Fast and accurate long-range phasing in a UK Biobank cohort

Nature Genetics

Volumn 48, Issue 7, 2016, Pages 811-816

  Loh, Po Ru ^a,b   Palamara, Pier Francesco ^a,b   Price, Alkes L ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CHROMOSOME 1; CHROMOSOME 10; CHROMOSOME 20; COHORT ANALYSIS; DIPLOIDY; EAGLE ALGORITHM; GENE CONVERSION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ALGORITHM; GENOTYPE; GENOTYPING TECHNIQUE; HAPLOTYPE; HETEROZYGOSITY; HIDDEN MARKOV MODEL; HOMOZYGOSITY; HUMAN; HUMAN GENOME; ICELANDER; LABORATORY; LONG RANGE PHASING; MAJOR CLINICAL STUDY; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED KINGDOM; ALGORITHM; BIOBANK; BIOLOGY; CAUCASIAN; DNA SEQUENCE; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; INHERITANCE; PROCEDURES; STATISTICS AND NUMERICAL DATA;

ALGORITHMS; BIOLOGICAL SPECIMEN BANKS; COHORT STUDIES; COMPUTATIONAL BIOLOGY; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETICS, POPULATION; GENOME, HUMAN; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INHERITANCE PATTERNS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; UNITED KINGDOM;

EID: 84976331409     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3571     Document Type: Article

References (49)

