These authors contributed equally to this work.
Accurate Imputation of Rare and Common Variants in a Founder Population From a Small Number of Sequenced Individuals
Article first published online: 28 MAR 2012
© 2012 Wiley-Liss, Inc.
Volume 36, Issue 4, pages 312–319, May 2012
How to Cite
Uricchio, L. H., Chong, J. X., Ross, K. D., Ober, C. and Nicolae, D. L. (2012), Accurate Imputation of Rare and Common Variants in a Founder Population From a Small Number of Sequenced Individuals. Genet. Epidemiol., 36: 312–319. doi: 10.1002/gepi.21623
Open source software will be made available to interested parties by e-mail request.
- Issue published online: 26 APR 2012
- Article first published online: 28 MAR 2012
- Manuscript Accepted: 9 JAN 2012
- Manuscript Revised: 4 JAN 2012
- Manuscript Received: 5 OCT 2011
- Exome sequencing;
- association study;
- IBD calculation;
- complex pedigrees;
Advances in DNA sequencing technologies have greatly facilitated the discovery of rare genetic variants in the human genome, many of which may contribute to common disease risk. However, evaluating their individual or even collective effects on disease risk requires very large sample sizes, which involves study designs that are often prohibitively expensive. We present an alternative approach for determining genotypes in large numbers of individuals for all variants discovered in the sequence of relatively few individuals. Specifically, we developed a new imputation algorithm that utilizes whole-exome sequencing data from 25 members of the South Dakota Hutterite population, and genome-wide single nucleotide polymorphism (SNP) genotypes from >1,400 individuals from the same founder population. The algorithm relies on identity-by-descent sharing of phased haplotypes, a different strategy than the linkage disequilibrium methods found in most imputation algorithms. We imputed genotypes discovered in the sequence data to on average ∼77% of chromosomes among the 1,400 individuals. Median R2 between imputed and directly genotyped data was >0.99. As expected, many variants that are vanishingly rare in European populations have risen to larger frequencies in the founder population and would be amenable to single-SNP analyses. Genet. Epidemiol. 36:312–319, 2012. © 2012 Wiley Periodicals, Inc.