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Lynn Jorde

Professor and Chair of Human Genetics

Human Population Genetics, Disease-gene Identification

Lynn Jorde

 

Molecular Biology Program

Education

B.A. University of New Mexico

Ph.D. University of New Mexico

Links

Lab Page

PubMed Literature Search

lbj@genetics.utah.edu

 

Research

Our laboratory has long been involved in studies of human genetic variation and disease. We realized the advantages of Utah’s large families for disease-gene identification, and we have carried out studies of human limb malformations, autism, hypertension, juvenile idiopathic arthritis, preterm birth, inflammatory bowel disease, amyotrophic lateral sclerosis, and a number of other Mendelian and common, complex diseases. I am a co-director of the Center for Genomic Medicine, an interdepartmental collaborative effort in which more than 12,000 members of large Utah disease pedigrees contained in the Utah Population Database have undergone whole-genome or exome sequencing to identify disease-causing genes. These projects now focus on more than 50 different disease phenotypes.

We published an analysis of the first whole-genome sequences (WGS) of a complete human family (Roach et al., 2010, Science). These data allowed us to directly estimate, for the first time, the intergenerational human mutation rate.  We have made extensive use of multigenerational Utah families to study the dynamics of mutation for single-nucleotide variants, structural variants, mobile elements, and tandem reeat polymorphisms.  We became interested in high-altitude adaptation and disease in Tibetan populations several years ago and, in a project led by one of my graduate students, published the first discoveries of natural selection on genes in the hypoxia-inducible factor pathway (Simonson et al., 2010, Science). For more than 15 years, we have carried out NIH-funded research on the evolution of mobile elements and their effects on the genome.

Genome Research Cover

 

