ArticleGenetics2012
Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- The Soifua Manuia reference panel with 2,570 Samoan haplotypes improves genotype imputation quality among Samoans.Communications biology · 2026Article
- Structural Variant Imputation in Samoans Using a Population-Specific Reference Panel.medRxiv : the preprint server for health sciences · 2026Article
- Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs.BMC genomics · 2021Article
- Current Developments in Detection of Identity-by-Descent Methods and Applications.Frontiers in genetics · 2021Review
- Identity-by-descent detection across 487,409 British samples reveals fine scale population structure and ultra-rare variant associations.Nature communications · 2020Article
- Evolutionary history of modern Samoans.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling.Genetics, selection, evolution : GSE · 2020Article
- Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data.BMC genomics · 2020Article
- Kinpute: using identity by descent to improve genotype imputation.Bioinformatics (Oxford, England) · 2019Article
- Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions.PLoS genetics · 2019Article
- A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals.Genetics, selection, evolution : GSE · 2017Article
- A method for the allocation of sequencing resources in genotyped livestock populations.Genetics, selection, evolution : GSE · 2017Article
- Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution.G3 (Bethesda, Md.) · 2016Article
- Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins.Nature communications · 2014Article
- Inference of identity by descent in population isolates and optimal sequencing studies.European journal of human genetics : EJHG · 2013Article
- Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage.BMC genomics · 2013Article
- Article
- Imputation of high-density genotypes in the Fleckvieh cattle population.Genetics, selection, evolution : GSE · 2013Article
- Imputation of rare variants in next-generation association studies.Human heredity · 2012Article
- DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation.American journal of human genetics · 2011Article
Corrections and comments
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome sequencing in an isolated population with few founders directly ascertains variants from the population bottleneck that may be rare elsewhere. In such populations, shared haplotypes allow imputation of variants in unsequenced samples without resorting to complex statistical methods as in studies of outbred cohorts. We focus on an isolated population cohort from the Pacific Island of Kosrae, Micronesia, where we previously collected SNP array and rich phenotype data for the majority of the population. We report identification of long regions with haplotypes co-inherited between pairs of individuals and methodology to leverage such shared genetic content for imputation. Our estimates show that sequencing as few as 40 personal genomes allows for inference in up to 60% of the 3000-person cohort at the average locus. We ascertained a pilot data set of whole-genome sequences from seven Kosraean individuals, with average 5× coverage. This assay identified 5,735,306 unique sites of which 1,212,831 were previously unknown. Additionally, these variants are unusually enriched for alleles that are rare in other populations when compared to geographic neighbors (published Korean genome SJK). We used the presence of shared haplotypes between the seven Kosraen individuals to estimate expected imputation accuracy of known and novel homozygous variants at 99.6% and 97.3%, respectively. This study presents whole-genome analysis of a homogenous isolate population with emphasis on optimal rare variant inference.
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