HGDP-CEPH Human Genome Diversity Cell Line Panel

A resource of 1063 cultured lymphoblastoid cell lines (LCLs) from 1050 individuals in 52 world populations and corresponding milligram quantities of DNA is banked at the Foundation Jean Dausset-CEPH in Paris. These LCLs were collected from various laboratories by the Human Genome Diversity Project (HGDP) and CEPH in order to provide unlimited supplies of DNA and RNA for studies of sequence diversity and history of modern human populations. Information for each LCL is limited to sex of the individual and population and geographic origin.
The table provides details of all the LCLs in the resource, uncorrected for duplicates (13 duplicate pairs), 2 genomically atypical samples, 13 pairs of duplicate LCLs and those from two genetically atypical individuals, and 96 pairs of close relatives (first and/or second degree relative pairs) LCLs for ("close") relative pairs. Sixteen LCLs differ in gender indicated on records and that determined by molecular typing. All samples used for this resource were collected with proper informed consent.

The DNAs have been distributed to 107 investigators (as of 1 December 2010) for genotyping and/or resequencing; the results are contributed to a central database. To date, the DNAs have been typed genome wide with almost 1 million SNPs, 843 microsatellites, and 51 small indel loci. Some 10,000 CNV calls from two different laboratories are included in the database. Nuclear and mitochondrial DNA regions have been resequenced. High throughput sequencing of entire HGDP-CEPH genomes and array captured targets is underway.

For more information contact , CEPH.


PUBLICATIONS ARISING FROM HGDP-CEPH HUMAN GENOME DIVERSITY PANEL

Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A, Chen Z, Chu J, Carcassi C, Contu L, Du R, Excoffier L, Ferrara GB, Friedlaender JS, Groot H, Gurwitz D, Jenkins T, Herrera RJ, Huang X, Kidd J, Kidd KK, Langaney A, Lin AA, Mehdi SQ, Parham P, Piazza A, Pistillo MP, Qian Y, Shu Q, Xu J, Zhu S, Weber JL, Greely HT, Feldman MW, Thomas G, Dausset J, Cavalli-Sforza LL. A human genome diversity cell line panel. Science. 2002 Apr 12;296(5566):261-2.

Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Genetic structure of human populations. Science. 2002 Dec 20;298(5602):2381-5.

Zhivotovsky LA, Rosenberg NA, Feldman MW. Features of evolution of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet. 2003 May;72(5):1171-86. Epub 2003 Apr 10.

Shi M, Caprau D, Romitti P, Christensen K, Murray JC. Genotype frequencies and linkage disequilibrium in the CEPH human diversity panel for variants in folate pathway genes MTHFR, MTHFD, MTRR, RFC1, and GCP2. Birth Defects Res A Clin Mol Teratol. 2003 Aug;67(8):545-9.

Horton R, Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. Read all about it: The Lancet's Paper of the Year. Lancet. 2003 Dec 20;362(9401):2101-3.

Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet. 2003 Dec;73(6):1402-22. Epub 2003 Nov 20.

Zhivotovsky LA, Underhill PA, Cinnio.lu C, Kayser M, Morar B, Kivisild T, Scozzari R, Cruciani F, Destro-Bisol G, Spedini G, Chambers GK, Herrera RJ, Yong KK, Gresham D, Tournev I, Feldman MW, Kalaydjieva L The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. Am J Hum Genet. 2004 Jan;74(1):50-61. Epub 2003 Dec 19.

Ramachandran S, Rosenberg NA, Zhivotovsky LA, Feldman MW. Robustness of the inference of human population structure: A comparison of X-chromosomal and autosomal microsatellites. Hum Genomics. 2004 Jan;1(2):87-97.

Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN. Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet. 2004 Jun;74(6):1111-20. Epub 2004 Apr 26.

Evans W, Fung HC, Steele J, Eerola J, Tienari P, Pittman A, Silva R, Myers A, Vrieze FW, Singleton A, Hardy J.  The tau H2 haplotype is almost exclusively Caucasian in origin. Neurosci Lett. 2004 Oct 21;369(3):183-5.

Zucchero TM, Cooper ME, Maher BS, Daack-Hirsch S, Nepomuceno B, Ribeiro L, Caprau D, Christensen K, Suzuki Y, Machida J, Natsume N, Yoshiura K, Vieira AR, Orioli IM, Castilla EE, Moreno L, Arcos-Burgos M, Lidral AC, Field LL, Liu YE, Ray A, Goldstein TH, Schultz RE, Shi M, Johnson MK, Kondo S, Schutte BC, Marazita ML, Murray JC. Interferon regulatory factor 6 (IRF6) gene variants and the risk of isolated cleft lip or palate. N Engl J Med. 2004 Aug 19;351(8):769-80.

González-Neira A, Calafell F, Navarro A, Lao O, Cann H, Comas D, Bertranpetit J. Geographic stratification of linkage disequilibrium: a worldwide population study in a region of chromosome 22. Hum Genomics. 2004 Nov;1(6):399-409.

Serre D, Paabo S Evidence for gradients of human genetic diversity within and among continents. Genome Res. 2004 Sep;14(9):1679-85.

Macpherson JM., Ramachandran S, Diamond L, Feldman MW. Demographic estimates from Y chromosome microsatellite polymorphisms: analysis of a worldwide sample. Hum Genomics. 2004 5: 345-354.

Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, Nibbs RJ, Freedman BI, Quinones MP, Bamshad MJ, Murthy KK, Rovin BH, Bradley W, Clark RA, Anderson SA, O'connell RJ, Agan BK, Ahuja SS, Bologna R, Sen L, Dolan MJ, Ahuja SK. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science. 2005 307:1434-1440

Barnholtz-Sloan JS, Pfaff CL, Chakraborty R, Long JC. Informativeness of the CODIS STR loci for admixture analysis. J Forensic Sci. 2005 Nov;50(6):1322-6.

Young JH, Chang YP, Kim JD, Chretien JP, Klag MJ, Levine MA, Ruff CB, Wang NY, Chakravarti A. Differential susceptibility to hypertension is due to selection during the out-of-Africa expansion. PLoS Genet. 2005 Dec;1(6):e82.

Cavalli-Sforza LL The Human Genome Diversity Project: past, present and future. Nat Rev Genet. 6: 333-40.

Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci U S A. 102:15942-7.

Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW. Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genet. 1: 660-671

Ramírez-Soriano A, Lao O, Soldevila M, Calafell F, Bertranpetit J, Comas D. Haplotype tagging efficiency in worldwide populations in CTLA4 gene. Genes Immun. 6: 646-57.

Barreiro LB, Patin E, Neyrolles O, Cann HM, Gicquel B, Quintana-Murci L. The heritage of pathogen pressures and ancient demography in the human innate-immunity CD209/CD209L Region. Am J Hum Genet. 77: 869-886.

Mekel-Bobrov N et al. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science 309:1720-1722.

González-Neira A, Ke X, Lao O, Calafell F, Navarro A, Comas D, Cann H, Bumpstead S, Ghori J, Hunt S, Deloukas P, Dunham I, Cardon LR, Bertranpetit J. The portability of tagSNPs across populations: a worldwide survey. Genome Res.16: 323-30.

Conrad DF, Jakobsson M, Coop G, Wen X, Wall JD, Rosenberg NA, Pritchard JK. A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet. 38: 1251-60.

Rosenberg NA et al Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet. 70: 841-7.

Rosenberg NA, Mahajan S, Gonzalez-Quevedo C, Blum MG, Nino-Rosales L, Ninis V, Das P, Hegde M, Molinari L, Zapata G, Weber JL, Belmont JW, Patel PI. Low levels of genetic divergence across geographically and linguistically diverse populations from India. PLoS Genet. 2: 2052-2061.

