Publications

Variation in proviral content among human genomes mediated by LTR recombination

Jainy Thomas, Hervé Perron, Cédric Feschotte

Mobile DNA 2018 9:36

Discovery of rare, diagnostic AluYb8/9 elements in diverse human populations

Julie Feusier, David J. Witherspoon, W. Scott Watkins, Clément Goubert, Thomas A. Sasani, and Lynn B. Jorde

Mob DNA.2017 Jul 27; 8: 9.

The evolving genetic risk for sporadic ALS

Summer B. Gibson, Jonathan M. Downie, Spyridoula Tsetsou, Julie E. Feusier, Karla P. Figueroa, Mark B. Bromberg, Lynn B. Jorde, Stefan M. Pulst

Neurology Jul 2017, 89 (3) 226-233

Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

Navin Rustagi, Anbo Zhou,W. Scott Watkins, Erika Gedvilaite, Shuoguo Wang, Naveen Ramesh, Donna Muzny, Richard A. Gibbs,Lynn B. Jorde,Fuli Yu and Jinchuan Xing

BMC Genomics201718:396

Evolutionary history of Tibetans inferred from whole-genome sequencing

Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, et al. (2017) Evolutionary history of Tibetans inferred from whole-genome sequencing. PLOS Genetics 13(4): e1006675.

A Genome-Wide Search for Greek and Jewish Admixture in the Kashmiri Population

Downie JM, Tashi T, Lorenzo FR, Feusier JE, Mir H, et al. (2016) A Genome-Wide Search for Greek and Jewish Admixture in the Kashmiri Population. PLOS ONE 11(8): e0160614.

Global diversity, population stratification, and selection of human copy-number variation.

Peter H. Sudmant, Swapan Mallick,Bradley J. Nelson, Fereydoun Hormozdiari, Niklas Krumm, John Huddleston, Bradley P. Coe, Carl Baker, Susanne Nordenfelt, Michael Bamshad, Lynn B. Jorde, Olga L. Posukh, Hovhannes Sahakyan, W. Scott Watkins, Levon Yepiskoposyan, M. Syafiq Abdullah, Claudio M. Bravi, Cristian Capelli, Tor Hervig, Joseph T. S. Wee, Chris Tyler-Smith, George van Driem, Irene Gallego Romero, Aashish R. Jha, Sena Karachanak-Yankova, Draga Toncheva, David Comas, Brenna Henn, Toomas Kivisild, Andres Ruiz-Linares, Antti Sajantila, Ene Metspalu, Jüri Parik, Richard Villems, Elena B. Starikovskaya, George Ayodo, Cynthia M. Beall, Anna Di Rienzo, Michael F. Hammer, Rita Khusainova, Elza Khusnutdinova, William Klitz, Cheryl Winkler, Damian Labuda, Mait Metspalu, Sarah A. Tishkoff, Stanislav Dryomov, Rem Sukernik, Nick Patterson, David Reich, Evan E. Eichler.

Science 2015 Sept 11; 349(6253)

The heritability of gestational age in a two-million member cohort: implications for spontaneous preterm birth.

Wu W1, Witherspoon DJ, Fraser A, Clark EA, Rogers A, Stoddard GJ, Manuck TA, Chen K, Esplin MS, Smith KR, Varner MW, Jorde LB.

Hum Genet 2015 July; 134:803–808

Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis.

Platt RN 2nd, Zhang Y, Witherspoon DJ, Xing J, Suh A, Keith MS, Jorde LB, Stevens RD, Ray DA.

Genome Biol Evol. 2015 May 25;7(6):1664-75.

The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades.

Hallast P, Batini C, Zadik D, Maisano Delser P, Wetton JH, Arroyo-Pardo E, Cavalleri GL, de Knijff P, Destro Bisol G, Dupuy BM, Eriksen HA, Jorde LB, King TE, Larmuseau MH, López de Munain A, López-Parra AM, Loutradis A, Milasin J, Novelletto A, Pamjav H, Sajantila A, Schempp W, Sears M, Tolun A, Tyler-Smith C, Van Geystelen A, Watkins S, Winney B, Jobling MA.

Mol Biol Evol. 2015 Mar;32(3):661-73.

Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR).

Nash D, Arrington CB, Kennedy BJ, Yandell M, Wu W, Zhang W, Ware S, Jorde LB, Gruber PJ, Yost HJ, Bowles NE, Bleyl SB.

PLoS One. 2015 Jun 29;10(6):e0131514.

Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry.

Viollet L, Glusman G, Murphy KJ, Newcomb TM1, Reyna SP, Sweney M, Nelson B, Andermann F, Andermann E, Acsadi G, Barbano RL, Brown C, Brunkow ME, Chugani HT, Cheyette SR, Collins A, DeBrosse SD, Galas D, Friedman J, Hood L, Huff C, Jorde LB, King MD, LaSalle B, Leventer RJ, Lewelt AJ, Massart MB, Mérida MR 2nd, Ptáček LJ, Roach JC, Rust RS, Renault F, Sanger TD, Sotero de Menezes MA, Tennyson R, Uldall P, Zhang Y, Zupanc M, Xin W, Silver K, Swoboda KJ.

PLoS One. 2015 May 21;10(5):e0127045.

A genetic mechanism for Tibetan high-altitude adaptation.

Lorenzo FR, Huff C, Myllymäki M, Olenchock B, Swierczek S, Tashi T, Gordeuk V6, Wuren T7, Ri-Li G7, McClain DA5, Khan TM8, Koul PA9, Guchhait P0, Salama ME, Xing J, Semenza GL, Liberzon E, Wilson A, Simonson TS, Jorde LB, Kaelin WG Jr, Koivunen P, Prchal JT.

