ArticleMolecular biology and evolution2014
Reducing pervasive false-positive identical-by-descent segments detected by large-scale pedigree analysis.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 53 citations in OpenAlex.
- Population genetic considerations for using biobanks as international resources in the pandemic era and beyond.BMC genomics · 2021Pooled it
- Article
- Characterizing identity by descent segments in Chinese interpopulation unrelated individual pairs.Molecular genetics and genomics : MGG · 2024Article
- Shortcomings of ethnicity-based carrier screening for conditions associated with Ashkenazi Jewish ancestry.Genetics in medicine open · 2024Article
- A computational approach for positive genetic identification and relatedness detection from low-coverage shotgun sequencing data.The Journal of heredity · 2023Article
- Review
- Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals.PLoS genetics · 2022Article
- Fine-scale population structure and demographic history of British Pakistanis.Nature communications · 2021Article
- Genetic landscape of Gullah African Americans.American journal of physical anthropology · 2021Article
- Rapid detection of identity-by-descent tracts for mega-scale datasets.Nature communications · 2021Article
- Personalized genealogical history of UK individuals inferred from biobank-scale IBD segments.BMC biology · 2021Article
- Article
- A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure.European journal of human genetics : EJHG · 2018Article
- 1000 human genomes carry widespread signatures of GC biased gene conversion.BMC genomics · 2018Article
- The promise of discovering population-specific disease-associated genes in South Asia.Nature genetics · 2017Article
- Benchmarking Relatedness Inference Methods with Genome-Wide Data from Thousands of Relatives.Genetics · 2017Article
- A fast and accurate method for detection of IBD shared haplotypes in genome-wide SNP data.European journal of human genetics : EJHG · 2017Article
- The time and place of European admixture in Ashkenazi Jewish history.PLoS genetics · 2017Article
- Clustering of 770,000 genomes reveals post-colonial population structure of North America.Nature communications · 2017Article
- Explosive genetic evidence for explosive human population growth.Current opinion in genetics & development · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Analysis of genomic segments shared identical-by-descent (IBD) between individuals is fundamental to many genetic applications, from demographic inference to estimating the heritability of diseases, but IBD detection accuracy in nonsimulated data is largely unknown. In principle, it can be evaluated using known pedigrees, as IBD segments are by definition inherited without recombination down a family tree. We extracted 25,432 genotyped European individuals containing 2,952 father-mother-child trios from the 23andMe, Inc. data set. We then used GERMLINE, a widely used IBD detection method, to detect IBD segments within this cohort. Exploiting known familial relationships, we identified a false-positive rate over 67% for 2-4 centiMorgan (cM) segments, in sharp contrast with accuracies reported in simulated data at these sizes. Nearly all false positives arose from the allowance of haplotype switch errors when detecting IBD, a necessity for retrieving long (>6 cM) segments in the presence of imperfect phasing. We introduce HaploScore, a novel, computationally efficient metric that scores IBD segments proportional to the number of switch errors they contain. Applying HaploScore filtering to the IBD data at a precision of 0.8 produced a 13-fold increase in recall when compared with length-based filtering. We replicate the false IBD findings and demonstrate the generalizability of HaploScore to alternative data sources using an independent cohort of 555 European individuals from the 1000 Genomes project. HaploScore can improve the accuracy of segments reported by any IBD detection method, provided that estimates of the genotyping error rate and switch error rate are available.
Indexed as
Identifiers
What OpenQuestion holds
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.