TY - BOOK AU - Menozzi, P. AU - Piazza, A. PY - 1994 DA - 1994// TI - The History and Geography of Human Genes PB - Princeton University Press CY - Princeton, NJ ID - Menozzi1994 ER - TY - JOUR AU - Rosenberg, N. A. AU - Pritchard, J. K. AU - Weber, J. L. AU - Cann, H. M. AU - Kidd, K. K. AU - Zhivotovsky, L. A. PY - 2002 DA - 2002// TI - Genetic structure of human populations JO - Science VL - 298 UR - https://doi.org/10.1126/science.1078311 DO - 10.1126/science.1078311 ID - Rosenberg2002 ER - TY - JOUR AU - Tang, H. AU - Jorgenson, E. AU - Gadde, M. AU - Kardia, S. L. AU - Rao, D. C. PY - 2006 DA - 2006// TI - Racial admixture and its impact on BMI and blood pressure in African and Mexican Americans JO - Hum Genet VL - 119 UR - https://doi.org/10.1007/s00439-006-0175-4 DO - 10.1007/s00439-006-0175-4 ID - Tang2006 ER - TY - JOUR AU - Cardon, L. R. AU - Palmer, L. J. PY - 2003 DA - 2003// TI - Population stratification and spurious allelic association JO - Lancet VL - 361 UR - https://doi.org/10.1016/S0140-6736(03)12520-2 DO - 10.1016/S0140-6736(03)12520-2 ID - Cardon2003 ER - TY - JOUR AU - Marchini, J. AU - Cardon, L. R. AU - Phillips, M. S. AU - Donnelly, P. PY - 2004 DA - 2004// TI - The effects of human population structure on large genetic association studies JO - Nat Genet VL - 36 UR - https://doi.org/10.1038/ng1337 DO - 10.1038/ng1337 ID - Marchini2004 ER - TY - JOUR AU - Price, A. L. AU - Zaitlen, N. A. AU - Reich, D. AU - Patterson, N. PY - 2010 DA - 2010// TI - New approaches to population stratification in genome-wide association studies JO - Nat Rev Genet VL - 11 UR - https://doi.org/10.1038/nrg2813 DO - 10.1038/nrg2813 ID - Price2010 ER - TY - JOUR AU - Pritchard, J. K. AU - Stephens, M. AU - Donnelly, P. PY - 2000 DA - 2000// TI - Inference of population structure using multilocus genotype data JO - Genetics VL - 155 ID - Pritchard2000 ER - TY - JOUR AU - Tang, H. AU - Peng, J. AU - Wang, P. AU - Risch, N. J. PY - 2005 DA - 2005// TI - Estimation of individual admixture: analytical and study design considerations JO - Genet Epidemiol VL - 28 UR - https://doi.org/10.1002/gepi.20064 DO - 10.1002/gepi.20064 ID - Tang2005 ER - TY - JOUR AU - Alexander, D. H. AU - Novembre, J. AU - Lange, K. PY - 2009 DA - 2009// TI - Fast model-based estimation of ancestry in unrelated individuals JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.094052.109 DO - 10.1101/gr.094052.109 ID - Alexander2009 ER - TY - STD TI - Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006; 2(12):e190. ID - ref10 ER - TY - JOUR AU - Li, J. Z. AU - Absher, D. M. AU - Tang, H. AU - Southwick, A. M. AU - Casto, A. M. AU - Ramachandran, S. PY - 2008 DA - 2008// TI - Worldwide human relationships inferred from genome-wide patterns of variation JO - Science VL - 319 UR - https://doi.org/10.1126/science.1153717 DO - 10.1126/science.1153717 ID - Li2008 ER - TY - JOUR AU - Altshuler, D. M. AU - Gibbs, R. A. AU - Peltonen, L. AU - Altshuler, D. M. AU - Gibbs, R. A. AU - Peltonen, L. PY - 2010 DA - 2010// TI - Integrating common and rare