Pereira RW, Santos SS, Pena SD. A novel polymorphic Alu insetion imbedded in a LINE 1 retrotransposon in the human X chromosome (DXS225): identification and worldwide population study. Genet. Mol. Res. 5:63-71.

Lao O, van Duijn K, Kersbergen P, de Knijff P, Kayser M. Proportioning whole-genome single-nucleotide polymorphism diversity for the identification of geographic population structure and genetic ancestry. Am J Hum Genet. 4: 680-690.

Bastos-Rodrigues L, Pimenta JR, Pena SD. The genetic structure of human populations studied through short insertion-deletion polymorphisms. Annals of Human Genetics 70:658-665.

Xue Y, Daly A, Yngvadottir B, Liu M, Coop G, Kim Y, Sabeti P, Chen Y, Stalker J, Huckle E, Burton J, Leonard S, Rogers J, Tyler-Smith C. Spread of an inactive form of caspase-12 in humans is due to recent positive selection. Am J of Hum Genet. 78:659-670.

Saunders MA, Good JM, Lawrence EC, Ferrell RE, Li WH, Nachman MW. Human adaptive evolution at myostatin (GDF8), a regulator of muscle growth. Am J Hum Genet. 79: 1089-1097.

Soldevila M, Andrés AM, Ramírez-Soriano A, Marquès-Bonet T, Calafell F, Navarro A, Bertranpetit J. The prion protein gene in humans revisited: lessons from a worldwide resequencing study. Genome Res. 16:231-9.

Akey JM et al. TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations. Human Molecular Genetics. 15: 2106-2113.

Paisan-Ruiz P et al. Testing association between LRRK2 and Parkinson.s disease and investigating linkage disequilibrium. Journal of Medical Genetics 2006;43:e09; doi:10.1136/jmg.2005.036889.

Patterson, N et al. Population structure and eigenanalysis. PLoS Genet. 2: 2074-2093.

Butty V, Roy M, Sabeti P, Besse W, Benoist C, Mathis D. Signatures of strong population differentiation shape extended haplotypes across the human CD28, CTLA4, and ICOS costimulatory genes. Proc Natl Acad Sci U S A.104: 570-5.

Lao O, de Gruijter JM, van Duijn K, Navarro A, Kayser M. Signatures of positive selection in genes associated with human skin pigmentation as revealed from analyses of single nucleotide polymorphisms. Ann Hum Genet. 71: 54-69.

Shimada MK, Panchapakesan K, Tishkoff SA, Nato AQ Jr, Hey J. Divergent Haplotypes and Human History as Revealed in a Worldwide Survey of X-Linked DNA Sequence Variation. Molecular Biology and Evolution 24:687-698.

Santos-Lopes SS, Pereira RW, Wilson IJ, Pena SD. A Worldwide Phylogeography for the Human X Chromosome. PLoS ONE 2(6): e557. doi:10.1371/journal.pone.0000557.

Kidd JM, Newman TL, Tuzun E, Kaul R, Eichler EE. Population stratification of a common gene deletion polymorphism. PLoS Genet. 3:584-592.

Nievergelt CM, Libiger O, Schork NJ. Generalized analysis of molecular variance. PLoS Genet. 3: 467-478.

Martin MP, Pascal V, Yeager M, Phair J, Kirk GD, Hoots K, O'brien SJ, Anderson SK, Carrington M. A mutation in KIR3DS1 that results in truncation and lack of cell surface expression. Immunogenetics 59: 823-829.

Graffelman J, Balding DJ, Gonzalez-Neira A, Bertranpetit J. Variation in estimated recombination rates across human populations. Hum Genet. 2007 122:301-10

Tibayrenc M. Human genetic diversity and the epidemiology of parasitic and other transmissible diseases. Adv Parasitol. 2007;64:377-422.

Sabeti PC et al. Genome-wide detection and chracterization of positive selection in human populations. Nature 449: 913-918.

Cavalli-Sforza LL. Human Evolution and Its Relevance for Genetic Epidemiology. Annu Rev Genomics Hum Genet. 2007;8:1-15.

Manica A, Amos W, Balloux F, Hanihara T. The effect of ancient population bottlenecks on human phenotypic variation. Nature 448: 346-349.

Wang S, Lewis CM, Jakobsson M, Ramachandran S, Ray N, Bedoya G, Rojas W, Parra MV, Molina JA, Gallo C, Mazzotti G, Poletti G, Hill K, Hurtado AM, Labuda D, Klitz W, Barrantes R, Bortolini MC, Salzano FM, Petzl-Erler ML, Tsuneto LT, Llop E, Rothhammer F, Excoffier L, Feldman MW, Rosenberg NA, Ruiz-Linares A. Genetic Variation and Population Structure in Native Americans. PLoS Genet. 3(11): e185 doi:10.1371.

Handley LJ, Manica A, Goudet J, Balloux F. Going the distance: human population genetics in a clinal world. TRENDS in Genetics. 23: 432-438.

Lalueza-Fox C, Römpler H, Caramelli D, Stäubert C, Catalano G, Hughes D, Rohland N, Pilli E, Longo L, Condemi S, de la Rasilla M, Fortea J, Rosas A, Stoneking M, Schöneberg T, Bertranpetit J, Hofreiter M. A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318: 1453-1454.

Balaresque PL, Ballereau SJ, Jobling MA. Challenges in human genetic diversity: demographic history and adaptation. Hum Mol Genet. 2007 16 Spec No. 2:R134-8.

Sistonen J, Sajantila A, Lao O, Corander J, Barbujani G, Fuselli S.  CYP2D6 worldwide genetic variation shows high frequency of altered activity variants and no continental structure. Pharmacogenet Genomics. 17: 93-101.

Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, Werner J, Villanea FA, Mountain JL, Misra R, Carter NP, Lee C, Stone AC. Diet and the evolution of human amylase gene copy number variation. Nat Genet. 39 :1256-60.

Friedlaender JS, Friedlaender FR, Reed FA, Kidd KK, Kidd JR, Chambers GK, Lea RA, Loo JH, Koki G, Hodgson JA, Merriwether DA, Weber JL. The genetic structure of Pacific Islanders. PLoS Genet. 4(1): e19 doi:10.1371.

Serre D, Montpetit A, Paré G, Engert JC, Yusuf S, Keavney B, Hudson TJ, Anand S. Correction of population stratification in large multi-ethnic association association studies. PLoS One 2(1): e1382 doi: 10.1371.

Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, Fung HC, Szpiech ZA, Degnan JH, Wang K, Guerreiro R, Bras JM, Schymick JC, Hernandez DG, Traynor BJ, Simon-Sanchez J, Matarin M, Britton A, van de Leemput J, Rafferty I, Bucan M, Cann HM, Hardy JA, Rosenberg NA, Singleton AB. Genotype, haplotype, and copy-number variation in worldwide human populations. Nature 451: 998-1003.

Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319: 1100-1104.

Xue Y, Sun D, Daly A, Yang F, Zhou X, Zhao M, Huang N, Zerjal T, Lee C, Carter NP, Hurles ME, Tyler-Smith C. Adaptive evolution of UGT2B17 copy-number variation. Am J Hum Genet. 83: 337-346.

Myles S, Davison D, Barrett J, Stoneking M, Timpson N. Worldwide population differentiation at disease-associated SNPs. BMC Medical Genomics. 1: 22.

Pemberton TJ, Jakobsson M, Conrad DF, Coop G, Wall JD, Pritchard JK, Patel PI, Rosenberg NA. Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Annals of Human Genetics 72: 535-546.

Bierut LJ, Stitzel JA, Wang JC, Hinrichs AL, Grucza RA, Xuei X, Saccone NL, Saccone SF, Bertelsen S, Fox L, Horton WJ, Breslau N, Budde J, Cloninger CR, Dick DM, Foroud T, Hatsukami D, Hesselbrock V, Johnson EO, Kramer J, Kuperman S, Madden PA, Mayo K, Nurnberger J Jr, Pomerleau O, Porjesz B, Reyes O, Schuckit M, Swan G, Tischfield JA, Edenberg HJ, Rice JP, Goate AM. Variants in the nicotinic receptors alter the risk for nicotinic dependence. Am J Psychiatry 165: 1163-1171.