1. Browning, S. R. & Browning, B. L. Haplotype phasing: existing methods and new developments. Nat. Rev. Genet. 12, 703-714 (2011).
2. Marchini, J., Howie, B., Myers, S., McVean, G. & Donnelly, P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906-913 (2007).
3. Marchini, J. & Howie, B. Genotype imputation for genome-wide association studies. Nat. Rev. Genet. 11, 499-511 (2010).
4. Li, Y., Willer, C. J., Ding, J., Scheet, P. & Abecasis, G. R. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet. Epidemiol. 34, 816-834 (2010).
5. Howie, B., Fuchsberger, C., Stephens, M., Marchini, J. & Abecasis, G. R. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat. Genet. 44, 955-959 (2012).
6. Stephens, M& Scheet, P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am. J. Hum. Genet. 76, 449-462 (2005).
7. Scheet, P. & Stephens, M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 78, 629-644 (2006).
8. Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084-1097 (2007).
9. Browning, B. L. & Browning, S. R. 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 (2009).
10. Delaneau, O., Marchini, J. & Zagury, J.-F. A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179-181 (2012).
11. Williams, A. L., Patterson, N., Glessner, J., Hakonarson, H. & Reich, D. Phasing of many thousands of genotyped samples. Am. J. Hum. Genet. 91, 238-251 (2012).
12. Delaneau, O., Zagury, J.-F. & Marchini, J. Improved whole-chromosome phasing for disease and population genetic studies. Nat. Methods 10, 5-6 (2013).
13. Kong, A. et al. Detection of sharing by descent, long-range phasing and haplotype imputation. Nat. Genet. 40, 1068-1075 (2008).
14. Stefansson, H. et al. Common variants conferring risk of schizophrenia. Nature 460, 744-747 (2009).
15. Kong, A. et al. Parental origin of sequence variants associated with complex diseases. Nature 462, 868-874 (2009).
16. Kong, A. et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature 467, 1099-1103 (2010).
17. Thorleifsson, G. et al. Common variants near CAV1 and CAV2 are associated with primary open-angle glaucoma. Nat. Genet. 42, 906-909 (2010).
18. Holm, H. et al. A rare variant in MYH6 is associated with high risk of sick sinus syndrome. Nat. Genet. 43, 316-320 (2011).
19. Rafnar, T. et al. Mutations in BRIP1 confer high risk of ovarian cancer. Nat. Genet. 43, 1104-1107 (2011).
20. Gudmundsson, J. et al. Discovery of common variants associated with low TSH levels and thyroid cancer risk. Nat. Genet. 44, 319-322 (2012).
21. Gudmundsson, J. et al. A study based on whole-genome sequencing yields a rare variant at 8q24 associated with prostate cancer. Nat. Genet. 44, 1326-1329 (2012).
22. Helgason, H. et al. A rare nonsynonymous sequence variant in C3 is associated with high risk of age-related macular degeneration. Nat. Genet. 45, 1371-1374 (2013).
23. Kong, A. et al. Common and low-frequency variants associated with genome-wide recombination rate. Nat. Genet. 46, 11-16 (2014).
24. Steinthorsdottir, V. et al. Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes. Nat. Genet. 46, 294-298 (2014).
25. Gudbjartsson, D. F. et al. Large-scale whole-genome sequencing of the Icelandic population. Nat. Genet. 47, 435-444 (2015).
26. Steinberg, S. et al. Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease. Nat. Genet. 47, 445-447 (2015).
27. Helgason, H. et al. Loss-of-function variants in ATM confer risk of gastric cancer. Nat. Genet. 47, 906-910 (2015).
28. Palin, K., Campbell, H., Wright, A. F., Wilson, J. F. & Durbin, R. Identity-by-descent-based phasing and imputation in founder populations using graphical models. Genet. Epidemiol. 35, 853-860 (2011).
29. O'Connell, J. et al. A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genet. 10, e1004234 (2014).
30. Sudlow, C. et al. UK Biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med. 12, e1001779 (2015).
31. Gusev, A. et al. Whole population, genome-wide mapping of hidden relatedness. Genome Res. 19, 318-326 (2009).
32. Browning, B. L. & Browning, S. R. A fast, powerful method for detecting identity by descent. Am. J. Hum. Genet. 88, 173-182 (2011).
33. Browning, B. L. & Browning, S. R. Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194, 459-471 (2013).
34. Banda, Y. et al. Characterizing race/ethnicity and genetic ancestry for 100, 000 subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. Genetics 200, 1285-1295 (2015).
35. Galinsky, K. J. et al. Fast principal-component analysis reveals convergent evolution of ADH1B in Europe and East Asia. Am. J. Hum. Genet. 98, 456-472 (2016).
36. O'Connell, J. et al. Haplotype estimation for biobank-scale data sets. Nat. Genet. http://dx. doi. org/10. 1038/ng. 3583 (2016).
37. Delaneau, O., Howie, B., Cox, A. J., Zagury, J.-F. & Marchini, J. Haplotype estimation using sequencing reads. Am. J. Hum. Genet. 93, 687-696 (2013).
38. Durbin, R. Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT). Bioinformatics 30, 1266-1272 (2014).
39. Browning, B. L. & Browning, S. R. Genotype imputation with millions of reference samples. Am. J. Hum. Genet. 98, 116-126 (2016).
40. Chen, C.-Y. et al. Improved ancestry inference using weights from external reference panels. Bioinformatics 29, 1399-1406 (2013).
41. Henn, B. M. et al. Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples. PLoS One 7, e34267 (2012).
42. Huang, L., Bercovici, S., Rodriguez, J. M. & Batzoglou, S. An effective filter for IBD detection in large data sets. PLoS One 9, e92713 (2014).
43. Rodriguez, J. M., Bercovici, S., Huang, L., Frostig, R. & Batzoglou, S. Parente2: a fast and accurate method for detecting identity by descent. Genome Res. 25, 280-289 (2015).
44. Bulik-Sullivan, B. K. et al. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47, 291-295 (2015).
45. Indyk, P. & Motwani, R. Approximate nearest neighbors: towards removing the curse of dimensionality. in Proc. 30th Ann. ACM Symposium Theory Computing 604-613 (ACM, 1998).
46. Gionis, A., Indyk, P. & Motwani, R. Similarity search in high dimensions via hashing. in Proc. 25th VLDB Conf. vol. 99, 518-529 (Morgan Kaufmann Publishers, 1999).
47. Li, N. & Stephens, M. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165, 2213-2233 (2003).
48. Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4, 7 (2015).
49. Kvale, M. N. et al. Genotyping informatics and quality control for 100, 000 subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. Genetics 200, 1051-1060 (2015).