Biomedical and Translational Informatics Laboratory

Publications - 2018

  • Buchanan, A. H., Manickam, K., Meyer, M. N., Wagner, J. K., Hallquist, M. L. G., Williams, J. L., Rahm, A. K., Williams, M. S., Chen, Z.-M. E., Shah, C. K., Garg, T. K., Lazzeri, A. L., Schwartz, M. L. B., Lindbuchler, D. M., Fan, A. L., Leeming, R., Servano, P. O., Smith, A. L., Vogel, V. G., … Murray, M. F. (2018). Early cancer diagnoses through BRCA1/2 screening of unselected adult Biobank participants. Genetics in Medicine, 20(5), 554–558. https://doi.org/10.1038/gim.2017.145
  • Zhana, J., Setten, J. van, Brody, J., Swenson, B., Butler, A. M., Campbell, H., … Baderab, J. S. (2018). Discovering patterns of pleiotropy in genome-wide association studies. bioRxiv , 273540. doi:10.1101/273540
  • Helle, E. I., Biegley, P., Knowles, J. W., Leader, J. B., Pendergrass, S., Yang, W., Reaven, G. R., Shaw, G. M., Ritchie, M., & Priest, J. R. (2018). First Trimester Plasma Glucose Values in Women without Diabetes are Associated with Risk for Congenital Heart Disease in Offspring. The Journal of Pediatrics., 195, 275–278. https://doi.org/10.1016/j.jpeds.2017.10.046
  • Bergmeijer, T. O., Reny, J.-L., Pakyz, R. E., Gong, L., Lewis, J. P., Kim, E.-Y., Aradi, D., Fernandez-Cadenas, I., Horenstein, R. B., Lee, M. T. M., Whaley, R. M., Montaner, J., Gensini, G. F., Cleator, J. H., Chang, K., Holmvang, L., Hochholzer, W., Roden, D. M., Winter, S., & Altman, R. B. (2018). Genome-wide and candidate gene approaches of clopidogrel efficacy using pharmacodynamic and clinical end points—Rationale and design of the International Clopidogrel Pharmacogenomics Consortium (ICPC). The American Heart Journal., 198, 152–159. https://doi.org/10.1016/j.ahj.2017.12.010
  • Ritchie, M. D., & Van Steen, K. (2018). The search for gene-gene interactions in genome-wide association studies: Challenges in abundance of methods, practical considerations, and biological interpretation. Annals of Translational Medicine, 6(8), 157–157. doi:10.21037/atm.2018.04.05
  • Buchanan, A. H., Manickam, K., Meyer, M. N., Wagner, J. K., Hallquist, M. L. G., Williams, J. L., … Murray, M. F. (2018). Early cancer diagnoses through BRCA1/2 screening of unselected adult Biobank participants. Genetics in Medicine, 20(5), 554–558. doi:10.1038/gim.2017.145
  • Gusarova, V., O’Dushlaine, C., Teslovich, T. M., Benotti, P. N., Mirshahi, T., Gottesman, O., … Gromada, J. (2018). Genetic inactivation of ANGPTL4 improves glucose homeostasis and is associated with reduced risk of diabetes. Nature Communications, 9(1). doi:10.1038/s41467-018-04611-z
  • Haas, D. W., Bradford, Y., Verma, A., Verma, S. S., Eron, J. J., Gulick, R. M., … Ritchie, M. D. (2018). Brain neurotransmitter transporter/receptor genomics and efavirenz Central Nervous System adverse events. Pharmacogenetics and Genomics, 28(7), 179–187. doi:10.1097/fpc.0000000000000341
  • Miller, J. E., Shivakumar, M. K., Risacher, S. L., Saykin, A. J., Ritchie, M. D., Nho, K., & Kim, D. (2018). P4‐238: Pathway Level Codon Bias Among Synonymous Rare Variants is Associated with Alzheimer’s Disease Imaging Biomarker. Alzheimer’s & Dementia : The Journal of the Alzheimer’s Association., 14(7S_Part_29). https://doi.org/10.1016/j.jalz.2018.07.059
  • Ritchie, M. D. (2018). Large-Scale Analysis of Genetic and Clinical Patient Data. Annual Review of Biomedical Data Science., 1(1), 263–274. https://doi.org/10.1146/annurev-biodatasci-080917-013508
  • van Setten, J., Brody, J. A., Jamshidi, Y., Swenson, B. R., Butler, A. M., Campbell, H., … Sotoodehnia, N. (2018). PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity. Nature Communications, 9(1). doi:10.1038/s41467-018-04766-9
  • Lee, J. J., Wedow, R., Okbay, A., Kong, E., Maghzian, O., Zacher, M., … Cesarini, D. (2018). Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals. Nature Genetics, 50(8), 1112–1121. doi:10.1038/s41588-018-0147-3
  • Manickam, K., Buchanan, A. H., Schwartz, M. L. B., Hallquist, M. L. G., Williams, J. L., Rahm, A. K., Rocha, H., Savatt, J. M., Evans, A. E., Butry, L. M., Lazzeri, A. L., Lindbuchler, D. M., Flansburg, C. N., Leeming, R., Vogel, V. G., Lebo, M. S., Mason-Suares, H. M., Hoskinson, D. C., Abul-Husn, N. S., & Dewey, F. E. (2018). Exome Sequencing–Based Screening for BRCA1/2 Expected Pathogenic Variants Among Adult Biobank Participants. JAMA Network Open., 1(5). https://doi.org/10.1001/jamanetworkopen.2018.2140
  • Ritchie. (2018). Methods of integrating genomics data. European Journal of Human Genetics., 26.
  • Klein. (2018). Pharmacogenomics Knowledge for Personalized Medicine. European Journal of Human Genetics.26.
  • Wei, W.-Q., Li, X., Feng, Q., Kubo, M., Kullo, I. J., Peissig, P. L., … Denny, J. C. (2018). LPA variants are associated with residual cardiovascular risk in patients receiving statins. Circulation, 138(17), 1839–1849. doi:10.1161/circulationaha.117.031356
  • Verma, S. S., Lucas, A., Zhang, X., Veturi, Y., Dudek, S., Li, B., … Ritchie, M. D. (2018). Collective feature selection to identify crucial epistatic variants. BioData Mining, 11(1). doi:10.1186/s13040-018-0168-6
  • Mosley, J. D., Benson, M. D., Smith, J. G., Melander, O., Ngo, D., Shaffer, C. M., … Wang, T. J. (2018). Probing the virtual proteome to identify novel disease biomarkers. Circulation, 138(22), 2469–2481. doi:10.1161/circulationaha.118.036063

