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Detection of sharing by descent, long-range phasing and haplotype imputation
Open accessAbstract
Uncertainty about the phase of strings of SNPs creates complications in genetic analysis, although methods have been developed for phasing population-based samples. However, these methods can only phase a small number of SNPs effectively and become unreliable when applied to SNPs spanning many linkage disequilibrium (LD) blocks. Here we show how to phase more than 1,000 SNPs simultaneously for a large fraction of the 35,528 Icelanders genotyped by Illumina chips. Moreover, haplotypes that are identical by descent (IBD) between close and distant relatives, for example, those separated by ten meioses or more, can often be reliably detected. This method is particularly powerful in studies of the inheritance of recurrent mutations and fine-scale recombinations in large sample sets. A further extension of the method allows us to impute long haplotypes for individuals who are not genotyped.
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“27,566 sequenced Icelanders that were sequenced to 30X and accurately phased using long-range phasing 21”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [21]
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Citations
Cites
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“Apart from being the first procedure that can systematically impute haplotypes into completely untyped individuals, our method can also be used in conjunction with previous methods for the imputation of untyped variants into individuals with other markers type”
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“Studying the inheritance of a recurrent deletion Recent studies support the notion that recurrent structural mutations may contribute substantially to the risks of psychiatric disorders such as autis”
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Thorgeirsson, T. E., Geller, F., Sulem, P., Rafnar, T., Wiste, A., Magnusson, K. P., Manolescu, A., Thorleifsson, G., Stefansson, H., Ingason, A., et al. (2008) · Nature · doi:10.1038/nature06846 · Cited by 1,523
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“Long-range phasing (Kong et al. 2008) uses IBD segments to resolve haplotype phasing inaccuracies.”
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Metadata
- Authors
- Kong, A., Masson, G., Frigge, M. L., Gylfason, A., Zusmanovich, P., Thorleifsson, G., Olason, P. I., Ingason, A., Steinberg, S., Rafnar, T., Sulem, P., Mouy, M., Jonsson, F., Thorsteinsdottir, U., Gudbjartsson, D. F., Stefansson, H., & Stefansson, K.
- Affiliations
- deCODE Genetics (Iceland) (IS)
- Corresponding author
- Kong, Augustine
- ORCID
- Venue
- Nature Genetics
- Published
- 2008-08-17
- Volume
- 40
- Issue
- 9
- Pages
- 1068-1075
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4540081
- OpenAlex
- W2115038037
- Cited by
- 447
- References
- 24
- Citations by year
- 2026: 12 · 2025: 12 · 2024: 22 · 2023: 19 · 2022: 29 · 2021: 34 · 2020: 23 · 2019: 22 · 2018: 30 · 2017: 29 · 2016: 24 · 2015: 33 · 2014: 33 · 2013: 31 · 2012: 32
- FWCI
- 11.81
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute on Drug Abuse (R01DA017932)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- haplotype imputation, identical by descent, linkage disequilibrium blocks, recurrent mutations, Icelanders
- MeSH terms
- Algorithms, Base Sequence, Female, Genetic Markers, Genetics, Population, Haplotypes, Humans, Iceland, Major Histocompatibility Complex, Male, Models, Genetic, Gene Deletion, Polymorphism, Single Nucleotide, Inheritance Patterns
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