Bio


My research interests primarily lie in two parts: 1) understanding genetic architecture of complex diseases and traits, and 2) clinical implementation of human genetics discoveries, for example, pharmacogenomics. I received my Ph.D. degree in Genomics and Computational Biology from University of Pennsylvania. My dissertation focused on identifying complex trait or disease-associated genes via genomic regulation-informed gene-based analyses. I am now a postdoctoral fellow in the Klein Lab (PharmGKB group). I am currently working on the Pharmacogenomics Clinical Annotation Tool (PharmCAT), a one-stop bioinformatics tool that analyzes pharmacogenomics variants from genotypic datasets and generates reports with genotype-based prescribing recommendations to supports clinical pharmacogenomics implementations and treatment decisions.

Professional Education


  • Bachelor of Science, Fudan University (2015)
  • Doctor of Philosophy, University of Pennsylvania (2020)
  • PhD, University of Pennsylvania, Genomics and Computational Biology (2020)
  • BS, Fudan University, Life Sciences (2015)

Stanford Advisors


Projects


  • Pharmacogenomics Clinical Annotation Tool (PharmCAT)

    Location

    Stanford, CA, USA

Lab Affiliations


All Publications


  • Influence of tissue context on gene prioritization for predicted transcriptome-wide association studies. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Li, B., Veturi, Y., Bradford, Y., Verma, S. S., Verma, A., Lucas, A. M., Haas, D. W., Ritchie, M. D. 2019; 24: 296–307

    Abstract

    Transcriptome-wide association studies (TWAS) have recently gained great attention due to their ability to prioritize complex trait-associated genes and promote potential therapeutics development for complex human diseases. TWAS integrates genotypic data with expression quantitative trait loci (eQTLs) to predict genetically regulated gene expression components and associates predictions with a trait of interest. As such, TWAS can prioritize genes whose differential expressions contribute to the trait of interest and provide mechanistic explanation of complex trait(s). Tissue-specific eQTL information grants TWAS the ability to perform association analysis on tissues whose gene expression profiles are otherwise hard to obtain, such as liver and heart. However, as eQTLs are tissue context-dependent, whether and how the tissue-specificity of eQTLs influences TWAS gene prioritization has not been fully investigated. In this study, we addressed this question by adopting two distinct TWAS methods, PrediXcan and UTMOST, which assume single tissue and integrative tissue effects of eQTLs, respectively. Thirty-eight baseline laboratory traits in 4,360 antiretroviral treatment-naïve individuals from the AIDS Clinical Trials Group (ACTG) studies comprised the input dataset for TWAS. We performed TWAS in a tissue-specific manner and obtained a total of 430 significant gene-trait associations (q-value < 0.05) across multiple tissues. Single tissue-based analysis by PrediXcan contributed 116 of the 430 associations including 64 unique gene-trait pairs in 28 tissues. Integrative tissue-based analysis by UTMOST found the other 314 significant associations that include 50 unique gene-trait pairs across all 44 tissues. Both analyses were able to replicate some associations identified in past variant-based genome-wide association studies (GWAS), such as high-density lipoprotein (HDL) and CETP (PrediXcan, q-value = 3.2e-16). Both analyses also identified novel associations. Moreover, single tissue-based and integrative tissuebased analysis shared 11 of 103 unique gene-trait pairs, for example, PSRC1-low-density lipoprotein (PrediXcan's lowest q-value = 8.5e-06; UTMOST's lowest q-value = 1.8e-05). This study suggests that single tissue-based analysis may have performed better at discovering gene-trait associations when combining results from all tissues. Integrative tissue-based analysis was better at prioritizing genes in multiple tissues and in trait-related tissue. Additional exploration is needed to confirm this conclusion. Finally, although single tissue-based and integrative tissue-based analysis shared significant novel discoveries, tissue context-dependency of eQTLs impacted TWAS gene prioritization. This study provides preliminary data to support continued work on tissue contextdependency of eQTL studies and TWAS.