Nat Genet. 2014 Sep;46(9):951-6

A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

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.

Nat Biotechnol. 2014 Jul;32(7):663-9.

Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data.

Kennedy B, Kronenberg Z, Hu H, Moore B, Flygare S, Reese MG, Jorde LB, Yandell M, Huff C.

Curr Protoc Hum Genet. 2014 Apr 24;81:6.14.1-25.

Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.

Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M.

Am J Hum Genet. 2014 Apr 3;94(4):599-610.

Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention.

dManuck TA, Watkins WS, Moore B, Esplin MS, Varner MW, Jackson GM, Yandell M, Jorde L.

Am J Obstet Gynecol. 2014 Apr;210(4):321.e1-321.e21.

Autoimmunity due to RAG deficiency and estimated disease incidence in RAG1/2 mutations.

Chen K, Wu W, Mathew D, Zhang Y, Browne SK, Rosen LB, McManus MP, Pulsipher MA, Yandell M, Bohnsack JF, Jorde LB, Notarangelo LD, Walter JE.

J Allergy Clin Immunol. 2014 Mar;133(3):880-2.e10.

Relationship estimation from whole-genome sequence data.

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.

PLoS Genet. 2014 Jan 30;10(1):e1004144.

Clinical and biochemical function of polymorphic NR0B1 GGAA-microsatellites in Ewing sarcoma: a report from the Children’s Oncology Group.

Monument MJ, Johnson KM, McIlvaine E, Abegglen L, Watkins WS, Jorde LB, Womer RB, Beeler N, Monovich L, Lawlor ER, Bridge JA, Schiffman JD, Krailo MD, Randall RL, Lessnick SL.

PLoS One. 2014 Aug 5;9(8):e104378.

Shared and unique signals of high-altitude adaptation in geographically distinct Tibetan populations.

Wuren T, Simonson TS, Qin G, Xing J, Huff CD, Witherspoon DJ, Jorde LB, Ge RL.

PLoS One. 2014 Mar 18;9(3):e88252.

Germline mutations in NFKB2 implicate the noncanonical NF-κB pathway in the pathogenesis of common variable immunodeficiency.

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.

Am J Hum Genet. 2013 Nov 7;93(5):812-24.

Meta-analysis confirms association between TNFA-G238A variant and JIA, and between PTPN22-C1858T variant and oligoarticular, RF-polyarticular and RF-positive polyarticular JIA.

Kaalla MJ, Broadaway KA, Rohani-Pichavant M, Conneely KN, Whiting A, Ponder L, Okou DT, Angeles-Han S, Rouster-Stevens K, Brown MR, Vogler LB, Jorde LB, Bohnsack JF, Epstein MP, Prahalad S.

Pediatr Rheumatol Online J. 2013 Oct 25;11(1):40.

Mobile Element Scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations.

David J Witherspoon, Yuhua Zhang, W. Scott Watkins, Hongseok Ha, Jinchuan Xing, Mark A. Batzer and Lynn B. Jorde.

Genome Res. 2013; 23: 1170-1181

Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World.

Watkins WS, Xing J, Huff C, Witherspoon DJ, Zhang Y, Perego UA, Woodward SR, Jorde LB.

BMC Genetics 2012 May 20;13:39

Genetic determinants of Tibetan high-altitude adaptation.

Simonson TS, McClain DA, Jorde LB, Prchal JT.

Hum Genet. 2011 Nov 9.

[Epub ahead of print]A comprehensive map of mobile element insertion polymorphisms in humans.

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.

PLoS Genet. 2011 Aug;7(8):e1002236. Epub 2011 Aug 18.Crohn’s disease and genetic hitchhiking at IBD5.

Huff CD, Witherspoon D, Zhang Y, Gatenbee C, Denson LA, Kugathasan S, Hakonarson H, Whiting A, Davis C, Wu W, Xing J, Watkins WS, Bamshad M, Bradfield JP, Bulayeva K, Simonson TS, Jorde LB, Guthery SL.

Mol Biol Evol. 2011 Aug 4. [Epub ahead of print]Hamartoma Syndromes, Exome Sequencing, and a Protean Puzzle.

Opitz JM, Jorde LB.

N Engl J Med. 2011 Aug 18;365(7):661-3. Epub 2011 Jul 27.A probabilistic disease-gene finder for personal genomes.

Yandell M, Huff CD, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG.

Genome Res. 2011 Sep;21(9):1529-42. Epub 2011 Jun 23.Using VAAST to Identify an X-Linked Disorder Resulting in Lethality in Male Infants Due to N-Terminal Acetyltransferase Deficiency.

Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ.

Am J Hum Genet. 2011 Jul 15;89(1):28-43. Epub 2011 Jun 23.Signatures of the pre-agricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages.

Batini C, Ferri G, Destro-Bisol G, Brisighelli F, Luiselli D, Sánchez-Diz P, Rocha J, Simonson T, Brehm A, Montano V, Elwali NE, Spedini G, Eugenia D’Amato M, Myres N, Ebbesen P, Comas D, Capelli C.

Mol Biol Evol. 2011 Apr 4. [Epub ahead of print]

Maximum-likelihood estimation of recent shared ancestry (ERSA).

Huff C, Witherspoon D, Simonson T, Xing J, Watkins S, Zhang Y, Tuohy T, Neklason D, Burt R, Guthery S, Woodward S, Jorde LB.

Genome Res. 2011 May;21(5):768-74. Epub 2011 Feb 8.

