ArticleGenetic epidemiology2012
Accurate imputation of rare and common variants in a founder population from a small number of sequenced individuals.
Article in Genetic epidemiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Current Developments in Detection of Identity-by-Descent Methods and Applications.Frontiers in genetics · 2021Review
- Kinpute: using identity by descent to improve genotype imputation.Bioinformatics (Oxford, England) · 2019Article
- Characterization of a Unique Form of Arrhythmic Cardiomyopathy Caused by Recessive Mutation in LEMD2.JACC. Basic to translational science · 2019Article
- Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy.Scientific reports · 2019Article
- Assigning breed origin to alleles in crossbred animals.Genetics, selection, evolution : GSE · 2016Article
- PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population.PLoS computational biology · 2015Article
- Using population isolates in genetic association studies.Briefings in functional genomics · 2014Review
- Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma.PloS one · 2014Article
- Robust rare variant association testing for quantitative traits in samples with related individuals.Genetic epidemiology · 2014Article
- Article
- The value of extended pedigrees for next-generation analysis of complex disease in the rhesus macaque.ILAR journal · 2013Review
- Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies.PloS one · 2013Article
- A population-based study of autosomal-recessive disease-causing mutations in a founder population.American journal of human genetics · 2012Article
- Genome-wide association study identifies candidate genes for male fertility traits in humans.American journal of human genetics · 2012Article
- Imputation of rare variants in next-generation association studies.Human heredity · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
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 R(2) 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.
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