    View details for PubMedID 30864331

    View details for PubMedCentralID PMC6417797

  • Collective feature selection to identify crucial epistatic variants BIODATA MINING Verma, S. S., Lucas, A., Zhang, X., Veturi, Y., Dudek, S., Li, B., Li, R., Urbanowicz, R., Moore, J. H., Kim, D., Ritchie, M. D. 2018; 11: 5

    Abstract

    Machine learning methods have gained popularity and practicality in identifying linear and non-linear effects of variants associated with complex disease/traits. Detection of epistatic interactions still remains a challenge due to the large number of features and relatively small sample size as input, thus leading to the so-called "short fat data" problem. The efficiency of machine learning methods can be increased by limiting the number of input features. Thus, it is very important to perform variable selection before searching for epistasis. Many methods have been evaluated and proposed to perform feature selection, but no single method works best in all scenarios. We demonstrate this by conducting two separate simulation analyses to evaluate the proposed collective feature selection approach.Through our simulation study we propose a collective feature selection approach to select features that are in the "union" of the best performing methods. We explored various parametric, non-parametric, and data mining approaches to perform feature selection. We choose our top performing methods to select the union of the resulting variables based on a user-defined percentage of variants selected from each method to take to downstream analysis. Our simulation analysis shows that non-parametric data mining approaches, such as MDR, may work best under one simulation criteria for the high effect size (penetrance) datasets, while non-parametric methods designed for feature selection, such as Ranger and Gradient boosting, work best under other simulation criteria. Thus, using a collective approach proves to be more beneficial for selecting variables with epistatic effects also in low effect size datasets and different genetic architectures. Following this, we applied our proposed collective feature selection approach to select the top 1% of variables to identify potential interacting variables associated with Body Mass Index (BMI) in ~ 44,000 samples obtained from Geisinger's MyCode Community Health Initiative (on behalf of DiscovEHR collaboration).In this study, we were able to show that selecting variables using a collective feature selection approach could help in selecting true positive epistatic variables more frequently than applying any single method for feature selection via simulation studies. We were able to demonstrate the effectiveness of collective feature selection along with a comparison of many methods in our simulation analysis. We also applied our method to identify non-linear networks associated with obesity.

    View details for DOI 10.1186/s13040-018-0168-6

    View details for Web of Science ID 000430966900001

    View details for PubMedID 29713383

    View details for PubMedCentralID PMC5907720

  • Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expression Li, B., Verma, S. S., Veturi, Y. C., Verma, A., Bradford, Y., Haas, D. W., Ritchie, M. D., Altman, R. B., Dunker, A. K., Hunter, L., Ritchie, M. D., Murray, T., Klein, T. E. WORLD SCIENTIFIC PUBL CO PTE LTD. 2018: 448–59

    Abstract

    Genome-wide association studies (GWAS) have been successful in facilitating the understanding of genetic architecture behind human diseases, but this approach faces many challenges. To identify disease-related loci with modest to weak effect size, GWAS requires very large sample sizes, which can be computational burdensome. In addition, the interpretation of discovered associations remains difficult. PrediXcan was developed to help address these issues. With built in SNP-expression models, PrediXcan is able to predict the expression of genes that are regulated by putative expression quantitative trait loci (eQTLs), and these predicted expression levels can then be used to perform gene-based association studies. This approach reduces the multiple testing burden from millions of variants down to several thousand genes. But most importantly, the identified associations can reveal the genes that are under regulation of eQTLs and consequently involved in disease pathogenesis. In this study, two of the most practical functions of PrediXcan were tested: 1) predicting gene expression, and 2) prioritizing GWAS results. We tested the prediction accuracy of PrediXcan by comparing the predicted and observed gene expression levels, and also looked into some potential influential factors and a filter criterion with the aim of improving PrediXcan performance. As for GWAS prioritization, predicted gene expression levels were used to obtain gene-trait associations, and background regions of significant associations were examined to decrease the likelihood of false positives. Our results showed that 1) PrediXcan predicted gene expression levels accurately for some but not all genes; 2) including more putative eQTLs into prediction did not improve the prediction accuracy; and 3) integrating predicted gene expression levels from the two PrediXcan whole blood models did not eliminate false positives. Still, PrediXcan was able to prioritize GWAS associations that were below the genome-wide significance threshold in GWAS, while retaining GWAS significant results. This study suggests several ways to consider PrediXcan's performance that will be of value to eQTL and complex human disease research.

    View details for Web of Science ID 000461831500041

    View details for PubMedID 29218904

    View details for PubMedCentralID PMC5749400