Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold

Bioinformatics

Volumn 29, Issue 1, 2013, Pages 84-91

  Menelaou, Androniki ^a   Marchini, Jonathan ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ALLELE; ARTICLE; CHROMOSOME 20; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENOTYPE; GENOTYPING TECHNIQUE; HAPLOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ALLELES; CHROMOSOMES, HUMAN, PAIR 20; GENE FREQUENCY; GENOTYPE; GENOTYPING TECHNIQUES; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84871736050     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts632     Document Type: Article

References (28)

1. Beckmann, L. (2010) Haplotype sharing methods. In Encyclopedia of Life Sciences. John Wiley & Sons, Ltd, Chichester.
2. Browning, B.L. and Browning, S.R. (2009) A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet., 84, 210-223.
3. Chapman, J. et al. (2003) Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum. Hered., 56, 18-31. (Pubitemid 37465067)
4. Coop, G. et al. (2010) Using environmental correlations to identify loci underlying local adaptation. Genetics, 185, 1411-1423.
5. Delaneau, O. et al. (2011) A linear complexity phasing method for thousands of genomes. Nat. Methods, 9, 179-181.
6. Golub, G.H. and Van Loan, C.F. (1996) Matrix computations. 3rd edn. John Hopkins University Press, Baltimore, MD.
7. He, D. et al. (2012) Hap-seq: an optimal algorithm for haplotype phasing with imputation using sequencing data. Lect. Notes Comput. Sci., 7262, 64-78.
8. Howie, B. et al. (2011) Genotype imputation with thousands of genomes. G3 (Bethesda, Md.), 1, 457-470.
9. Howie, B.N. et al. (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS. Genet., 5, e1000529.
10. International HapMap 3 Consortium (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52-58.
11. Kim, S.Y. et al. (2010) Design of association studies with pooled or un-pooled next-generation sequencing data. Genet. Epidemiol., 34, 479-491.
12. Kong, A. et al. (2008) Detection of sharing by descent, long-range phasing and haplotype imputation. Nat. Genet., 40, 1068-1075.
13. Le, S.Q. and Durbin, R. (2011) SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res., 21, 952-960.
14. Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
15. Li, J. and Jiang, T. (2005) Haplotype-based linkage disequilibrium mapping via direct data mining. Bioinformatics, 21, 4384-4393. (Pubitemid 41782929)
16. Li, Y. et al. (2011) Low-coverage sequencing: implications for design of complex trait association studies. Genome Res., 21, 940-951.
17. Li, Y. et al. (2010) Mach: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol., 34, 816-834.
18. Manolio, T.A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
19. Marchini, J. and Howie, B. (2010) Genotype imputation for genome-wide association studies. Nat. Rev. Genet., 11, 499-511.
20. Marchini, J. et al. (2007) A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet., 39, 906-913. (Pubitemid 47014502)
21. McCarthy, M.I. et al. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet., 9, 356-369. (Pubitemid 351556063)
22. Nicholson, G. et al. (2002) Assessing population differentiation and isolation from single-nucleotide polymorphism data. J. R. Stat. Soc. B, 64, 695-715.
23. O'Connell, J. and Marchini, J. (2012) Joint genotype calling with array and sequence data. Genet. Epidemiol., 36, 527-537.
24. Pasaniuc, B. et al. (2012) Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat. Genet., 44, 631-635.
25. Stephens, M. and Donnelly, P. (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum Genet., 73, 1162-1169. (Pubitemid 37414228)
26. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65.
27. Tychonoff, A.N. (1943) On the stability of inverse problems. Doklady. Akademii. Nauk. SSSR, 39, 195-198.
28. Wen, X. and Stephens, M. (2010) Using linear predictors to impute allele frequencies from summary or pooled genotype data. Ann. Appl. Stat., 4, 1158-1182.