He W, Neil S, Kulkarni H, Wright E, Agan BK, Marconi VC, Dolan MJ, Weiss RA, Ahuja SK. Duffy Antigen Receptor for Chemokines Mediates trans-Infection of HIV-1 from Red Blood Cells to Target Cells and Affects HIV-AIDS Susceptibility. Cell Host & Microbe 4: 52.62.

Bryk J, Hardouin E, Pugach I, Hughes D, Strotmann R, Stoneking M, Myles S. et al. Positive Selection in East Asians for an EDAR Allele that Enhances NF-.B Activation. PLoS ONE 3(5): e2209 doi:10.1371/journal.pone.0002209.

Hillmer AM, Brockschmidt FF, Hanneken S, Eigelshoven S, Steffens M, Flaquer A, Herms S, Becker T, Kortüm AK, Nyholt DR, Zhao ZZ, Montgomery GW, Martin NG, Mühleisen TW, Alblas MA, Moebus S, Jöckel KH, Bröcker-Preuss M, Erbel R, Reinartz R, Betz RC, Cichon S, Propping P, Baur MP, Wienker TF, Kruse R, Nöthen MM. Susceptibility variants for male pattern baldness on chromosome 20p11. Nature Genetics 40:1279-1281.

Ferrer-Admetlla A, Bosch E, Sikora M, Marquès-Bonet T, Ramírez-Soriano A, Muntasell A, Navarro A, Lazarus R, Calafell F, Bertranpetit J, Casals F. Balancing selection is the main force shaping the evolution of innate immunity genes. J Immunol. 181: 1315-22.

Tarazona-Santos E, Bernig T, Burdett L, Magalhaes WC, Fabbri C, Liao J, Redondo RA, Welch R, Yeager M, Chanock SJ. CYBB, an NADPH-oxidase gene: restricted diversity in humans and evidence for differential long-term purifying selection on transmembrane and cytosolic domains. Hum Mutat. 29: 623-32.

Wall JD, Cox MP, Mendez FL, Woerner A, Severson T, Hammer MF. A novel DNA sequence database for analyzing human demographic history. Genome Res 18: 1354-1361.

Szpiech ZA, Jakobsson M, Rosenberg NA. ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24: 2498-2504.

Balaresque P, Bowden GR, Parkin EJ, Omran GA, Heyer E, Quintana-Murci L, Roewer L, Stoneking M, Nasidze I, Carvalho-Silva DR, Tyler-Smith C, de Knijff P, Jobling MA. Dynamic nature of the proximal AZFc region of the human Y chromosome: multiple independent deletion and duplication events revealed by microsatellite analysis. Hum Mutat. 29:1171-80.

Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 18: 830-838.

Tian C, Kosoy R, Lee A, Ransom M, Belmont JW, Gregersen PK, Seldin MF. Analysis of East Asia genetic substructure using genome-wide SNP arrays. PLoS ONE. 3: e3862. doi:10.1371.

Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, Redon R. Copy number variation and evolution in humans and chimpanzees. Genome Res. 18: 1698-1710, 2008.

Xu S, Jin L. A genome-wide analysis of admixture in Uyghurs and a high-density admixture map for disease-gene discovery. Am J Hum Genet. 2008 Sep;83(3):322-36.

Hancock AM, Witonsky DB, Gordon AS, Eshel G, Pritchard JK, Coop G, Di Rienzo A. Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet. 2008 Feb;4(2):e3

Colobran R, Adreani P, Ashhab Y, Llano A, Esté JA, Dominguez O, Pujol-Borrell R, Juan M.  Population structure in copy number variation and SNPs in the CCL4L chemokine gene. Genes Immun. 9: 279-88.

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. A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nat Genet. 41:187-91.

Hofer T, Ray N, Wegmann D, Excoffier L. Large Allele Frequency Differences between Human Continental Groups are more Likely to have Occurred by Drift During range Expansions than by Selection. Annals of Human Genetics 73: 95-108.

Rosenberg NA, Jakobsson M. The relationship between homozygosity and the frequency of the most frequent allele. Genetics. 2008 Aug;179(4):2027-36.

Wall JD, Cox MP, Mendez FL, Woerner A, Severson T, Hammer MF. A novel DNA sequence database for analyzing human demographic history. Genome Res. 2008 Aug;18(8):1354-61.

Hammer MF, Mendez FL, Cox MP, Woerner AE, Wall JD. Sex-biased evolutionary forces shape genomic patterns of human diversity.r PLoS Genet. 2008 Sep26;4(9):e1000202.

Ramachandran S, Rosenberg NA, Feldman MW, Wakeley J. Population differentiation and migration: coalescence times in a two-sex island model for autosomal and X-linked loci. Theor Popul Biol. 2008 Dec;74(4):291-301.

Fumagalli M, Cagliani R, Pozzoli U, Riva S, Comi GP, Menozzi G, Bresolin N, Sironi M. Widespread balancing selection and pathogen-driven selection at blood group antigen genes. Genome Res. 2009 Feb;19(2):199-212.

DeGiorgio M, Rosenberg NA. An unbiased estimatorof gene diversity in samples containing related individuals. Mol Biol Evol. 2009 Mar;26(3):501-12.

Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D, Krauss RM, Myers RM, Ridker PM, Chasman DI, Mefford H, Ying P, Nickerson DA, Eichler EE. Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet. 84: 148-161.

Yngvadottir B, Xue Y, Searle S, Hunt S, Delgado M, Morrison J, Whittaker P, Deloukas P, Tyler-Smith C. A Genome-wide Survey of the Prevalence and Evolutionary Forces Acting on Human Nonsense SNPs. Am J Hum Genet. 84: 224-234.

Huang L, Li Y, Singleton AB, Hardy JA, Abecasis G, Rosenberg NA, Scheet P. Genotype-Imputation Accuracy across Worldwide Human Populations. Am J Hum Genet. 84: 235-250.

Auton A, Bryc K, Boyko AR, Lohmueller KE, Novembre J, Reynolds A, Indap A, Wright MH, Degenhardt JD, Gutenkunst RN, King KS, Nelson MR, Bustamante CD. Global distribution of genomic diversity underscores rich complex history of continental human populations. Genome Res. 19:795-803.

Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ, Absher D, Srinivasan BS, Barsh GS, Myers RM, Feldman MW, Pritchard JK. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19: 826-37.

Tishkoff SA, Reed FA, Friedlaender FR, Ehret C, Ranciaro A, Froment A, Hirbo JB, Awomoyi AA, Bodo JM, Doumbo O, Ibrahim M, Juma AT, Kotze MJ, Lema G, Moore JH, Mortensen H, Nyambo TB, Omar SA, Powell K, Pretorius GS, Smith MW, Thera MA, Wambebe C, Weber JL, Williams SM. The Genetic Structure and History of Africans and African Americans. Science 324: 1035-44.

Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, Absher D, Myers RM, Cavalli-Sforza LL, Feldman MW, Pritchard JK. The Role of Geography in Human Adaptation. PLoS Genet 5(6): e1000500. doi:10.1371.

Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, Beaty TH, Mathias R, Reich D, Myers S. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 2009 5:e1000519

Hunley KL, Healy ME, Long JC. The global pattern of gene identity variation reveals a history of long-range migrations, bottlenecks, and local mate exchange: implications for biological race. Am J Phys Anthropol. 2009 May;139(1):35-46.

Biswas S, Scheinfeldt LB, Akey JM. Genome-wide insights into the patterns and determinants of fine-scale population structure in humans.r  Am J Hum Genet. 2009 May;84(5):641-50.

