ArticleBioinformatics (Oxford, England)2010
Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Accurate detection of identity-by-descent segments in human ancient DNA.Nature genetics · 2024Article
- Integrating omics for a better understanding of Inflammatory Bowel Disease: a step towards personalized medicine.Journal of translational medicine · 2019Review
- RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts.Genome biology · 2019Article
- Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype.PLoS computational biology · 2017Article
- An efficient method to handle the 'large p, small n' problem for genomewide association studies using Haseman-Elston regression.Journal of genetics · 2016Article
- PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population.PLoS computational biology · 2015Article
- Parente2: a fast and accurate method for detecting identity by descent.Genome research · 2015Article
- Relatedness in the post-genomic era: is it still useful?Nature reviews. Genetics · 2015Review
- Using haplotypes for the prediction of allelic identity to fine-map QTL: characterization and properties.Genetics, selection, evolution : GSE · 2014Article
- Deciphering the fine-structure of tribal admixture in the Bedouin population using genomic data.Heredity · 2014Article
- An effective filter for IBD detection in large data sets.PloS one · 2014Article
- Detection of identity by descent using next-generation whole genome sequencing data.BMC bioinformatics · 2012Article
- Detecting rare variant associations by identity-by-descent mapping in case-control studies.Genetics · 2012Article
- Obtaining accurate p values from a dense SNP linkage scan.Human heredity · 2012Article
- Integration of SNP genotyping confidence scores in IBD inference.Bioinformatics (Oxford, England) · 2011Article
- Reconstruction of genealogical relationships with applications to Phase III of HapMap.Bioinformatics (Oxford, England) · 2011Article
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4 authors.
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Abstract
motivationAssociation analysis is the method of choice for studying complex multifactorial diseases. The premise of this method is that affected persons contain some common genomic regions with similar SNP alleles and such areas will be found in this analysis. An important disadvantage of GWA studies is that it does not distinguish between genomic areas that are inherited from a common ancestor [identical by descent (IBD)] and areas that are identical merely by state [identical by state (IBS)]. Clearly, areas that can be marked with higher probability as IBD and have the same correlation with the disease status of identical areas that are more probably only IBS, are better candidates to be causative, and yet this distinction is not encoded in standard association analysis.
resultsWe develop a factorial hidden Markov model-based algorithm for computing genome-wide IBD sharing. The algorithm accepts as input SNP data of measured individuals and estimates the probability of IBD at each locus for every pair of individuals. For two g-degree relatives, when g > or = 8, the computation yields a precision of IBD tagging of over 50% higher than previous methods for 95% recall. Our algorithm uses a first-order Markovian model for the linkage disequilibrium process and employs a reduction of the state space of the inheritance vector from being exponential in g to quadratic. The higher accuracy along with the reduced time complexity marks our method as a feasible means for IBD mapping in practical scenarios. AVAILABILITY: A software implementation, called IBDMAP, is freely available at http://bioinfo.cs.technion.ac.il/IBDmap.
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