ArticleGenome research2009
Whole population, genome-wide mapping of hidden relatedness.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 257 papers, 3 of them syntheses that pooled it.
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Who cites it
257 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Population genetic considerations for using biobanks as international resources in the pandemic era and beyond.BMC genomics · 2021Pooled it
- A Prospective Analysis of Genetic Variants Associated with Human Lifespan.G3 (Bethesda, Md.) · 2019Pooled it
- IBS-CNN: a novel computer vision-based kinship classification model for high-density SNP microarray.International journal of legal medicine · 2026Article
- DRIVE v3: Command Line Application for Identity-by-Descent Haplotype Clustering in Large Biobank Scale Data.Genetic epidemiology · 2026Article
- HiFiMAP: High-resolution fast identity-by-descent mapping test.medRxiv : the preprint server for health sciences · 2026Article
- A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis.Genome research · 2026Article
- Leveraging ancestral recombination graphs for scalable mixed-model analysis of complex traits.Cell genomics · 2026Article
- RaPID2: a parallel scalable framework for identity-by-descent segment detection via parallel PBWT.Bioinformatics advances · 2026Article
- 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
- Refining rare disease variant discovery in an isolated Andean community through imputation-enhanced IBD and kinship inference from whole exome sequencing data.Human molecular genetics · 2025Article
- SPC: a SPectral Component approach leveraging Identity-by-Descent graphs to address recent population structure in genomic analysis.medRxiv : the preprint server for health sciences · 2025Article
- Identifying individuals with rare disease variants by inferring shared ancestral haplotypes from SNP array data.NAR genomics and bioinformatics · 2025Article
- Distribution of runs of homozygosity in Lactuca species and its implications for plant breeding and evolutionary conservation.BMC genomics · 2025Article
- EMIBD9: Estimating 9 condensed IBD coefficients, inbreeding and relatedness from marker genotypes.Heredity · 2025Article
- Runs of Homozygosity Preliminary Investigation in Pig Breeds.Animals : an open access journal from MDPI · 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
- Multiple-Wave Admixture and Adaptive Evolution of the Pamirian Wakhi People.Molecular biology and evolution · 2024Article
- Modeling recent positive selection using identity-by-descent segments.American journal of human genetics · 2024Article
197 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on a dictionary of haplotypes that is used to efficiently discover short exact matches between individuals. We then expand these matches using dynamic programming to identify long, nearly identical segmental sharing that is indicative of relatedness. We use GERMLINE to comprehensively survey hidden relatedness both in the HapMap as well as in a densely typed island population of 3000 individuals. We verify that GERMLINE is in concordance with other methods when they can process the data, and also facilitates analysis of larger scale studies. We bolster these results by demonstrating novel applications of precise analysis of hidden relatedness for (1) identification and resolution of phasing errors and (2) exposing polymorphic deletions that are otherwise challenging to detect. This finding is supported by concordance of detected deletions with other evidence from independent databases and statistical analyses of fluorescence intensity not used by GERMLINE.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.