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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
A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data
Stephens, M., & Donnelly, P. (2003) · The American Journal of Human Genetics · doi:10.1086/379378 · Cited by 3,516 · cited 1×
“In general, consider a SNP that is heterozygous (1,2) in A and all of his”
BackgroundA new multipoint method for genome-wide association studies by imputation of genotypes
Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007) · Nature Genetics · doi:10.1038/ng2088 · Cited by 2,609 · cited 1×
“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”
MethodScheet, P. A., & Stephens, M. (2006) · The American Journal of Human Genetics · doi:10.1086/502802 · Cited by 1,959
Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia
Walsh, T., McClellan, J. M., McCarthy, S. E., Addington, A. M., Pierce, S. B., Cooper, G. M., Nord, A. S., Kusenda, M., Malhotra, D., Bhandari, A., et al. (2008) · Science · doi:10.1126/science.1155174 · Cited by 1,800
A high-resolution recombination map of the human genome
Kong, A., Gudbjartsson, D. F., Sainz, J., Jonsdottir, G. M., Gudjonsson, S. A., Richardsson, B., Sigurdardottir, S. L., Barnard, J., Hallbeck, B., Másson, G., et al. (2002) · Nature Genetics · doi:10.1038/ng917 · Cited by 1,750 · cited 1×
“Genetically, the target region is approximately 6 cM (ref”
BackgroundSelf-citationLarge recurrent microdeletions associated with schizophrenia.
GROUP, Stefansson, H., Rujescu, D., Cichon, S., Pietiläinen, O. P. H., Ingason, A., Steinberg, S., Fossdal, R., Sigurdsson, E., Sigmundsson, T., et al. (2008) · Nature · doi:10.1038/nature07229 · Cited by 1,745
Self-citationAssociation between Microdeletion and Microduplication at 16p11.2 and Autism
Weiss, L. A., Shen, Y., Korn, J. M., Arking, D. E., Miller, D. T., Fossdal, R., Saemundsen, E., Stefansson, H., Ferreira, M. A. R., Green, T., et al. (2008) · New England Journal of Medicine · doi:10.1056/nejmoa075974 · Cited by 1,666 · cited 1×
“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”
BackgroundA variant associated with nicotine dependence, lung cancer and peripheral arterial disease
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
Self-citationAmos, C. I., Wu, X., Broderick, P., Gorlov, I. P., Gu, J., Eisen, T., Dong, Q., Zhang, Q., Gu, X., Vijayakrishnan, J., et al. (2008) · Nature Genetics · doi:10.1038/ng.109 · Cited by 1,310 · cited 1×
“Here we focus on a region around the nicotinic acetylcholine receptor gene cluster ( CHRNA5 , CHRNA3 and CHRNB4 ) on 15q25 where variants, including allele T of SNP rs1051730, were recently shown to associate with smoking behavior, lung cancer and peripheral arterial diseas”
BackgroundHung, R. J., McKay, J. D., Gaborieau, V., Boffetta, P., Hashibe, M., Zaridze, D., Mukeria, A., Szeszenia-Dabrowska, N., Lissowska, J., Rudnai, P., et al. (2008) · Nature · doi:10.1038/nature06885 · Cited by 1,275
A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome
Myers, S., Bottolo, L., Freeman, C., McVean, G., & Donnelly, P. (2005) · Science · doi:10.1126/science.1117196 · Cited by 1,134 · cited 1×
“Studying fine-scale recombination There is much interest in recombination hot spots and their evolutio”
BackgroundLee, J. A., Carvalho, C. M. B., & Lupski, J. R. (2007) · Cell · doi:10.1016/j.cell.2007.11.037 · Cited by 914
Saccone, S. F., Hinrichs, A. L., Saccone, N. L., Chase, G. A., Konvicka, K., Madden, P. A. F., Breslau, N., Johnson, E. O., Hatsukami, D., Pomerleau, O., et al. (2007) · Human Molecular Genetics · doi:10.1093/hmg/ddl438 · Cited by 850 · cited 1×
“Here we focus on a region around the nicotinic acetylcholine receptor gene cluster ( CHRNA5 , CHRNA3 and CHRNB4 ) on 15q25 where variants, including allele T of SNP rs1051730, were recently shown to associate with smoking behavior, lung cancer and peripheral arterial diseas”
BackgroundAssociation Between Microdeletion and Microduplication at 16p11.2 and Autism
Weiss, L. A., Shen, Y., Korn, J. M., Arking, D. E., Miller, D. T., Fossdal, R., Sæmundsen, E., Stefánsson, H., Ferreira, M. A. R., Green, T. J., et al. (2008) · Obstetrical & Gynecological Survey · doi:10.1097/01.ogx.0000316305.61461.6f · Cited by 647
