Biomedical and Translational Informatics Laboratory

  • Verma, A., Tsao, N., Thomann, L., Ho, Y. L., Carr, R., Crawford, D., Efird, J., Huffman, J., Hung, A., Ivey, K., Iyengar, S., Levin, M., Luoh, S. W., Lynch, J., Natarajan, P., Pyarajan, S., Bick, A., Costa, L., Genovese, G., … Liao, K. (2021). A phenome-wide association study of genes associated with covid-19 severity reveals shared genetics with rheumatic conditions. Arthritis & Rheumatology. https://pesquisa.bvsalud.org/global-literature-on-novel-coronavirus-2019-ncov/resource/pt/covidwho-1728538
  • Sun, L., Surya, S., Goodman, N., Le, A., Kelly, G., Owoyemi, O., Desai, H., Zheng, C., DeLuca, S., Good, M., Hussain, J., Jeffries, S., Kry, Y., Kugler, E., Mansour, M., Ndicu, J., Osei-Akoto, A., Prior, T., Pundock, S., … DeMichele, A. (2021). SARS-COV-2 seropositivity and seroconversion in patients undergoing active cancer-directed therapy (preprint). Pesquisa. https://pesquisa.bvsalud.org/global-literature-on-novel-coronavirus-2019-ncov/resource/fr/ppmedrxiv-21249810
  • Williams, A. T., Shrine, N., Naghra-van Gijzel, H., Betts, J. C., Chen, J., Hessel, E. M., John, C., Packer, R., Reeve, N. F., Yeo, A. J., Abner, E., Åsvold, B. O., Auvinen, J., Bartz, T. M., Bradford, Y., Brumpton, B., Campbell, A., Cho, M. H., Chu, S., & Crosslin, D. R. (2021). Genome-wide association study of susceptibility to hospitalised respiratory infections. Wellcome Open Research., 6(290). https://doi.org/10.12688/wellcomeopenres.17230.2
  • Hartwell, E. E., Merikangas, A. K., Verma, S. S., Ritchie, M. D., Kranzler, H. R., & Kember, R. L. (2021). Genetic liability for substance use associated with medical comorbidities in Electronic Health Records of African‐ and european‐ancestry individuals. Addiction Biology, 27(1). https://doi.org/10.1111/adb.13099
  • Park, J., Packard, E. A., Levin, M. G., Judy, R. L., Damrauer, S. M., Day, S. M., Ritchie, M. D., & Rader, D. J. (2021). A genome-first approach to rare variants in hypertrophic cardiomyopathy genes mybpc3 and myh7 in a medical biobank. Human Molecular Genetics, 31(5), 827–837. https://doi.org/10.1093/hmg/ddab249
  • Ahmadmehrabi, S., Li, B., Hui, D., Park, J., Ritchie, M., Rader, D. J., Ruckenstein, M. J., Epstein, D. J., & Brant, J. (2021). A genome‐first approach to rare variants in dominant postlingual hearing loss genes in a large adult population. Otolaryngology–Head and Neck Surgery, 166(4), 746–752. https://doi.org/10.1177/01945998211029544
  • Verma, S. S., Chung, W. K., Dudek, S., Williamson, J. L., Verma, A., Robinson, S., … Ritchie, M. D. (2021). Research on COVID-19 through patient-reported data: a survey for observational studies in the COVID-19 pandemic. Journal of Clinical and Translational Science5(1), e17. doi:10.1017/cts.2020.509
  • Park, J., Lucas, A.M., Zhang, X. et al. Exome-wide evaluation of rare coding variants using electronic health records identifies new gene–phenotype associations. Nat Med 27, 66–72 (2021). https://doi.org/10.1038/s41591-020-1133-8
  • Kosmicki, J. A., Horowitz, J. E., Banerjee, N., Lanche, R., Marcketta, A., Maxwell, E., ... & Ferreira, M. A. (2021). A catalog of associations between rare coding variants and COVID-19 outcomes (preprint).