Xing J, Watkins WS, Witherspoon DJ, Zhang Y, Guthery SL, Thara R, Mowry BJ, Bulayeva K, Weiss RB, Jorde LB. Fine-scaled human genetic structure revealed by SNP microarrays. Genome Res. 2009 May;19(5) 815-25.

Schroeder KB, Jakobsson M, Crawford MH, Schurr TG, Boca SM, Conrad DF, Tito RY, Osipova LP, Tarskaia LA, Zhadanov SI, Wall JD, Pritchard JK, Malhi RS, Smith DG, Rosenberg NA. Haplotypic background of a private allele at high frequency in the Americas. Mol Biol Evol. 2009 May;26(5):995-1016.

Shringarpure S, Xing EP. mStruct: inference of population structure in light of both genetic admixing and allele mutations. Genetics. 182: 575-93.

Scheinfeldt LB, Biswas S, Madeoy J, Connelly CF, Schadt EE, Akey JM. Population genomic analysis of ALMS1 in humans reveals a surprisingly complex evolutionary history. Mol Biol Evol. 2009 Jun;26(6):1357-67.

Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Riva S, Clerici M, Bresolin N, Sironi M. Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions. J Exp Med. 2009 Jun 8;206(6):1395-408.

Bosch E, Laayouni H, Morcillo-Suarez C, Casals F, Moreno-Estrada A, Ferrer-Admetlla A, Gardner M, Rosa A, Navarro A, Comas D, Graffelman J, Calafell F, Bertranpetit J. Decay of linkage disequilibrium within genes across HGDP-CEPH human samples: most population isolates do not show increased LD. BMC Genomics. Jul 28;10:338.

Vermeulen M, Wollstein A, van der Gaag K, Lao O, Xue Y, Wang Q, Roewer L, Knoblauch H, Tyler-Smith C, de Knijff P, Kayser M. Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms. Forensic Sci Int Genet. 3: 205-213.

Moreno-Estrada A, Tang K, Sikora M, Marquès-Bonet T, Casals F, Navarro A, Calafell F, Bertranpetit J, Stoneking M, Bosch E. Interrogating 11 fast-evolving genes for signatures of recent positive selection in worldwide human populations. Mol Biol Evol. 26:2285-2297.

DeGiorgio M, Jakobsson M, Rosenberg NA. Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proc Natl Acad Sci U S A. 2009 Sep 22;106(38):16057-62.

Kersbergen P, van Duijn K, Kloosterman AD, den Dunnen JT, Kayser M, de Knijff P. Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans. BMC Genet. Oct 27;10:69.

Huang L, Wang C, Rosenberg NA. The relationship between imputation error and statistical power in genetic association studies in diverse populations. Am J Hum Genet. 2009 Nov;85(5):692-8.

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Xu S, Yin X, Li S, Jin W, Lou H, Yang L, Gong X, Wang H, Shen Y, Pan X, He Y, Yang Y, Wang Y, Fu W, An Y, Wang J, Tan J, Qian J, Chen X, Zhang X, Sun Y, Zhang X, Wu B, Jin L. Genomic dissection of population substructure of Han Chinese and its implication in association studies. Am J Hum Genet. 2009 Dec;85(6):762-74.

Kopelman NM, Stone L, Wang C, Gefel D, Feldman MW, Hillel J, Rosenberg NA. Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations. BMC Genet. 2009 Dec 8;10:80.

Pemberton TJ, Sandefur CI, Jakobsson M, Rosenberg NA Sequence determinants of human microsatellite variability. BMC Genomics. 2009 Dec 16;10:612.

Romero IG, Manica A, Goudet J, Handley LL, Balloux F.  How accurate is the current picture of human genetic variation? Heredity. 2009 Feb;102(2):120-6.

Zakharia F, Basu A, Absher D, Assimes TL, Go AS, Hlatky MA, Iribarren C, Knowles JW, Li J, Narasimhan B, Sidney S, Southwick A, Myers RM, Quertermous T, Risch N, Tang H.   Characterizing the admixed African ancestry of African Americans. Genome Biol. 2009;10(12):R141.

Ji LD, Xu J, Wu DD, Xie SD, Tang NL, Zhang YP.  Association of disease-predisposition polymorphisms of the melatonin receptors and sunshine duration in the global human populations. J Pineal Res. 2010 Mar;48(2):133-41.

Patterson N, Petersen DC, van der Ross RE, Sudoyo H, Glashoff RH, Marzuki S, Reich D, Hayes VM. Genetic structure of a unique admixed population: implications for medical research. Hum Mol Genet. 2010 Feb 1;19(3):411-9. Epub 2009 Nov 5.

Grossman SR, Shylakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, Lander ES, Schaffner SF, Sabeti PC A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327: 883-886.

Shi W, Ayub Q, Vermeulen M, Shao RG, Zuniga S, van der Gaag K, de Knijff P, Kayser M, Xue Y, Tyler-Smith C. A Worldwide Survey of Human Male Demographic History Based on Y-SNP and Y-STR Data from the HGDP-CEPH Populations. Mol. Biol. Evol. 27: 385-393.

Hao K, Chudin E, Greenawalt D, Schadt EE  Magnitude of stratification in human populations and impacts on genome wide association studies. PLoS One. 2010 Jan 13;5(1):e8695.

Li R, Li Y, Zheng H, Luo R, Zhu H, Li Q, Qian W, Ren Y, Tian G, Li J, Zhou G, Zhu X, Wu H, Qin J, Jin X, Li D, Cao H, Hu X, Blanche H, Cann H, Zhang X, Li S, Bolund L, Kristiansen K, Yang H, Wang J, Wang J. Building the sequence map of the human pan-genome. Nat Biotechnol. 2010 Jan;28(1):57-63.

Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M. Genome-wide identification of susceptibility alleles for viral infections through a population genetics approach.  PLoS Genet. 2010 Feb 19;6(2):e1000849.

Pozzoli U, Fumagalli M, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M. The role of protozoa-driven selection in shaping human genetic variability. Trends Genet. 2010 Mar;26(3):95-9.

Guerreiro RJ, Washecka N, Hardy J, Singleton A. A thorough assessment of benign genetic variability in GRN and MAPT. Hum Mutat. 2010 Feb;31(2):E1126-40.

Pritchard JK, Pickrell JK, Coop G. The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Curr Biol. 2010 Feb 23;20(4):R208-15.

Lemmers RJ, van der Vliet PJ, van der Gaag KJ, Zuniga S, Frants RR, de Knijff P, van der Maarel SM. Worldwide population analysis of the 4q and 10q subtelomeres identifies only four discrete interchromosomal sequence transfers in human evolution. Am J Hum Genet. 2010 Mar 12;86(3):364-77

Phillips C, Fernandez-Formoso L, Garcia-Magariños M, Porras L, Tvedebrink T, Amigo J, Fondevila M, Gomez-Tato A, Alvarez-Dios J, Freire-Aradas A, Gomez-Carballa A, Mosquera-Miguel A, Carracedo A, Lareu MV. Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel. Forensic Sci Int Genet. 2010 Mar 5.

Walsh S, Liu F, Ballantyne KN, van Oven M, Lao O, Kayser M. IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Sci Int Genet. 2010 Mar 27.

Guerreiro RJ, Baquero M, Blesa R, Boada M, Brás JM, Bullido MJ, Calado A, Crook R, Ferreira C, Frank A, Gómez-Isla T, Hernández I, Lleó A, Machado A, Martínez-Lage P, Masdeu J, Molina-Porcel L, Molinuevo JL, Pastor P, Pérez-Tur J, Relvas R, Oliveira CR, Ribeiro MH, Rogaeva E, Sa A, Samaranch L, Sánchez-Valle R, Santana I, Tàrraga L, Valdivieso F, Singleton A, Hardy J, Clarimón J. Genetic screening of Alzheimer's disease genes in Iberian and African samples yields novel mutations in presenilins and APP. Neurobiol Aging. 2010 May;31(5):725-31.

