Northwestern University Feinberg School of Medicine
Center for Genetic Medicine
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Publications & Collaborations

 eMERGE Phase IV

  1. Agrawal S, Heiss MS, Fenter RB, Abramova TV, Perera MA, Pacheco JA, Smith ME, Rasmussen-Torvik LJ, George AL Jr. Impact of CYP2C9-Interacting Drugs on Warfarin Pharmacogenomics. Clin Transl Sci. 2020 Sep;13(5):941-949. doi: 10.1111/cts.12781. Epub 2020 Apr 9.PMID: 32270628
  2. Gacita AM, Dellefave-Castillo L, Page PGT, Barefield DY, Wasserstrom JA, Puckelwartz MJ, Nobrega MA, McNally EM. Altered Enhancer and Promoter Usage Leads to Differential Gene Expression in the Normal and Failed Human Heart. Circ Heart Fail. 2020 Oct;13(10):e006926. doi: 10.1161/CIRCHEARTFAILURE.120.006926. Epub 2020 Sep 30. PMID: 32993371
  3. Gordon AS, Zouk H, Venner E, Eng CM, Funke BH, Amendola LM, Carrell DS, Chisholm RL, Chung WK, Denny JC, Fedotov A, Hakonarson H, Kullo IJ, Larson EB, Leduc MS, Leppig KA, Lennon NJ, Linder JE, Muzny DM, Prows CA, Rasmussen-Torvik LJ, Rasouly HM, Roden DM, Rosenthal EA, Smith ME, Stanaway IB, Van Driest SL, Walker K, Wiesner GL, Williams MS, Witkowski L, Crosslin DR, Gibbs RA, Rehm HL, Jarvik GP. Frequency of genomic secondary findings among 21,915 eMERGE network participants. eMERGE Clinical Annotation Working Group.Genet Med. 2020 Sep;22(9):1470-1477. doi: 10.1038/s41436-020-0810-9. Epub 2020 Jun 17.PMID: 32546831
  4. Hoell C, Aufox S, Nashawaty N, Myers MF, Smith ME. Comprehension and personal value of negative non-diagnostic genetic panel testing. J Genet Couns. 2020 Sep 18. doi: 10.1002/jgc4.1327. Epub ahead of print. PMID: 32945059
  5. Hoell C, Wynn J, Rasmussen LV, Marsolo K, Aufox SA, Chung WK, Connolly JJ, Freimuth RR, Kochan D, Hakonarson H, Harr M, Holm IA, Kullo IJ, Lammers PE, Leppig KA, Leslie ND, Myers MF, Sharp RR, Smith ME, Prows CA. Participant choices for return of genomic results in the eMERGE Network. Genet Med. 2020 Nov;22(11):1821-1829. doi: 10.1038/s41436-020-0905-3. Epub 2020 Jul 16.PMID: 32669677
  6. Joo YY, Actkins K, Pacheco JA, Basile AO, Carroll R, Crosslin DR, Day F, Denny JC, Velez Edwards DR, Hakonarson H, Harley JB, Hebbring SJ, Ho K, Jarvik GP, Jones M, Karaderi T, Mentch FD, Meun C, Namjou B, Pendergrass S, Ritchie MD, Stanaway IB, Urbanek M, Walunas TL, Smith ME, Chisholm RL, Kho AN, Davis L, Hayes MG. PCOS Consortium. A Polygenic and Phenotypic Risk Prediction for Polycystic Ovary Syndrome Evaluated by Phenome-Wide Association Studies International. J Clin Endocrinol Metab. 2020 Jun 1;105(6):1918-36. doi: 10.1210/clinem/dgz326. PMID: 31917831
  7. Kawai VK, Shi M, Feng Q, Chung CP, Liu G, Cox NJ, Jarvik GP, Lee MTM, Hebbring SJ, Harley JB, Kaufman KM, Namjou B, Larson E, Gordon AS, Roden DM, Stein CM, Mosley JD; eMERGE Investigators. Pleiotropy in the Genetic Predisposition to Rheumatoid Arthritis: A Phenome-Wide Association Study and Inverse Variance-Weighted Meta-Analysis. Arthritis Rheumatol. 2020 Sep;72(9):1483-1492. doi: 10.1002/art.41291. Epub 2020 Aug 6. PMID: 32307929
  8. Lynch JA, Sharp RR, Aufox SA, Bland ST, Blout C, Bowen DJ, Buchanan AH, Halverson C, Harr M, Hebbring SJ, Henrikson N, Hoell C, Holm IA, Jarvik G, Kullo IJ, Kochan DC, Larson EB, Lazzeri A, Leppig KA, Madden J, Marasa M, Myers MF, Peterson J, Prows CA, Kulchak Rahm A, Ralston J, Milo Rasouly H, Scrol A, Smith ME, Sturm A, Stuttgen K, Wiesner G, Williams MS, Wynn J, Williams JL. Understanding the Return of Genomic Sequencing Results Process: Content Review of Participant Summary Letters in the eMERGE Research Network. J Pers Med. 2020 May 13;10(2):38. doi: 10.3390/jpm10020038.PMID: 32413979
