期刊
NATURE COMMUNICATIONS
卷 5, 期 -, 页码 -出版社
NATURE PORTFOLIO
DOI: 10.1038/ncomms4934
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资金
- Medical Research Council [G0801823]
- BBSRC [BB/I02593X/1] Funding Source: UKRI
- MRC [G0801823] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/I02593X/1] Funding Source: researchfish
- Medical Research Council [G0801823] Funding Source: researchfish
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. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants.
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