References

  1. Workalemahu T, Avery C, Lopez S, Blue NR, Wallace A, Quinlan AR, Coon H, Warner D, Varner MW, Branch DW, Jorde LB, Silver RM. 2023. Whole-genome sequencing analysis in families with recurrent pregnancy loss: A pilot study. PLoS One18: e0281934.
  2. Steely CJ, Watkins WS, Baird L, Jorde LB. 2022. The mutational dynamics of short tandem repeats in large, multigenerational families. Genome Biol23: 253.
  3. Workalemahu T, Page JM, Meeks H, Yu Z, Guinto E, Fraser A, Varner MW, Theilen LH, Quinlan A, Coon H, Enquobahrie DA, Ananth CV, Tekola-Ayele F, Jorde LB, Silver RM. 2022. Familial aggregation of stillbirth: A pedigree analysis of a matched case-control study. BJOG : an international journal of obstetrics and gynaecologydoi:10.1111/1471-0528.17301.
  4. Feusier JE, Arunachalam S, Tashi T, Baker MJ, VanSant-Webb C, Ferdig A, Welm BE, Rodriguez-Flores JL, Ours C, Jorde LB, Prchal JT, Mason CC. 2021. Large-Scale Identification of Clonal Hematopoiesis and Mutations Recurrent in Blood Cancers. Blood Cancer Discov 2: 226-237.
  5. Belyeu JR, Brand H, Wang H, Zhao X, Pedersen BS, Feusier J, Gupta M, Nicholas TJ, Brown J, Baird L, Devlin B, Sanders SJ, Jorde LB, Talkowski ME, Quinlan AR. 2021. De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families. Am J Hum Genet 108: 597-607.
  6. Steely CJ, Russell KL, Feusier JE, Qiao Y, Tavtigian SV, Marth G, Jorde LB. 2021. Mobile element insertions and associated structural variants in longitudinal breast cancer samples. Sci Rep 11: 13020.
  7. Russell KL, Downie JM, Gibson SB, Tsetsou S, Keefe MD, Duran JA, Figueroa KP, Bromberg MB, Murtaugh LC, Bonkowsky JL, Pulst SM, Jorde LB. 2021. Pathogenic effect of TP73 Gene Variants in People With Amyotrophic Lateral Sclerosis. Neurology doi:10.1212/wnl.0000000000012285.
  8. Watkins WS, Feusier JE, Thomas J, Goubert C, Mallick S, Jorde LB. 2020. The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity. Genome Biol Evol 12: 779-794.
  9. Van Tassell JC, Shimbo D, Hess R, Kittles R, Wilson JG, Jorde LB, Li M, Lange LA, Lange EM, Muntner P, Bress AP. 2020. Association of West African ancestry and blood pressure control among African Americans taking antihypertensive medication in the Jackson Heart Study. J Clin Hypertens (Greenwich) 22: 157-166.
  10. Jorde LB, Bamshad MJ. 2020. Genetic Ancestry Testing: What Is It and Why Is It Important? Jama 323: 1089-1090.
  11. Goubert C, Thomas J, Payer LM, Kidd JM, Feusier J, Watkins WS, Burns KH, Jorde LB, Feschotte C. 2020. TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. Nucleic Acids Res 48: e36.
  12. Cawthon RM, Meeks HD, Sasani TA, Smith KR, Kerber RA, O'Brien E, Baird L, Dixon MM, Peiffer AP, Leppert MF, Quinlan AR, Jorde LB. 2020. Germline mutation rates in young adults predict longevity and reproductive lifespan. Sci Rep 10: 10001.
  13. Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, Jorde LB, Quinlan AR. 2019. Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. Elife 8.
  14. Periyasamy S, John S, Padmavati R, Rajendren P, Thirunavukkarasu P, Gratten J, Vinkhuyzen A, McRae A, Holliday EG, Nyholt DR, Nancarrow D, Bakshi A, Hemani G, Nertney D, Smith H, Filippich C, Patel K, Fowdar J, McLean D, Tirupati S, Nagasundaram A, Gundugurti PR, Selvaraj K, Jegadeesan J, Jorde LB, Wray NR, Brown MA, Suetani R, Giacomotto J, Thara R, Mowry BJ. 2019. Association of Schizophrenia Risk With Disordered Niacin Metabolism in an Indian Genome-wide Association Study. JAMA Psychiatry 76: 1026-1034.
  15. Feusier J, Watkins WS, Thomas J, Farrell A, Witherspoon DJ, Baird L, Ha H, Xing J, Jorde LB. 2019. Pedigree-based estimation of human mobile element retrotransposition rates. Genome Res 29: 1567-1577.
  16. Al-Agha AE, Ahmed IA, Nuebel E, Moriwaki M, Moore B, Peacock KA, Mosbruger T, Neklason DW, Jorde LB, Yandell M et al. 2018. Primary Ovarian Insufficiency and Azoospermia in Carriers of a Homozygous PSMC3IP Stop Gain Mutation. J Clin Endocrinol Metab 103: 555-563.
  17. Booth JN, III, Li M, Shimbo D, Hess R, Irvin MR, Kittles R, Wilson JG, Jorde LB, Cheung AK, Lange LA et al. 2018. West African Ancestry and Nocturnal Blood Pressure in African Americans: The Jackson Heart Study. Am J Hypertens 31: 706-714.\
  18. Chen JS, Hu F, Kugathasan S, Jorde LB, Nix D, Rutherford A, Denson L, Watkins WS, Prahalad S, Huff C et al. 2018. Targeted Gene Sequencing in Children with Crohn's Disease and Their Parents: Implications for Missing Heritability. G3 (Bethesda) 8: 2881-2888.
  19. Flygare S, Hernandez EJ, Phan L, Moore B, Li M, Fejes A, Hu H, Eilbeck K, Huff C, Jorde L et al. 2018. The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool. BMC Bioinformatics 19: 57.
  20. Gao Z, Moorjani P, Sasani TA, Pedersen BS, Quinlan AR, Jorde LB, Amster G, Przeworski M. 2019. Overlooked roles of DNA damage and maternal age in generating human germline mutations. Proc Natl Acad Sci U S A 116: 9491-9500.
  21. Moriwaki M, Moore B, Mosbruger T, Neklason DW, Yandell M, Jorde LB, Welt CK. 2017. POLR2C Mutations Are Associated With Primary Ovarian Insufficiency in Women. Journal of the Endocrine Society1: 162-173.
  22. Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD. 2017 Evolutionary history of Tibetans inferred from whole-genome sequencing. PLoS Genet. 13(4):e1006675.
  23. Rustagi N, Zhou A, Watkins WS, Gedvilaite E, Wang S, Ramesh N, Muzny D, Gibbs RA, Jorde LB, Yu F, Xing J. 2017 Extremely low-coverage whole genome sequencing in South Asians captures population genomics information. BMC Genomics. 18(1):396.