  9. Murugan M, Babb LJ, Overby Taylor C, Rasmussen LV, Freimuth RR, Venner E, Yan F, Yi V, Granite SJ, Zouk H, Aronson SJ, Power K, Fedotov A, Crosslin DR, Fasel D, Jarvik GP, Hakonarson H, Bangash H, Kullo IJ, Connolly JJ, Nestor JG, Caraballo PJ, Wei W, Wiley K, Rehm HL, Gibbs RA. Genomic considerations for FHIR®; eMERGE implementation lessons. J Biomed Inform. 2021 Jun;118:103795. doi: 10.1016/j.jbi.2021.103795. Epub 2021 Apr 28. PMID: 33930535
  10. Pottinger TD, Pesce LL, Gacita A, Montefiori L, Hodge N, Kearns S, Salamone IM, Pacheco JA, Rasmussen-Torvik LJ, Smith ME, Chisholm R, Nobrega MA, McNally EM, Puckelwartz MJ. Trajectory analysis of cardiovascular phenotypes from biobank data uncovers novel genetic associations. BioRxiv paper. https://doi.org/10.1101/2020.05.10.087130. 27 Oct 2020. https://doi.org/10.1161/res.127.suppl_1.439 Circulation Research. 2020;127:A439
  11. Pottinger TD, Puckelwartz MJ, Pesce LL, Robinson A, Kearns S, Pacheco JA, Rasmussen-Torvik LJ, Smith ME, Chisholm R, McNally EM. Pathogenic and Uncertain Genetic Variants Have Clinical Cardiac Correlates in Diverse Biobank Participants. J Am Heart Assoc. 2020 Feb 4;9(3):e013808. doi: 10.1161/JAHA.119.013808. Epub 2020 Feb 3. PMID: 32009526
  12. Rasmussen LV, Connolly JJ, Del Fiol G, Freimuth RR, Pet DB, Peterson JF, Shirts BH, Starren JB, Williams MS, Walton N, Taylor CO. Infobuttons for Genomic Medicine: Requirements and Barriers. Appl Clin Inform 2021; 12(02): 383-390. DOI: 10.1055/s-0041-1729164
  13. Rasmussen LV, Hoell C, Smith ME, Chisholm R, Starren J, Aufox S, Luo Y, Rasmussen-Torvik LJ. Solutions for unexpected challenges encountered when integrating research genomics results into the EHR. CC BY 4.0 · ACI Open 2020; 04(02): e132-e135. DOI: 10.1055/s-0040-1719059
  14. Rosenthal EA, Crosslin DR, Gordon AS, Carrell DS, Stanaway IB, Larson EB, Grafton J, Wei WQ, Denny JC, Feng QP, Shah AS, Sturm AC, Ritchie MD, Pacheco JA, Hakonarson H, Rasmussen-Torvik LJ, Connolly JJ, Fan X, Safarova M, Kullo IJ, Jarvik GP. Association between triglycerides, known risk SNVs and conserved rare variation in SLC25A40 in a multi-ancestry cohort.BMC Med Genomics. 2021 Jan 6;14(1):11. doi: 10.1186/s12920-020-00854-2.PMID: 33407432
  15. Wiesner GL, Kulchak Rahm A, Appelbaum P, Aufox S, Bland ST, Blout CL, Christensen KD, Chung WK, Clayton EW, Green RC, Harr MH, Henrikson N, Hoell C, Holm IA, Jarvik GP, Kullo IJ, Lammers PE, Larson EB, Lindor NM, Marasa M, F Myers M, Peterson JF, Prows CA, Ralston JD, Milo Rasouly H, Sharp RR, Smith ME, Van Driest SL, Williams JL, Williams MS, Wynn J, Leppig KA. Returning Results in the Genomic Era: Initial Experiences of the eMERGE Network. J Pers Med. 2020 Apr 27;10(2):30. doi: 10.3390/jpm10020030. PMID: 32349224

 eMERGE Phase III

  1. Almoguera B, Vazquez L, Mentch F, Connolly J, Pacheco JA, Sundaresan AS, Peissig PL, Linneman JG, McCarty CA, Crosslin D, Carrell DS, Lingren T, Namjou-Khales B, Harley JB, Larson E, Jarvik GP, Brilliant M, Williams MS, Kullo IJ, Hysinger EB, Sleiman PM, Hakonarson H. Identification of Four Novel Loci in Asthma in European American and African American Populations. Am J Respir Crit Care Med. 2017 Feb 15;195(4):456-463. doi: 10.1164/rccm.201604-0861OC. PMID: 27611488
  2. Antommaria AHM, Brothers KB, Myers JA, Feygin YB, Aufox SA, Brilliant MH, Conway P, Fullerton SM, Garrison NA, Horowitz CR, Jarvik GP, Li R, Ludman EJ, McCarty CA, McCormick JB, Mercaldo ND, Myers MF, Sanderson SC, Shrubsole MJ, Schildcrout JS, Williams JL, Smith ME, Clayton EW, Holm IA. Parents' attitudes toward consent and data sharing in biobanks: A multisite experimental survey. AJOB Empir Bioeth. 2018 Jul-Sep;9(3):128-142. doi: 10.1080/23294515.2018.1505783. Epub 2018 Sep 21.
