Graduate School
- PhD, University of Colorado Denver (2018)
Undergraduate School
- BS, Brigham Young University (UT) (2008)
Department
Biomedical InformaticsProfessional Titles
- Research Instructor
Publications
- Jacoby E, Quan D, Todd E, Shortt J, Smith H, Rafaels N, Crooks K. Prevalence of Pathogenic Transthyretin Gene Variants in the Rocky Mountain Region. Muscle Nerve. 2025 Feb;71(2):252-256. PubMed PMID: 39655870
- Jones MK, Nicklawsky A, Shortt J, Pattee J, Kennerley V, Eule CJ, Candelario N, O'Donnell PH, Flaig TW. Pharmacogenomics of chemotherapy induced peripheral neuropathy using an electronic health record-derived definition: a genome-wide association study. Support Care Cancer. 2025 Apr 8;33(5):362. PubMed PMID: 40198382
- Vargas LB, Meyer MC, Konigsberg IR, Kakar A, Carry PM, Li Y, Jones AC, Tiwari HK, Srinivasasainagendra V, Armstrong ND, Kenny EE, Pasaniuc B, Irvin MR, Cho MH, Stanislawski MA, Raghavan S, Shortt JA, Lange LA, Lange EM. Ancestry Calibration of Polygenic Risk Scores Improves Risk Stratification and Effect Estimation in African American Adults. medRxiv. 2025 Jun 18. PubMed PMID: 40585132
- Brasher MS, Fisher MJ, Wild CS, Shortt JA, Miller K, Johnson RK, Rafaels NM, Kudron EL, Brooks IM, Crooks KR, Oser SM, Oser TK, Cole JB, Wiley LK, Raghavan S, Rasouli N, Lin M, Gignoux CR. Enabling reproducible type 1 diabetes polygenic risk scoring for clinical and translational applications. medRxiv. 2025 Jul 17. PubMed PMID: 40791684
- Lazorwitz A, Aquilante CL, Shortt JA, Gignoux CR, Teal S, Sheeder J. Pharmacogenomics of the Etonogestrel Contraceptive Implant: A Genome-Wide Association Study of Steady-State Etonogestrel Concentrations. O G Open. 2025 Feb;2(1):e066. PubMed PMID: 41000562
- Guo B, Cai Y, Kim D, Smit RAJ, Wang Z, Iyer KR, Hilliard AT, Haessler J, Tao R, Broadaway KA, Wang Y, Pozdeyev N, Stæger FF, Yang C, Vanderwerff B, Patki AD, Stalbow L, Lin M, Rafaels N, Shortt J, Wiley L, Stanislawski M, Pattee J, Davis L, Straub PS, Shuey MM, Cox NJ, Lee NR, Jørgensen ME, Bjerregaard P, Larsen C, Hansen T, Moltke I, Meigs JB, Stram DO, Yin X, Zhou X, Chang KM, Clarke SL, Guarischi-Sousa R, Lankester J, Tsao PS, Buyske S, Graff M, Raffield LM, Sun Q, Wilkens LR, Carlson CS, Easton CB, Liu S, Manson JE, Marchand LL, Haiman CA, Mohlke KL, Gordon-Larsen P, Albrechtsen A, Boehnke M, Rich SS, Manichaikul A, Rotter JI, Yousri NA, Irvin RM, Gignoux C, North KE, Loos RJF, Assimes TL, Peters U, Kooperberg C, Raghavan S, Highland HM, Darst BF. Polygenic risk score for type 2 diabetes shows context-dependent effects across populations. Nat Commun. 2025 Oct 1;16(1):8632. PubMed PMID: 41034193
- O'Brien KA, Toledo-Jaldin L, Gu W, Houck JA, Lazo-Vega L, Miranda-Garrido V, Yung HW, Yasini H, Moore LG, Reisz JA, Simonson TS, Shortt J, Stalker M, D'Alessandro A, Julian CG. Dysregulated Fatty Acid Metabolism in Preeclampsia Among Highland Andeans: Insights Into Adaptive and Maladaptive Placental Metabolic Phenotypes. FASEB J. 2025 Nov 30;39(22):e71254. PubMed PMID: 41273236
