Genotype Imputation with Millions of Reference Samples

American Journal of Human Genetics

Volumn 98, Issue 1, 2016, Pages 116-126

  Browning, Brian L ^a   Browning, Sharon R ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BEAGLE; COMPUTER; CONTROLLED STUDY; GENETIC VARIABILITY; GENOTYPE; INFORMATION PROCESSING; MEMORY; NONHUMAN; PRIORITY JOURNAL; REFERENCE DATABASE; SIMULATION; VELOCITY; GENETIC DATABASE; STANDARD;

DATABASES, GENETIC; GENOTYPE; REFERENCE STANDARDS;

EID: 84954234248     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2015.11.020     Document Type: Article

References (28)

1. J. Marchini, and B. Howie Genotype imputation for genome-wide association studies Nat. Rev. Genet. 11 2010 499 511
2. J. Marchini, B. Howie, S. Myers, G. McVean, and P. Donnelly A new multipoint method for genome-wide association studies by imputation of genotypes Nat. Genet. 39 2007 906 913
3. A.R. Wood, T. Esko, J. Yang, S. Vedantam, T.H. Pers, S. Gustafsson, A.Y. Chu, K. Estrada, J. Luan, Z. Kutalik, et al. Electronic Medical Records and Genomics (eMERGE) Consortium MIGen Consortium PAGE Consortium LifeLines Cohort Study Defining the role of common variation in the genomic and biological architecture of adult human height Nat. Genet. 46 2014 1173 1186
4. E.K. Speliotes, C.J. Willer, S.I. Berndt, K.L. Monda, G. Thorleifsson, A.U. Jackson, H. Lango Allen, C.M. Lindgren, J. Luan, R. Mägi, et al. MAGIC Procardis Consortium Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index Nat. Genet. 42 2010 937 948
5. C.J. Willer, E.M. Schmidt, S. Sengupta, G.M. Peloso, S. Gustafsson, S. Kanoni, A. Ganna, J. Chen, M.L. Buchkovich, S. Mora, et al. Global Lipids Genetics Consortium Discovery and refinement of loci associated with lipid levels Nat. Genet. 45 2013 1274 1283
6. Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
7. K.A. Frazer, D.G. Ballinger, D.R. Cox, D.A. Hinds, L.L. Stuve, R.A. Gibbs, J.W. Belmont, A. Boudreau, P. Hardenbol, S.M. Leal, et al. International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs Nature 449 2007 851 861
8. G.R. Abecasis, D. Altshuler, A. Auton, L.D. Brooks, R.M. Durbin, R.A. Gibbs, M.E. Hurles, G.A. McVean 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
9. G.R. Abecasis, A. Auton, L.D. Brooks, M.A. DePristo, R.M. Durbin, R.E. Handsaker, H.M. Kang, G.T. Marth, G.A. McVean 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes Nature 491 2012 56 65
10. A. Auton, L.D. Brooks, R.M. Durbin, E.P. Garrison, H.M. Kang, J.O. Korbel, J.L. Marchini, S. McCarthy, G.A. McVean, G.R. Abecasis 1000 Genomes Project Consortium A global reference for human genetic variation Nature 526 2015 68 74
11. B.L. Browning, and S.R. Browning A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals Am. J. Hum. Genet. 84 2009 210 223
12. B.N. Howie, P. Donnelly, and J. Marchini A flexible and accurate genotype imputation method for the next generation of genome-wide association studies PLoS Genet. 5 2009 e1000529
13. B.L. Browning, and S.R. Browning Detecting identity by descent and estimating genotype error rates in sequence data Am. J. Hum. Genet. 93 2013 840 851
14. B. Howie, J. Marchini, and M. Stephens Genotype imputation with thousands of genomes G3 (Bethesda) 1 2011 457 470
15. B. Howie, C. Fuchsberger, M. Stephens, J. Marchini, and G.R. Abecasis Fast and accurate genotype imputation in genome-wide association studies through pre-phasing Nat. Genet. 44 2012 955 959
16. N. Li, and M. Stephens Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data Genetics 165 2003 2213 2233
17. Y. Li, C.J. Willer, J. Ding, P. Scheet, and G.R. Abecasis MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes Genet. Epidemiol. 34 2010 816 834
18. L.R. Rabiner A tutorial on Hidden Markov-models and selected applications in speech recognition Proc. IEEE 77 1989 257 286
19. J.A. Grice, R. Hughey, and D. Speck Reduced space sequence alignment Comput. Appl. Biosci. 13 1997 45 53
20. R. Wheeler, and R. Hughey Optimizing reduced-space sequence analysis Bioinformatics 16 2000 1082 1090
21. P. Danecek, A. Auton, G. Abecasis, C.A. Albers, E. Banks, M.A. DePristo, R.E. Handsaker, G. Lunter, G.T. Marth, S.T. Sherry, et al. 1000 Genomes Project Analysis Group The variant call format and VCFtools Bioinformatics 27 2011 2156 2158
22. J. Huang, B. Howie, S. McCarthy, Y. Memari, K. Walter, J.L. Min, P. Danecek, G. Malerba, E. Trabetti, H.F. Zheng, et al. UK10K Consortium Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel Nat. Commun. 6 2015 8111
23. G.K. Chen, P. Marjoram, and J.D. Wall Fast and flexible simulation of DNA sequence data Genome Res. 19 2009 136 142
24. C. Fuchsberger, G.R. Abecasis, and D.A. Hinds minimac2: faster genotype imputation Bioinformatics 31 2015 782 784
25. International HapMap Consortium A haplotype map of the human genome Nature 437 2005 1299 1320
26. S.R. Browning, and B.L. Browning Accurate non-parametric estimation of recent effective population size from segments of identity by descent Am. J. Hum. Genet. 97 2015 404 418
27. M.D. Mailman, M. Feolo, Y. Jin, M. Kimura, K. Tryka, R. Bagoutdinov, L. Hao, A. Kiang, J. Paschall, L. Phan, and et al. The NCBI dbGaP database of genotypes and phenotypes Nat. Genet. 39 2007 1181 1186
28. I. Lappalainen, J. Almeida-King, V. Kumanduri, A. Senf, J.D. Spalding, S. Ur-Rehman, G. Saunders, J. Kandasamy, M. Caccamo, R. Leinonen, and et al. The European Genome-phenome Archive of human data consented for biomedical research Nat. Genet. 47 2015 692 695