genetic variation in diverse human populations JO - Nature VL - 467 UR - https://doi.org/10.1038/nature09298 DO - 10.1038/nature09298 ID - Altshuler2010 ER - TY - JOUR AU - Nelson, M. R. AU - Bryc, K. AU - King, K. S. AU - Indap, A. AU - Boyko, A. R. AU - Novembre, J. PY - 2008 DA - 2008// TI - The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research JO - Am J Hum Genet VL - 83 UR - https://doi.org/10.1016/j.ajhg.2008.08.005 DO - 10.1016/j.ajhg.2008.08.005 ID - Nelson2008 ER - TY - JOUR AU - Xing, J. AU - Watkins, W. S. AU - Witherspoon, D. J. AU - Zhang, Y. AU - Guthery, S. L. AU - Thara, R. PY - 2009 DA - 2009// TI - Fine-scaled human genetic structure revealed by SNP microarrays JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.085589.108 DO - 10.1101/gr.085589.108 ID - Xing2009 ER - TY - JOUR AU - Xing, J. AU - Watkins, W. S. AU - Shlien, A. AU - Walker, E. AU - Huff, C. D. AU - Witherspoon, D. J. PY - 2010 DA - 2010// TI - Toward a more uniform sampling of human genetic diversity: a survey of worldwide populations by high-density genotyping JO - Genomics VL - 96 UR - https://doi.org/10.1016/j.ygeno.2010.07.004 DO - 10.1016/j.ygeno.2010.07.004 ID - Xing2010 ER - TY - STD TI - Alexander DH, Lange K. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics. 2011; 12:246. ID - ref16 ER - TY - JOUR AU - Kiezun, A. AU - Garimella, K. AU - Do, R. AU - Stitziel, N. O. AU - Neale, B. M. AU - McLaren, P. J. PY - 2012 DA - 2012// TI - Exome sequencing and the genetic basis of complex traits JO - Nat Genet VL - 44 UR - https://doi.org/10.1038/ng.2303 DO - 10.1038/ng.2303 ID - Kiezun2012 ER - TY - JOUR AU - Abecasis, G. R. AU - Auton, A. AU - Brooks, L. D. AU - DePristo, M. A. AU - Durbin, R. M. AU - Handsaker, R. E. PY - 2012 DA - 2012// TI - An integrated map of genetic variation from 1,092 human genomes JO - Nature VL - 491 UR - https://doi.org/10.1038/nature11632 DO - 10.1038/nature11632 ID - Abecasis2012 ER - TY - STD TI - Guo Y, Long J, He J, Li CI, Cai Q, Shu XO, et al. Exome sequencing generates high quality data in non-target regions. BMC Genomics. 2012; 13:194. ID - ref19 ER - TY - JOUR AU - Skotte, L. AU - Korneliussen, T. S. AU - Albrechtsen, A. PY - 2013 DA - 2013// TI - Estimating individual admixture proportions from next generation sequencing data JO - Genetics VL - 195 UR - https://doi.org/10.1534/genetics.113.154138 DO - 10.1534/genetics.113.154138 ID - Skotte2013 ER - TY - JOUR AU - Hu, Y. AU - Willer, C. AU - Zhan, X. AU - Kang, H. M. AU - Abecasis, G. R. PY - 2013 DA - 2013// TI - Accurate local-ancestry inference in exome-sequenced admixed individuals via off-target sequence reads JO - Am J Hum Genet VL - 93 UR - https://doi.org/10.1016/j.ajhg.2013.10.008 DO - 10.1016/j.ajhg.2013.10.008 ID - Hu2013 ER - TY - JOUR AU - Wang, C. AU - Zhan, X. AU - Bragg-Gresham, J. AU - Kang, H. M. AU - Stambolian, D. AU - Chew, E. Y. PY - 2014 DA - 2014// TI - Ancestry estimation and control of population stratification for sequence-based association studies JO - Nat Genet VL - 46 UR - https://doi.org/10.1038/ng.2924 