  • Liu, X., Verma, A., Garcia, G., Ramage, H., Lucas, A., Myers, R. L., Michaelson, J. J., Coryell, W., Kumar, A., Charney, A. W., Kazanietz, M. G., Rader, D. J., Ritchie, M. D., Berrettini, W. H., Schultz, D. C., Cherry, S., Damoiseaux, R., Arumugaswami, V., & Klein, P. S. (2021). Targeting the coronavirus nucleocapsid protein through GSK-3 inhibition. Proceedings of the National Academy of Sciences, 118(42). https://doi.org/10.1073/pnas.2113401118
  • Li, R., Duan, R., Zhang, X. et al. Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics. Nat Commun 12, 168 (2021). https://doi.org/10.1038/s41467-020-20211-2
  • Gu, X., Yang, H., Sheng, X., Ko, Y.-A., Qiu, C., Park, J., Huang, S., Kember, R., Judy, R. L., Park, J., Damrauer, S. M., Nadkarni, G., Loos, R. J., My, V. T., Chaudhary, K., Bottinger, E. P., Paranjpe, I., Saha, A., Brown, C., … Susztak, K. (2021). Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity. Science Translational Medicine, 13(576). https://doi.org/10.1126/scitranslmed.aaz1458
  • Kember, R. L., Merikangas, A. K., Verma, S. S., Verma, A., Judy, R., Damrauer, S. M., Ritchie, M. D., Rader, D. J., Bućan, M., Abecasis, G., Baras, A., Cantor, M., Coppola, G., Economides, A., Lotta, L., Overton, J. D., Reid, J. G., Shuldiner, A., Beechert, C., & Forsythe, C. (2021). Polygenic Risk of Psychiatric Disorders Exhibits Cross-trait Associations in Electronic Health Record Data From European Ancestry Individuals. Biological Psychiatry., 89(3), 236–245. https://doi.org/10.1016/j.biopsych.2020.06.026
  • Sun, L., Surya, S., Le, A. N., Desai, H., Doucette, A., Gabriel, P., Ritchie, M. D., Rader, D., Maillard, I., Bange, E., Huang, A. C., Vonderheide, R. H., DeMichele, A., Verma, A., Mamtani, R., & Maxwell, K. N. (2021). Rates of covid-19–related outcomes in cancer compared with Noncancer patients. JNCI Cancer Spectrum, 5(1). https://doi.org/10.1093/jncics/pkaa120
  • Drivas, T. G., Lucas, A., Zhang, X., & Ritchie, M. D. (2021). Mendelian pathway analysis of laboratory traits reveals distinct roles for ciliary subcompartments in common disease pathogenesis. The American Journal of Human Genetics, 108(3), 482–501. https://doi.org/10.1016/j.ajhg.2021.02.008
  • Lee, D.S.M., Park, J., Kromer, A. et al. Disrupting upstream translation in mRNAs is associated with human disease. Nat Commun 12, 1515 (2021). https://doi.org/10.1038/s41467-021-21812-1
  • Assimes, T., Tcheandjieu, C., Zhu, X., Hilliard, A., Clarke, S., Napolioni, V., Ma, S., Fang, H., Gorman, B. R., Lee, K. M., Chen, F., Pyarajan, S., Song, R., Plomondon, M., Maddox, T., Waldo, S., Sinnott-Armstrong, N., Ho, Y.-L., Wojcik, G., … Huang, J. (2021). A Large-Scale Multi-Ethnic Genome-Wide Association Study of Coronary Artery Disease. https://doi.org/10.21203/rs.3.rs-275591/v1
  • Georgakis, M. K., Malik, R., Li, X., Gill, D., Levin, M. G., Vy, H. M., Judy, R., Ritchie, M., Verma, S. S., Nadkarni, G. N., Damrauer, S. M., Theodoratou, E., & Dichgans, M. (2021). Genetically downregulated interleukin-6 signaling is associated with a favorable cardiometabolic profile. Circulation, 143(11), 1177–1180. https://doi.org/10.1161/circulationaha.120.052604
  • Lau-Min, K. S., Asher, S. B., Chen, J., Domchek, S. M., Feldman, M., Joffe, S., Landgraf, J., Speare, V., Varughese, L. A., Tuteja, S., VanZandbergen, C., Ritchie, M. D., & Nathanson, K. L. (2021). Real-world integration of genomic data into the electronic health record: the PennChart Genomics Initiative. Genetics in Medicine: Official Journal of the American College of Medical Genetics., 23(4), 603–605. https://doi.org/10.1038/s41436-020-01056-y
  • Shang, N., Khan, A., Polubriaginof, F. et al. Medical records-based chronic kidney disease phenotype for clinical care and “big data” observational and genetic studies. npj Digit. Med. 4, 70 (2021). https://doi.org/10.1038/s41746-021-00428-1
  • Li, B., Veturi, Y., Verma, A., Bradford, Y., Daar, E. S., Gulick, R. M., Riddler, S. A., Robbins, G. K., Lennox, J. L., Haas, D. W., & Ritchie, M. D. (2021). Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults. PLOS Genetics, 17(4). https://doi.org/10.1371/journal.pgen.1009464
  • Basile AO, Verma A, Tang LA, et al. Rapid Identification and Phenotyping of Nonalcoholic Fatty Liver Disease Patients Using an Algorithmic Approach in Diverse, Urban Healthcare Systems. medRxiv; 2021. DOI: 10.1101/2021.04.27.21256139.
