Reich Lab Publications
2009
Price AL, Helgason A, P Snaebjorn, S Hreinn, St. Clair D, Andreassen OA, Reich D, Kong A, Stefansson K (2009) The impact of divergence time on the nature of population structure: An example from Iceland. PLoS Genet 5, e1000505.
Cheng CY, Kao WH, Patterson N, Tandon A, Haiman CA, Harris TB, Xing C, John EM, Ambrosone CB, Brancati FL, Coresh J, Press MF, Parekh RS, Klag MJ, Meoni LA, Hsueh WC, Fejerman L, Pawlikowska L, Freedman ML, Jandorf LH, Bandera EV, Ciupak GL, Nalls MA, Akylbekova EL, Orwoll ES, Leak TS, Miljkovic I, Li R, Ursin G, Bernstein L, Ardlie K, Taylor HA, Boerwinckle E, Zmuda JM, Henderson BE, Wilson JG, Reich D (2009) Admixture mapping of 15,280 African Americans identifies obesity susceptibility Loci on chromosomes 5 and X. PLoS Genet. 5, e1000490. (Supplementary Materials)
Sun JX, Mullikin JC, Patterson N, Reich DE (2009) Microsatellites are molecular clocks that support accurate inferences about history. Mol Biol Evol. 26, 1017-1027.
Mallick S, Gnerre S, Muller P, Reich D (2009) The difficulty of avoiding false positives in genome scans for natural selection. Genome Research 19, 922-933 (Supplementary Materials )
De Jager PL, Baecher-Allan C, Maier LM, Arthur AT, Ottoboni L, Barcellos L, McCauley JL, Sawcer S, Goris A, Saarela J, Yelensky R, Price A, Leppa V, Patterson N, de Bakker PI, Tran D, Aubin C, Pobywajlo S, Rossin E, Hu X, Ashley CW, Choy E, Rioux JD, Pericak-Vance MA, Ivinson A, Booth DR, Stewart GJ, Palotie A, Peltonen L, Dubois B, Haines JL, Weiner HL, Compston A, Hauser SL, Daly MJ, Reich D, Oksenberg JR, Hafler DA (2009) The role of the CD58 locus in multiple sclerosis. Proc Natl Acad Sci USA, 106, 5264-5269. (Supplementary Materials)
Reich D, Nalls MA, Kao WHL, Akylbekova EL, Tandon A, Patterson N, Mullikin J, Hsueh W-C, Cheng C-Y, Coresh J, Boerwinkle B, Li M, Waliszewska A, Neubauer J, Li R, Leak TS, Ekunwe L, Files JC, Hardy CL, Zmuda JM, Taylor HA, Ziv E, Harris TB, Wilson JG (2009) Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy Antigen Receptor for Chemokines gene. PLoS Genetics 5, e1000360.
Dhandapany PS, Sadayappan S, Xue Y, Powell GT, Rani DS, Nallari P, Rai TS, Khullar M, Soares P, Bahl A, Tharkan JM, Vaideeswar P, Rathinavel A, Narasimhan C, Ayapati DR, Ayub Q, Mehdi SQ, Oppenheimer S, Richards MB, Price AL, Patterson N, Reich D, Singh L, Tyler-Smith C, Thangaraj K (2009) A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nature Genetics 41, 187-191. (Supplementary Materials )
Deo RC, Reich D, Tandon A, Akylbekova E, Patterson N, Waliszewska A, Kathiresan S, Sarpong D, Taylor HA Jr, Wilson JG (2009) Genetic differences between the determinants of lipid profile phenotypes in African and European Americans: the Jackson Heart Study. PLoS Genet. 5, e1000342. (Supplementary Materials)
Keinan A, Mullikin JC, Patterson N, Reich D (2009) Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nature Genetics, 41, 66-70 (2009). (Supplementary Materials)
2008
Price AL, Patterson N, Hancks DC, Myers S, Reich D, Cheung VG, Spielman RS (2008) Effects of cis and trans genetic ancestry on gene expression in African Americans. PLoS Genetics 4, e1000294.
Kao WH, Klag MJ, Meoni LA, Reich D, Berthier-Schaad Y, Li M, Coresh J, Patterson N, Tandon A, Powe NR, Fink NE, Sadler JH, Weir MR, Abboud HE, Adler SG, Divers J, Iyengar SK, Freedman BI, Kimmel PL, Knowler WC, Kohn OF, Kramp K, Leehey DJ, Nicholas SB, Pahl MV, Schelling JR, Sedor JR, Thornley-Brown D, Winkler CA, Smith MW, Parekh RS; Family Investigation of Nephropathy and Diabetes Research Group (2008) MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nature Genetics 40, 1185-1192. (Supplementary Materials)
Price AL, Weale ME, Patterson N, Myers SR, Need AC, Shianna KV, Ge D, Rotter JI, Torres E, Taylor KD, Goldstein DB, Reich D (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am J Hum Genet. 83, 132-135.
