Journal article
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
O Delaneau, J Marchini, GA McVeanh, P Donnelly, G Lunter, S Myers, A Gupta-Hinch, Z Iqbal, I Mathieson, A Rimmer, DK Xifara, A Kerasidou, C Churchhouse, DM Altshuler, SB Gabriel, ES Lander, N Gupta, MJ Daly, MA DePristo, E Banks Show all
Nature Communications | NATURE PORTFOLIO | Published : 2014
DOI: 10.1038/ncomms4934
Abstract
A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community...
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Awarded by UK Research and Innovation
Funding Acknowledgements
J.M. and O.D. acknowledge support from the Medical Research Council (G0801823). We thank Androniki Menelaou, Bryan Howie and members of the 1000 Genomes analysis group for their comments.