Parente2: a fast and accurate method for detecting identity by descent
Online Publication Date2014-10-01
Print Publication Date2015-02
Permanent link to this recordhttp://hdl.handle.net/10754/599140
MetadataShow full item record
AbstractIdentity-by-descent (IBD) inference is the problem of establishing a genetic connection between two individuals through a genomic segment that is inherited by both individuals from a recent common ancestor. IBD inference is an important preceding step in a variety of population genomic studies, ranging from demographic studies to linking genomic variation with phenotype and disease. The problem of accurate IBD detection has become increasingly challenging with the availability of large collections of human genotypes and genomes: Given a cohort's size, a quadratic number of pairwise genome comparisons must be performed. Therefore, computation time and the false discovery rate can also scale quadratically. To enable accurate and efficient large-scale IBD detection, we present Parente2, a novel method for detecting IBD segments. Parente2 is based on an embedded log-likelihood ratio and uses a model that accounts for linkage disequilibrium by explicitly modeling haplotype frequencies. Parente2 operates directly on genotype data without the need to phase data prior to IBD inference. We evaluate Parente2's performance through extensive simulations using real data, and we show that it provides substantially higher accuracy compared to previous state-of-the-art methods while maintaining high computational efficiency.
CitationRodriguez JM, Bercovici S, Huang L, Frostig R, Batzoglou S (2014) Parente2: a fast and accurate method for detecting identity by descent. Genome Res 25: 280–289. Available: http://dx.doi.org/10.1101/gr.173641.114.
SponsorsThis material is based upon work supported in part by the National Science Foundation Graduate Research Fellowship under grant no. DGE-1147470. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. This work is also supported by a grant from the Stanford-KAUST alliance for academic excellence. L.H. was supported in part by a Stanford Graduate Fellowship. We thank Dorna Kashef-Haghighi for producing Figure 1.
PublisherCold Spring Harbor Laboratory
PubMed Central IDPMC4315301
CollectionsPublications Acknowledging KAUST Support
- Fast and Accurate Shared Segment Detection and Relatedness Estimation in Un-phased Genetic Data via TRUFFLE.
- Authors: Dimitromanolakis A, Paterson AD, Sun L
- Issue date: 2019 Jul 3
- HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination.
- Authors: Zhang K, Sun F, Zhao H
- Issue date: 2005 Jan 1
- Haplotype reconstruction in large pedigrees with untyped individuals through IBD inference.
- Authors: Li X, Li J
- Issue date: 2011 Nov
- Reducing pervasive false-positive identical-by-descent segments detected by large-scale pedigree analysis.
- Authors: Durand EY, Eriksson N, McLean CY
- Issue date: 2014 Aug
- Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies.
- Authors: Levine AP, Connor TM, Oygar DD, Neild GH, Segal AW, Maxwell PH, Gale DP
- Issue date: 2015 Mar 10