  3. Aronson S, Babb L, Ames D, Gibbs RA, Venner E, Connelly JJ, Marsolo K, Weng C, Williams MS, Hartzler AL, Liang WH, Ralston JD, Devine EB, Murphy S, Chute CG, Caraballo PJ, Kullo IJ, Freimuth RR, Rasmussen LV, Wehbe FH, Peterson JF, Robinson JR, Wiley K, Overby Taylor C; eMERGE Network EHRI Working Group. Empowering genomic medicine by establishing critical sequencing result data flows: the eMERGE example. J Am Med Inform Assoc. 2018 Oct 1;25(10):1375-1381. doi: 10.1093/jamia/ocy051.
  4. Aziz A, Kawamoto K, Eilbeck K, Williams MS, Freimuth RR, Hoffman MA, Rasmussen LV, Overby CL, Shirts BH, Hoffman JM, Welch BM. The genomic CDS sandbox: An assessment among domain experts. J Biomed Inform. 2016 Apr;60:84-94. doi: 10.1016/j.jbi.2015.12.019. PMID: 26778834
  5. Baldridge AS, Pacheco JA, Aufox SA, Kim KY, Silverstein JC, Denham W, Hungness E, Smith ME, Allen NB, Greenland P, Rasmussen-Torvik LJ. Factors Associated With Long-Term Weight Loss Following Bariatric Surgery Using 2 Methods for Repeated Measures Analysis. Am J Epidemiol. 2015 Aug 1;182(3):235-43. doi: 10.1093/aje/kwv039. PMID: 26093003
  6. Bielinski SJ, Pathak J, Carrell DS, Takahashi PY, Olson JE, Larson NB, Liu H, Sohn S, Wells QS, Denny JC, Rasmussen-Torvik LJ, Pacheco JA, Jackson KL, Lesnick TG, Gullerud RE, Decker PA, Pereira NL, Ryu E, Dart RA, Peissig P, Linneman JG, Jarvik GP, Larson EB, Bock JA, Tromp GC, de Andrade M, Roger VL. A Robust e-Epidemiology Tool in Phenotyping Heart Failure with Differentiation for Preserved and Reduced Ejection Fraction: the Electronic Medical Records and Genomics (eMERGE) Network. J Cardiovasc Transl Res. 2015 Nov;8(8):475-83. doi: 10.1007/s12265-015-9644-2. PMID: 26195183
  7. Borthwick KM, Smelser DT, Bock JA, Elmore JR, Ryer EJ, Ye Z, Pacheco JA, Carrell DS, Michalkiewicz M, Thompson WK, Pathak J, Bielinski SJ, Denny JC, Linneman JG, Peissig PL, Kho AN, Gottesman O, Parmar H, Kullo IJ, McCarty CA, Böttinger EP, Larson EB, Jarvik GP, Harley JB, Bajwa T, Franklin DP, Carey DJ, Kuivaniemi H, Tromp G. ePhenotyping for Abdominal Aortic Aneurysm in the Electronic Medical Records and Genomics (eMERGE) Network: Algorithm Development and Konstanz Information Miner Workflow. Int J Biomed Data Min. 2015 Dec;4(1). pii: 113. PMID: 27054044
  8. Bush WS, Crosslin DR, Owusu-Obeng A, Wallace J, Almoguera B, Basford MA, Bielinski SJ, Carrell DS, Connolly JJ, Crawford D, Doheny KF, Gallego CJ, Gordon AS, Keating B, Kirby J, Kitchner T, Manzi S, Mejia AR, Pan V, Perry CL, Peterson JF, Prows CA, Ralston J, Scott SA, Scrol A, Smith M, Stallings SC, Veldhuizen T, Wolf W, Volpi S, Wiley K, Li R, Manolio T, Bottinger E, Brilliant MH, Carey D, Chisholm RL, Chute CG, Haines JL, Hakonarson H, Harley JB, Holm IA, Kullo IJ, Jarvik GP, Larson EB, McCarty CA, Williams MS, Denny JC, Rasmussen-Torvik LJ, Roden DM, Ritchie MD. Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network. Clin Pharmacol Ther. 2016 Aug;100(2):160-9. doi: 10.1002/cpt.350. PMID: 26857349
  9. De R, Verma SS, Drenos F, Holzinger ER, Holmes MV, Hall MA, Crosslin DR, Carrell DS, Hakonarson H, Jarvik G, Larson E, Pacheco JA, Rasmussen-Torvik LJ, Moore CB, Asselbergs FW, Moore JH, Ritchie MD, Keating BJ, Gilbert-Diamond D. Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR). BioData Min. 2015 Dec 14;8:41. doi: 10.1186/s13040-015-0074-0. PMID: 26674805
  10. Dumitrescu L, Ritchie MD, Denny JC, El Rouby NM, McDonough CW, Bradford Y, Ramirez AH, Bielinski SJ, Basford MA, Chai HS, Peissig P, Carrell D, Pathak J, Rasmussen LV, Wang X, Pacheco JA, Kho AN, Hayes MG, Matsumoto M, Smith ME, Li R, Cooper-DeHoff RM, Kullo IJ, Chute CG, Chisholm RL, Jarvik GP, Larson EB, Carey D, McCarty CA, Williams MS, Roden DM, Bottinger E, Johnson JA, de Andrade M, Crawford DC. Genome-wide study of resistant hypertension identified from electronic health records. PLoS One. 2017 Feb 21;12(2):e0171745. doi: 10.1371/journal.pone.0171745. PMID: 28222112
  11. Fort DG, Herr TM, Shaw PL, Gutzman KE, Starren JB. Mapping the evolving definitions of translational research. J Clin Transl Sci. 2017 Feb;1(1):60-66. doi: 10.1017/cts.2016.10. Epub 2017 Feb 2. Review. PMID: 28480056
  12. Fossey R, Kochan D, Winkler E, Pacyna JE, Olson J, Thibodeau S, Connolly JJ, Harr M, Behr MA, Prows CA, Cobb B, Myers MF, Leslie ND, Namjou-Khales B, Milo Rasouly H, Wynn J, Fedotov A, Chung WK, Gharavi A, Williams JL, Pais L, Holm I, Aufox S, Smith ME, Scrol A, Leppig K, Jarvik GP, Wiesner GL, Li R, Stroud M, Smoller JW, Sharp RR, Kullo IJ. Ethical Considerations Related to Return of Results from Genomic Medicine Projects: The eMERGE Network (Phase III) Experience. J Pers Med. 2018 Jan 3;8(1). pii: E2. doi: 10.3390/jpm8010002.