Ancestry of the Iban is predominantly southeast asian: genetic evidence from autosomal, mitochondrial, and y chromosomes.

Simonson TS, Xing J, Barrett R, Jerah E, Loa P, Zhang Y, Watkins WS, Witherspoon DJ, Huff CD, Woodward S, Mowry B, Jorde LB.

PLoS One. 2011 Jan 31;6(1):e16338.

Genetic diversity in India and the inference of Eurasian population expansion.

Xing J, Watkins WS, Hu Y, Huff CD, Sabo A, Muzny DM, Bamshad MJ, Gibbs RA, Jorde LB, Yu F.

Genome Biol. 2010;11(11):R113. Epub 2010 Nov 24.

Genotype Data, Supplemental Materials

Insights into the demographic history of African Pygmies from complete mitochondrial genomes.

Batini C, Lopes J, Behar DM, Calafell F, Jorde LB, van der Veen L, Quintana-Murci L, Spedini G, Destro-Bisol G, Comas D.

Mol Biol Evol. 2011 Feb;28(2):1099-110. Epub 2010 Nov 1.

A map of human genome variation from population-scale sequencing.

1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA.

Nature. 2010 Oct 28;467(7319):1061-73.

Ancestry and disease in the age of genomic medicine.

Rotimi CN, Jorde LB.

N Engl J Med. 2010 Oct 14;363(16):1551-8.

Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping.

Xing J, Watkins WS, Shlien A, Walker E, Huff CD, Witherspoon DJ, Zhang Y, Simonson TS, Weiss RB, Schiffman JD, Malkin D, Woodward SR, Jorde LB.

Genomics. 2010 Oct;96(4):199-210. Epub 2010 Jul 16.

Genotype Data, Supplemental Figures, Supplemental Table

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing.

Witherspoon DJ, Xing J, Zhang Y, Watkins WS, Batzer MA, Jorde LB.

BMC Genomics. 2010 Jun 30;11(1):410.

Quantification of the familial contribution to juvenile idiopathic arthritis.

Prahalad S, Zeft A, Pimentel R, Clifford B, McNally B, Mineau G, Jorde L, Bohnsack J.

Arthritis Rheum. 2010 Aug;62(8):2525-9.

Genetic Evidence for High-Altitude Adaptation in Tibet.

Simonson TS, Yang Y, Huff CD, Yun H, Qin G, Witherspoon DJ, Bai Z, Lorenzo FR, Xing J, Jorde LB, Prchal JT, Ge R.

Science. 2010 Jul 2;329(5987):72-5. Epub 2010 May 13.

Supplemental Material

Comment in: Science. 2010 Jul 2;329(5987):40-1.

AGT Genetic Variation, Plasma AGT, and Blood Pressure: An Analysis of the Utah Genetic Reference Project Pedigrees.

Watkins WS, Rohrwasser A, Peiffer A, Leppert MF, Lalouel JM, Jorde LB.

Am J Hypertens. 2010 Aug;23(8):917-23. Epub 2010 Apr 22.

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing.

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.

Science. 2010 Apr 30;328(5978):636-9. Epub 2010 Mar 10.

Limited Distribution of a Cardiomyopathy-Associated Variant in India.

Simonson TS, Zhang Y, Huff CD, Xing J, Watkins WS, Witherspoon DJ, Woodward SR, Jorde LB.

Ann Hum Genet. 2010 Mar;74(2):184-8. Epub 2010 Feb 18.

Mobile elements reveal small population size in the ancient ancestors of Homo sapiens.Huff CD, Xing J, Rogers AR, Witherspoon D, Jorde LB.

Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):2147-52. Epub 2010 Jan 19.

Supplemental Table 1, Supplemental Table 2, Supplemental Table 3, Supplemental Table 4

Alu repeats increase local recombination rates.

Witherspoon DJ, Watkins WS, Zhang Y, Xing J, Tolpinrud WL, Hedges DJ, Batzer MA, Jorde LB.

BMC Genomics. 2009 Nov 16;10(1):530.

Common variants on chromosome 2 and risk of primary open-angle glaucoma in the Afro-Caribbean population of Barbados.

Jiao X, Yang Z, Yang X, Chen Y, Tong Z, Zhao C, Zeng J, Chen H, Gibbs D, Sun X, Li B, Wakins WS, Meyer C, Wang X, Kasuga D, Bedell M, Pearson E, Weinreb RN, Leske MC, Hennis A, Dewan A, Nemesure B, Jorde LB, Hoh J, Hejtmancik JF, Zhang K.

Proc Natl Acad Sci U S A. 2009 Oct 6;106(40):17105-10. Epub 2009 Sep 24.

Genotype-phenotype analysis of angiotensinogen polymorphisms and essential hypertension: the importance of haplotypes.

Watkins WS, Hunt SC, Williams GH, Tolpinrud W, Jeunemaitre X, Lalouel JM, Jorde LB.

J Hypertens. 2010 Jan;28(1):65-75. Epub 2009 Sep 16.

Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis.

Prahalad S, Hansen S, Whiting A, Guthery SL, Clifford B, McNally B, Zeft AS, Bohnsack JF, Jorde LB.

Arthritis Rheum. 2009 Jul;60(7):2124-30.

Genetic adaptation to extreme hypoxia: Study of high-altitude pulmonary edema in a three-generation Han Chinese family.

Lorenzo V F, Yang Y, Simonson TS, Nussenzveig R, Jorde LB, Prchal JT, Ge RL.

Blood Cells Mol Dis. 2009 Nov-Dec;43(3):221-5. Epub 2009 May 29.

Mobile elements create structural variation: analysis of a complete human genome.