  24. Gibson SB, Downie JM, Tsetsou S, Feusier JE, Figueroa KP, Bromberg MB, Jorde LB, Pulst SM. 2017 The evolving genetic risk for sporadic ALS. Neurology. 89(3):226-33.
  25. Manuck TA, Watkins WS, Esplin MS, Biggio J, Bukowski R, Parry S, Zhan H, Huang H, Andrews W, Saade G, Sadovsky Y, Reddy UM, Ilekis J, Yandell M, Varner MW, Jorde LB. 2017 Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth: a case-control study. BJOG : an international journal of obstetrics and gynaecology.
  26. Downie JM, Tashi T, Lorenzo FR, Feusier JE, Mir H, Prchal JT, Jorde LB, Koul PA. 2016 A Genome-Wide Search for Greek and Jewish Admixture in the Kashmiri Population. PLoS One. 11(8):e0160614.
  27. Mallick S, Li H, Lipson M, Mathieson I, …, Jorde LB, et al. 2016 The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 538(7624):201-6.
  28. Nance D, Campbell RA, Rowley JW, Downie JM, Jorde LB, Kahr WH, Mereby SA, Tolley ND, Zimmerman GA, Weyrich AS, Rondina MT. 2016 Combined Variants in Factor VIII and Prostaglandin Synthase-1 Amplify Hemorrhage Severity Across Three Generations of Descendants. Journal of thrombosis and haemostasis.
  29. Staples J, Witherspoon DJ, Jorde LB, Nickerson DA, Below JE, Huff CD. 2016. PADRE: Pedigree-Aware Distant-Relationship Estimation. Am J Hum Genet. 99(1):154-62.
  30. Simonson TS, Huff CD, Witherspoon DJ, Prchal JT, Jorde LB. 2015. Adaptive genetic changes related to haemoglobin concentration in native high-altitude Tibetans. Experimental physiology. 100(11):1263-8.
  31. Wu W, Witherspoon DJ, Fraser A, Clark EA, Rogers A, Stoddard GJ, Manuck TA, Chen K, Esplin MS, Smith KR, Varner MW, Jorde LB. 2015. The heritability of gestational age in a two-million member cohort: implications for spontaneous preterm birth. Hum Genet. 134(7):803-8.
  32. Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR, 1000 Genomes Consortium. 2015. A global reference for human genetic variation. Nature. 526(7571):68-74.
  33. Sudmant PH, Mallick S, Nelson BJ, Hormozdiari F, Krumm N, Huddleston J, Coe BP, Baker C, Nordenfelt S, Bamshad M, Jorde LB, Posukh OL, Sahakyan H, Watkins WS, Yepiskoposyan L, Abdullah MS, Bravi CM, Capelli C, Hervig T, Wee JT, Tyler-Smith C, van Driem G, Romero IG, Jha AR, Karachanak-Yankova S, Toncheva D, Comas D, Henn B, Kivisild T, Ruiz-Linares A, Sajantila A, Metspalu E, Parik J, Villems R, Starikovskaya EB, Ayodo G, Beall CM, Di Rienzo A, Hammer M, Khusainova R, Khusnutdinova E, Klitz W, Winkler C, Labuda D, Metspalu M, Tishkoff SA, Dryomov S, Sukernik R, Patterson N, Reich D, Eichler EE. 2015. Global diversity, population stratification, and selection of human copy number variation. Science. 349: 1181.
  34. Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, Li H, Garg V, Moore B, Hood L, Galas DJ, Srivastava D, Reese MG, Jorde LB, Yandell M, Huff CD. 2014. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat Biotechnol. 32(7):663-9.
  35. Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M. 2014. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet. 94(4):599-610.
  36. Li H, Glusman G, Hu H, Shankaracharya, Caballero J, Hubley R, Witherspoon D, Guthery SL, Mauldin DE, Jorde LB, Hood L, Roach JC, Huff CD. 2014. Relationship estimation from whole-genome sequence data. PLoS Genet. 10(1):e1004144.
  37. Chen K, Coonrod EM, Kumánovics A, Franks ZF, Durtschi JD, Margraf RL, Wu W, Heikal NM, Augustine NH, Ridge PG, Hill HR, Jorde LB, Weyrich AS, Zimmerman GA, Gundlapalli AV, Bohnsack JF, Voelkerding KV. 2013. Germline mutations in NFKB2 implicate the noncanonical NF-κB pathway in the pathogenesis of common variable immunodeficiency. Am J Hum Genet. 93(5):812-24.
  38. Xing J, Wuren T, Simonson TS, Watkins WS, Witherspoon DJ, Wu W, Qin G, Huff CD, Jorde LB, Ge RL. 2013. Genomic analysis of natural selection and phenotypic variation in high-altitude mongolians. PLoS Genet. 9(7):e1003634.
  39. Witherspoon DJ, Zhang Y, Xing J, Watkins WS, Ha H, Batzer MA, Jorde LB. 2013. Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. Genome Res. 23(7):1170-81.
  40. Xing J, Witherspoon DJ, Jorde LB. 2013. Mobile element biology: new possibilities with high-throughput sequencing. Trends Genet. 29(5):280-9.
  41. Heinzen EL, Swoboda KJ, Hitomi Y, Gurrieri F, Nicole S, de Vries B, Tiziano FD, Fontaine B, Walley NM, Heavin S, …, Jorde LB, et al. 2012. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood. Nat Genet. 44(9):1030-4.
  42. Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT; 1000 Genomes Project. 2011. A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 7(8):e1002236.
  43. Huff CD, Witherspoon DJ, Zhang Y, Gatenbee C, Denson LA, Kugathasan S, Hakonarson H, Whiting A, Davis CT, Wu W, Xing J, Watkins WS, Bamshad MJ, Bradfield JP, Bulayeva K, Simonson TS, Jorde LB, Guthery SL. Crohn's disease and genetic hitchhiking at IBD5. Mol Biol Evol. 29(1):101-11.
  44. Huff CD, Witherspoon DJ, Simonson TS, Xing J, Watkins WS, Zhang Y, Tuohy TM, Neklason DW, Burt RW, Guthery SL, Woodward SR, Jorde LB. 2011. Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Res. 21(5):768-74.
  45. Simonson TS, Yang Y, Huff CD, Yun H, Qin G, Witherspoon DJ, Bai Z, Lorenzo FR, Xing J, Jorde LB*, Prchal JT, Ge R. 2010. Genetic evidence for high-altitude adaptation in Tibet. Science 329(5987):72-5. (*co-senior author)
  46. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ. 2010. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328(5978):636-9.
Last Updated: 1/11/24