All Publications


  • Outgroup Machine Learning Approach Identifies Single Nucleotide Variants in Noncoding DNA Associated with Autism Spectrum Disorder Varma, M., Paskov, K., Jung, J., Chrisman, B., Stockham, N., Washington, P., Wall, D., Altman, R. B., Dunker, A. K., Hunter, L., Ritchie, M. D., Murray, T., Klein, T. E. WORLD SCIENTIFIC PUBL CO PTE LTD. 2019: 260–71
  • Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks. Cell Ruzzo, E. K., Pérez-Cano, L. n., Jung, J. Y., Wang, L. K., Kashef-Haghighi, D. n., Hartl, C. n., Singh, C. n., Xu, J. n., Hoekstra, J. N., Leventhal, O. n., Leppä, V. M., Gandal, M. J., Paskov, K. n., Stockham, N. n., Polioudakis, D. n., Lowe, J. K., Prober, D. A., Geschwind, D. H., Wall, D. P. 2019; 178 (4): 850–66.e26

    Abstract

    We performed a comprehensive assessment of rare inherited variation in autism spectrum disorder (ASD) by analyzing whole-genome sequences of 2,308 individuals from families with multiple affected children. We implicate 69 genes in ASD risk, including 24 passing genome-wide Bonferroni correction and 16 new ASD risk genes, most supported by rare inherited variants, a substantial extension of previous findings. Biological pathways enriched for genes harboring inherited variants represent cytoskeletal organization and ion transport, which are distinct from pathways implicated in previous studies. Nevertheless, the de novo and inherited genes contribute to a common protein-protein interaction network. We also identified structural variants (SVs) affecting non-coding regions, implicating recurrent deletions in the promoters of DLG2 and NR3C2. Loss of nr3c2 function in zebrafish disrupts sleep and social function, overlapping with human ASD-related phenotypes. These data support the utility of studying multiplex families in ASD and are available through the Hartwell Autism Research and Technology portal.

    View details for DOI 10.1016/j.cell.2019.07.015

    View details for PubMedID 31398340

  • Coalitional Game Theory Facilitates Identification of Non-Coding Variants Associated With Autism. Biomedical informatics insights Sun, M. W., Gupta, A., Varma, M., Paskov, K. M., Jung, J., Stockham, N. T., Wall, D. P. 2019; 11: 1178222619832859

    Abstract

    Studies on autism spectrum disorder (ASD) have amassed substantial evidence for the role of genetics in the disease's phenotypic manifestation. A large number of coding and non-coding variants with low penetrance likely act in a combinatorial manner to explain the variable forms of ASD. However, many of these combined interactions, both additive and epistatic, remain undefined. Coalitional game theory (CGT) is an approach that seeks to identify players (individual genetic variants or genes) who tend to improve the performance-association to a disease phenotype of interest-of any coalition (subset of co-occurring genetic variants) they join. This method has been previously applied to boost biologically informative signal from gene expression data and exome sequencing data but remains to be explored in the context of cooperativity among non-coding genomic regions. We describe our extension of previous work, highlighting non-coding chromosomal regions relevant to ASD using CGT on alteration data of 4595 fully sequenced genomes from 756 multiplex families. Genomes were encoded into binary matrices for three types of non-coding regions previously implicated in ASD and separated into ASD (case) and unaffected (control) samples. A player metric, the Shapley value, enabled determination of individual variant contributions in both sets of cohorts. A total of 30 non-coding positions were found to have significantly elevated player scores and likely represent significant contributors to the genetic coordination underlying ASD. Cross-study analyses revealed that a subset of mutated non-coding regions (all of which are in human accelerated regions (HARs)) and related genes are involved in biological pathways or behavioral outcomes known to be affected in autism, suggesting the importance of single nucleotide polymorphisms (SNPs) within HARs in ASD. These findings support the use of CGT in identifying hidden yet influential non-coding players from large-scale genomic data, to better understand the precise underpinnings of complex neurodevelopmental disorders such as autism.

    View details for PubMedID 30886520

  • Analysis of Sex and Recurrence Ratios in Simplex and Multiplex Autism Spectrum Disorder Implicates Sex-Specific Alleles as Inheritance Mechanism Chrisman, B., Varma, M., Washington, P., Paskov, K., Stockham, N., Jung, J., Wall, D. P., Zheng, H., Callejas, Z., Griol, D., Wang, H., Hu, Schmidt, H., Baumbach, J., Dickerson, J., Zhang, L. IEEE. 2018: 1470–77