  13. Gallego CJ, Burt A, Sundaresan AS, Ye Z, Shaw C, Crosslin DR, Crane PK, Fullerton SM, Hansen K, Carrell D, Kuivaniemi H, Derr K, de Andrade M, McCarty CA, Kitchner TE, Ragon BK, Stallings SC, Papa G, Bochenek J, Smith ME, Aufox SA, Pacheco JA, Patel V, Friesema EM, Erwin AL, Gottesman O, Gerhard GS, Ritchie M, Motulsky AG, Kullo IJ, Larson EB, Tromp G, Brilliant MH, Bottinger E, Denny JC, Roden DM, Williams MS, Jarvik GP. Penetrance of Hemochromatosis in HFE Genotypes Resulting in p.Cys282Tyr and p.[Cys282Tyr];[His63Asp] in the eMERGE Network. Am J Hum Genet. 2015 Oct 1;97(4):512-20. doi: 10.1016/j.ajhg.2015.08.008. PMID: 26365338
  14. Garrison NA, Sathe NA, Antommaria AH, Holm IA, Sanderson SC, Smith ME, McPheeters ML, Clayton EW. A systematic literature review of individuals' perspectives on broad consent and data sharing in the United States. Genet Med. 2016 Jul;18(7):663-71. doi: 10.1038/gim.2015.138. PMID: 26583683
  15. Heatherly R, Rasmussen LV, Peissig PL, Pacheco JA, Harris P, Denny JC, Malin BA. A multi-institution evaluation of clinical profile anonymization. J Am Med Inform Assoc. 2016 Apr;23(e1):e131-7. doi: 10.1093/jamia/ocv154. PMID: 26567325
  16. Herr TM, Bielinski SJ, Bottinger E, Brautbar A, Brilliant M, Chute CG, Cobb BL, Denny JC, Hakonarson H, Hartzler AL, Hripcsak G, Kannry J, Kohane IS, Kullo IJ, Lin S, Manzi S, Marsolo K, Overby CL, Pathak J, Peissig P, Pulley J, Ralston J, Rasmussen L, Roden DM, Tromp G, Uphoff T, Weng C, Wolf W, Williams MS, Starren J. Practical considerations in genomic decision support: The eMERGE experience. J Pathol Inform. 2015 Sep 28;6:50. doi: 10.4103/2153-3539.165999. PMID: 26605115
  17. Herr TM, Bielinski SJ, Bottinger E, Brautbar A, Brilliant M, Chute CG, Denny J, Freimuth RR, Hartzler A, Kannry J, Kohane IS, Kullo IJ, Lin S, Pathak J, Peissig P, Pulley J, Ralston J, Rasmussen L, Roden D, Tromp G, Williams MS, Starren J. A conceptual model for translating omic data into clinical action. J Pathol Inform. 2015 Aug 31;6:46. doi: 10.4103/2153-3539.163985. PMID: 26430534
  18. Hylind R, Smith M, Rasmussen-Torvik L, Aufox S. Great expectations: patient perspectives and anticipated utility of non-diagnostic genomic-sequencing results. Journal of community genetics. 2018 Jan;9(1):19-26.