  • Volpi S, Bult CJ, Chisholm RL, Deverka PA, Ginsburg GS, Jacob HJ, Kasapi M, McLeod HL, Roden DM, Williams MS, Green ED, Rodriguez LL, Aronson S, Cavallari LH, Denny JC, Dressler LG, Johnson JA, Klein TE, Leeder JS, Piquette-Miller M, Perera M, Rasmussen-Torvik LJ, Rehm HL, Ritchie MD, Skaar TC, Wagle N, Weinshilboum R, Weitzel KW, Wildin R, Wilson J, Manolio TA, Relling MV. Research Directions in the Clinical Implementation of Pharmacogenomics: An Overview of US Programs and Projects. Clin Pharmacol Ther. 2018 Feb 20. doi: 10.1002/cpt.1048. PMID:29460415. 
  • Nielsen JB, Fritsche LG, Zhou W, Teslovich TM, Holmen OL, Gustafsson S, Gabrielsen ME, Schmidt EM, Beaumont R, Wolford BN, Lin M, Brummett CM, Preuss MH, Refsgaard L, Bottinger EP, Graham SE, Surakka I, Chu Y, Skogholt AH, Dalen H, Boyle AP, Oral H, Herron TJ, Kitzman J, Jalife J, Svendsen JH, Olesen MS, Njølstad I, Løchen ML, Baras A, Gottesman O, Marcketta A, O'Dushlaine C, Ritchie MD, Wilsgaard T, Loos RJF, Frayling TM, Boehnke M, Ingelsson E, Carey DJ, Dewey FE, Kang HM, Abecasis GR, Hveem K, Willer CJ. Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development. Am J Hum Genet. 2018 Jan 4;102(1):103-115. PMID: 29290336
  • Li B, Verma SS, Veturi YC, Verma A, Bradford Y, Haas DW, Ritchie MD. Evaluation of PrediXcan for prioritizing GWAS associations and predicting gene expression. Pac Symp Biocomput. 2018;23:448-459. PMID: 29218904. PMCID: PMC5749400
  • Veturi Y, Ritchie MD. How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures? Pac Symp Biocomput. 2018; 23:228-239. PMID: 29218884. PMCID: PMC5785784
  • Verma A, Bradford Y, Dudek SM, Verma SS, Pendergrass SA, Ritchie MD. A simulation study investigating power of Phenome-Wide Association Studies. BMC Bioinformatics, 2018 Apr 4;19(1):120. doi: 10.1186/s12859-018-2135-0. PMID:29618318
  • Verma SS, Josyula N, Verma A, Zhang X, Veturi Y, Dewey FE, Hartzel DN, Lavage DR, Leader J, Ritchie MD, Pendergrass SA. Rare variants in drug target genes contributing to complex diseases, phenome-wide. Sci Rep. 2018 Mar 15;8(1):4624. doi: 10.1038/s41598-018-22834-4. PMID:29545597; PMCID:PMC5854600
  • Verma A, Lucas A, Verma SS, Zhang Y, Josyula N, Khan A, Hartzel DN, Lavage DR, Leader J, Ritchie MD, Pendergrass SA. PheWAS and Beyond: The Landscape of Associations with Medical Diagnoses and Clinical Measures across 38,662 Individuals from Geisinger. Am J Hum Genet. 2018 Mar 19. pii: S0002-9297(18)30062-4. doi: 10.1016/j.ajhg.2018.02.017. PMID:29606303
  • Basile AO, Ritchie MD. Informatics and machine learning to define the phenotype.  Expert Rev Mol Diagn. 2018 Mar;18(3):219-226. doi: 10.1080/14737159.2018.1439380. Epub 2018 Feb 16. PMID:29431517
  • Verma SS, Ritchie MD. Another Round of "Clue" to Uncover the Mystery of Complex Traits. Genes (Basel). 2018 Jan 25;9(2). pii: E61. PMID: 29370075