ArticleAmerican journal of human genetics2021
Distinguishing pedigree relationships via multi-way identity by descent sharing and sex-specific genetic maps.
Article in American journal of human genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Single Nucleotide Polymorphisms in Distant Kinship Inference and Forensic Genetic Genealogy.International journal of molecular sciences · 2026Review
- A novel method for across-chromosome phasing without relative data.Bioinformatics (Oxford, England) · 2026Article
- Article
- Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses.HGG advances · 2025Article
- Ancient DNA reveals the population interactions and a Neolithic patrilineal community in Northern Yangtze Region.Nature communications · 2025Article
- Article
- Genomic profiling of a six-generation patrilineal family of the Ming-Qing dynasties in China.iScience · 2025Article
- clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.Genomics, proteomics & bioinformatics · 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
- Reconstructing parent genomes using siblings and other relatives.bioRxiv : the preprint server for biology · 2024Article
- Biobank-scale inference of multi-individual identity by descent and gene conversion.American journal of human genetics · 2024Article
- Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques.bioRxiv : the preprint server for biology · 2024Article
- Biobank-scale inference of multi-individual identity by descent and gene conversion.bioRxiv : the preprint server for biology · 2023Article
- RaPID-Query for fast identity by descent search and genealogical analysis.Bioinformatics (Oxford, England) · 2023Article
- Parent-offspring inference in inbred populations.Molecular ecology resources · 2022Article
- Evaluating the utility of identity-by-descent segment numbers for relatedness inference via information theory and classification.G3 (Bethesda, Md.) · 2022Article
- A machine learning approach for missing persons cases with high genotyping errors.Frontiers in genetics · 2022Article
- Bonsai: An efficient method for inferring large human pedigrees from genotype data.American journal of human genetics · 2021Article
- Rapid, Phase-free Detection of Long Identity-by-Descent Segments Enables Effective Relationship Classification.American journal of human genetics · 2020Article
- A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data.American journal of human genetics · 2020Article
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5 authors.
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Abstract
The proportion of samples with one or more close relatives in a genetic dataset increases rapidly with sample size, necessitating relatedness modeling and enabling pedigree-based analyses. Despite this, relatives are generally unreported and current inference methods typically detect only the degree of relatedness of sample pairs and not pedigree relationships. We developed CREST, an accurate and fast method that identifies the pedigree relationships of close relatives. CREST utilizes identity by descent (IBD) segments shared between a pair of samples and their mutual relatives, leveraging the fact that sharing rates among these individuals differ across pedigree configurations. Furthermore, CREST exploits the profound differences in sex-specific genetic maps to classify pairs as maternally or paternally related-e.g., paternal half-siblings-using the locations of autosomal IBD segments shared between the pair. In simulated data, CREST correctly classifies 91.5%-100% of grandparent-grandchild (GP) pairs, 80.0%-97.5% of avuncular (AV) pairs, and 75.5%-98.5% of half-siblings (HS) pairs compared to PADRE's rates of 38.5%-76.0% of GP, 60.5%-92.0% of AV, 73.0%-95.0% of HS pairs. Turning to the real 20,032 sample Generation Scotland (GS) dataset, CREST identified seven pedigrees with incorrect relationship types or maternal/paternal parent sexes, five of which we confirmed as mistakes, and two with uncertain relationships. After correcting these, CREST correctly determines relationship types for 93.5% of GP, 97.7% of AV, and 92.2% of HS pairs that have sufficient mutual relative data; the parent sex in 100% of HS and 99.6% of GP pairs; and it completes this analysis in 2.8 h including IBD detection in eight threads.
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