failure and distant metastases. Proportional hazards were used to analyze the effect of family history and confounding variables (that is age, stage, biopsy Gleason score, initial PSA levels, surgical specimen Gleason score, extracapsular extension, lymph node metastasis, seminal vesicle invasion and surgical margin involvement) on treatment outcome.Median followup was 30 months. Of all cases 12% had a positive family history. Younger age was the only factor associated with positive family history, with 18% of patients younger than 65 years having a positive family history versus 6% of older patients (chi-square p <0.001). The 5-year biochemical relapse-free survival rate for the entire group was 64%. The 5-year biochemical relapse-free survival rates for patients with negative family history versus positive history were 66% and 46%, respectively (p = 0.001). A multivariate time-to-failure analysis using the proportional hazards model was performed based on family history, age (less than 65 versus 65 to 69 versus 70 or greater, initial PSA (10 or less versus greater than 10), biopsy Gleason score (6 or less versus 7 or greater), clinical T stage (T1-T2A versus T2B-C), prostatectomy specimen Gleason score (6 or less versus 7 or greater), extracapsular extension, seminal vesicle involvement, surgical margin involvement and lymph node involvement. After adjusting for the potential confounding factors, positive family history remained strongly associated with biochemical failure. The clinical failure rate for the entire group was 14%. The 5-year local failure rate was 7%, with positive surgical margins being the only independent predictor of local failure. The 5-year distant metastasis rate was 8%, with family history and initial PSA levels being independent predictors of distant relapse.Our study suggests that patients with a familial prostate cancer have a higher likelihood of biochemical failure after radical prostatectomy than patients with sporadic cancer. This effect is independent of pretreatment or pathological factors. Our results suggest that the higher failure rates associated with familial prostate cancer are mainly secondary to higher distant relapse rates, and that familial prostate cancer may be more biologically aggressive than sporadic cancers.

    View details for DOI 10.1016/S0022-5347(01)68194-1

    View details for Web of Science ID A1997YE61700046

    View details for PubMedID 9366343

  • A sigmoidoscopy-based case-control study of polyps: Macronutrients, fiber and meat consumption INTERNATIONAL JOURNAL OF CANCER Haile, R. W., Witte, J. S., Longnecker, M. P., PROBSTHENSCH, N., Chen, M. J., Harper, J., Frankl, H. D., Lee, E. R. 1997; 73 (4): 497-502

    Abstract

    We conducted a large, sigmoidoscopy-based case-control study to examine the relation of intake of macronutrients, meat, and fiber to occurrence of adenomas of the large bowel. Cases were subjects diagnosed for the first time with one or more histologically confirmed adenomas. Controls had no polyps of any type at sigmoidoscopy, had no history of polyps, and were individually matched to cases by gender, age, date of sigmoidoscopy, and Kaiser Center. The response rate was 84% for cases and 82% for controls. Complete dietary data for 488 matched pairs were available. All odds ratios are from matched analyses adjusted for energy. We observed positive associations with risk of adenomas for calories, animal fat, saturated fat, red meat, and the ratio of red meat to poultry and fish. Protective effects were observed for vegetable protein, carbohydrates, and dietary fiber. The fiber effects diminished after adjusting for fruits and vegetables. Results after mutually adjusting for the effects of saturated fat, fiber and the ratio of red meat to chicken and fish suggest that each of these variables has an effect on risk of adenomas that is independent of the other 2 exposures.

    View details for Web of Science ID A1997YG99200007

    View details for PubMedID 9389562

  • Family history of prostate cancer in patients with localized prostate cancer: An independent predictor of treatment outcome JOURNAL OF CLINICAL ONCOLOGY Kupelian, P. A., Kupelian, V. A., Witte, J. S., Macklis, R., Klein, E. A. 1997; 15 (4): 1478-1480

    Abstract

    To determine if familial prostate cancer patients have a less favorable prognosis than patients with sporadic prostate cancer after treatment for localized disease with either radiotherapy (RT) or radical prostatectomy (RP).One thousand thirty-eight patients treated with either RT (n = 583) or RP (n = 455) were included in this analysis. These patients were noted as having a positive family history if they confirmed the diagnosis of prostate cancer in a first-degree relative. The outcome of interest was biochemical relapse-free survival (bRFS). We used proportional hazards to analyze the effect of the presence of family history and other potential confounding variables (ie, age, treatment modality, stage, biopsy Gleason sum [GS], and initial prostate-specific antigen [iPSA] levels) on treatment outcome.Eleven percent of all patients had a positive family history. The 5-year bRFS rates for patients with negative and positive family histories were 52% and 29%, respectively (P < .001). The potential confounders with bRFS rates were iPSA levels, biopsy GS, and clinical tumor stage; treatment modality and age did not appear to be associated with outcome. After adjusting for potential confounders, family history of prostate cancer remained strongly associated with biochemical failure.This is the first study to demonstrate that the presence of a family history of prostate cancer correlates with treatment outcome in a large unselected series of patients. Our findings suggest that familial prostate cancer may have a more aggressive course than nonfamilial prostate cancer, and that clinical and/or pathologic parameters may not adequately predict this course.