Reich D, Price AL, Patterson N (2008) Principal component analysis of genetic data. Nat Genet. 40, 491-492.
Caswell JL, Mallick S, Richter DJ, Neubauer J, Schirmer C, Gnerre S, Reich D (2008) Analysis of chimpanzee history based on genome sequence alignments. PLoS Genetics, 4: e1000057. (Supplementary Materials)
Myers S, Fefferman C, Patterson N (2008) Can one learn history from the allelic spectrum? Theoretical Population Biology, 73, 342-348.
Nalls MA, Wilson JG, Patterson NJ, Tandon A, Zmuda JM, Huntsman S, Garcia M, Hu D, Li R, Beamer BA, Patel KV, Akylbekova EL, Files JC, Hardy CL, Buxbaum SG, Taylor HA, Reich D, Harris TB, Ziv E (2008) Admixture Mapping of White Cell Count: Genetic Locus Responsible for Lower White Blood Cell Count in the Health ABC and Jackson Heart Studies. Am J Hum Genet. 82, 81–87.
Seldin MF, Price AL (2008) Application of Ancestry Informative Markers to Association Studies in European Americans. PLoS Genetics 4:e5
Price AL, Butler J, Patterson N, Capelli C, Pascali VL, Scarnicci F, Ruiz-Linares A, Groop L, Saetta AA, Korkolopoulou P, Seligsohn U, Waliszewska A, Schirmer C, Ardlie K, Ramos A, Nemesh J, Arbeitman L, Goldstein DB, Reich D, Hirschhorn JN (2008) Discerning the Ancestry of European Americans in Genetic Association Studies. PLoS Genetics 4:e236. (Supplementary Materials)
2007
Deo R, Patterson N, Tandon A, McDonald G, Haiman CA, Ardlie K, Henderson BE, Henderson SO, Reich D (2007) A High-Density Admixture Scan in 1,670 African Americans with Hypertension. PLoS Genetics 3:e196.
Keinan A, Mullikin JC, Patterson N, Reich D (2007) Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than Europeans. Nature Genetics 39, 1251-1255. (Supplementary Materials, Raw Data Available Online)
Haiman CA, Le Marchand L, Yamamato J, Stram DO, Sheng X, Kolonel LN, Wu AH, Reich D, Henderson BE (2007) A common genetic risk factor for colorectal and prostate cancer. Nature Genetics 39, 954-956. (Supplementary Materials).
Ayodo G, Price AL, Keinan A, Ajwang A, Otieno MF, Orago ASS, Patterson N, Reich D (2007) Combining Evidence of Natural Selection with Association Analysis Increases Power to Detect Malaria-Resistance Variants. Am J Hum Genet. 81, 234-242.
Yu F, Hill RS, Schaffner SF, Sabeti PC, Wang ET, Mignault AA, Ferland RJ, Moyzis RK, Walsh CA, Reich D (2007) Technical Comment on Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens. Science 316, 370. (Supplementary Materials)
Becquet C, Patterson N, Stone AC, Przeworski M, Reich D (2007) Genetic Structure of Chimpanzee Populations. PLoS Genetics 3: e66. (Supplementary Materials)
Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MC, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, Reich D (2007) A genomewide admixture map for Latino populations. Am J Hum Genet. 80, 1024-1036. (Supplementary Materials)
Haiman CA, Patterson N, Freedman ML, Myers SR, Pike MC, Waliszewska A, Neubauer J, Tandon A, Schirmer C, McDonald GJ, Greenway SC, Stram DO, Le Marchand L, Kolonel LN, Frasco M, Wong D, Pooler LC, Ardlie K, Oakley-Girvan I, Whittemore AS, Cooney KA, John EM, Ingles SA, Altshuler D, Henderson BE, Reich D (2007) Multiple regions within 8q24 independently affect risk for prostate cancer. Nature Genetics 39, 638-644. (Supplementary Materials)
Reich D, Patterson N, Ramesh V, De Jager PL, McDonald GJ, Tandon A, Choy E, Hu D, Tamraz B, Pawlikowska L, Wassel-Fyr C, Huntsman S, Waliszewska A, Rossin E, Li R, Garcia M, Reiner A, Ferrell R, Cummings S, Kwok PY, Harris T, Zmuda JM, Ziv E; Health, Aging and Body Composition (Health ABC) Study (2007) Admixture mapping of an allele affecting interleukin 6 soluble receptor and interleukin 6 levels. Am J Hum Genet. 80, 716-726. (Supplementary Materials)
Wassel Fyr CL, Kanaya AM, Cummings SR, Reich D, Hsueh WC, Reiner AP, Harris TB, Moffett S, Li R, Ding J, Miljkovic-Gacic I, Ziv E for the Health, Aging, Body Composition Study (2007) Genetic admixture, adipocytokines, and adiposity in Black Americans: the Health, Aging, and Body Composition study. Human Genetics 121, 615-624.