Xing J, Zhang Y, Han K, Salem AH, Sen SK, Huff CD, Zhou Q, Kirkness EF, Levy S, Batzer MA, Jorde LB.

Genome Res. 2009 Sep;19(9):1516-26. Epub 2009 May 13.

Supplemental Table 1, Supplemental Table 2, Supplemental Table 3, Supplemental Alignments

Estimating the age of retrotransposon subfamilies using maximum likelihood.

Marchani EE, Xing J, Witherspoon DJ, Jorde LB, Rogers AR.

Genomics. 2009 Jul;94(1):78-82. Epub 2009 Apr 18.

Fine-scaled human genetic structure revealed by SNP microarrays.

Xing J, Watkins WS, Witherspoon DJ, Zhang Y, Guthery SL, Thara R, Mowry BJ, Bulayeva K, Weiss RB, Jorde LB.

Genome Res. 2009 May;19(5):815-25.

Genotype Data, Supplemental Figures, Supplemental Table 1, Supplemental Table 2,

Lack of association between beta 2-adrenergic receptor polymorphisms and juvenile idiopathic arthritis.

Pont-Kingdon G, Bohnsack J, Sumner K, Whiting A, Clifford B, Guthery SS, Jorde LB, Lyon E, Prahalad S.

Scand J Rheumatol. 2009 Mar-Apr;38(2):91-5.

Strong evidence for a novel schizophrenia risk locus on chromosome 1p31.1 in homogeneous pedigrees from Tamil Nadu, India.

Holliday EG, Nyholt DR, Tirupati S, John S, Ramachandran P, Ramamurti M, Ramadoss AJ, Jeyagurunathan A, Kottiswaran S, Smith HJ, Filippich C, Nertney DA, Nancarrow DJ, Hayward NK, Watkins WS, Jorde LB, Thara R, Mowry BJ.

Am J Psychiatry. 2009 Feb;166(2):206-15. Epub 2008 Oct 1. Erratum in: Am J Psychiatry. 2009 Feb;166(2):238.

Watkins WS, Thara R, Mowry BJ, Zhang Y, Witherspoon DJ, Tolpinrud W, Bamshad MJ, Tiripati S, Padmavati R, Smith H, Nancarrow D, Filippich C, Jorde LB.

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms.

BMC Genet. 2008 Dec 12;9(1):86.

Xing J, Watkins WS, Zhang Y, Witherspoon DJ, Jorde LB.

High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

Genomics. 2008 Dec;92(6):452-6 Epub 2008 Sep 27. Supplemental Data

Kugathasan S, Baldassano RN, Bradfield JP, Sleiman PM, Imielinski M, Guthery SL, Cucchiara S, Kim CE, Frackelton EC, Annaiah K, Glessner JT, Santa E, Willson T, Eckert AW, Bonkowski E, Shaner JL, Smith RM, Otieno FG, Peterson N, Abrams DJ, Chiavacci RM, Grundmeier R, Mamula P, Tomer G, Piccoli DA, Monos DS, Annese V, Denson LA, Grant SF, Hakonarson H.

Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease.

Nat Genet. 2008 Oct;40(10):1211-5. Epub 2008 Aug 31.

Yang Z, Stratton C, Francis PJ, Kleinman ME, Tan PL, Gibbs D, Tong Z, Chen H, Constantine R, Yang X, Chen Y, Zeng J, Davey L, Ma X, Hau VS, Wang C, Harmon J, Buehler J, Pearson E, Patel S, Kaminoh Y, Watkins S, Luo L, Zabriskie NA, Bernstein PS, Cho W, Schwager A, Hinton DR, Klein ML, Hamon SC, Simmons E, Yu B, Campochiaro B, Sunness JS, Campochiaro P, Jorde L, Parmigiani G, Zack DJ, Katsanis N, Ambati J, Zhang K.

Toll-like Receptor 3 and Geographic Atrophy in Age-Related Macular Degeneration.

N Engl J Med. 2008 Oct 2;359(14):1456-63. Epub 2008 Aug 27.

Guthery SL, Dong L, Dean JM, Holubkov R.

US estimates of hospitalized pediatric patients with ulcerative colitis: implications for multicenter clinical studies.

Inflamm Bowel Dis. 2008 Sep;14(9):1253-8.

Marchani EE, Watkins WS, Bulayeva K, Harpending HC, Jorde LB.

Culture creates genetic structure in the Caucasus: Autosomal, mitochondrial, and Y-chromosomal variation in Daghestan.

BMC Genet. 2008 Jul 17;9(1):47.

Gangwal K, Sankar S, Hollenhorst PC, Kinsey M, Haroldsen SC, Shah AA, Boucher KM, Watkins WS, Jorde LB, Graves BJ, Lessnick SL.

Microsatellites as EWS/FLI response elements in Ewing’s sarcoma.

Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):10149-54. Epub 2008 Jul 14.

Xing J, Witherspoon DJ, Watkins WS, Zhang Y, Tolpinrud W, Jorde LB.

HapMap tagSNP transferability in multiple populations: General guidelines.

Genomics. 2008 Jul; 92(1):41-51. Epub 2008 May 14..

Prahalad S, Bohnsack JF, Whiting A, Clifford B, Jorde LB, Guthery SL, Thompson SD, Glass DN, Bamshad MJ.

Lack of association of functional CTLA4 polymorphisms with juvenile idiopathic arthritis.