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22.

Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, Fortea J, Rosas A, Lachmann M, Hannon GJ, Pääbo S. Targeted investigation of the Neandertal genome by array-based sequence capture. Science. 2010 May 7;328(5979):723-5.

Santos C, Phillips C, Fondevila M, Porras-Hurtado L, Carracedo A, Souto L, Lareu MV. A study of East Timor variability using the SNPforID 52-plex SNP panel. Forensic Sci Int Genet. 2010 May 10.

Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, Boehnke M. Genome-wide association studies in diverse populations. Nat Rev Genet. 2010 May;11(5):356-66.

Hancock AM, Witonsky DB, Ehler E, Alkorta-Aranburu G, Beall C, Gebremedhin A, Sukernik R, Utermann G, Pritchard J, Coop G, Di Rienzo A. Colloquium paper: human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency. Proc Natl Acad Sci U S A. 2010 May 11;107 Suppl 2:8924-30.

Biffi A, Anderson CD, Nalls MA, Rahman R, Sonni A, Cortellini L, Rost NS, Matarin M, Hernandez DG, Plourde A, de Bakker PI, Ross OA, Greenberg SM, Furie KL, Meschia JF, Singleton AB, Saxena R, Rosand J. Principal-component analysis for assessment of population stratification in mitochondrial medical genetics. Am J Hum Genet. 2010 Jun 11;86(6):904-17.

Ross KA, Bigham AW, Edwards M, Gozdzik A, Suarez-Kurtz G, Parra EJ. Worldwide allele frequency distribution of four polymorphisms associated with warfarin dose requirements. J Hum Genet. 2010 Jun 17.

Gil Atzmon, Li Hao, Itsik Pe'er, Christopher Velez, Alexander Pearlman, Pier Francesco Palamara, Bernice Morrow, Eitan Friedman, Carole Oddoux, Edward Burns, Harry Ostrer. Abraham's Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry. Am J Hum Genet. 2010 June; 86(6):850-859.

Oleksyk TK, Nelson GW, An P, Kopp JB, Winkler CA. Worldwide distribution of the MYH9 kidney disease susceptibility alleles and haplotypes: evidence of historical selection in Africa. PLoS One. 2010 Jul 9;5(7):e11474.

Behar DM, Yunusbayev B, Metspalu M, Metspalu E, Rosset S, Parik J, Rootsi S, Chaubey G, Kutuev I, Yudkovsky G, Khusnutdinova EK, Balanovsky O, Semino O, Pereira L, Comas D, Gurwitz D, Bonne-Tamir B, Parfitt T, Hammer MF, Skorecki K, Villems R. The genome-wide structure of the Jewish people. Nature 2010 Jul 8;466(7303):238-42.

Kehdy FS, Pena SD. Worldwide diversity of the Y-chromosome tetra-local microsatellite DYS464. Genet Mol Res. 2010 Aug 3;9(3):1525-34.

Coop G, Witonsky D, Di Rienzo A, Pritchard JK. Using environmental correlations to identify loci underlying local adaptation. Genetics. 2010 Aug;185(4):1411-23.

Hancock AM, Alkorta-Aranburu G, Witonsky DB, Di Rienzo A. Adaptations to new environments in humans: the role of subtle allele frequency shifts. Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2459-68.

Fumagalli M, Pozzoli U, Cagliani R, Comi GP, Bresolin N, Clerici M, Sironi M. The landscape of human genes involved in the immune response to parasitic worms. BMC Evol Biol. 2010 Aug 31;10:264.

Moreno-Estrada A, Aparicio-Prat E, Sikora M, Engelken J, Ramirez-Soriano A, Calafell F, Bosch E. African signatures of recent positive selection in human FOXI1. BMC Evol Biol. 2010 Sep 1;10(1):267.

The International HapMap 3 Consortium; Principal investigators, Altshuler DM, Gibbs RA, Peltonen L; Project coordination leaders, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E; Manuscript writing group, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA; Genotyping and QC, de Bakker PI Co-Leader, Deloukas P Co-Leader, Gabriel SB, Gwilliam R, Hunt S, Inouye M Co-Leader, Jia X, Palotie A, Parkin M Co-Leader, Whittaker P; ENCODE 3 sequencing and SNP discovery, Yu F Leader, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Marie Muzny D; Copy number variation typing and analysis, Barnes C, Darvishi K, Hurles M Co-Leader, Korn JM, Kristiansson K, Lee C, McCarroll SA Co-Leader, Nemesh J; Population analysis, Dermitzakis E, Keinan A Leader, Montgomery SB, Pollack S, Price AL, Soranzo N; Low frequency variation analysis, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F Leader; Linkage disequilibrium and haplotype sharing analysis, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF Leader, Zhang Q; Imputation, Ghori MJ, McGinnis R Co-Leader, McLaren W, Pollack S, Price AL Co-Leader, Schaffner SF Co-Leader, Takeuchi F; Natural selection, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC Leader; Community engagement and sample collection groups, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Cristina Manca M, Marshall PA, Matsuda I, Ngare D, Ota Wang V, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C; Scientific management, Brooks LD, McEwen JE. Integrating common and rare genetic variation in diverse human populations. Nature. 2010 Sep 2;467(7311):52-58.

Listman JB, Malison RT, Sanichwankul K, Ittiwut C, Mutirangura A, Gelernter J. Southeast Asian origins of five Hill Tribe populations and correlation of genetic to linguistic relationships inferred with genome-wide SNP data. Am J Phys Anthropol. 2010 Oct 26. [Epub ahead of print]

Fumagalli M, Cagliani R, Riva S, Pozzoli U, Biasin M, Piacentini L, Comi GP, Bresolin N, Clerici M, Sironi M. Population genetics of IFIH1: ancient population structure, local selection, and implications for susceptibility to type 1 diabetes. Mol Biol Evol. 2010 Nov;27(11):2555-66.

Aggarwal S, Negi S, Jha P, Singh PK, Stobdan T, Pasha MA, Ghosh S, Agrawal A. Indian Genome Variation Consortium, Prasher B, Mukerji M. EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda. Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18961-6.

Zhang J. Ancestral informative marker selection and population structure visualization using sparse laplacian eigenfunctions. PLoS One. 2010 Nov 4;5(11):e13734.

Huyghe JR, Fransen E, Hannula S, Van Laer L, Van Eyken E, Mäki-Torkko E, Aikio P, Sorri M, Huentelman MJ, Camp GV. A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies. Eur J Hum Genet. 2010 Dec 8. [Epub ahead of print]

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010 Dec 23;468(7327):1053-60.

Bigham A, Bauchet M, Pinto D, Mao X, Akey JM, Mei R, Scherer SW, Julian CG, Wilson MJ, López Herráez D, Brutsaert T, Parra EJ, Moore LG, Shriver MD. Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data. PLoS Genet. 2010 Sep 9;6(9). pii: e1001116.

Mosher JT, Pemberton TJ, Harter K, Wang C, Buzbas EO, Dvorak P, Simón C, Morrison SJ, Rosenberg NA. Lack of population diversity in commonly used human embryonic stem-cell lines. N Engl J Med. 2010 Jan 14;362(2):183-5.

Wang C, Szpiech ZA, Degnan JH, Jakobsson M, Pemberton TJ, Hardy JA, Singleton AB, Rosenberg NA. Comparing spatial maps of human population-genetic variation using Procrustes analysis. Stat Appl Genet Mol Biol. 2010;9(1):Article 13.

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. Toward a more uniform sampling of human genetic diversity: a survey of worldwide populations by high-density genotyping. Genomics. 2010 Oct;96(4):199-210.