DO - 10.1038/ng.2924 ID - Wang2014 ER - TY - STD TI - Nocedal J, Wright SJ. Numerical optimization: Springer; 2000. [http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20&path=ASIN/0387987932] ID - ref23 ER - TY - JOUR AU - Byrd, R. AU - Lu, P. AU - Nocedal, J. AU - Zhu, C. PY - 1995 DA - 1995// TI - A Limited Memory Algorithm for Bound Constrained Optimization JO - SIAM J Sci Comput VL - 16 UR - https://doi.org/10.1137/0916069 DO - 10.1137/0916069 ID - Byrd1995 ER - TY - JOUR AU - Li, H. AU - Ruan, J. AU - Durbin, R. PY - 2008 DA - 2008// TI - Mapping short DNA sequencing reads and calling variants using mapping quality scores JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.078212.108 DO - 10.1101/gr.078212.108 ID - Li2008 ER - TY - JOUR AU - Li, R. AU - Li, Y. AU - Fang, X. AU - Yang, H. AU - Wang, J. AU - Kristiansen, K. PY - 2009 DA - 2009// TI - SNP detection for massively parallel whole-genome resequencing JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.088013.108 DO - 10.1101/gr.088013.108 ID - Li2009 ER - TY - JOUR AU - Bansal, V. AU - Harismendy, O. AU - Tewhey, R. AU - Murray, S. S. AU - Schork, N. J. AU - Topol, E. J. PY - 2010 DA - 2010// TI - Accurate detection and genotyping of SNPs utilizing population sequencing data JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.100040.109 DO - 10.1101/gr.100040.109 ID - Bansal2010 ER - TY - STD TI - Bansal V, Tewhey R, Leproust EM, Schork NJ. Efficient and cost effective population resequencing by pooling and in-solution hybridization. PLoS ONE. 2011; 6(3):e18353. ID - ref28 ER - TY - JOUR AU - Nejentsev, S. AU - Walker, N. AU - Riches, D. AU - Egholm, M. AU - Todd, J. A. PY - 2009 DA - 2009// TI - Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes JO - Science VL - 324 UR - https://doi.org/10.1126/science.1167728 DO - 10.1126/science.1167728 ID - Nejentsev2009 ER - TY - JOUR AU - Rivas, M. A. AU - Beaudoin, M. AU - Gardet, A. AU - Stevens, C. AU - Sharma, Y. AU - Zhang, C. K. PY - 2011 DA - 2011// TI - Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.952 DO - 10.1038/ng.952 ID - Rivas2011 ER - TY - JOUR AU - Diogo, D. AU - Kurreeman, F. AU - Stahl, E. A. AU - Liao, K. P. AU - Gupta, N. AU - Greenberg, J. D. PY - 2013 DA - 2013// TI - Rare, low-frequency, and common variants in the protein-coding sequence of biological candiyear genes from GWASs contribute to risk of rheumatoid arthritis JO - Am J Hum Genet VL - 92 UR - https://doi.org/10.1016/j.ajhg.2012.11.012 DO - 10.1016/j.ajhg.2012.11.012 ID - Diogo2013 ER - TY - JOUR AU - Scott-Van Zeeland, A. A. AU - Bloss, C. S. AU - Tewhey, R. AU - Bansal, V. AU - Torkamani, A. AU - Libiger, O. PY - 2014 DA - 2014// TI - Evidence for the role of EPHX2 gene variants in anorexia nervosa JO - Mol Psychiatry VL - 19 UR - https://doi.org/10.1038/mp.2013.91 DO - 10.1038/mp.2013.91 ID - Scott-Van Zeeland2014 ER - TY - JOUR AU - Kim, S. Y. AU - Li, Y. AU - Guo, Y. AU - Li, R. AU - Holmkvist, J. AU - Hansen, T. PY - 2010 DA - 2010// TI - Design of association studies with