ArticleGenetics2012
Inferring coancestry in population samples in the presence of linkage disequilibrium.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Exploring how space, time, and sampling impact our ability to measure genetic structure acrossFrontiers in epidemiology · 2023Article
- Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing.International journal of molecular sciences · 2021Review
- A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data.American journal of human genetics · 2020Article
- Estimating Relatedness Between Malaria Parasites.Genetics · 2019Article
- Correlations between relatives: From Mendelian theory to complete genome sequence.Genetic epidemiology · 2019Article
- Efficient Estimation of Realized Kinship from Single Nucleotide Polymorphism Genotypes.Genetics · 2017Article
- Identity by descent fine mapping of familial adult myoclonus epilepsy (FAME) to 2p11.2-2q11.2.Human genetics · 2016Article
- Pedigree-Free Descent-Based Gene Mapping from Population Samples.Human heredity · 2015Article
- A renewal theory approach to IBD sharing.Theoretical population biology · 2014Article
- Reducing pervasive false-positive identical-by-descent segments detected by large-scale pedigree analysis.Molecular biology and evolution · 2014Article
- Genome-wide patterns of identity-by-descent sharing in the French Canadian founder population.European journal of human genetics : EJHG · 2014Article
- Bayesian inference of local trees along chromosomes by the sequential Markov coalescent.Journal of molecular evolution · 2014Article
- Joint inference of identity by descent along multiple chromosomes from population samples.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Combining information from linkage and association mapping for next-generation sequencing longitudinal family data.BMC proceedings · 2014Article
- Efficient identification of equivalences in dynamic graphs and pedigree structures.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Review
- Improving the accuracy and efficiency of identity-by-descent detection in population data.Genetics · 2013Article
- Article
- The geography of recent genetic ancestry across Europe.PLoS biology · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
In both pedigree linkage studies and in population-based association studies there has been much interest in the use of modern dense genetic marker data to infer segments of gene identity by descent (ibd) among individuals not known to be related, to increase power and resolution in localizing genes affecting complex traits. In this article, we present a hidden Markov model (HMM) for ibd among a set of chromosomes and describe methods and software for inference of ibd among the four chromosomes of pairs of individuals, using either phased (haplotypic) or unphased (genotypic) data. The model allows for missing data and typing error, but does not model linkage disequilibrium (LD), because fitting an accurate LD model requires large samples from well-studied populations. However, LD remains a major confounding factor, since LD is itself a reflection of coancestry at the population level. To study the impact of LD, we have developed a novel simulation approach to generate realistic dense marker data for the same set of markers but at varying levels of LD. Using this approach, we present results of a study of the impact of LD on the sensitivity and specificity of our HMM model in estimating segments of ibd among sets of four chromosomes and between genotype pairs. We show that, despite not incorporating LD, our model has been quite successful in detecting segments as small as 10(6) bp (1 Mpb); we present also comparisons with fastIBD which uses an LD model in estimating ibd.
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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.