DeGiorgio M, Jankovic I, Rosenberg NA. Unbiased estimation of gene diversity in samples containing related individuals: exact variance and arbitrary ploidy. Genetics. 2010 Dec;186(4):1367-87.

Hancock AM, Clark VJ, Qian Y, Di Rienzo A. Population genetic analysis of the uncoupling proteins supports a role for UCP3 in human cold resistance. Mol Biol Evol. 2011 Jan;28(1):601-14

Leutenegger AL, Sahbatou M, Gazal S, Cann H, Génin E. Consanguinity around the world: what do the genomic data of the HGDP-CEPH diversity panel tell us? Eur J Hum Genet. 2011 May;19(5):583-7.

Campbell CD, Sampas N, Tsalenko A, Sudmant PH, Kidd JM, Malig M, Vu TH, Vives L, Tsang P, Bruhn L, Eichler EE. Population-genetic properties of differentiated human copy-number polymorphisms. Am J Hum Genet. 2011 Mar 11;88(3):317-32.

Casto AM, Feldman MW.  Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? PLoS Genet. 2011 Jan 6;7(1):e1001266.

Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, Rodríguez-Botigué L, Ramachandran S, Hon L, Brisbin A, Lin AA, Underhill PA, Comas D, Kidd KK, Norman PJ, Parham P, Bustamante CD, Mountain JL, Feldman MW. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5154-62

Pino-Yanes M, Corrales A, Basaldúa S, Hernández A, Guerra L, Villar J, Flores C. North african influences and potential bias in case-control association studies in the spanish population. PLoS One. 2011 Mar 30;6(3):e18389.

Ghahramani Seno MM, Kwan BY, Lee-Ng KK, Moessner R, Lionel AC, Marshall CR, Scherer SW. Human PTCHD3 nulls: rare copy number and sequence variants suggest a non-essential gene. BMC Med Genet. 2011 Mar 26;12:45.

Konyukh M, Delorme R, Chaste P, Leblond C, Lemière N, Nygren G, Anckarsäter H, Rastam M, Ståhlberg O, Amsellem F, Gillberg IC, Mouren-Simeoni MC, Herbrecht E, Fauchereau F, Toro R, Gillberg C, Leboyer M, Bourgeron T. Variations of the candidate SEZ6L2 gene on Chromosome 16p11.2 in patients with autism spectrum disorders and in human populations. PLoS One. 2011 Mar 4;6(3):e17289.

Moorjani P, Patterson N, Hirschhorn JN, Keinan A, Hao L, Atzmon G, Burns E, Ostrer H, Price AL, Reich D. The history of african gene flow into southern Europeans, Levantines, and Jews. PLoS Genet. 2011 Apr;7(4):e1001373.

Ding K, Kullo IJ. Geographic differences in allele frequencies of susceptibility SNPs for cardiovascular disease. BMC Med Genet. 2011 Apr 20;12:55.

Hancock AM, Witonsky DB, Alkorta-Aranburu G, Beall CM, Gebremedhin A, Sukernik R, Utermann G, Pritchard JK, Coop G, Di Rienzo A. Adaptations to climate-mediated selective pressures in humans. PLoS Genet. 2011 Apr;7(4):e1001375.

Cruciani F, Trombetta B, Massaia A, Destro-Bisol G, Sellitto D, Scozzari R. A revised root for the human y chromosomal phylogenetic tree: the origin of patrilineal diversity in Africa. Am J Hum Genet. 2011 Jun 10;88(6):814-8.

Manry J, Laval G, Patin E, Fornarino S, Tichit M, Bouchier C, Barreiro LB, Quintana-Murci L. Evolutionary genetics evidence of an essential, nonredundant role of the IFN-γ pathway in protective immunity. Hum Mutat. 2011 Jun; 32(6):633-42.

Mirabello L, Yeager M, Chowdhury S, Qi L, Deng X, Wang Z, Hutchinson A, Savage SA. Worldwide genetic structure in 37 genes important in telomere biology. Heredity (Edinb). 2011 Jul 6. doi: 10.1038/hdy.2011.55.

Narang A, Jha P, Rawat V, Mukhopadhyay A, Dash D; Indian Genome Variation Consortium, Basu A, Mukerji M. Recent admixture in an Indian population of African ancestry. Am J Hum Genet. 2011 Jul 15;89(1):111-20.

Szpiech ZA, NA Rosenberg NA. On the size distribution of private microsatellite alleles. Theor Popul Biol. 2011 Sep;80(2):100-13.

Bhatia G, Patterson N, Pasaniuc B, Zaitlen N, Genovese G, Pollack S, Mallick S, Myers S, Tandon A, Spencer C, Palmer CD, Adeyemo AA, Akylbekova EL, Cupples LA, Divers J, Fornage M, Kao WH, Lange L, Li M, Musani S, Mychaleckyj JC, Ogunniyi A, Papanicolaou G, Rotimi CN, Rotter JI, Ruczinski I, Salako B, Siscovick DS, Tayo BO, Yang Q, McCarroll S, Sabeti P, Lettre G, De Jager P, Hirschhorn J, Zhu X, Cooper R, Reich D, Wilson JG, Price AL. Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection. Am J Hum Genet. 2011 Sep 9;89(3):368-81.

Hammer MF, Woerner AE, Mendez FL, Watkins JC, Wall JD. Genetic evidence for archaic admixture in Africa. Proc Natl Acad Sci U S A. 2011 Sep13;108(37):15123-8.

Novembre J, Ramachandran S. Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet. 2011 Sep 22;12: 245-74.

Guinan KJ. Worldwide Distribution of Type II Diabetes-Associated TCF7L2 SNPs: Evidence for Stratification in Europe. Biochem Genet. 2011 Sep 7. [Epub ahead of print]

Scheinfeldt LB, Biswas S, Madeoy J, Connelly CF, Akey JM. Clusters of adaptive evolution in the human genome. Front Genet. 2011;2:50. Epub 2011 Sep 9.

Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MT, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Gallego Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science. 2011 Oct 7;334(6052):94-8.

Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, Ko AM, Ko YC, Jinam TA, Phipps ME, Saitou N, Wollstein A, Kayser M, Pääbo S, Stoneking M. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am J Hum Genet. 2011 Oct 7;89(4):516-28.

M DeGiorgio M, Degnan JH, Rosenberg NA. Coalescence-time distributions in a serial founder model of human evolutionary history. Genetics. 2011 Oct;189(2):579-93.

Boca SM, Rosenberg NA. Mathematical properties of Fst between admixed populations and their parental source populations. Theor Popul Biol. 2011 Nov;80(3):208-16.

Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admettla A, Pattini L, Nielsen R. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet. 2011 Nov;7(11):e1002355.

Vasseur E, Patin E, Laval G, Pajon S, Fornarino S, Crouau-Roy B, Quintana-Murci L. The selective footprints of viral pressures at the human RIG-I-like receptor family. Hum Mol Genet. 2011 Nov 15;20(22):4462-74.

Fornarino S, Laval G, Barreiro LB, Manry J, Vasseur E, Quintana-Murci L. Evolution of the TIR domain-containing adaptors in humans: swinging between constraint and adaptation. Mol Biol Evol. 2011 Nov;28(11):3087-97.

Eriksson A, Manica A.  Detecting and Removing Ascertainment Bias in Microsatellites from the HGDP-CEPH Panel. G3 (Bethesda). 2011 Nov;1(6):479-88.

Manry J, Laval G, Patin E, Fornarino S, Itan Y, Fumagalli M, Sironi M, Tichit M, Bouchier C, Casanova JL, Barreiro LB, Quintana-Murci L. Evolutionary genetic dissection of human interferons. J Exp Med. 2011 Dec 19;208(13):2747-59.

