ArticleEuropean journal of human genetics : EJHG2013
Using identity by descent estimation with dense genotype data to detect positive selection.
Article in European journal of human genetics : EJHG, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 57 citations in OpenAlex.
- Gene × sex interactions on cognition in the Philadelphia neurodevelopmental cohort.Biology of sex differences · 2026Article
- Identity by descent and local ancestry mapping of HCV spontaneous clearance in populations of diverse ancestries.BMC genomics · 2025Article
- Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations.Bioinformatics (Oxford, England) · 2025Article
- FiMAP: A fast identity-by-descent mapping test for biobank-scale cohorts.PLoS genetics · 2023Article
- Molecular characterization of doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic (BSSS) maize population.Frontiers in plant science · 2023Article
- Single-step genomic prediction of Eucalyptus dunnii using different identity-by-descent and identity-by-state relationship matrices.Heredity · 2021Article
- Genetic influences on externalizing psychopathology overlap with cognitive functioning and show developmental variation.European psychiatry : the journal of the Association of European Psychiatrists · 2021Article
- Genetic influence on cognitive development between childhood and adulthood.Molecular psychiatry · 2021Article
- Correspondence Between Genomic- and Genealogical/Coalescent-Based Inference of Homozygosity by Descent in Large French-Canadian Genealogies.Frontiers in genetics · 2021Article
- Probabilistic Estimation of Identity by Descent Segment Endpoints and Detection of Recent Selection.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
- Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners.Frontiers in genetics · 2020Review
- Kinpute: using identity by descent to improve genotype imputation.Bioinformatics (Oxford, England) · 2019Article
- Detecting the dominance component of heritability in isolated and outbred human populations.Scientific reports · 2018Article
- Analysis of type 2 diabetes and obesity genetic variants in Mexican Pima Indians: Marked allelic differentiation among Amerindians at HLA.Annals of human genetics · 2018Article
- Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens.PLoS genetics · 2018Article
- Molecular Population Genetics.Genetics · 2017Review
- Robust Inference of Identity by Descent from Exome-Sequencing Data.American journal of human genetics · 2016Article
- Conflation of Short Identity-by-Descent Segments Bias Their Inferred Length Distribution.G3 (Bethesda, Md.) · 2016Article
- Pairwise Kinship Analysis by the Index of Chromosome Sharing Using High-Density Single Nucleotide Polymorphisms.PloS one · 2016Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Identification of genomic loci and segments that are identical by descent (IBD) allows inference on problems such as relatedness detection, IBD disease mapping, heritability estimation and detection of recent or ongoing positive selection. Here, employing a novel statistical method, we use IBD to find signals of selection in the Maasai from Kinyawa, Kenya (MKK). In doing so, we demonstrate the advantage of statistical tools that can probabilistically estimate IBD sharing without having to thin genotype data because of linkage disequilibrium (LD), and that allow for both inbreeding and more than one allele to be shared IBD. We use our novel method, GIBDLD, to estimate IBD sharing between all pairs of individuals at all genotyped SNPs in the MKK, and, by looking for genomic regions showing excess IBD sharing in unrelated pairs, find loci that are known to have undergone recent selection (eg, the LCT gene and the HLA region) as well as many novel loci. Intriguingly, those loci that show the highest amount of excess IBD, with the exception of HLA, also show a substantial number of unrelated pairs sharing all four of their alleles IBD. In contrast to other IBD detection methods, GIBDLD provides accurate probabilistic estimates at each locus for all nine possible IBD sharing states between a pair of individuals, thus allowing for consanguinity, while also modeling LD, thus removing the need to thin SNPs. These characteristics will prove valuable for those doing genetic studies, and estimating IBD, in the wide variety of human populations.
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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.