  19. Jackson KL, Mbagwu M, Pacheco JA, Baldridge AS, Viox DJ, Linneman JG, Shukla SK, Peissig PL, Borthwick KM, Carrell DA, Bielinski SJ, Kirby JC, Denny JC, Mentch FD, Vazquez LM, Rasmussen-Torvik LJ, Kho AN. Performance of an electronic health record-based phenotype algorithm to identify community associated methicillin-resistant Staphylococcus aureus cases and controls for genetic association studies. BMC Infect Dis. 2016 Nov 17;16(1):684. PMID: 27855652
  20. Jiang G, Kiefer RC, Rasmussen LV, Solbrig HR, Mo H, Pacheco JA, Xu J, Montague E, Thompson WK, Denny JC, Chute CG, Pathak J. Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution. J Biomed Inform. 2016 Aug;62:232-42. doi: 10.1016/j.jbi.2016.07.008. PMID: 27392645
  21. Jiang G, Solbrig HR, Kiefer R, Rasmussen LV, Mo H, Speltz P, Thompson WK, Denny JC, Chute CG, Pathak J. A Standards-based Semantic Metadata Repository to Support EHR-driven Phenotype Authoring and Execution. Stud Health Technol Inform. 2015;216:1098. PMID: 26262397
  22. Jones GT, Tromp G, Kuivaniemi H, Gretarsdottir S, Baas AF, Giusti B, Strauss E, Van't Hof FN, Webb TR, Erdman R, Ritchie MD, Elmore JR, Verma A, Pendergrass S, Kullo IJ, Ye Z, Peissig PL, Gottesman O, Verma SS, Malinowski J, Rasmussen-Torvik LJ, Borthwick KM, Smelser DT, Crosslin DR, de Andrade M, Ryer EJ, McCarty CA, Böttinger EP, Pacheco JA, Crawford DC, Carrell DS, Gerhard GS, Franklin DP, Carey DJ, Phillips VL, Williams MJ, Wei W, Blair R, Hill AA, Vasudevan TM, Lewis DR, Thomson IA, Krysa J, Hill GB, Roake J, Merriman TR, Oszkinis G, Galora S, Saracini C, Abbate R, Pulli R, Pratesi C, Saratzis A, Verissimo AR, Bumpstead S, Badger SA, Clough RE, Cockerill G, Hafez H, Scott DJ, Futers TS, Romaine SP, Bridge K, Griffin KJ, Bailey MA, Smith A, Thompson MM, van Bockxmeer FM, Matthiasson SE, Thorleifsson G, Thorsteinsdottir U, Blankensteijn JD, Teijink JA, Wijmenga C, de Graaf J, Kiemeney LA, Lindholt JS, Hughes A, Bradley DT, Stirrups K, Golledge J, Norman PE, Powell JT, Humphries SE, Hamby SE, Goodall AH, Nelson CP, Sakalihasan N, Courtois A, Ferrell RE, Eriksson P, Folkersen L, Franco-Cereceda A, Eicher JD, Johnson AD, Betsholtz C, Ruusalepp A, Franzén O, Schadt EE, Björkegren JL, Lipovich L, Drolet AM, Verhoeven EL, Zeebregts CJ, Geelkerken RH, van Sambeek MR, van Sterkenburg SM, de Vries JP, Stefansson K, Thompson JR, de Bakker PI, Deloukas P, Sayers RD, Harrison SC, van Rij AM, Samani NJ, Bown MJ. Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci. Circ Res. 2017 Jan 20;120(2):341-353. doi: 10.1161/CIRCRESAHA.116.308765. PMID: 27899403
  23. Keswani RN, Law R, Ciolino JD, Lo AA, Gluskin AB, Bentrem DJ, Komanduri S, Pacheco JA, Grande D, Thompson WK. Adverse events after surgery for nonmalignant colon polyps are common and associated with increased length of stay and costs. Gastrointest Endosc. 2016 Aug;84(2):296-303.e1. doi: 10.1016/j.gie.2016.01.048. PMID:26828760
  24. Kirby JC, Speltz P, Rasmussen LV, Basford M, Gottesman O, Peissig PL, Pacheco JA, Tromp G, Pathak J, Carrell DS, Ellis SB, Lingren T, Thompson WK, Savova G, Haines J, Roden DM, Harris PA, Denny JC. PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J Am Med Inform Assoc. 2016 Nov;23(6):1046-1052. doi: 10.1093/jamia/ocv202. PMID: 27026615
