ArticleGenetics2025
A rapid accurate approach to inferring pedigrees in endogamous populations.
Article in Genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Recovering the precolonial population structure of Khoe-San descendant populations.Science advances · 2026Article
- IBS-CNN: a novel computer vision-based kinship classification model for high-density SNP microarray.International journal of legal medicine · 2026Article
- Single Nucleotide Polymorphisms in Distant Kinship Inference and Forensic Genetic Genealogy.International journal of molecular sciences · 2026Review
- No evidence for disassortative mating based on HLA in a small-scale, endogamous population.bioRxiv : the preprint server for biology · 2025Article
- COMPADRE: Combined pedigree-aware distant relatedness estimation for improved pedigree reconstruction.American journal of human genetics · 2025Article
- Recovering the pre-colonial population structure of Khoe-San descendant populations.bioRxiv : the preprint server for biology · 2025Article
- clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.Genomics, proteomics & bioinformatics · 2025Article
- Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine.American journal of human genetics · 2024Article
- Increased homozygosity due to endogamy results in fitness consequences in a human population.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RaPID-Query for fast identity by descent search and genealogical analysis.Bioinformatics (Oxford, England) · 2023Article
- Examination of runs of homozygosity in relation to height in an endogamous Namibian population.American journal of biological anthropology · 2023Article
- Hunter-gatherer genomes reveal diverse demographic trajectories during the rise of farming in Eastern Africa.Current biology : CB · 2022Article
- Article
- Bonsai: An efficient method for inferring large human pedigrees from genotype data.American journal of human genetics · 2021Article
- Fast and Robust Identity-by-Descent Inference with the Templated Positional Burrows-Wheeler Transform.Molecular biology and evolution · 2021Article
- Distinguishing pedigree relationships via multi-way identity by descent sharing and sex-specific genetic maps.American journal of human genetics · 2021Article
- RAFFI: Accurate and fast familial relationship inference in large scale biobank studies using RaPID.PLoS genetics · 2021Article
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13 authors.
Funding
Abstract
Accurate reconstruction of pedigrees from genetic data remains a challenging problem. Many relationship categories (e.g. half-sibships vs avuncular) can be difficult to distinguish without external information. Pedigree inference algorithms are often trained on European-descent families in urban locations. Thus, existing methods tend to perform poorly in endogamous populations for which there may be reticulations within the pedigrees and elevated haplotype sharing. We present a simple, rapid algorithm which initially uses only high-confidence first-degree relationships to seed a machine learning step based on summary statistics of identity-by-descent sharing. One of these statistics, our "haplotype score," is novel and can be used to: (1) distinguish half-sibling pairs from avuncular or grandparent-grandchildren pairs; and (2) assign individuals to ancestor vs descendant generation. We test our approach in a sample of 700 individuals from northern Namibia, sampled from an endogamous population called the Himba. Due to a culture of concurrent relationships in the Himba, there is a high proportion of half-sibships. We accurately identify first through fourth-degree relationships and distinguish between various second-degree relationships: half-sibships, avuncular pairs, and grandparent-grandchildren. We further validate our approach in a second African-descent dataset, the Barbados Asthma Genetics Study, and a European-descent founder population from Quebec. Accurate reconstruction of relatives facilitates estimation of allele frequencies, tracing allele trajectories, improved phasing, heritability and other population genomic questions.
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