    View details for DOI 10.1200/JCO.1997.15.4.1478

    View details for Web of Science ID A1997WX65100026

    View details for PubMedID 9193343

  • A nested approach to evaluating dose-response and trend ANNALS OF EPIDEMIOLOGY Witte, J. S., Greenland, S. 1997; 7 (3): 188-193

    Abstract

    Conventional dose-response and trend analysis fits either a linear or categorical logistic model and tests the resulting coefficients. These analyses, however, are based on implausible assumptions.We present an alternative approach that uses likelihood ratio tests to compare nested regression models and determine when a model is rich enough to capture the data trends.For illustration, we apply this approach to data on diet and colorectal polyps.Comparison of linear and quadratic spline logistic models indicates that the conventional approach of using only a linear logistic model would not appropriately describe the association between intake of fruits and vegetables and colorectal polyps in our data. Graphical checking further supports this conclusion.

    View details for DOI 10.1016/S1047-2797(96)00159-7

    View details for Web of Science ID A1997WX57800005

    View details for PubMedID 9141641

  • Meat preparation and colorectal adenomas in a large sigmoidoscopy-based case-control study in California (United States) CANCER CAUSES & CONTROL PROBSTHENSCH, N. M., Sinha, R., Longnecker, M. P., Witte, J. S., Ingles, S. A., Frankl, H. D., Lee, E. R., Haile, R. W. 1997; 8 (2): 175-183

    Abstract

    The often observed association between red meat and colorectal cancer could be due in part to mutagens, such as heterocyclic amines (HCA), that are present in cooked meat. HCAs are highly mutagenic and cause intestinal tumors in animals. The hypothesis that HCAs are also carcinogenic to humans remains to be substantiated in epidemiologic studies. We determined the associations of meat preparation and frequency of intake (proxy variables for HCA exposure, since HCA concentration depends on the type of meat and the way it is cooked) with the prevalence of distal colorectal adenomas in a sigmoidoscopy-based case-control study of 488 matched pairs of subjects from two California (United States) Kaiser Permanente Medical Centers. A more than twofold difference in adenoma prevalence between subjects at extreme ends of estimated HCA intake was observed. For subjects who ate red meat more than once per week, fried it more than 10 percent of the time, and ate it with a darkly browned surface, compared with subjects who ate red meat one time or less per week, fried it 10 or less percent of the time, and ate it with a lightly browned surface, the odds ratio was 2.2 (95 percent confidence interval = 1.1-4.3). Adenoma prevalence also increased with frequency of frying red meat (P trend = 0.004). These results are consistent with a carcinogenic effect of HCA.

    View details for Web of Science ID A1997WU35100008

    View details for PubMedID 9134241

  • Diet and premenopausal bilateral breast cancer: A case-control study BREAST CANCER RESEARCH AND TREATMENT Witte, J. S., Ursin, G., Siemiatycki, J., Thompson, W. D., PAGANINIHILL, A., Haile, R. W. 1997; 42 (3): 243-251

    Abstract

    We investigated associations between diet and premenopausal bilateral breast cancer in a familial matched case-control study. We studied 140 cases from population-based registries in Los Angeles County (California) and Connecticut, and from the major hospitals in the southern parts of the Province of Quebec. Unaffected sisters of the cases served as matched controls (222 total). Dietary intake were assessed with a food frequency questionnaire. Total fat, monounsaturated fat, polyunsaturated fat, oleic acid, and linoleic acid intake was inversely associated with premenopausal bilateral breast cancer risk. Consumption of carbohydrates (and sweetened beverages) was associated with an increased risk. We observed no associations for dietary fiber, antioxidants, or major food groupings, but we did observe inverse associations for intake of low fat dairy products and tofu. These findings suggest that monounsaturated and polyunsaturated fats, as well as soy foods, might reduce the risk of premenopausal bilateral breast cancer.

    View details for Web of Science ID A1997WM10800006

    View details for PubMedID 9065608

  • Modeling age of onset and residual familial correlations for the linkage analysis of bipolar disorder Schnell, A. H., Karunaratne, P. M., Witte, J. S., Dawson, D. V., Elston, R. C. WILEY-LISS. 1997: 675-680

    Abstract

    We applied regressive modeling to the data described by Stine et al. [1995] and further explored the possible linkage of bipolar disorder to marker D18S41 on chromosome 18. We performed analyses to determine age-dependent penetrance functions that best fit the data and that allow for residual familial correlations. Specifically, we introduce here a simple method to allow for a sibling correlations. that is not due to segregation at the linked locus, and then extend the results of Stine et al. [1995] by using the best fitting "regressive" model of this kind as input into a lod score linkage analysis. Although a formal segregation analysis was not attempted, a surprising finding was that, except for doubtful linkage to D18S41, there is little evidence for genetic transmission of bipolar disorder in these families.