- Guare LA, Das J, Caruth L, Rajagopalan A, Akerele AT, Brumpton BM, Chen TT, Kottyan L, Lin YF, Moreno E, Mulford AJ, Dombrovska MS, Luo Y, Rovite V, Sanders AR, Teerlink C, Candelieri D, Elhadad N, Hill A, Jarvik GP, Jaworski J, Lynch J, Namba S, Okada Y, Shi Y, Shirai Y, Shortt J, Wei WQ, Weng C, Yamamoto Y, Biobank PM, Genetics Center R, Meta-Analysis Initiative GB, Chapman S, Zhou W, Edwards T, Senapati S, Velez Edwards DR, Setia-Verma S. Expanding the genetic landscape of endometriosis: Integrative -omics analyses implicate key genes and pathways in a multi-ancestry study of over one million women. Res Sq. 2025 Dec 4. PubMed PMID: 41377979
- Schneider K, Chowdhury M, Tepper M, Khan J, Shortt JA, Gignoux C, Layer R. GenoSiS: A Biobank-Scale Genotype Similarity Search Architecture for Creating Dynamic Patient-Match Cohorts. bioRxiv. 2024 Nov 3. PubMed PMID: 39554195
- Wiley LK, Shortt JA, Roberts ER, Lowery J, Kudron E, Lin M, Mayer D, Wilson M, Brunetti TM, Chavan S, Phang TL, Pozdeyev N, Lesny J, Wicks SJ, Moore ET, Morgenstern JL, Roff AN, Shalowitz EL, Stewart A, Williams C, Edelmann MN, Hull M, Patton JT, Axell L, Ku L, Lee YM, Jirikowic J, Tanaka A, Todd E, White S, Peterson B, Hearst E, Zane R, Greene CS, Mathias R, Coors M, Taylor M, Ghosh D, Kahn MG, Brooks IM, Aquilante CL, Kao D, Rafaels N, Crooks KR, Hess S, Barnes KC, Gignoux CR. Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine. Am J Hum Genet. 2024 Jan 4;111(1):11-23. PubMed PMID: 38181729
- Pozdeyev N, Dighe M, Barrio M, Raeburn C, Smith H, Fisher M, Chavan S, Rafaels N, Shortt JA, Lin M, Leu MG, Clark T, Marshall C, Haugen BR, Subramanian D, Crooks K, Gignoux C, Cohen T. Thyroid Cancer Polygenic Risk Score Improves Classification of Thyroid Nodules as Benign or Malignant. J Clin Endocrinol Metab. 2024 Jan 18;109(2):402-412. PubMed PMID: 37683082
- O'Brien KA, Gu W, Houck JA, Holzner LMW, Yung HW, Armstrong JL, Sowton AP, Baxter R, Darwin PM, Toledo-Jaldin L, Lazo-Vega L, Moreno-Aramayo AE, Miranda-Garrido V, Shortt JA, Matarazzo CJ, Yasini H, Burton GJ, Moore LG, Simonson TS, Murray AJ, Julian CG. Genomic Selection Signals in Andean Highlanders Reveal Adaptive Placental Metabolic Phenotypes That Are Disrupted in Preeclampsia. Hypertension. 2024 Feb;81(2):319-329. PubMed PMID: 38018457
- Kullo IJ, Conomos MP, Nelson SC, Adebamowo SN, Choudhury A, Conti D, Fullerton SM, Gogarten SM, Heavner B, Hornsby WE, Kenny EE, Khan A, Khera AV, Li Y, Martin I, Mercader JM, Ng M, Raffield LM, Reiner A, Rowley R, Schaid D, Stilp A, Wiley K, Wilson R, Witte JS, Natarajan P. The PRIMED Consortium: Reducing disparities in polygenic risk assessment. Am J Hum Genet. 2024 Dec 5;111(12):2594-2606. PubMed PMID: 39561770
- Lo Faro V, Bhattacharya A, Zhou W, Zhou D, Wang Y, Läll K, Kanai M, Lopera-Maya E, Straub P, Pawar P, Tao R, Zhong X, Namba S, Sanna S, Nolte IM, Okada Y, Ingold N, MacGregor S, Snieder H, Surakka I, Shortt J, Gignoux C, Rafaels N, Crooks K, Verma A, Verma SS, Guare L, Rader DJ, Willer C, Martin AR, Brantley MA Jr, Gamazon ER, Jansonius NM, Joos K, Cox NJ, Hirbo J. Novel ancestry-specific primary open-angle glaucoma loci and shared biology with vascular mechanisms and cell proliferation. Cell Rep Med. 2024 Feb 20;5(2):101430. PubMed PMID: 38382466
