ArticlePLoS genetics2014
A general approach for haplotype phasing across the full spectrum of relatedness.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 385 papers, 11 of them syntheses that pooled it.
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Who cites it
385 citing papers in PubMed, 11 syntheses or guidelines pooled it.
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- Genome-Wide Meta-Analysis Identifies Multiple Novel Rare Variants to Predict Common Human Infectious Diseases Risk.International journal of molecular sciences · 2023Pooled it
- Genetic effects on the timing of parturition and links to fetal birth weight.Nature genetics · 2023Pooled it
- Taste receptor polymorphisms and longevity: a systematic review and meta-analysis.Aging clinical and experimental research · 2021Pooled it
- Large trans-ethnic meta-analysis identifies AKR1C4 as a novel gene associated with age at menarche.Human reproduction (Oxford, England) · 2021Pooled it
- Family-based genome-wide association study of leprosy in Vietnam.PLoS pathogens · 2020Trial
- Western Hunter-Gatherer genetic ancestry contributes to human longevity in the Italian population.GeroScience · 2026Article
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- Circulating erythropoietin concentration associates with thromboembolism in sickle cell disease.British journal of haematology · 2026Article
- Defining Pseudo-Haplotype Analysis Reveals Multi-Gene Genetic Pattern Across BAF Chromatin Remodeling Complexes.bioRxiv : the preprint server for biology · 2026Article
- [Association analysis between genetic nurturing effects ofBeijing da xue xue bao. Yi xue ban = Journal of Peking University. Health sciences · 2026Article
- Association and risk prediction of 19 complex diseases with polygenic scores and socioeconomic status.Communications medicine · 2026Article
325 more citing papers are in PubMed but not listed here.
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27 authors.
Funding
Abstract
Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses. Using genotypes from six cohorts from isolated populations and two cohorts from non-isolated populations, we have investigated the performance of different phasing methods designed for nominally 'unrelated' individuals. We find that SHAPEIT2 produces much lower switch error rates in all cohorts compared to other methods, including those designed specifically for isolated populations. In particular, when large amounts of IBD sharing is present, SHAPEIT2 infers close to perfect haplotypes. Based on these results we have developed a general strategy for phasing cohorts with any level of implicit or explicit relatedness between individuals. First SHAPEIT2 is run ignoring all explicit family information. We then apply a novel HMM method (duoHMM) to combine the SHAPEIT2 haplotypes with any family information to infer the inheritance pattern of each meiosis at all sites across each chromosome. This allows the correction of switch errors, detection of recombination events and genotyping errors. We show that the method detects numbers of recombination events that align very well with expectations based on genetic maps, and that it infers far fewer spurious recombination events than Merlin. The method can also detect genotyping errors and infer recombination events in otherwise uninformative families, such as trios and duos. The detected recombination events can be used in association scans for recombination phenotypes. The method provides a simple and unified approach to haplotype estimation, that will be of interest to researchers in the fields of human, animal and plant genetics.
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