ArticleGenome research2015
Parente2: a fast and accurate method for detecting identity by descent.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
10 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- A Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data.American journal of human genetics · 2020Article
- RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts.Genome biology · 2019Article
- Efficient haplotype matching between a query and a panel for genealogical search.Bioinformatics (Oxford, England) · 2019Article
- Fast and Accurate Shared Segment Detection and Relatedness Estimation in Un-phased Genetic Data via TRUFFLE.American journal of human genetics · 2019Article
- Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype.PLoS computational biology · 2017Article
- Fast and accurate long-range phasing in a UK Biobank cohort.Nature genetics · 2016Article
- A Pipeline for Classifying Relationships Using Dense SNP/SNV Data and Putative Pedigree Information.Genetic epidemiology · 2016Article
- A method for positive forensic identification of samples from extremely low-coverage sequence data.BMC genomics · 2015Article
- HaploShare: identification of extended haplotypes shared by cases and evaluation against controls.Genome biology · 2015Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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.
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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.