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Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

Publication ,  Journal Article
Delaneau, O; Marchini, J; 1000 Genomes Project Consortium,
Published in: Nature communications
June 2014

A major use of the 1000 Genomes Project (1000 GP) 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 1000 GP 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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Published In

Nature communications

DOI

EISSN

2041-1723

ISSN

2041-1723

Publication Date

June 2014

Volume

5

Start / End Page

3934

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Microarray Analysis
  • Humans
  • Haplotypes
  • Genome-Wide Association Study
  • Genome, Human
  • Gene Frequency
  • Alleles
  • Algorithms
 

Citation

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Delaneau, O., Marchini, J., & 1000 Genomes Project Consortium, . (2014). Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature Communications, 5, 3934. https://doi.org/10.1038/ncomms4934
Delaneau, Olivier, Jonathan Marchini, and Jonathan 1000 Genomes Project Consortium. “Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.Nature Communications 5 (June 2014): 3934. https://doi.org/10.1038/ncomms4934.
Delaneau O, Marchini J, 1000 Genomes Project Consortium. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature communications. 2014 Jun;5:3934.
Delaneau, Olivier, et al. “Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.Nature Communications, vol. 5, June 2014, p. 3934. Epmc, doi:10.1038/ncomms4934.
Delaneau O, Marchini J, 1000 Genomes Project Consortium. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature communications. 2014 Jun;5:3934.

Published In

Nature communications

DOI

EISSN

2041-1723

ISSN

2041-1723

Publication Date

June 2014

Volume

5

Start / End Page

3934

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Microarray Analysis
  • Humans
  • Haplotypes
  • Genome-Wide Association Study
  • Genome, Human
  • Gene Frequency
  • Alleles
  • Algorithms