  • Holmes, J. H., Beinlich, J., Boland, M. R., Bowles, K. H., Chen, Y., Cook, T. S., Demiris, G., Draugelis, M., Fluharty, L., Gabriel, P. E., Grundmeier, R., Hanson, C. W., Herman, D. S., Himes, B. E., Hubbard, R. A., Kahn, C. E., Kim, D., Koppel, R., Long, Q., … Moore, J. H. (2021). Why is the electronic health record so challenging for research and clinical care? Methods of Information in Medicine, 60(01/02), 032–048. https://doi.org/10.1055/s-0041-1731784
  • Ahmadmehrabi, S., Li, B., Park, J. et al. Genome-first approach to rare EYA4 variants and cardio-auditory phenotypes in adults. Hum Genet 140, 957–967 (2021). https://doi.org/10.1007/s00439-021-02263-6
  • Hall, M. A., Wallace, J., Lucas, A. M., Bradford, Y., Verma, S. S., Müller-Myhsok, B., Passero, K., Zhou, J., McGuigan, J., Jiang, B., Pendergrass, S. A., Zhang, Y., Peissig, P., Brilliant, M., Sleiman, P., Hakonarson, H., Harley, J. B., Kiryluk, K., Van Steen, K., … Ritchie, M. D. (2021). Novel edge encoding method enhances ability to identify genetic interactions. PLOS Genetics, 17(6). https://doi.org/10.1371/journal.pgen.1009534
  • Kosmicki, J. A., Horowitz, J. E., Banerjee, N., Lanche, R., Marcketta, A., Maxwell, E., Bai, X., Sun, D., Backman, J. D., Sharma, D., Kury, F. S. P., Kang, H. M., O’Dushlaine, C., Yadav, A., Mansfield, A. J., Li, A. H., Watanabe, K., Gurski, L., McCarthy, S. E., … Ferreira, M. A. R. (2021). Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals. The American Journal of Human Genetics, 108(7), 1350–1355. https://doi.org/10.1016/j.ajhg.2021.05.017
  • Veturi, Y., Lucas, A., Bradford, Y. et al. A unified framework identifies new links between plasma lipids and diseases from electronic medical records across large-scale cohorts. Nat Genet 53, 972–981 (2021). https://doi.org/10.1038/s41588-021-00879-y
  • Wang, L., Desai, H., Le, A., Hausler, R., Verma, S., Verma, A., Judy, R., Doucette, A., Gabriel, P., Damrauer, S., Ritchie, M., Rader, D., Kember, R., & Maxwell, K. (2021). Abstract LB222: Performance of polygenic risk scores for GI cancer prediction in an academic biobank. Cancer Research, 81(13_Supplement). https://doi.org/10.1158/1538-7445.am2021-lb222
  • Zhang, C., Verma, A., Feng, Y., Melo, M. C., McQuillan, M., Hansen, M., Lucas, A., Park, J., Ranciaro, A., Thompson, S., Rubel, M. A., Campbell, M. C., Beggs, W., Hirbo, J., Mpoloka, S. W., Mokone, G. G., Nyambo, T., Meskel, D. W., Belay, G., … Tishkoff, S. (2021). Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-COV-2 infection. Medrxiv. https://doi.org/10.1101/2021.06.28.21259529
  • Banday, A. R., Stanifer, M. L., Florez-Vargas, O., Onabajo, O. O., Zahoor, M. A., Papenberg, B. W., Ring, T. J., Lee, C.-H., Andreakos, E., Arons, E., Barsh, G., Biesecker, L. G., Boyle, D. L., Burnett-Hartman, A., Carrington, M., Chang, E., Choe, P. G., Chrisholm, R. L., Dalgard, C., … Prokunina-Olsson, L. (2021). Genetic regulation of OAS1 nonsense-mediated decay underlies association with risk of severe COVID-19. Medrxiv. https://doi.org/10.1101/2021.07.09.21260221
  • Chung, W. K., Brothers, K., Bradbury, A., Chanprasert, S., Orlando, L., Torkamani, A., Zierhut, H., Ritchie, M. D., Phillips, M., Schoden, J., Maiese, D., Hendershot, T., Hamilton, C. M., & Ramos, E. M. (2021). Genomic Medicine Implementation Protocols in the PHENX toolkit: Tools for Standardized Data Collection. Genetics in Medicine, 23(9), 1783–1788. https://doi.org/10.1038/s41436-021-01183-0
  • Bone, W. P., Bellomo, T., Chen, B. Y., Gawronski, K. A., Zhang, D., Park, J., Levin, M., Tsao, N., Klarin, D., lynch, julie, Assimes, T. L., Gaziano, M., Wilson, P., Cho, K., Vujkovic, M., O’Donnell, C. J., Chang, K.-M., Tsao, P. S., Rader, D. J., … Voight, B. F. (2021). Abstract MP16: Multi-trait GWAS of atherosclerosis detects novel loci and potential therapeutic targets. Arteriosclerosis, Thrombosis, and Vascular Biology, 41(Suppl_1). https://doi.org/10.1161/atvb.41.suppl_1.mp16
  • Li B and Ritchie MD (2021) From GWAS to Gene: Transcriptome-Wide Association Studies and Other Methods to Functionally Understand GWAS Discoveries. Front. Genet. 12:713230. doi: 10.3389/fgene.2021.713230
  • Hartwell, E., Merikangas, A., Verma, S., Ritchie, M., Center, R. G., Kranzler, H., & Kember, R. (2021). 17. DIFFERENCES IN PHENOTYPIC ASSOCIATIONS OF GENETIC LIABILITY FOR SUBSTANCE USE BY ANCESTRY AND SEX. European Neuropsychopharmacology51, e49.