  25. Liu CT, Raghavan S, Maruthur N, Kabagambe EK, Hong J, Ng MC, Hivert MF, Lu Y, An P, Bentley AR, Drolet AM, Gaulton KJ, Guo X, Armstrong LL, Irvin MR, Li M, Lipovich L, Rybin DV, Taylor KD, Agyemang C, Palmer ND, Cade BE, Chen WM, Dauriz M, Delaney JA, Edwards TL, Evans DS, Evans MK, Lange LA, Leong A, Liu J, Liu Y, Nayak U, Patel SR, Porneala BC, Rasmussen-Torvik LJ, Snijder MB, Stallings SC, Tanaka T, Yanek LR, Zhao W, Becker DM, Bielak LF, Biggs ML, Bottinger EP, Bowden DW, Chen G, Correa A, Couper DJ, Crawford DC, Cushman M, Eicher JD, Fornage M, Franceschini N, Fu YP, Goodarzi MO, Gottesman O, Hara K, Harris TB, Jensen RA, Johnson AD, Jhun MA, Karter AJ, Keller MF, Kho AN, Kizer JR, Krauss RM, Langefeld CD, Li X, Liang J, Liu S, Lowe WL Jr, Mosley TH, North KE, Pacheco JA, Peyser PA, Patrick AL, Rice KM, Selvin E, Sims M, Smith JA, Tajuddin SM, Vaidya D, Wren MP, Yao J, Zhu X, Ziegler JT, Zmuda JM, Zonderman AB, Zwinderman AH; AAAG Consortium.; CARe Consortium.; COGENT-BP Consortium.; eMERGE Consortium.; MEDIA Consortium., Adeyemo A, Boerwinkle E, Ferrucci L, Hayes MG, Kardia SL, Miljkovic I, Pankow JS, Rotimi CN, Sale MM, Wagenknecht LE, Arnett DK, Chen YD, Nalls MA; MAGIC Consortium., Province MA, Kao WH, Siscovick DS, Psaty BM, Wilson JG, Loos RJ, Dupuis J, Rich SS, Florez JC, Rotter JI, Morris AP, Meigs JB. Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin. Am J Hum Genet. 2016 Jul 7;99(1):56-75. doi: 10.1016/j.ajhg.2016.05.006. PMID: 27321945
  26. Luo Y, Thompson WK, Herr TM, Zeng Z, Berendsen MA, Jonnalagadda SR, Carson MB, Starren J. Natural Language Processing for EHR-Based Pharmacovigilance: A Structured Review. Drug Saf. 2017 Nov;40(11):1075-1089. doi: 10.1007/s40264-017-0558-6. Review. PMID: 28643174
  27. Mo H, Jiang G, Pacheco JA, Kiefer R, Rasmussen LV, Pathak J, Denny JC, Thompson WK. A Decompositional Approach to Executing Quality Data Model Algorithms on the i2b2 Platform. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:167-75.PMID: 27570665
  28. Mo H, Pacheco JA, Rasmussen LV, Speltz P, Pathak J, Denny JC, Thompson WK. A Prototype for Executable and Portable Electronic Clinical Quality Measures Using the KNIME Analytics Platform. AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:127-31. PMID: 26306254
  29. Mo H, Thompson WK, Rasmussen LV, Pacheco JA, Jiang G, Kiefer R, Zhu Q, Xu J, Montague E, Carrell DS, Lingren T, Mentch FD, Ni Y, Wehbe FH, Peissig PL, Tromp G, Larson EB, Chute CG, Pathak J, Denny JC, Speltz P, Kho AN, Jarvik GP, Bejan CA, Williams MS, Borthwick K, Kitchner TE, Roden DM, Harris PA. Desiderata for computable representations of electronic health records-driven phenotype algorithms. J Am Med Inform Assoc. 2015 Nov;22(6):1220-30. doi: 10.1093/jamia/ocv112. PMID: 26342218
  30. Mosley JD, Benson MD, Smith JG, Melander O, Ngo D, Shaffer CM, Ferguson JF, Herzig MS, McCarty CA, Chute CG, Jarvik GP, Gordon AS, Palmer MR, Crosslin DR, Larson EB, Carrell DS, Kullo IJ, Pacheco JA, Peissig PL, Brilliant MH, Kitchner TE, Linneman JG, Namjou B, Williams MS, Ritchie MD, Borthwick KM, Kiryluk K, Mentch FD, Sleiman PM, Karlson EW, Verma SS, Zhu Y, Vasan RS, Yang Q, Denny JC, Roden DM, Gerszten RE, Wang TJ. Probing the Virtual Proteome to Identify Novel Disease Biomarkers. Circulation. 2018 Nov 27;138(22):2469-2481. doi: 10.1161/CIRCULATIONAHA.118.036063.
  31. Mosley JD, Feng Q, Wells QS, Van Driest SL, Shaffer CM, Edwards TL, Bastarache L, Wei WQ, Davis LK, McCarty CA, Thompson W, Chute CG, Jarvik GP, Gordon AS, Palmer MR, Crosslin DR, Larson EB, Carrell DS, Kullo IJ, Pacheco JA, Peissig PL, Brilliant MH, Linneman JG, Namjou B, Williams MS, Ritchie MD, Borthwick KM, Verma SS, Karnes JH, Weiss ST, Wang TJ, Stein CM, Denny JC, Roden DM.. A study paradigm integrating prospective epidemiologic cohorts and electronic health records to identify disease biomarkers. Nature communications. 2018 Aug 30;9(1):3522.