Shaffer JR, Kammerer CM, Reich D, McDonald G, Patterson N, Goodpaster B, Bauer DC, Li J, Newman AB, Cauley JA, Harris TB, Tylavsky F, Ferrell RE, Zmuda JM; for the Health ABC study (2007) Genetic markers for ancestry are correlated with body composition traits in older African Americans. Osteoporosis International 18, 733-741.
2006
Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genetics 2:e190.
Freedman ML, Haiman CA, Patterson N, McDonald GJ, Tandon A, Waliszewska A, Penney K, Steen RG, Ardlie K, John EM, Oakley-Girvan I, Whittemore AS, Cooney KA, Ingles SA, Altshuler D, Henderson BE, Reich D (2006) Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc. Natl. Acad. Sci. USA. 103, 14068-14073 (Supp. Notes) (Supp. Tables).
Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 38, 904-909 (Supplementary Materials) (EIGENSTRAT software).
Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D (2006) Genetic evidence for complex speciation of humans and chimpanzees. Nature 441, 1103-1108 (Supplementary Materials) (Raw Data Available Online) (Correspondence with John Wakeley March 2008).
Lohmueller KE, Mauney MM, Reich D, Braverman JM (2006) Variants associated with common disease are not unusually differentiated in frequency across populations. Am J Hum Genet. 78, 130-136.
Bonnen PE, Pe'er I, Plenge RM, Salit J, Lowe JK, Shapero MH, Lifton RP, Breslow JL, Daly MJ, Reich DE, Jones KW, Stoffel M, Altshuler D, Friedman JM (2006) Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia. Nat Genet. 38, 214-217.
2005
Reich D, Patterson N (2005) Will admixture mapping work to find disease genes? Philos Trans R Soc Lond B Biol Sci. 360, 1605-1607.
Reich D, Patterson N, Jager PL, McDonald GJ, Waliszewska A, Tandon A, Lincoln RR, Deloa C, Fruhan SA, Cabre P, Bera O, Semana G, Kelly MA, Francis DA, Ardlie K, Khan O, Cree BA, Hauser SL, Oksenberg JR, Hafler DA (2005) A whole-genome admixture scan finds a candidate gene for multiple sclerosis susceptibility. Nat Genet. 37, 1113-1118 (Supplementary Methods) (Supplementary Tables).
Chimpanzee Sequencing and Analysis Consortium (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 437, 69-87.
Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE, McVean GA, Gabriel SB, Reich D, Donnelly P, Altshuler D (2005) Comparison of fine-scale recombination rates in humans and chimpanzees. Science 308, 107-111.
Sabeti PC, Walsh E, Schaffner SF, Varilly P, Fry B, Hutcheson HB, Cullen M, Mikkelsen TS, Roy J, Patterson N, Cooper R, Reich D, Altshuler D, O'Brien S, Lander ES (2005) The case for selection at CCR5-Delta32. PLoS Biol. 3:e378.
Patterson NJ (2005) How old is the most recent ancestor of two copies of an allele? Genetics 169, 1093-1104.
Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D (2005) Calibrating a coalescent simulation of human genome sequence variation. Genome Res. 15, 1576-1583.
2004
Freedman ML*, Reich D*, Penney KL, McDonald GJ, Mignault AA, Patterson N, Gabriel SB, Topol EJ, Smoller JW, Pato CN, Pato MT, Petryshen T, Kolonel LN, Lander ES, Sklar P, Henderson B, Hirschhorn J, Altshuler D (2004). Assessing the impact of population stratification on genetic association studies. Nature Genetics 36, 388-393.
Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager P, Yi Z, De Thé G, Essex M, Kanki PJ, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Hafler DA, Altshuler D, Gilbert DA, O’Brien SJ, Reich D (2004). A high density admixture map for disease gene discovery in African Americans. Am J Hum Genet. 74, 979-1000 (Online Table A) (Online Table B).
Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O’Brien SJ, Altshuler D, Daly M, Reich D (2004). Methods for high-density admixture mapping of disease genes. Am J Hum Genet. 74, 1001-1013 (ANCESTRYMAP software).
Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN (2004). Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet. 74, 1111-1120.
Cree BA, Khan O, Bourdette D, Goodin DS, Cohen JA, Marrie RA, Glidden D, Weinstock-Guttman B, Reich D, Patterson N, Haines JL, Pericak-Vance M, Deloa C, Oksenberg JR, Hauser SL. (2004) Clinical characteristics of African Americans vs Caucasian Americans with multiple sclerosis. Neurology. 63, 2039-45.
Oksenberg JR, Barcellos LF, Cree BA, Baranzini SE, Bugawan TL, Khan O, Lincoln RR, Swerdlin A, Mignot E, Lin L, Goodin D, Erlich HA, Schmidt S, Thomson G, Reich DE, Pericak-Vance MA, Haines JL, Hauser SL (2004) Mapping multiple sclerosis susceptibility to the HLA-DR locus in African Americans. Am. J. Hum. Genet. 74, 160-167.
2003
Reich DE, Gabriel SB and Altshuler D (2003) “Quality and completeness of SNP databases,” Nature Genetics 33, 457-458.
2002
Reich DE*, Schaffner, SF*, Daly, MJ, McVean, G. Mullikin, JC, Higgins, JM, Richter, DJ, Lander, ES, Altshuler, D (2002) “The landscape of human genome sequence variation: the role of gene history, mutation and recombination,” Nature Genetics 32, 135-142.
Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GM, Ackerman HC, Campbell SJ, Altshuler D, Kwiatkowski D, Ward R, Lander ES (2002) “Detecting recent positive selection in the human genome from haplotype structure,” Nature 419, 832-837.
2001
Reich DE, Goldstein, DB (2001) “Detecting associations in case-control studies while correcting for population stratification,” Genetic Epidemiology 20, 4-16.
Reich DE, Lander ES (2001) “On the allelic spectrum of human disease,” TIG 17, 502-510.
Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES (2001) “Linkage disequilibrium in the human genome,” Nature 411, 199-204.
The International SNP Map Working Group (2001) "A map of human genome sequence variation containing 1.4 million SNPs," Nature 409, 928-933.
2000
Lindblad-Toh K, Winchester E, Daly MJ, Wang DG, Hirschhorn JN, Laviolette JP, Ardlie K, Reich DE, Robinson E, Sklar P, Shah N, Thomas D, Fan JB, Gingeras T, Warrington J, Patil N, Hudson TJ, Lander ES (2000) “Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse,” Nature Genetics 24, 381-386.
1999
Reich DE, Wayne RK, Goldstein DB (1998) “Genetic evidence for a recent origin by hybridization of red wolves,” Molecular Ecology 8, 139-145.
Goldstein DB, Reich, DE, Bradman N, Usher S, Seligsohn U, Peretz H. (1999) “Age estimates for two common mutations causing Factor XI deficiency,” Am. J. Hum. Genet. 64, 1071-1075.
Goldstein DB, Roemer GW, Smith DA, Reich DE, Bergman A, Wayne RK (1999) “Inferring population structure and demographic history in a natural model system,” Genetics 151, 797-801.
Reich DE, Feldman MW, Goldstein DB (1999) “Statistical properties of two tests that use multilocus data sets to detect population expansions,” Mol. Biol. Evol. 16, 453-466.
Reich DE, Goldstein DB (1999) “Estimating the ages of mutations using variation at linked markers,” in Microsatellites: Evolution & Applications, Oxford University Press.
1998
Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, Carrington M, Winkler C, Huttley GA, Allikmets R, Schriml L, Gerrard B, Malasky M, Ramos MD, Morlot S, Tzetis M, Oddoux C, di Giovine FS, Nasioulas G, Chandler D, Aseev M, Hanson M, Kalaydjieva L, Glavac D, Gasparini P, Kanavakis E, Claustres M, Kambouris M, Ostrer H, Duff G, Baranov V, Sibul H, Metspalu A, Goldman D, Martin N, Duffy D, Schmidtke J, Estivill X, O’Brien SJ, Dean M (1998) “Dating the origin of the CCR5-D32 AIDS resistance allele by the coalescence of haplotypes,” Am. J. Hum. Genet. 62, 1507-1515.
Reich DE, Goldstein DB (1998) “Genetic evidence for a Paleolithic human population expansion in Africa,” Proc. Natl. Acad. Sci. USA 95, 8119-8123.