Thorlacius, S., Ólafsdóttir, G. H., Tryggvadóttír, L., Neuhausen, S. L., Jonasson, J. G., Tavtigian, S. V., Tulinius, H., Ogmundsdottir, H. M., & Eyfjord, J. E. (1996) · Nature Genetics · doi:10.1038/ng0596-117 · Cited by 523
Coop, G., Wen, X., Ober, C., Pritchard, J. K., & Przeworski, M. (2008) · Science · doi:10.1126/science.1151851 · Cited by 372 · cited 1×
“Apart from methods that estimate historic recombination rates on the basis of LD patterns, a recent study has investigated recombination events directly by utilizing high-density SNP data from 725 related individuals falling into 82 nuclear familie”
MethodComparison of Fine-Scale Recombination Rates in Humans and Chimpanzees
Winckler, W., Myers, S. R., Richter, D. J., Onofrio, R. C., McDonald, G. J., Bontrop, R. E., McVean, G., Gabriel, S., Reich, D., Donnelly, P., et al. (2005) · Science · doi:10.1126/science.1105322 · Cited by 357 · cited 1×
“Studying fine-scale recombination There is much interest in recombination hot spots and their evolutio”
BackgroundA Comparison of Phasing Algorithms for Trios and Unrelated Individuals
Marchini, J., Cutler, D., Patterson, N., Stephens, M., Eskin, E., Halperin, E., Lin, S., Qin, Z. S., Munro, H. M., Abecasis, G. R., et al. (2006) · The American Journal of Human Genetics · doi:10.1086/500808 · Cited by 341
HAPLO: A Program Using the EM Algorithm to Estimate the Frequencies of Multi-site Haplotypes
Hawley, M. E., & Kídd, K. K. (1995) · Journal of Heredity · doi:10.1093/oxfordjournals.jhered.a111613 · Cited by 323 · cited 2×
“If a surrogate relative C with Erdös distance K+1 is homozygous (1,1), then the haplotype of A through”
BackgroundHaplotype reconstruction from genotype data using Imperfect Phylogeny
Halperin, E., & Eskin, E. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth149 · Cited by 219
In silico method for inferring genotypes in pedigrees
Burdick, J. T., Chen, W., Abecasis, G. R., & Cheung, V. G. (2006) · Nature Genetics · doi:10.1038/ng1863 · Cited by 145 · cited 1×
“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”
MethodFactors influencing recombination frequency and distribution in a human meiotic crossover hotspot
Jeffreys, A. J., & Neumann, R. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi232 · Cited by 144 · cited 1×
“Studying fine-scale recombination There is much interest in recombination hot spots and their evolutio”
BackgroundGuðmundsson, J., Jóhannesdóttir, G., Arason, A., Bergþorsson, J. Þ., Ingvarsson, S., Egilsson, V., & Barkardottir, R. B. (1996) · PubMed Central · Cited by 70
And What is Your Erdös Number?
Goffman, C. (1969) · American Mathematical Monthly · doi:10.1080/00029890.1969.12000324 · Cited by 48
And What Is Your Erdos Number?
Goffman, C. (1969) · The American Mathematical Monthly · doi:10.2307/2317868
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Self-citationHowie, B. N., Donnelly, P., & Marchini, J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000529 · Cited by 3,928
“One way of understanding our approach is by comparison to the phasing method of Kong et al. [19].”
MethodGenome-wide association studies
Uffelmann, E., Huang, Q. Q., Munung, N. S., de Vries, J., Okada, Y., Martin, A. R., Martin, H. C., Lappalainen, T., & Posthuma, D. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-021-00056-9 · Cited by 1,849
Reference-based phasing using the Haplotype Reference Consortium panel
Loh, P.-R., Danecek, P., Palamara, P. F., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, G. R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3679 · Cited by 1,723
“We and others have recently developed methods that achieve very high statistical phasing accuracy in cohorts comprising a large fraction of a population [8] or containing >100,000 samples [13, 14].”
MethodA mutation in APP protects against Alzheimer’s disease and age-related cognitive decline
Jonsson, T., Atwal, J. K., Steinberg, S., Snaedal, J., Jonsson, P. V., Bjornsson, S., Stefansson, H., Sulem, P., Gudbjartsson, D., Maloney, J., et al. (2012) · Nature · doi:10.1038/nature11283 · Cited by 1,738
Self-citation
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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