Parente2: a fast and accurate method for detecting identity by descent

Handle URI:
http://hdl.handle.net/10754/599140
Title:
Parente2: a fast and accurate method for detecting identity by descent
Authors:
Rodriguez, Jesse M.; Bercovici, Sivan; Huang, Lin; Frostig, Roy; Batzoglou, Serafim
Abstract:
Identity-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.
Citation:
Rodriguez 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.
Publisher:
Cold Spring Harbor Laboratory Press
Journal:
Genome Research
Issue Date:
1-Oct-2014
DOI:
10.1101/gr.173641.114
PubMed ID:
25273070
PubMed Central ID:
PMC4315301
Type:
Article
ISSN:
1088-9051; 1549-5469
Sponsors:
This 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.
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Full metadata record

DC FieldValue Language
dc.contributor.authorRodriguez, Jesse M.en
dc.contributor.authorBercovici, Sivanen
dc.contributor.authorHuang, Linen
dc.contributor.authorFrostig, Royen
dc.contributor.authorBatzoglou, Serafimen
dc.date.accessioned2016-02-25T13:53:37Zen
dc.date.available2016-02-25T13:53:37Zen
dc.date.issued2014-10-01en
dc.identifier.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.en
dc.identifier.issn1088-9051en
dc.identifier.issn1549-5469en
dc.identifier.pmid25273070en
dc.identifier.doi10.1101/gr.173641.114en
dc.identifier.urihttp://hdl.handle.net/10754/599140en
dc.description.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.en
dc.description.sponsorshipThis 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.en
dc.publisherCold Spring Harbor Laboratory Pressen
dc.subject.meshPedigreeen
dc.titleParente2: a fast and accurate method for detecting identity by descenten
dc.typeArticleen
dc.identifier.journalGenome Researchen
dc.identifier.pmcidPMC4315301en
dc.contributor.institutionBiomedical Informatics Program.en
dc.contributor.institutionDepartment of Computer Science, Stanford University, Stanford, California 94305, USA.en

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