Arthritis Rheum. 2008 Jun 24;58(7):2147-2152

Tong Z, Yang Z, Patel S, Chen H, Gibbs D, Yang X, Hau VS, Kaminoh Y, Harmon J, Pearson E, Buehler J, Chen Y, Yu B, Tinkham NH, Zabriskie NA, Zeng J, Luo L, Sun JK, Prakash M, Hamam RN, Tonna S, Constantine R, Ronquillo CC, Sadda S, Avery RL, Brand JM, London N, Anduze AL, King GL, Bernstein PS, Watkins S; Genetics of Diabetes and Diabetic Complication Study Group, Jorde LB, Li DY, Aiello LP, Pollak MR, Zhang K.

Promoter polymorphism of the erythropoietin gene in severe diabetic eye and kidney complications.

Proc Natl Acad Sci U S A. 2008 May 13;105(19):6998-7003. Epub 2008 May 5.

Eriksson AW, Fellman J, Jorde LB, Pitkänen K.

Temporal, seasonal, and regional differences in births and deaths in Aland (Finland).

Hum Biol. 2008 Apr;80(2):125-40.

Guthery SL, Gross TG.

Assessing the risk of epstein-barr virus-related lymphoproliferative disorders before administration of visilizumab.

Gastroenterology. 2008 Mar;134(3):895-6. No abstract available.

Xing J, Witherspoon DJ, Ray DA, Batzer MA, Jorde LB.

Mobile DNA elements in primate and human evolution.

Am J Phys Anthropol. 2007 Dec; 134(S45):2-19

Guthery SL, Salisbury BA, Pungliya MS, Stephens JC, Bamshad M.

The structure of common genetic variation in United States populations.

Am J Hum Genet. 2007 Dec;81(6):1221-31.

Bamshad M, Guthery SL.

Race, genetics and medicine: does the color of a leopard’s spots matter?

Curr Opin Pediatr. 2007 Dec;19(6):613-8.

Witherspoon DJ, Wooding S, Rogers AR, Marchani EE, Watkins WS, Batzer MA, Jorde LB.

Genetic Similarities Within and Between Human Populations.

Genetics. 2007 May;176(1):351-9.

Rogers AR, Wooding S, Huff CD, Batzer MA, Jorde LB.

Ancestral Alleles and Population Origins: Inferences Depend on Mutation Rate.

Mol Biol Evol. 2007 Apr;24(4):990-7.

Toydemir RM, Brassington AE, Bayrak-Toydemir P, Krakowiak PA, Jorde LB, Whitby FG, Longo N, Viskochil DH, Carey JC, Bamshad MJ.

A novel mutation in FGFR3 causes camptodactyly, tall stature, and hearing loss (CATSHL) syndrome.

Am J Hum Genet. 2006 Nov;79(5):935-41.

Toydemir RM, Chen H, Proud VK, Martin R, van Bokhoven H, Hamel BC, Tuerlings JH, Stratakis CA, Jorde LB, Bamshad MJ.

Trismus-pseudocamptodactyly syndrome is caused by recurrent mutation of MYH8.

Am J Med Genet A. 2006 Nov 15;140(22):2387-93.
Witherspoon DJ, Marchani EE, Watkins WS, Ostler CT, Wooding SP, Anders BA, Fowlkes JD, Boissinot S, Furano AV, Ray DA, Rogers AR, Batzer MA, Jorde LB.

Human Population Genetic Structure and Diversity Inferred from Polymorphic L1(LINE-1) and Alu Insertions.

Hum Hered. 2006 Sep 21;62(1):30-46.

Kim UK, Wooding S, Riaz N, Jorde LB, Drayna D.

Variation in the human TAS1R taste receptor genes.

Chem Senses. 2006 Sep;31(7):599-611.

Prahalad S, Bohnsack JF, Jorde LB, Whiting A, Clifford B, Dunn D, Weiss R, Moroldo M, Thompson SD, Glass DN, Bamshad MJ.

Association of two functional polymorphisms in the CCR5 gene with juvenile rheumatoid arthritis.

Genes Immun. 2006 Sep;7(6):468-75.

Toydemir RM, Rutherford A, Whitby FG, Jorde LB, Carey JC, Bamshad MJ.

Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome.

Nat Genet. 2006 May;38(5):561-5.

Wooding S, Jorde LB.

Duplication and divergence in humans and chimpanzees.

Bioessays. 2006 Apr;28(4):335-8.

Watkins WS, Prasad BV, Naidu JM, Rao BB, Bhanu BA, Ramachandran B, Das PK, Gai PB, Reddy PC, Reddy PG, Sethuraman M, Bamshad MJ, Jorde LB.

Diversity and divergence among the tribal populations of India.

Ann Hum Genet. 2005 Nov;69(Pt 6):680-92.

Hedges DJ, Cordaux R, Xing J, Witherspoon DJ, Rogers AR, Jorde LB, Batzer MA.

Modeling the amplification dynamics of human Alu retrotransposons.

PLoS Comput Biol. 2005 Sep;1(4):e44. Epub 2005 Sep 30.

Karafet TM, Lansing JS, Redd AJ, Reznikova S, Watkins JC, Surata SP, Arthawiguna WA, Mayer L, Bamshad M, Jorde LB, Hammer MF.

Balinese Y-chromosome perspective on the peopling of Indonesia: genetic contributions from pre-neolithic hunter-gatherers, Austronesian farmers, and Indian traders.

Hum Biol. 2005 Feb;77(1):93-114.

Kim U, Wooding S, Ricci D, Jorde LB, Drayna D.

Worldwide haplotype diversity and coding sequence variation at human bitter taste receptor loci.

Hum Mutat. 2005 Sep;26(3):199-204.