Huang L, Jakobsson M, Pemberton TJ, Ibrahim M, Nyambo T, Omar S, Pritchard JK, Tishkoff SA, Rosenberg NA. Haplotype variation and genotype imputation in African populations. Genet Epidemiol. 2011 Dec;35(8):766-80

Ramachandran S, Rosenberg NA. A test of the influence of continental axes of orientation on patterns of human gene flow. Am J Phys Anthropol. 2011 Dec;146(4):515-29.

Metspalu M, Romero IG, Yunusbayev B, Chaubey G, Mallick CB, Hudjashov G, Nelis M, Mägi R, Metspalu E, Remm M, Pitchappan R, Singh L, Thangaraj K, Villems R, Kivisild T. Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. Am J Hum Genet. 2011 Dec 9;89(6):731-44.

Rosenberg NA. A Population-Genetic Perspective on the Similarities and Differences among Worldwide Human Populations. Hum Biol. 2011 Dec;83 (6):659-84.

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. Crohn's disease and genetic hitchhiking at IBD5. Mol Biol Evol (2012) Jan;29(1): 101-111.

Reddy SB, Rosenberg NA. Refining the relationship between homozygosity and the frequency of the most frequent allele. J Math Biol. 2012 Jan;64(1-2):87-108.

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Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of Population Structure using Dense Haplotype Data. PLoS Genet. 2012 Jan;8(1):e1002453.

Veeramah KR, Wegmann D, Woerner A, Mendez FL, Watkins JC, Destro-Bisol G, Soodyall H, Louie L, Hammer MF. An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomalresequencing data. Mol Biol Evol. 2012 Feb;29(2):617-30.

Li H, Wang JX, Wu DD, Wang HW, Tang NL, Zhang YP. The Origin and Evolution of Variable Number Tandem Repeat of CLEC4M Gene in the Global Human Population. PLoS One. 2012;7(1):e30268.

Pereira R, Phillips C, Pinto N, Santos C, Dos Santos SE, Amorim A, Carracedo A, Gusmão L. Straightforward Inference of Ancestry and Admixture Proportions throughAncestry-Informative Insertion Deletion Multiplexing. PLoS One. 2012; 7(1):e29684.

Hodo?lugil U, Mahley RW. Turkish Population Structure and Genetic Ancestry Reveal Relatedness among Eurasian Populations. Ann Hum Genet. 2012 Mar;76(2):128-41.

Henn BM, Hon L, Macpherson JM, Eriksson N, Saxonov S, Pe'er I, Mountain JL. Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples. PLoS One. 2012;7(4):e34267.

Hofer T, Foll M, Excoffier L. Evolutionary forces shaping genomic islands of population differentiation in humans. BMC Genomics. 2012 Mar 22; 13: 107.

Chen R, Corona E, Sikora M, Dudley JT, Morgan AA, Moreno-Estrada A, Nilsen GB,Ruau D, Lincoln SE, Bustamante CD, Butte AJ. Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation among Human Populations, Compared to Other Diseases. PLoS Genet. 2012 Apr;8(4):e1002621.

Manichaikul A, Palmas W, Rodriguez CJ, Peralta CA, Divers J, Guo X, Chen WM, Wong Q, Williams K, Kerr KF, Taylor KD, Tsai MY, Goodarzi MO, Sale MM, Diez-Roux AV, Rich SS, Rotter JI, Mychaleckyj JC. Population structure of hispanics in the United States: the multi-ethnic study of atherosclerosis. PLoS Genet. 2012 Apr;8(4):e1002640.

Tucci A, Charlesworth G, Sheerin UM, Plagnol V, Wood NW, Hardy J. Study of the genetic variability in a Parkinson's Disease gene: EIF4G1. Neurosci Lett. 2012. Apr 23. [Epub ahead of print]

Piras IS, De Montis A, Calò CM, Marini M, Atzori M, Corrias L, Sazzini M, Boattini A, Vona G, Contu L. Genome-wide scan with nearly 700,000 SNPS in two Sardinian sub-populations suggests some regions as candidate targets for positive selection. Eur J Hum Genet. 2012 Apr 25. doi: 10.1038/ejhg.2012.65.

Ameur A, Enroth S, Johansson A, Zaboli G, Igl W, Johansson AC, Rivas MA, Daly MJ, Schmitz G, Hicks AA, Meitinger T, Feuk L, van Duijn C, Oostra B, Pramstaller PP, Rudan I, Wright AF, Wilson JF, Campbell H, Gyllensten U. Genetic Adaptation of Fatty-Acid Metabolism: A Human-Specific Haplotype Increasing the Biosynthesis of Long-Chain Omega-3 and Omega-6 Fatty Acids. Am J Hum Genet. 2012 May 4;90(5):809-820.

Watkins WS, Xing J, Huff C, Witherspoon DJ, Zhang Y, Perego UA, Woodward SR, Jorde LB. Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World. BMC Genet. 2012 May 20;13(1):39.

Ji LD, Qiu YQ, Xu J, Irwin DM, Tam SC, Tang NL, Zhang YP. Genetic adaptation of the hypoxia-inducible factor pathway to oxygen pressure among Eurasian human populations. Mol Biol Evol. 2012 May 23.

Mendez FL, Watkins JC, Hammer MF. Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations. Mol Biol Evol. 2012 Jun;29(6):1513-20.

Machado LR, Hardwick RJ, Bowdrey J, Bogle H, Knowles TJ, Sironi M, Hollox EJ. Evolutionary History of Copy-Number-Variable Locus for the Low-Affinity Fc? Receptor: Mutation Rate, Autoimmune Disease, and the Legacy of Helminth Infection. Am J Hum Genet. 2012 Jun 8;90(6):973-985.

Kiryluk K, Li Y, Sanna-Cherchi S, Rohanizadegan M, Suzuki H, et al. Geographic Differences in Genetic Susceptibility to IgA Nephropathy: GWAS Replication Study and Geospatial Risk Analysis. PLoS Genet 8(6): e1002765. doi:10.1371/journal.pgen.1002765

Fondevila M, Phillips C, Santos C, Freire Aradas A, Vallone PM, Butler JM, Lareu MV, Carracedo A. Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies. Forensic Sci Int Genet. 2012 Jun 29. pii: S1872-4973(12)00140-8. doi: 10.1016/j.fsigen.2012.06.007.

Kuhn PC, Horimoto AR, Sanches JM, Vieira Filho JP, Franco L, Fabbro AD, Franco LJ, Pereira AC, Moises RS. Genome-wide analysis in brazilian xavante indians reveals low degree of admixture. PLoS One. 2012;7(8):e42702.  

Levran O, Awolesi O, Shen PH, Adelson M, Kreek MJ. Estimating ancestral proportions in a multi-ethnic US sample: implications for studies of admixed populations. Hum Genomics. 2012 Jul 5;6(1):2.

Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, Parra MV, Rojas W, Duque C, Mesa N, García LF, Triana O, Blair S, Maestre A, Dib JC, Bravi CM, Bailliet G, Corach D, Hünemeier T, Bortolini MC, Salzano FM, Petzl-Erler ML, Acuña-Alonzo V, Aguilar-Salinas C, Canizales-Quinteros S, Tusié-Luna T, Riba L, Rodríguez-Cruz M, Lopez-Alarcón M, Coral-Vazquez R, Canto-Cetina T, Silva-Zolezzi I, Fernandez-Lopez JC, Contreras AV, Jimenez-Sanchez G, Gómez-Vázquez MJ, Molina J, Carracedo A, Salas A, Gallo C, Poletti G, Witonsky DB, Alkorta-Aranburu G, Sukernik RI, Osipova L, Fedorova SA, Vasquez R, Villena M, Moreau C, Barrantes R, Pauls D, Excoffier L, Bedoya G, Rothhammer F, Dugoujon JM, Larrouy G, Klitz W, Labuda D, Kidd J, Kidd K, Di Rienzo A, Freimer NB, Price AL, Ruiz-Linares A. Reconstructing Native American population history. Nature. 2012 Aug 16;488(7411):370-4.  

