Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Jun 17;8(Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo):S16.
doi: 10.1186/1753-6561-8-S1-S16. eCollection 2014.

Imputation in families using a heuristic phasing approach

August N Blackburn  1 , Angela K Dean  2 , Donna M Lehman  2
Affiliations

Imputation in families using a heuristic phasing approach

August N Blackburn et al. BMC Proc. .

Abstract

Whole genome sequencing (WGS) remains prohibitively expensive, which has encouraged the development of methods to impute WGS data into nonsequenced individuals using a framework of single nucleotide polymorphisms genotyped for genome-wide association studies (GWAS). Although successful methods have been developed for cohorts of unrelated individuals, current imputation methods in related individuals are limited by pedigree size, by the distance of relationships, or by computation time. In this article, we describe a method for imputation in arbitrarily shaped multigenerational pedigrees that can impute genotypes across distantly related individuals based on identity by descent. We evaluate this approach using GWAS data and apply this approach to WGS data distributed for Genetic Analysis Workshop 18.

PubMed Disclaimer

Figures

Figure 1
Figure 1
An example pedigree partially simulated from pedigree 10 from Genetic Analysis Workshop 18 data. Founders are shown in red, individuals carrying nonfounding chromosomes that are the product of a single meiosis are shown in blue, and individuals carrying nonfounding chromosomes that are products of two or more meioses are shown in yellow.
See this image and copyright information in PMC

References

    1. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet. 2012;44:955–959. doi: 10.1038/ng.2354. - DOI - PMC - PubMed
    1. Abecasis GR, Cherny SS, Cookson WO, Cardon LR. Merlin--rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet. 2002;30:97–101. doi: 10.1038/ng786. - DOI - PubMed
    1. Chen GK, Wang K, Stram AH, Sobel EM, Lange K. Mendel-GPU: haplotyping and genotype imputation on graphics processing units. Bioinformatics. 2012;28:2979–2980. doi: 10.1093/bioinformatics/bts536. - DOI - PMC - PubMed
    1. Wijsman EM, Rothstein JH, Thompson EA. Multipoint linkage analysis with many multiallelic or dense diallelic markers: Markov chain-Monte Carlo provides practical approaches for genome scans on general pedigrees. Am J Hum Genet. 2006;79:846–858. doi: 10.1086/508472. - DOI - PMC - PubMed
    1. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST. et al.The variant call format and VCFtools. Bioinformatics. 2011;27:2156–2158. doi: 10.1093/bioinformatics/btr330. - DOI - PMC - PubMed

LinkOut - more resources