Shriver MD, Mei R, Parra EJ, Sonpar V, Halder I, Tishkoff SA, Schurr TG, Zhadanov SI, Osipova LP, Brutsaert TD, Friedlaender J, Jorde LB, Watkins WS, Bamshad MJ, Gutierrez G, Loi H, Matsuzaki H, Kittles RA, Argyropoulos G, Fernandez JR, Akey JM, Jones KW.

Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation.

Hum Genomics. 2005 Jun;2(2):81-9.

Nakajima T, Wooding S, Satta Y, Jinnai N, Goto S, Hayasaka I, Saitou N, Guan-Jun J, Tokunaga K, Jorde LB, Emi M, Inoue I.

Evidence for natural selection in the HAVCR1 gene: high degree of amino-acid variability in the mucin domain of human HAVCR1 protein.

Genes Immun. 2005 Aug;6(5):398-406.

Jorde LB.

Evolution. Where we’re hot, they’re not.

Science. 2005 Apr 1;308(5718):60-2.

Wooding S, Stone AC, Dunn DM, Mummidi S, Jorde LB, Weiss RK, Ahuja S, Bamshad MJ.

Contrasting effects of natural selection on human and chimpanzee CC chemokine receptor 5.

Am J Hum Genet. 2005 Feb;76(2):291-301. Epub 2004 Dec 29. Erratum in: Am J Hum Genet. 2005 Apr;76(4):715.

Carter AB, Salem AH, Hedges DJ, Keegan CN, Kimball B, Walker JA, Watkins WS, Jorde LB, Batzer MA.

Genome-wide analysis of the human Alu Yb-lineage.

Hum Genomics. 2004 Mar;1(3):167-78.

Jorde LB.

Genetic variation and cardiovascular care.

Manag Care. 2004 Oct;13(10 Suppl):9-12.

Jorde LB, Wooding SP.

Genetic variation, classification and ‘race’.

Nat Genet. 2004 Nov;36(11 Suppl):S28-33.

Wooding S, Ostler C, Prasad BV, Watkins WS, Sung S, Bamshad M, Jorde LB.

Directional migration in the Hindu castes: inferences from mitochondrial, autosomal and Y-chromosomal data.

Hum Genet. 2004 Aug;115(3):221-9. Epub 2004 Jul 1.

Sakagami T, Witherspoon DJ, Nakajima T, Jinnai N, Wooding S, Jorde LB, Hasegawa T, Suzuki E, Gejyo F, Inoue I.

Local adaptation and population differentiation at the interleukin 13 and interleukin 4 loci.

Genes Immun. 2004 Aug;5(5):389-97.

Nakajima T, Wooding S, Sakagami T, Emi M, Tokunaga K, Tamiya G, Ishigami T, Umemura S, Munkhbat B, Jin F, Guan-Jun J, Hayasaka I, Ishida T, Saitou N, Pavelka K, Lalouel JM, Jorde LB, Inoue I.

Natural selection and population history in the human angiotensinogen gene (AGT): 736 complete AGT sequences in chromosomes from around the world.

Am J Hum Genet. 2004 May;74(5):898-916. Epub 2004 Apr 9.

Bulayeva K, Jorde LB, Ostler C, Watkins S, Bulayev O, Harpending H.

Genetics and population history of Caucasus populations.

Hum Biol. 2003 Dec;75(6):837-53.

Xing J, Salem AH, Hedges DJ, Kilroy GE, Watkins WS, Schienman JE, Stewart CB, Jurka J, Jorde LB, Batzer MA.

Comprehensive analysis of two Alu Yd subfamilies.

J Mol Evol. 2003;57 Suppl 1:S76-89.

Wooding S, Kim UK, Bamshad MJ, Larsen J, Jorde LB, Drayna D.

Natural selection and molecular evolution in PTC, a bitter-taste receptor gene.

Am J Hum Genet. 2004 Apr;74(4):637-46. Epub 2004 Mar 2.

Callinan PA, Hedges DJ, Salem AH, Xing J, Walker JA, Garber RK, Watkins WS, Bamshad MJ, Jorde LB, Batzer MA.

Comprehensive analysis of Alu-associated diversity on the human sex chromosomes.

Gene. 2003 Oct 23;317(1-2):103-10.

Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA.

Alu elements and hominid phylogenetics.

Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12787-91. Epub 2003 Oct 15.

Toomajian C, Ajioka RS, Jorde LB, Kushner JP, Kreitman M.

A method for detecting recent selection in the human genome from allele age estimates.

Genetics. 2003 Sep;165(1):287-97.

Sung SS, Brassington AM, Krakowiak PA, Carey JC, Jorde LB, Bamshad M.

Mutations in TNNT3 cause multiple congenital contractures: a second locus for distal arthrogryposis type 2B.

Am J Hum Genet. 2003 Jul;73(1):212-4.

Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AM, Carroll ML, Nguyen SV, Walker JA, Prasad BV, Reddy PG, Das PK, Batzer MA, Jorde LB.

Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms.

Genome Res. 2003 Jul;13(7):1607-18. Epub 2003 Jun 12.

Brassington AM, Sung SS, Toydemir RM, Le T, Roeder AD, Rutherford AE, Whitby FG, Jorde LB, Bamshad MJ.

Expressivity of Holt-Oram syndrome is not predicted by TBX5 genotype.

Am J Hum Genet. 2003 Jul;73(1):74-85. Epub 2003 Jun 3.

Salem AH, Kilroy GE, Watkins WS, Jorde LB, Batzer MA.

Recently integrated Alu elements and human genomic diversity.

Mol Biol Evol. 2003 Aug;20(8):1349-61. Epub 2003 May 30.