    View details for DOI 10.1002/(SICI)1098-2272(1997)14:6<675::AID-GEPI21>3.3.CO;2-V

    View details for Web of Science ID 000071121800022

    View details for PubMedID 9433562

  • Relation of vegetable, fruit, and grain consumption to colorectal adenomatous polyps AMERICAN JOURNAL OF EPIDEMIOLOGY Witte, J. S., Longnecker, M. P., Bird, C. L., Lee, E. R., Frankl, H. D., Haile, R. W. 1996; 144 (11): 1015-1025

    Abstract

    Previous studies suggest that colorectal cancer risk decreases with higher intake of vegetables, fruits, and grains. Few studies, however, have examined these factors in relation to occurrence of colorectal polyps. The authors used case-control data from 488 matched pairs to evaluate associations of vegetables, fruits, and grains with polyps. Subjects were southern Californians aged 50-74 years who had a sigmoidoscopy in 1991-1993. Diet in the year before sigmoidoscopy was measured with a food frequency questionnaire. Frequent consumption of vegetables, fruits, and grains was associated with decreased polyp prevalence. Specifically, the adjusted odds ratio comparing the highest with the lowest quintile of intake for vegetables was 0.47 (95% confidence interval (CI) 0.29-0.76), for fruits was 0.65 (95% CI 0.40-1.05), and for grains was 0.55 (95% CI 0.33-0.91). The authors also found inverse associations for high carotenoid vegetables, cruciferae, high vitamin C fruits, garlic, and tofu (or soybeans). After further adjusting for potentially anticarcinogenic constituents of these foods, high carotenoid vegetables, cruciferous vegetables, garlic, and tofu (or soybeans) remained inversely associated with polyps. These findings support the hypothesis that high intake of vegetables, fruits, or grains decreases the risk of polyps and suggest that any protective effects might reflect unmeasured constituents in these foods.

    View details for Web of Science ID A1996VV53500002

    View details for PubMedID 8942431

  • Agreement in alcohol consumption levels as measured by two different questionnaires JOURNAL OF STUDIES ON ALCOHOL Witte, J. S., Haile, R. W. 1996; 57 (4): 406-409

    Abstract

    We evaluated the agreement in reported alcohol consumption between a standard food frequency questionnaire (FFQ) and a risk factor questionnaire (RFQ) developed for a genetic epidemiologic study of breast cancer.The FFQ measured intake of alcoholic beverages by asking which of nine levels were consumed during a single time period. In contrast, the RFQ used open-ended questions to measure intake of alcoholic beverages during numerous time periods. Subjects (N = 765) completed both questionnaires at home.Mean daily alcohol consumption levels were consistently higher in the FFQ than in the RFQ; for example, the mean alcohol consumption for all subjects was 7.0 g/day in the FFQ versus 5.3 g/day in the RFQ. Moreover, the RFQ overestimated the number of nondrinkers relative to the FFQ. Nonetheless, the Spearman correlation coefficients between daily alcohol consumption levels as measured by the two questionnaires were relatively high: total alcohol, r = 0.72; beer, r = 0.69; wine, r = 0.69; and distilled spirits, r = 0.54.The reasonable agreement between these questionnaires supports the validity of historical alcohol consumption levels measured by the RFQ.

    View details for Web of Science ID A1996UR80200011

    View details for PubMedID 8776682

  • Simulation study of hierarchical regression STATISTICS IN MEDICINE Witte, J. S., Greenland, S. 1996; 15 (11): 1161-1170

    Abstract

    Hierarchical regression - which attempts to improve standard regression estimates by adding a second-stage 'prior' regression to an ordinary model - provides a practical approach to evaluating multiple exposures. We present here a simulation study of logistic regression in which we compare hierarchical regression fitted by a two-stage procedure to ordinary maximum likelihood. The simulations were based on case-control data on diet and breast cancer, where the hierarchical model uses a second-stage regression to pull conventional dietary-item estimates toward each other when they have similar levels of food constituents. Our results indicate that hierarchical modelling of continuous covariates offers worthwhile improvement over ordinary maximum-likelihood, provided one does not underspecify the second-stage standard deviations.

    View details for DOI 10.1002/(SICI)1097-0258(19960615)15:11<1161::AID-SIM221>3.0.CO;2-7

    View details for Web of Science ID A1996UR76800006

    View details for PubMedID 8804145

  • Association within twin pairs for a dichotomous trait GENETIC EPIDEMIOLOGY Olson, J. M., Witte, J. S., Elston, R. C. 1996; 13 (5): 489-499

    Abstract

    We propose an odds-ratio measure of twin association for a dichotomous trait. This odds ratio can be estimated without arbitrarily specifying an index twin and without estimating additional nuisance parameters. Tests of association and confidence intervals may be computed easily, in contrast to those proposed previously [Donner et al. (1995) Genet Epidemiol 12:267-277] for a correlation measure of association. For testing homogeneity of association in two samples of twins, monozygotic and dizygotic, we propose a large-sample test and an exact test, both based on the odds-ratio parameterization. Large-sample tests of homogeneity are slightly anticonservative when some cell counts are small, and the exact test may be preferred in these situations. We also propose a long-linear parameterization useful for modeling more complex data sets.

    View details for DOI 10.1002/(SICI)1098-2272(1996)13:5<489::AID-GEPI5>3.0.CO;2-Y

    View details for Web of Science ID A1996VN71900005

    View details for PubMedID 8905395