pooled or un-pooled next-generation sequencing data JO - Genet Epidemiol VL - 34 UR - https://doi.org/10.1002/gepi.20501 DO - 10.1002/gepi.20501 ID - Kim2010 ER - TY - JOUR AU - Eskin, I. AU - Hormozdiari, F. AU - Conde, L. AU - Riby, J. AU - Skibola, C. F. AU - Eskin, E. PY - 2013 DA - 2013// TI - eALPS: estimating abundance levels in pooled sequencing using available genotyping data JO - J Comput Biol VL - 20 UR - https://doi.org/10.1089/cmb.2013.0105 DO - 10.1089/cmb.2013.0105 ID - Eskin2013 ER - TY - JOUR AU - Purcell, S. AU - Neale, B. AU - Todd-Brown, K. AU - Thomas, L. AU - Ferreira, M. A. AU - Bender, D. ,. PY - 2007 DA - 2007// TI - PLINK: a tool set for whole-genome association and population-based linkage analyses JO - Am J Hum Genet VL - 81 UR - https://doi.org/10.1086/519795 DO - 10.1086/519795 ID - Purcell2007 ER - TY - STD TI - Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I, et al. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 2009; 5(6):e1000519. ID - ref36 ER - TY - JOUR AU - Zhu, C. AU - Byrd, R. H. AU - Lu, P. AU - Nocedal, J. PY - 1997 DA - 1997// TI - Algorithm 778: L-BFGS-B: fortran subroutines for large-scale bound-constrained optimization JO - ACM Trans Math Softw VL - 23 UR - https://doi.org/10.1145/279232.279236 DO - 10.1145/279232.279236 ID - Zhu1997 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - STD TI - Libiger O, Schork NJ. A method for inferring an individual’s genetic ancestry and degree of admixture associated with six major continental populations. Front Genet. 2012; 3:322. ID - ref39 ER - TY - JOUR AU - Vieira, F. G. AU - Fumagalli, M. AU - Albrechtsen, A. AU - Nielsen, R. PY - 2013 DA - 2013// TI - Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation JO - Genome Res. VL - 23 UR - https://doi.org/10.1101/gr.157388.113 DO - 10.1101/gr.157388.113 ID - Vieira2013 ER - TY - STD TI - Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, et al. Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet. 2013; 9(12):e1004023. ID - ref41 ER - TY - JOUR AU - Sankararaman, S. AU - Sridhar, S. AU - Kimmel, G. AU - Halperin, E. PY - 2008 DA - 2008// TI - Estimating local ancestry in admixed populations JO - Am J Hum Genet VL - 82 UR - https://doi.org/10.1016/j.ajhg.2007.09.022 DO - 10.1016/j.ajhg.2007.09.022 ID - Sankararaman2008 ER - TY - JOUR AU - Tang, H. AU - Coram, M. AU - Wang, P. AU - Zhu, X. AU - Risch, N. PY - 2006 DA - 2006// TI - Reconstructing genetic ancestry blocks in admixed individuals JO - Am J Hum Genet VL - 79 UR - https://doi.org/10.1086/504302 DO - 10.1086/504302 ID - Tang2006 ER - TY - JOUR AU - Maples, B. K. AU - Gravel, S. AU - Kenny, E. E. AU - Bustamante, C. D. PY - 2013 DA - 2013// TI - RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference JO - Am J Hum Genet VL - 93 UR - https://doi.org/10.1016/j.ajhg.2013.06.020 DO - 10.1016/j.ajhg.2013.06.020 ID - Maples2013 ER - TY - STD TI - Brown R, Pasaniuc B. Enhanced methods for local ancestry assignment in sequenced admixed individuals. PLoS Comput Biol. 2014; 10(4):e1.003555. ID - ref45 ER -