Vincent BJ, Myers JS, Ho HJ, Kilroy GE, Walker JA, Watkins WS, Jorde LB, Batzer MA.

Following the LINEs: an analysis of primate genomic variation at human-specific LINE-1 insertion sites.

Mol Biol Evol. 2003 Aug;20(8):1338-48. Epub 2003 May 30.

Sung SS, Brassington AM, Grannatt K, Rutherford A, Whitby FG, Krakowiak PA, Jorde LB, Carey JC, Bamshad M.

Mutations in genes encoding fast-twitch contractile proteins cause distal arthrogryposis syndromes.

Am J Hum Genet. 2003 Mar;72(3):681-90.

Salem AH, Myers JS, Otieno AC, Watkins WS, Jorde LB, Batzer MA.

LINE-1 preTa elements in the human genome.

J Mol Biol. 2003 Feb 28;326(4):1127-46.

Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB.

Human population genetic structure and inference of group membership.

Am J Hum Genet. 2003 Mar;72(3):578-89. Epub 2003 Jan 28.

Wooding SP, Watkins WS, Bamshad MJ, Dunn DM, Weiss RB, Jorde LB.

DNA sequence variation in a 3.7-kb noncoding sequence 5′ of the CYP1A2 gene: implications for human population history and natural selection.

Am J Hum Genet. 2002 Sep;71(3):528-42. Epub 2002 Aug 9.

Lum JK, Jorde LB, Schiefenhovel W.

Affinities among Melanesians, Micronesians, and Polynesians: a neutral biparental genetic perspective.

Hum Biol. 2002 Jun;74(3):413-30.

Bamshad MJ, Mummidi S, Gonzalez E, Ahuja SS, Dunn DM, Watkins WS, Wooding S, Stone AC, Jorde LB, Weiss RB, Ahuja SK.

A strong signature of balancing selection in the 5′ cis-regulatory region of CCR5.

Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10539-44. Epub 2002 Jul 29.

Myers JS, Vincent BJ, Udall H, Watkins WS, Morrish TA, Kilroy GE, Swergold GD, Henke J, Henke L, Moran JV, Jorde LB, Batzer MA.

A comprehensive analysis of recently integrated human Ta L1 elements.

Am J Hum Genet. 2002 Aug;71(2):312-26. Epub 2002 Jun 17.

Yu N, Chen FC, Ota S, Jorde LB, Pamilo P, Patthy L, Ramsay M, Jenkins T, Shyue SK, Li WH.

Larger genetic differences within africans than between Africans and Eurasians.

Genetics. 2002 May;161(1):269-74.

Luo HR, Lu XM, Yao YG, Horie N, Takeishi K, Jorde LB, Zhang YP.

Length polymorphism of thymidylate synthase regulatory region in Chinese populations and evolution of the novel alleles.

Biochem Genet. 2002 Feb;40(1-2):41-51.

Redd AJ, Roberts-Thomson J, Karafet T, Bamshad M, Jorde LB, Naidu JM, Walsh B, Hammer MF.

Gene flow from the Indian subcontinent to Australia: evidence from the Y chromosome.

Curr Biol. 2002 Apr 16;12(8):673-7.

Wooding S, Rogers A.

The matrix coalescent and an application to human single-nucleotide polymorphisms.

Genetics. 2002 Aug;161(4):1641-50. Download pdf

Nakajima T, Jorde LB, Ishigami T, Umemura S, Emi M, Lalouel JM, Inoue I.

Nucleotide diversity and haplotype structure of the human angiotensinogen gene in two populations.

Am J Hum Genet. 2002 Jan;70(1):108-23. Epub 2001 Nov 30. Download pdf

Jorde LB, Watkins WS, Bamshad MJ.

Population genomics: a bridge from evolutionary history to genetic medicine.

Hum Mol Genet. 2001 Oct 1;10(20):2199-207. Download pdf

Jorde LB.

Consanguinity and prereproductive mortality in the Utah Mormon population.

Hum Hered. 2001;52(2):61-5. Download pdf

Carroll ML, Roy-Engel AM, Nguyen SV, Salem AH, Vogel E, Vincent B, Myers J, Ahmad Z, Nguyen L, Sammarco M, Watkins WS, Henke J, Makalowski W, Jorde LB, Deininger PL, Batzer MA.

Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity.

J Mol Biol. 2001 Aug 3;311(1):17-40. Download pdf

Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, Rao BB, Naidu JM, Prasad BV, Reddy PG, Rasanayagam A, Papiha SS, Villems R, Redd AJ, Hammer MF, Nguyen SV, Carroll ML, Batzer MA, Jorde LB.

Genetic evidence on the origins of Indian caste populations.

Genome Res. 2001 Jun;11(6):994-1004. [Download commentary by P. Majumder] Download pdf

Jorde LB, Shortsleeve PA, Henry JW, Vanburen RT, Hutchinson LE, Rigley TM.

Genetic analysis of the Utah population: a comparison of STR and VNTR loci.

Hum Biol. 2000 Dec;72(6):927-36.

Watkins WS, Ricker CE, Bamshad MJ, Carroll ML, Nguyen SV, Batzer MA, Harpending HC, Rogers AR, Jorde LB.

Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms.

Am J Hum Genet. 2001 Mar;68(3):738-52. Epub 2001 Feb 15. Download pdf

Yu N, Zhao Z, Fu YX, Sambuughin N, Ramsay M, Jenkins T, Leskinen E, Patthy L, Jorde LB, Kuromori T, Li WH. Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1.

Mol Biol Evol. 2001 Feb;18(2):214-22. Download pdf

Fischer PR, Thacher TD, Pettifor JM, Jorde LB, Eccleshall TR, Feldman D.

