ArticleAmerican journal of human genetics2020
Rapid, Phase-free Detection of Long Identity-by-Descent Segments Enables Effective Relationship Classification.
Article in American journal of human genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Blocks of Identity by Descent Reveal the Dual Role Played by Reef Fish Larvae for Retention and Dispersal.Molecular ecology · 2026Article
- IBS-CNN: a novel computer vision-based kinship classification model for high-density SNP microarray.International journal of legal medicine · 2026Article
- Bioarchaeological analysis illustrates the life of a 16th-century Sámi individual from Kitka, Kuusamo, northern Finland.BMC genomics · 2026Article
- Census and genetic analysis of the United States marmoset population.bioRxiv : the preprint server for biology · 2026Article
- Exome sequencing and analysis of 44,028 British South Asians enriched for high autozygosity.Nature genetics · 2026Article
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- Comparative assessment of SNP genotyping assays for challenging forensic samples utilizing ancient DNA methods.Genome biology · 2025Article
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- COMPADRE: Combined pedigree-aware distant relatedness estimation for improved pedigree reconstruction.American journal of human genetics · 2025Article
- Use of Estonian Biobank data and participant recall to improve Wilson's disease management.European journal of human genetics : EJHG · 2025Article
- STREAM-PRS: a multi-tool pipeline for streamlining polygenic risk score computation.Genome medicine · 2025Article
- Genotype imputation from low-coverage data for medical and population genetic analyses.Genome research · 2025Article
- Power and Limitations of Inferring Genetic Ancestry.Annals of human genetics · 2025Review
- Archaeogenetics reveals fine-scale genetic continuity and patterns of kinship and health in medieval Finland.iScience · 2025Article
- Article
- clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.Genomics, proteomics & bioinformatics · 2025Article
- Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden.Genome biology · 2025Article
- Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A likelihood ratio framework for inferring close kinship from dynamically selected SNPs.Frontiers in genetics · 2025Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Identity-by-descent (IBD) segments are a useful tool for applications ranging from demographic inference to relationship classification, but most detection methods rely on phasing information and therefore require substantial computation time. As genetic datasets grow, methods for inferring IBD segments that scale well will be critical. We developed IBIS, an IBD detector that locates long regions of allele sharing between unphased individuals, and benchmarked it with Refined IBD, GERMLINE, and TRUFFLE on 3,000 simulated individuals. Phasing these with Beagle 5 takes 4.3 CPU days, followed by either Refined IBD or GERMLINE segment detection in 2.9 or 1.1 h, respectively. By comparison, IBIS finishes in 6.8 min or 7.8 min with IBD2 functionality enabled: speedups of 805-946× including phasing time. TRUFFLE takes 2.6 h, corresponding to IBIS speedups of 20.2-23.3×. IBIS is also accurate, inferring ≥7 cM IBD segments at quality comparable to Refined IBD and GERMLINE. With these segments, IBIS classifies first through third degree relatives in real Mexican American samples at rates meeting or exceeding other methods tested and identifies fourth through sixth degree pairs at rates within 0.0%-2.0% of the top method. While allele frequency-based approaches that do not detect segments can infer relationship degrees faster than IBIS, the fastest are biased in admixed samples, with KING inferring 30.8% fewer fifth degree Mexican American relatives correctly compared with IBIS. Finally, we ran IBIS on chromosome 2 of the UK Biobank dataset and estimate its runtime on the autosomes to be 3.3 days parallelized across 128 cores.
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