  32. Mosley JD, Shaffer CM, Van Driest SL, Weeke PE, Wells QS, Karnes JH, Velez Edwards DR, Wei WQ, Teixeira PL, Bastarache L, Crawford DC, Li R, Manolio TA, Bottinger EP, McCarty CA, Linneman JG, Brilliant MH, Pacheco JA, Thompson W, Chisholm RL, Jarvik GP, Crosslin DR, Carrell DS, Baldwin E, Ralston J, Larson EB, Grafton J, Scrol A, Jouni H, Kullo IJ, Tromp G, Borthwick KM, Kuivaniemi H, Carey DJ, Ritchie MD, Bradford Y, Verma SS, Chute CG, Veluchamy A, Siddiqui MK, Palmer CN, Doney A, MahmoudPour SH, Maitland-van der Zee AH, Morris AD, Denny JC, Roden DM. A genome-wide association study identifies variants in KCNIP4 associated with ACE inhibitor-induced cough. Pharmacogenomics J. 2016 Jun;16(3):231-7. doi: 10.1038/tpj.2015.51. PMID: 26169577
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 eMERGE Phase II

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Electronic Medical Records and Genomics (eMERGE) Consortium; MIGen Consortium; PAGE Consortium; LifeLines Cohort Study, Amouyel P, Asselbergs FW, Assimes TL, Bochud M, Boehm BO, Boerwinkle E, Bottinger EP, Bouchard C, Cauchi S, Chambers JC, Chanock SJ, Cooper RS, de Bakker PI, Dedoussis G, Ferrucci L, Franks PW, Froguel P, Groop LC, Haiman CA, Hamsten A, Hayes MG, Hui J, Hunter DJ, Hveem K, Jukema JW, Kaplan RC, Kivimaki M, Kuh D, Laakso M, Liu Y, Martin NG, März W, Melbye M, Moebus S, Munroe PB, Njølstad I, Oostra BA, Palmer CN, Pedersen NL, Perola M, Pérusse L, Peters U, Powell JE, Power C, Quertermous T, Rauramaa R, Reinmaa E, Ridker PM, Rivadeneira F, Rotter JI, Saaristo TE, Saleheen D, Schlessinger D, Slagboom PE, Snieder H, Spector TD, Strauch K, Stumvoll M, Tuomilehto J, Uusitupa M, van der Harst P, Völzke H, Walker M, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Zanen P, Deloukas P, Heid IM, Lindgren CM, Mohlke KL, Speliotes EK, Thorsteinsdottir U, Barroso I, Fox CS, North KE, Strachan DP, Beckmann JS, Berndt SI, Boehnke M, Borecki IB, McCarthy MI, Metspalu A, Stefansson K, Uitterlinden AG, van Duijn CM, Franke L, Willer CJ, Price AL, Lettre G, Loos RJ, Weedon MN, Ingelsson E, O'Connell JR, Abecasis GR, Chasman DI, Goddard ME, Visscher PM, Hirschhorn JN, Frayling TM. 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  14. Kullo IJ, Haddad R, Prows CA, Holm I, Sanderson SC, Garrison NA, Sharp RR, Smith ME, Kuivaniemi H, Bottinger EP, Connolly JJ, Keating BJ, McCarty CA, Williams MS, Jarvik GP. Return of results in the genomic medicine projects of the eMERGE network. Front Genet. 2014 Mar 26;5:50. doi: 10.3389/fgene.2014.00050. eCollection 2014. PubMed PMID: 24723935; PubMed Central PMCID: PMC3972474.
  15. Muthalagu A, Pacheco JA, Aufox S, Peissig PL, Fuehrer JT, Tromp G, Kho AN, Rasmussen-Torvik LJ. A Rigorous Algorithm To Detect And Clean Inaccurate Adult Height Records Within EHR Systems. Appl Clin Inform. 2014 Feb 19;5(1):118-26. doi: 10.4338/ACI-2013-09-RA-0074. eCollection 2014. PubMed PMID: 24734128; PubMedCentral PMCID: PMC3974252.
  16. Shameer K, Denny JC, Ding K, Jouni H, Crosslin DR, de Andrade M, Chute CG, Peissig P, Pacheco JA, Li R, Bastarache L, Kho AN, Ritchie MD, Masys DR, Chisholm RL, Larson EB, McCarty CA, Roden DM, Jarvik GP, Kullo IJ. A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. Hum Genet. 2014 Jan;133(1):95-109. doi: 10.1007/s00439-013-1355-7. Epub 2013 Sep 12. PubMed PMID: 24026423; PubMed Central PMCID: PMC3880605.
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  18. Denny JC, Bastarache L, Ritchie MD, Carroll RJ, Zink R, Mosley JD, Field JR, Pulley JM, Ramirez AH, Bowton E, Basford MA, Carrell DS, Peissig PL, Kho AN, Pacheco JA, Rasmussen LV, Crosslin DR, Crane PK, Pathak J, Bielinski SJ, Pendergrass SA, Xu H, Hindorff LA, Li R, Manolio TA, Chute CG, Chisholm RL, Larson EB, Jarvik GP, Brilliant MH, McCarty CA, Kullo IJ, Haines JL, Crawford DC, Masys DR, Roden DM. Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data. Nat Biotechnol. 2013 Dec;31(12):1102-10. PubMed PMID: 24270849; PubMed Central PMCID: PMC3969265.
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 eMERGE Phase I

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  5. McCarty CA, Chisholm RL, Chute CG, Kullo I, Jarvik G, Larson EB, Li R, Masys DR, Ritchie MD, Roden DM, Struewing JP, Wolf WA. “The eMERGE Network: A Consortium of Biorepositories Linked to Electronic Medical Records Data for Conducting Genomic Studies.” BMC Genomics. 2011 Jan 26. PMID: 21269473.
  6. Edwards KL, Lemke AA, Trinidad SB, Lewis, Starks, Quinn-Griffin, Wiesner, GRRIP Consortium. “Attitudes toward Genetic Research Review: Results from a Survey of Human Genetics Researchers.” Public Health Genomics 2011;14:337–345. PMID: 21487211.