Mendez FL, Watkins JC, Hammer MF. A Haplotype at STAT2 Introgressed from Neanderthals and Serves as a Candidate of Positive Selection in Papua New Guinea. Am J Hum Genet. 2012 Aug 10;91(2):265-74.

Wang C, Zöllner S, Rosenberg NA. A quantitative comparison of the similarity between genes and geography in worldwide human populations. PLoS Genet. 2012 Aug;8(8):e1002886. doi: 10.1371/journal.pgen.1002886

Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ. Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet. 2012 Aug 10;91(2):275-92.

Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science. 2012 Oct 12;338(6104):222-6.

Schlebusch CM, Skoglund P, Sjödin P, Gattepaille LM, Hernandez D, Jay F, Li S, De Jongh M, Singleton A, Blum MG, Soodyall H, Jakobsson M. Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. Science. 2012 Oct 19;338(6105):374-9.

Hollenbach JA, Nocedal I, Ladner MB, Single RM, Trachtenberg EA. Killer cell immunoglobulin-like receptor (KIR) gene content variation in the HGDP-CEPH populations. Immunogenetics. 2012 Oct;64(10):719-37.

Pickrell JK, Patterson N, Barbieri C, Berthold F, Gerlach L, Güldemann T, Kure B, Mpoloka SW, Nakagawa H, Naumann C, Lipson M, Loh PR, Lachance J, Mountain J, Bustamante CD, Berger B, Tishkoff SA, Henn BM, Stoneking M, Reich D, Pakendorf B. The genetic prehistory of southern Africa. Nat Commun. 2012 Oct 16;3:1143. doi: 10.1038/ncomms2140.

Magalhães TR, Casey JP, Conroy J, Regan R, Fitzpatrick DJ, Shah N, Sobral J, Ennis S. HGDP and HapMap Analysis by Ancestry Mapper Reveals Local and Global Population Relationships.  PLoS One. 2012;7(11):e49438. Epub 2012 Nov 26. doi: 10.1371/journal.pone.0049438.

Lee S, Kang J, Oh J. A 2-phased approach for detecting multiple loci associations with traits. Int J Data Min Bioinform. 2012;6(5):535-56.

Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012 Nov;8(11):e1002967. doi: 10.1371/journal.pgen.1002967.

Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Genschoreck T, Webster T, Reich D. Ancient admixture in human history. Genetics. 2012 Nov;192(3):1065-93. doi: 10.1534/genetics.112.145037.

Alkorta-Aranburu G, Beall CM, Witonsky DB, Gebremedhin A, Pritchard JK, Di Rienzo A. The genetic architecture of adaptations to high altitude in ethiopia. PLoS Genet. 2012 Dec;8(12):e1003110. doi: 10.1371/journal.pgen.1003110.

Patillon B, Luisi P, Blanché H, Patin E, Cann HM, Génin E, Sabbagh A. Positive Selection in the Chromosome 16 VKORC1 Genomic Region Has Contributed to the Variability of Anticoagulant Response in Humans. PLoS One. 2012;7(12):e53049. doi: 10.1371/journal.pone.0053049

Manta FS, Pereira R, Caiafa A, Silva DA, Gusmão L, Carvalho EF. Analysis of genetic ancestry in the admixed Brazilian population from Rio de Janeiro using 46 autosomal ancestry-informative indel markers. Ann Hum Biol. 2013 Jan; 40(1):94-8

Schlebusch CM, Lewis CM Jr, Vahter M, Engström K, Tito RY, Obregón-Tito AJ, Huerta D, Polo SI, Medina AC, Brutsaert TD, Concha G, Jakobsson M, Broberg K. Possible Positive Selection for an Arsenic-Protective Haplotype in Humans. Environ Health Perspect. 2013 Jan;121(1):53-58.

Di Gaetano C, Matullo G, Piazza A, Ursino M, Gasparini M. A proximity-based method to identify genomic regions correlated with a continuously varying environmental variable. Evol Bioinform Online. 2013;9:29-42

Gumus E, Gormez Z, Kursun O. Multi objective SNP selection using pareto optimality. Comput Biol Chem. 2013 Apr;43:23-8.

Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B. Inferring admixture histories of human populations using linkage disequilibrium. Genetics. 2013 Apr;193(4):1233-54.

Holmes LV, Strain L, Staniforth SJ, Moore I, Marchbank K, Kavanagh D, Goodship JA, Cordell HJ, Goodship TH. Determining the Population Frequency of the CFHR3/CFHR1 Deletion at 1q32. PLoS One. 2013 Apr 16;8(4):e60352. doi:10.1371/journal.pone.0060352.

Bassaganyas L, Riveira-Muñoz E, García-Aragonés M, González JR, Cáceres M, Armengol L, Estivill X. Worldwide population distribution of the common LCE3C-LCE3B deletion associated with psoriasis and other autoimmune disorders. BMC Genomics. 2013 Apr 17;14(1):261. [Epub ahead of print]

Pemberton TJ, DeGiorgio M, Rosenberg NA. Population structure in a comprehensive genomic data set on human microsatellite variation. G3 (Bethesda) 2013 May 3(5):891-907.

Cagliani R, Pozzoli U, Forni D, Cassinotti A, Fumagalli M, Giani M, Fichera M, Lombardini M, Ardizzone S, Asselta R, de Franchis R, Riva S, Biasin M, Comi GP, Bresolin N, Clerici M, Sironi M. Crohn's disease Loci are common targets of protozoa-driven selection. Mol Biol Evol. 2013 May;30(5):1077-87. doi: 10.1093/molbev/mst020.

Lipson M, Loh PR, Levin A, Reich D, Patterson N, Berger B. Efficient moment-based inference of admixture parameters and sources of gene flow.Mol Biol Evol. 2013 May 24 [Epub ahead of print] doi:10.1093/molbev/mst099.  

Corona E, Chen R, Sikora M, Morgan AA, Patel CJ, Ramesh A, Bustamante CD, Butte AJ. Analysis of the genetic basis of disease in the context of worldwide human relationships and migration. PLoS Genet. 2013 May;9(5):e1003447. doi: 10.1371/journal.pgen.1003447.

Hsu I, Chen R, Ramesh A, Corona E, Kang HP, Ruau D, Butte AJ. Systematic Identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS). BMC Med Genet. 2013 Jun doi: 10.1186/1471-2350-14-62.

Forni D, Cagliani R, Pozzoli U, Colleoni M, Riva S, Biasin M, Filippi G, De Gioia L, Gnudi F, Comi GP, Bresolin N, Clerici M, Sironi M. A 175 million year history of T cell regulatory molecules reveals widespread selection, with adaptive evolution of disease alleles. Immunity. 2013 Jun 27;38(6):1129-41.

Nievergelt CM, Maihofer AX, Shekhtman T, Libiger O, Wang X, Kidd KK, Kidd JR. Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel. Investig Genet. 2013 Jul 1;4(1):13. doi: 10.1186/2041-2223-4-13.

Aigner J, Villatoro S, Rabionet R, Roquer J, Jiménez-Conde J, Martí E, Estivill X. A common 56-kilobase deletion in a primate-specific segmentalduplication creates a novel butyrophilin-like protein. BMC Genet. 2013 Jul6;14:61. doi: 10.1186/1471-2156-14-61.

Phillips C, Kind S, Fernandez-Formoso L, Gelabert-Besada M, Carracedo A, LareuMV. Global population variability in Promega PowerPlex CS7, D6S1043, and Penta B STRs. Int J Legal Med. 2013 Sep;127(5):901-6.

Alsmadi O, Thareja G, Alkayal F, Rajagopalan R, John SE, Hebbar P, Behbehani K, Thanaraj TA. Genetic substructure of kuwaiti population reveals migration history. PLoS One. 2013 Sep 16;8(9):e74913. doi: 10.1371/journal.pone.0074913.

  


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