ArticleAmerican journal of human genetics2013
Detecting identity by descent and estimating genotype error rates in sequence data.
Article in American journal of human genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers.
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Who cites it
119 citing papers in PubMed.
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- Population-scale genomic medicine with the Hong Kong Genome Project.Nature medicine · 2026Article
- Systematic analysis of loss-of-function variants across MODY genes demonstrates gene-specific effects and expands the spectrum of INS variants causing MODY.Diabetologia · 2026Article
- Article
- Population discontinuity in the Paris Basin linked to evidence of the Neolithic decline.Nature ecology & evolution · 2026Article
- Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Across Urban, Rural, and Forested Environments in Gabon.Molecular ecology · 2026Article
- Distinct Genetic Footprint of Adaptation Observed WithinResearch and reports in tropical medicine · 2026Article
- Genetic characterization of commercial spring maize germplasm in Northern China for hybrid breeding and trait improvement.Frontiers in plant science · 2026Article
- TS-IBD: An efficient ancestral recombination graph-based identity by descent segment detection method.Human population genetics and genomics · 2026Article
- Identifying Single-Origin Rare Variants in Population Genomic Data.Molecular biology and evolution · 2025Article
- Inferring Domestic Goat Demographic History Through Ancient Genome Imputation.Genome biology and evolution · 2025Article
- Article
- Identity-By-Descent Mapping Using Multi-Individual IBD With Genome-Wide Multiple Testing Adjustment.Genetic epidemiology · 2025Article
- The genomic footprints of migration: how ancient DNA reveals our history of mobility.Genome biology · 2025Review
- clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.Genomics, proteomics & bioinformatics · 2025Article
- Article
- Neanderthal introgressed ancestry reveals human genomic regions enriched with recessive deleterious mutations.bioRxiv : the preprint server for biology · 2025Article
- Estimating effective population size trajectories from time-series identity-by-descent segments.Genetics · 2025Article
- The population genetics of convergent adaptation in maize and teosinte is not locally restricted.eLife · 2025Article
- A likelihood ratio framework for inferring close kinship from dynamically selected SNPs.Frontiers in genetics · 2025Article
59 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Existing methods for identity by descent (IBD) segment detection were designed for SNP array data, not sequence data. Sequence data have a much higher density of genetic variants and a different allele frequency distribution, and can have higher genotype error rates. Consequently, best practices for IBD detection in SNP array data do not necessarily carry over to sequence data. We present a method, IBDseq, for detecting IBD segments in sequence data and a method, SEQERR, for estimating genotype error rates at low-frequency variants by using detected IBD. The IBDseq method estimates probabilities of genotypes observed with error for each pair of individuals under IBD and non-IBD models. The ratio of estimated probabilities under the two models gives a LOD score for IBD. We evaluate several IBD detection methods that are fast enough for application to sequence data (IBDseq, Beagle Refined IBD, PLINK, and GERMLINE) under multiple parameter settings, and we show that IBDseq achieves high power and accuracy for IBD detection in sequence data. The SEQERR method estimates genotype error rates by comparing observed and expected rates of pairs of homozygote and heterozygote genotypes at low-frequency variants in IBD segments. We demonstrate the accuracy of SEQERR in simulated data, and we apply the method to estimate genotype error rates in sequence data from the UK10K and 1000 Genomes projects.
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