  7. Lemke AA, Smith ME, Wolf WA, Trinidad SB, and the GRRIP consortium. “Broad Data Sharing in Genetic Research: Views of Institutional Review Board Professionals.” IRB: Ethics & Human Research 33, no. 3 (2011): 1-5. PMID: 21736136.
  8. Clayton EW, Smith ME, Fullerton SM, Burke W, McCarty CA, Koenig B, McGuire AL, Beskow LM, Dressler L, Lemke AA, Ramos EM, Rodriguez LL, for the Consent and Community Consultation Working Group of the eMERGE Consortium. “Confronting Real-Time Ethical Issues in the eMERGE (electronic Medical Records and Genomics) Consortium.” Genet Med. 2010 Oct; 12 (10): 616-620. PMID: 20733502.
  9. Schildcrout, Basford, Pulley, Masys DR, Roden DM, Wang, Chute CG, Kull, Carrell, Peissig PL, Kho AN, Denny JC. “An analytical approach to characterize morbidity profile dissimilarity between distinct cohorts using electronic medical records.” J Biomed Inform. 2010 Aug 3. PMID:20688191.
  10. Edwards, Lemke AA, Trinidad SB, Lewis, Starks, Snappin, Quinn-Griffin, Wiesner, Burke, GRRIP Consortium. “Comparison of Attitudes toward Genetic Research Review: Results from a Survey of Human Genetics Researchers and Professionals Involved in Human Subjects Protections.” J Empir Res Hum Res Ethics. 2010 Mar;5(1):83-91. PMID: 20235866.
  11. Lemke AA, Wolf WA, Hebert-Beirne, J, Smith ME. “Public and biobank participant attitudes toward genetic research participation and data sharing,” [published online ahead of Epub January 15, 2010] Public Health Genomics. PMID: 20805700.
  12. Lemke AA, Wu J, Brown E, Lam A, Pulley J, Waudby C. “Community Engagement Methods Utilized by Six Electronic Medical Record-Linked Biobanks in the United States.” Genomics, Society, and Policy. 2010; 6 (3): 35-52. ISSN: 1746-5354.
  13. Pacheco JA, Avila PC, Thompson JA, Law M, Quraishi JA, Greiman AK, Just EM, Kho AN. “A Highly Specific Algorithm for Identifying Asthma Cases and Controls for Genome-Wide Association Studies.” AMIA Annu Symp Proc. 2009 Nov. 14; 2009: 497–501. PMID: 20351906
  14. Khoury MJ, McBride CM, Schully SD, Ioannidis JP, Feero WG, Janssens AC, Gwinn M, Simons-Morton DG, Bernhardt JM, Cargill M, Chanock SJ, Church GM, Coates RJ, Collins FS, Croyle RT, Davis BR, Downing GJ, Duross A, Friedman S, Gail MH, Ginsburg GS, Green RC, Greene MH, Greenland P, Gulcher JR, Hsu A, Hudson KL, Kardia SL, Kimmel PL, Lauer MS, Miller AM, Offit K, Ransohoff DF, Roberts JS, Rasooly RS, Stefansson K, Terry SF, Teutsch SM, Trepanier A, Wanke KL, Witte JS, Xu J; Centers for Disease Control and Prevention. “The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop.” Genet Med. 2009 Aug;11(8):559-67. PMID: 19617843.

Collaborations

  1. African American Type 2 Diabetes Genetics Consortium (MEDIA): Don Bowden (Wake Forest) leads a collaborative group of ~12 sites including Northwestern and Vanderbilt. This consortium conducted a meta-analysis of genomic determinants of Type 2 Diabetes in African Americans. Paper is submitted to Nature Genetics, with multiple eMERGE investigators and the eMERGE consortium represented as authors.
  2. GIANT Consortium: Meta-analysis of height from >100,000 subjects across multiple studies.  Awaiting draft of manuscript from consortium lead analysts.
  3. Height in African Americans (w/ Cincinnati Children’s Hospital)
  4. COGENT (Continental Origins of Genetic Traits): New meta-analysis consortium focused on African-American and Latino populations; NU participates in trait-specific working group (for height & RBC phenotypes)
  5. GIANT Consortium: meta-analysis of height from >100,000 subjects across multiple studies. 
  6. Vitamin D Related Innate Immunity in Influenza (with VU)
  7. PAGE (Population Architecture using Genomics and Epidemiology)
  8. CTSAwith Mayo (neutropenia and thrombocytopenia)
  9. CAGE (QRS in African Americans with VU)
  10. eMERGE Urological GWAS: RO1 application with University of Washington
  11. UCSF:  Genomewide Association Studies of HbA1c and Body Weight Change
    in Patients on Metformin for Type 2 Diabetes
  12. HAPO-GENEVA: meta-analysis of eMERGE African Ancestry with Afro-Caribs (for height phenotype)
  13. Vitamin D related Innate Immunity in Influenza (with VU)
  14. AAA Genotyping: collaboration with Geisinger
  15. De-ID Project (Anonymization of clinical codes in support of genome-phenome association studies)
  16. AAGILE/MEDIA:  Fasting Glucose meta-analysis
  17. Electronic Consent Project: collaboration with the University of Iowa

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