  • Arthur VL, Li Z, Cao R, Oetting WS, Israni AK, Jacobson PA, Ritchie MD, Guan W and Chen J (2021) A Multi-Marker Test for Analyzing Paired Genetic Data in Transplantation. Front. Genet. 12:745773. doi: 10.3389/fgene.2021.745773
  • Liu, X., Verma, A., Garcia, G., Ramage, H., Lucas, A., Myers, R. L., Michaelson, J. J., Coryell, W., Kumar, A., Charney, A. W., Kazanietz, M. G., Rader, D. J., Ritchie, M. D., Berrettini, W. H., Schultz, D. C., Cherry, S., Damoiseaux, R., Arumugaswami, V., & Klein, P. S. (2021). Targeting the coronavirus nucleocapsid protein through GSK-3 inhibition. Proceedings of the National Academy of Sciences, 118(42). https://doi.org/10.1073/pnas.2113401118
  • Wen, J., Fu, C. H. Y., Tosun, D., Veturi, Y., Yang, Z., Abdulkadir, A., Mamourian, E., Srinivasan, D., Bao, J., Erus, G., Shou, H., Habes, M., Doshi, J., Varol, E., Mackin, S. R., Sotiras, A., Fan, Y., Saykin, A. J., Sheline, Y. I., … Davatzikos, C. (2021). Multidimensional representations in late-life depression: convergence in neuroimaging, cognition, clinical symptomatology and genetics. Arxiv. https://doi.org/https://doi.org/10.48550/arXiv.2110.11347
  • Li, B., Veturi, Y., Lucas, A., Bradford, Y., Verma, S. S., Verma, A., Park, J., Wei, W.-Q., Feng, Q., Namjou, B., Kiryluk, K., Kullo, I., Luo, Y., Pividori, M., Im, H. K., Greene, C. S., & Ritchie, M. D. (2021). Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked Biobank Data. Medrxiv. https://doi.org/10.1101/2021.10.21.21265225
  • Scott, W. K., Ritchie, M. D., Haines, J. L., & Pericak‐Vance, M. A. (2021). Designing a study for identifying genes in complex traits. Genetic Analysis of Complex Diseases, 1–12. https://doi.org/10.1002/9781119104100.ch1
  • Pendergrass, S. A., & Ritchie, M. D. (2021). Sample size, power, and Data Simulation. Genetic Analysis of Complex Diseases, 278–297. https://doi.org/10.1002/9781119104100.ch12
  • McCauley, J. L., Veturi, Y., Verma, S. S., & Ritchie, M. D. (2021). Genome‐Wide association studies. Genetic Analysis of Complex Diseases, 205–227. https://doi.org/10.1002/9781119104100.ch9
  • Scott, W. K., & Ritchie, M. D. (2021). Genetic analysis of complex disease. Wiley-Blackwell.
  • Singhal, P., Guerraty, M. A., Kim, D., Rader, D. J., Ritchie, M. D., & Verma, A. (2021). Abstract 12957: Determining Disease Co-Occurrence Architecture of Hypertensive Heart Disease in Penn Medicine Biobank Using Longitudinal EHR Data Linked With PMBB Participants. Circulation Hypertension and Nephrology, 144(A12957). https://doi.org/https://doi.org/10.1161/circ.144.suppl_1.12957
  • Reza, N., Bone, W. P., Singhal, P., Yang, Y., Verma, A., Murthy, A. C., Denduluri, S., Adusumalli, S., Ritchie, M., & Cappola, T. P. (2021). Abstract 11946: Comparison of Unsupervised Learning Approaches Applied to Electronic Health Record Traits in Heart Failure. Circulation Health Tech, 144(A11946). https://doi.org/https://www.ahajournals.org/doi/abs/10.1161/circ.144.suppl_1.11946