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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness
PLoS Genetics, Volume 10, No. 4, Article e1004234, Year 2014
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Description
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. © 2014 O'Connell et al.
Available Materials
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Authors & Co-Authors
O'Connell, Jared
United Kingdom, Oxford
The Wellcome Centre for Human Genetics
United Kingdom, Oxford
University of Oxford
Gurdasani, Deepti
United Kingdom, Hinxton
Wellcome Sanger Institute
United Kingdom, Cambridge
University of Cambridge
Delaneau, Olivier
United Kingdom, Oxford
University of Oxford
Pirastu, Nicola N.
Italy, Trieste
Università Degli Studi Di Trieste
Ulivi, Sheila
Italy, Trieste
Irccs Burlo Garofolo
Cocca, Massimiliano
Italy, Milan
Irccs Ospedale San Raffaele
Traglia, Michela
Italy, Milan
Irccs Ospedale San Raffaele
Huang, Jie
United Kingdom, Hinxton
Wellcome Sanger Institute
Huffman, Jennifer E.
United Kingdom, Edinburgh
Mrc Human Genetics Unit
Rudan, Igor
United Kingdom, Edinburgh
The University of Edinburgh
McQuillan, Ruth
United Kingdom, Edinburgh
The University of Edinburgh
Fraser, Ross M.
United Kingdom, Edinburgh
The University of Edinburgh
Campbell, Harry
United Kingdom, Edinburgh
The University of Edinburgh
Polašek, Ozren
Croatia, Split
University of Split
Asiki, Gershim
Uganda, Entebbe
Uganda Virus Research Institute
Ekoru, Kenneth
France, Paris
Conservatoire National Des Arts et Metiers
Hayward, Caroline
United Kingdom, Edinburgh
Mrc Human Genetics Unit
Wright, Alan F.
United Kingdom, Edinburgh
Mrc Human Genetics Unit
Vitart, Véronique
United Kingdom, Edinburgh
Mrc Human Genetics Unit
Navarro, Pau
United Kingdom, Edinburgh
Mrc Human Genetics Unit
Zagury, Jean François
France, Paris
Conservatoire National Des Arts et Metiers
Wilson, James F.
United Kingdom, Edinburgh
The University of Edinburgh
Toniolo, Daniela
Italy, Milan
Irccs Ospedale San Raffaele
Gasparini, Paolo P.
Italy, Trieste
Università Degli Studi Di Trieste
Soranzo, Nicole
United Kingdom, Hinxton
Wellcome Sanger Institute
Sandhu, Manjinder Singh
United Kingdom, Hinxton
Wellcome Sanger Institute
United Kingdom, Cambridge
University of Cambridge
Marchini, Jonathan L.
United Kingdom, Oxford
The Wellcome Centre for Human Genetics
United Kingdom, Oxford
University of Oxford
Statistics
Citations: 534
Authors: 27
Affiliations: 12
Identifiers
Doi:
10.1371/journal.pgen.1004234
e-ISSN:
15537404
Research Areas
Genetics And Genomics
Study Design
Cohort Study