- Hou K, Gogarten S, Kim J, Hua X, Dias JA, Sun Q, Wang Y, Tan T, Atkinson EG, Martin A, Shortt J, Hirbo J, Li Y, Pasaniuc B, Zhang H. Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations. Bioinformatics. 2024 Mar 29;40(4). PubMed PMID: 38490256
- Kanai M, Elzur R, Zhou W, Daly MJ, Finucane HK. Meta-analysis fine-mapping is often miscalibrated at single-variant resolution. Cell Genom. 2022 Dec 14;2(12). PubMed PMID: 36643910
- . A first update on mapping the human genetic architecture of COVID-19. Nature. 2022 Aug;608(7921):E1-E10. PubMed PMID: 35922517
- Johnson RK, Marker KM, Mayer D, Shortt J, Kao D, Barnes KC, Lowery JT, Gignoux CR. COVID-19 Surveillance in the Biobank at the Colorado Center for Personalized Medicine: Observational Study. JMIR Public Health Surveill. 2022 Jun 13;8(6):e37327. PubMed PMID: 35486493
- Harrison GF, Leaton LA, Harrison EA, Kichula KM, Viken MK, Shortt J, Gignoux CR, Lie BA, Vukcevic D, Leslie S, Norman PJ. Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1. PLoS Comput Biol. 2022 Feb;18(2):e1009059. PubMed PMID: 35192601
- D'Antonio M, Nguyen JP, Arthur TD, Matsui H, D'Antonio-Chronowska A, Frazer KA. SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues. Cell Rep. 2022 Jun 14;39(11):110968. PubMed PMID: 35705058
- Zhou W, Kanai M, Wu K, Rasheed H, Tsuo K, Hirbo J, Wang Y, Bhattacharya A, Zhao H, Namba S, Surakka I, Wolford B, Lo Faro V, Lopera-Maya E, Läll K, Favé M, Partanen J, Chapman S, Karjalainen J, Kurki M, Maasha M, Brumpton B, Chavan S, Chen T, Daya M, Ding Y, Feng Y, Guare L, Gignoux C, Graham S, Hornsby W, Ingold N, Ismail S, Johnson R, Laisk T, Lin K, Lv J, Millwood I, Moreno-Grau S, Nam K, Palta P, Pandit A, Preuss M, Saad C, Setia-Verma S, Thorsteinsdottir U, Uzunovic J, Verma A, Zawistowski M, Zhong X, Afifi N, Al-Dabhani K, Al Thani A, Bradford Y, Campbell A, Crooks K, de Bock G, Damrauer S, Douville N, Finer S, Fritsche L, Fthenou E, Gonzalez-Arroyo G, Griffiths C, Guo Y, Hunt K, Ioannidis A, Jansonius N, Konuma T, Lee M, Lopez-Pineda A, Matsuda Y, Marioni R, Moatamed B, Nava-Aguilar M, Numakura K, Patil S, Rafaels N, Richmond A, Rojas-Muñoz A, Shortt J, Straub P, Tao R, Vanderwerff B, Vernekar M, Veturi Y, Barnes K, Boezen M, Chen Z, Chen C, Cho J, Smith G, Finucane H, Franke L, Gamazon E, Ganna A, Gaunt T, Ge T, Huang H, Huffman J, Katsanis N, Koskela J, Lajonchere C, Law M, Li L, Lindgren C, Loos R, MacGregor S, Matsuda K, Olsen C, Porteous D, Shavit J, Snieder H, Takano T, Trembath R, Vonk J, Whiteman D, Wicks S, Wijmenga C, Wright J, Zheng J, Zhou X, Awadalla P, Boehnke M, Bustamante C, Cox N, Fatumo S, Geschwind D, Hayward C, Hveem K, Kenny E, Lee S, Lin Y, Mbarek H, Mägi R, Martin H, Medland S, Okada Y, Palotie A, Pasaniuc B, Rader D, Ritchie M, Sanna S, Smoller J, Stefansson K, van Heel D, Walters R, Zöllner S, Martin A, Willer C, Daly M, Neale B. Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease. Cell Genomics. 2022/10; 2(10):100192.