Vitamin D receptor polymorphisms and nutritional rickets in Nigerian children.

J Bone Miner Res. 2000 Nov;15(11):2206-10.

Bulaj ZJ, Ajioka RS, Phillips JD, LaSalle BA, Jorde LB, Griffen LM, Edwards CQ, Kushner JP.

Disease-related conditions in relatives of patients with hemochromatosis.

N Engl J Med. 2000 Nov 23;343(21):1529-35.

Jorde LB.

Linkage disequilibrium and the search for complex disease genes.

Genome Res. 2000 Oct;10(10):1435-44. Download pdf

Zhao Z, Jin L, Fu YX, Ramsay M, Jenkins T, Leskinen E, Pamilo P, Trexler M, Patthy L, Jorde LB, Ramos-Onsins S, Yu N, Li WH. Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22.

Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11354-8. Download pdf

Kivisild T, Villems R, Jorde LB, Bamshad M, Kumar S, Hedrick P, Dowling T, Stoneking M, Parsons TJ, Irwin JA, Awadalla P, Eyre-Walker A, Smith JM.

Questioning Evidence for Recombination in Human Mitochondrial DNA.

Science. 2000 Jun 16;288(5473):1931a. Download pdf

Jorde LB, Watkins WS, Bamshad MJ, Dixon ME, Ricker CE, Seielstad MT, Batzer MA.

The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data.

Am J Hum Genet. 2000 Mar;66(3):979-88. Download pdf

Bamshad M, Jorde LB, Carey JC.

Getting a LEAD on EEC.

Am J Med Genet. 2000 Jan 17;90(2):183-4.

Jorde LB, Watkins WS, Kere J, Nyman D, Eriksson AW.

Gene mapping in isolated populations: new roles for old friends?

Hum Hered. 2000 Jan-Feb;50(1):57-65.

Wooding S.

PRoMT: inferring demographic history from DNA sequences.

Bioinformatics. 2000 Mar;16(3):298-9. Download pdf

Wooding S, Rogers A.

A Pleistocene population X-plosion?

Hum Biol. 2000 Aug;72(4):693-5. Download pdf

Ding YC, Wooding S, Harpending HC, Chi HC, Li HP, Fu YX, Pang JF, Yao YG, Yu JG, Moyzis R, Zhang Y. Population structure and history in East Asia.

Proc Natl Acad Sci U S A. 2000 Dec 5;97(25):14003-6 Download pdf

Watkins WS, Bamshad M, Dixon ME, Bhaskara Rao B, Naidu JM, Reddy PG, Prasad BV, Das PK, Reddy PC, Gai PB, Bhanu A, Kusuma YS, Lum JK, Fischer P, Jorde LB. (1999)

Multiple Origins of the mtDNA 9-bp Deletion in Populations of South India. Am. J. Phys. Anthropol. 109:147-58 Download pdf

Bamshad M, Le T, Watkins WS, Dixon ME, Kramer BE, Roeder AD, Carey JC, Root S, Schinzel A, Van Maldergem L, Gardner RJ, Lin RC, Seidman CE, Seidman JG, Wallerstein R, Moran E, Sutphen R, Campbell CE, Jorde LB. (1999)

The spectrum of mutations in TBX3: Genotype/Phenotype relationship in ulnar-mammary syndrome. Am. J. Hum. Genet. 64:1550-62 Download pdf

L.B. Jorde,W.S. Watkins, J. Kere, D. Nyman, A.W. Eriksson. (1999)

Gene Mapping in Isolated Populations: New Roles for Old Friends? Human Heredity 50:57-65 Download pdf

Lynn B. Jorde, Michael Bamshad, and Alan R. Rogers. (1998)

Using mitochondrial and nuclear DNA markers to reconstruct human evolution BioEssays 20:126-136 Download pdf

Kivisild T, Bamshad MJ, Kaldma K, Metspalu M, Metspalu E, Reidla M, Laos S, Parik J, Watkins WS, Dixon ME, Papiha SS, Mastana SS, Mir MR, Ferak V, Villems R. (1999)

Deep common ancestry of indian and western-Eurasian mitochondrial DNA lineages. Curr Biol. 9:1331-4 Download pdf

Gonzalez E, Bamshad M, Sato N, Mummidi S, Dhanda R, Catano G, Cabrera S, McBride M, Cao XH, Merrill G, O’Connell P, Bowden DW, Freedman BI, Anderson SA, Walter EA, Evans JS, Stephan KT, Clark RA, Tyagi S, Ahuja SS, Dolan MJ, Ahuja SK. (1998)

Race-specific HIV-1 disease-modifying effects associated with CCR5 haplotypes. Proc. Natl. Acad. Sci. 96:12004-12009 Download pdf

Bamshad MJ, Watkins WS, Dixon ME, Jorde LB, Rao BB, Naidu JM, Prasad BV, Rasanayagam A, Hammer MF. (1998)

Female gene flow stratifies Hindu castes. Nature 395:651-2 Download pdf

Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST. (1998)

Genetic traces of ancient demography. Proc. Natl. Acad. Sci. USA 95:1961-7 Download pdf

Jorde LB, Rogers AR, Bamshad M, Watkins WS, Krakowiak P, Sung S, Kere J, Harpending HC. (1997)

Microsatellite diversity and the demographic history of modern humans. Proc. Natl. Acad. Sci. USA. 94:3100-3 Download pdf

Wooding, S., Ward, R.H. (1997)

Phylogeography and Pleistocene evolution in the North American black bear. Molecular Biology and Evolution 14:1096-1105 Download pdf