- Shortt JA, Timm LE, Hales NR, Nikolakis ZL, Schield DR, Perry BW, Liu Y, Zhong B, Castoe TA, Carlton EJ, Pollock DD. Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts. Sci Rep. 2021 Mar 25;11(1):6884. PubMed PMID: 33767307
- Deng Z, Zhen J, Harrison GF, Zhang G, Chen R, Sun G, Yu Q, Nemat-Gorgani N, Guethlein LA, He L, Tang M, Gao X, Cai S, Palmer WH, Shortt JA, Gignoux CR, Carrington M, Zou H, Parham P, Hong W, Norman PJ. Adaptive Admixture of HLA Class I Allotypes Enhanced Genetically Determined Strength of Natural Killer Cells in East Asians. Mol Biol Evol. 2021 May 19;38(6):2582-2596. PubMed PMID: 33616658
- Stanislawski MA, Lange LA, Raffield LM, Zakai NA, Meyer M, Ferrier K, Szeto MD, Leavitt C, Shortt JA, Thornton TA, Tracy RP, Auer PL, Reiner AP, Lange EM, Olson NC. Soluble CD14 Levels in the Jackson Heart Study: Associations With Cardiovascular Disease Risk and Genetic Variants. Arterioscler Thromb Vasc Biol. 2021 Jun;41(6):e369-e378. PubMed PMID: 33910371
- Lazorwitz A, Aquilante CL, Shortt JA, Sheeder J, Teal S, Gignoux CR. Applicability of ancestral genotyping in pharmacogenomic research with hormonal contraception. Clin Transl Sci. 2021 Sep;14(5):1713-1718. PubMed PMID: 33650294
- Warshauer EM, Brown A, Fuentes I, Shortt J, Gignoux C, Montinaro F, Metspalu M, Youssefian L, Vahidnezhad H, Jacków J, Christiano AM, Uitto J, Fajardo-Ramírez ÓR, Salas-Alanis JC, McGrath JA, Consuegra L, Rivera C, Maier PA, Runfeldt G, Behar DM, Skorecki K, Sprecher E, Palisson F, Norris DA, Bruckner AL, Kogut I, Bilousova G, Roop DR. Ancestral patterns of recessive dystrophic epidermolysis bullosa mutations in Hispanic populations suggest sephardic ancestry. Am J Med Genet A. 2021 Nov;185(11):3390-3400. PubMed PMID: 34435747
- . Mapping the human genetic architecture of COVID-19. Nature. 2021 Dec;600(7889):472-477. PubMed PMID: 34237774
- Shortt JA, Ruggiero RP, Cox C, Wacholder AC, Pollock DD. Finding and extending ancient simple sequence repeat-derived regions in the human genome. Mob DNA. 2020;11:11. PubMed PMID: 32095164
- Leaton LA, Shortt J, Kichula KM, Tao S, Nemat-Gorgani N, Mentzer AJ, Oppenheimer SJ, Deng Z, Hollenbach JA, Gignoux CR, Guethlein LA, Parham P, Carrington M, Norman PJ. Conservation, Extensive Heterozygosity, and Convergence of Signaling Potential All Indicate a Critical Role for KIR3DL3 in Higher Primates. Front Immunol. 2019;10:24. PubMed PMID: 30745901
- Pasquesi GIM, Adams RH, Card DC, Schield DR, Corbin AB, Perry BW, Reyes-Velasco J, Ruggiero RP, Vandewege MW, Shortt JA, Castoe TA. Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nat Commun. 2018 Jul 17;9(1):2774. PubMed PMID: 30018307