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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
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“It is possible that Beagle could produce better results with different settings, although we tried varying both the model-fitting parameters (niterations, nsamples) and the model-building parameters (scale, shift) without observing a meaningful change in accuracy (data not shown).”
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Self-citationClonal hematopoiesis, with and without candidate driver mutations, is common in the elderly
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“Similar to Kong et al. (2008) [12], we took each individual in turn and at each locus we calculated the number of other individuals that share an IBD segment (excluding closely related individuals with relatedness rw0:125).”
BackgroundResultFine-scale recombination rate differences between sexes, populations and individuals
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InfluentialMutations in BRIP1 confer high risk of ovarian cancer
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Gudbjartsson, D. F., Þorgeirsson, G., Sulem, P., Helgadóttir, A., Gylfason, A., Saemundsdottir, J., Björnsson, E., Norddahl, G. L., Jónasdóttir, Á., Jónasdóttir, A., et al. (2019) · Journal of the American College of Cardiology · doi:10.1016/j.jacc.2019.10.019 · Cited by 227
“The sequence variants identified in subjects who underwent whole-genome sequencing were imputed into 151,677 Icelanders who had been genotyped with various Illumina (San Diego, California) SNP chips and their genotypes phased using long-range phasing (25,28) (Online Appendix).”
MethodSelf-citationAmini, S., Pushkarev, D., Christiansen, L., Kostem, E., Royce, T., Turk, C., Pignatelli, N., Adey, A., Kitzman, J. O., Vijayan, K., et al. (2014) · Nature Genetics · doi:10.1038/ng.3119 · Cited by 189
High-Resolution Detection of Identity by Descent in Unrelated Individuals
Browning, S. R., & Browning, B. L. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.02.021 · Cited by 216
“Greater power to detect IBD will lead to increased power for IBD mapping, as well as to increased accuracy from IBD-based genotype imputation and phasing.(6) Current IBD resolution may be somewhat restricted by the relative scarcity of low-frequency variants on existing SNP arrays.”
BackgroundMethodInfluentialDruet, T., & Georges, M. (2009) · Genetics · doi:10.1534/genetics.109.108431 · Cited by 217
Haplotype estimation for biobank-scale data sets
O’Connell, J., Sharp, K., Shrine, N. R. G., Wain, L. V., Hall, I. P., Tobin, M. D., Zagury, J., Delaneau, O., & Marchini, J. (2016) · Nature Genetics · doi:10.1038/ng.3583 · Cited by 205
Cryptic Distant Relatives Are Common in Both Isolated and Cosmopolitan Genetic Samples
Henn, B. M., Hon, L., Macpherson, J. M., Eriksson, N., Saxonov, S., Pe’er, I., & Mountain, J. L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034267 · Cited by 197
“[36] suggest that a large sample of individuals with European ancestry is likely to include many pairs of 2 through 9 cousins.”
InfluentialDNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis
Kular, L., Liu, Y., Ruhrmann, S., Zheleznyakova, G. Y., Marabita, F., Gómez-Cabrero, D., James, T., Ewing, E., Lindén, M., Górnikiewicz, B., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04732-5 · Cited by 212
Price, A. L., Helgason, A., Þorleifsson, G., McCarroll, S. A., Kong, A., & Stefánsson, K. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001317 · Cited by 198
“Given long-range phased Illumina 300K data [15] for a pair of individuals, we partitioned the genome into 2cM blocks and for each block performed 262 = 4 comparisons between haplotypes from the two individuals.”
MethodSelf-citationIdentity by Descent Between Distant Relatives: Detection and Applications
Browning, S. R., & Browning, B. L. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155534 · Cited by 206
Kuriyama, S., Metoki, H., Kikuya, M., Obara, T., Ishikuro, M., Yamanaka, C., Nagai, M., Matsubara, H., Kobayashi, T., Sugawara, J., et al. (2019) · International Journal of Epidemiology · doi:10.1093/ije/dyz169 · Cited by 196
“The inclusion of all family members from three generations enables a direct haplotype assessment.(65) Familial information may enable the estimation of genetic and non-genetic familial transmission and aid investigations of the effects of assortative mating on offspring characteristics, intergenerational (dis)similari…”
BackgroundA sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer
Kiemeney, L. A. L. M., Sulem, P., Besenbacher, S., Vermeulen, S. H. H. M., Sigurðsson, Á., Þorleifsson, G., Gudbjartsson, D. F., Stacey, S., Guðmundsson, J., Zanon, C., et al. (2010) · Nature Genetics · doi:10.1038/ng.558 · Cited by 190
“The genotypes of these variants were imputed into 561 UBC cases and 35,684 controls genotyped in the Icelandic study group by using a method of long-range phasing and haplotypin”
MethodSelf-citationInvestigative genetic genealogy: Current methods, knowledge and practice
Kling, D., Phillips, C., Kennett, D., & Tillmar, A. O. (2021) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2021.102474 · Cited by 199
Helgadóttir, A., Grétarsdóttir, S., Þorleifsson, G., Hólm, H., Patel, R. S., Guðnason, Þ., Jones, G. T., van Rij, A. M., Eapen, D. J., Baas, A. F., et al. (2012) · Journal of the American College of Cardiology · doi:10.1016/j.jacc.2012.01.078 · Cited by 185
“As the LPA SNPs were not represented on available genome-wide chips, genotypes for the Icelandic samples were imputed using methods previously described (21).”
MethodSelf-citationGuðmundsson, J., Sulem, P., Gudbjartsson, D. F., Másson, G., Agnarsson, B. A., Benediktsdóttir, K. R., Sigurðsson, Á., Magnússon, Ó. Þ., Gudjonsson, S. A., Magnúsdóttir, D. N., et al. (2012) · Nature Genetics · doi:10.1038/ng.2437 · Cited by 188
Self-citationLoss-of-function variants in ATM confer risk of gastric cancer
Helgason, H., Rafnar, Þ., Ólafsdóttir, H. S., Jonasson, J. G., Sigurðsson, Á., Stacey, S., Jónasdóttir, A., Tryggvadóttír, L., Alexiusdottir, K. K., Haraldsson, Á., et al. (2015) · Nature Genetics · doi:10.1038/ng.3342 · Cited by 180
Self-citationGrarup, N., Sulem, P., Sandholt, C. H., Þorleifsson, G., Ahluwalia, T. S., Steinthórsdóttir, V., Bjarnason, H., Gudbjartsson, D. F., Magnússon, Ó. Þ., Sparsø, T., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003530 · Cited by 177
“In Iceland, a large population-based resource has been generated applying WGS and highly accurate imputation of the sequence information into a large fraction of the population [20,21].”
MethodSelf-citationA Fast and Simple Method for Detecting Identity-by-Descent Segments in Large-Scale Data
Zhou, Y., Browning, S. R., & Browning, B. L. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.02.010 · Cited by 175
Relatedness disequilibrium regression estimates heritability without environmental bias
Young, A. I., Frigge, M. L., Gudbjartsson, D. F., Thorleifsson, G., Bjornsdottir, G., Sulem, P., Masson, G., Thorsteinsdottir, U., Stefansson, K., & Kong, A. (2018) · Nature Genetics · doi:10.1038/s41588-018-0178-9 · Cited by 173
Self-citationCommon and rare variants associated with kidney stones and biochemical traits
Oddsson, Á., Sulem, P., Helgason, H., Edvardsson, V. O., Þorleifsson, G., Sveinbjörnsson, G., Haraldsdottir, E., Eyjolfsson, G. I., Sigurðardóttir, Ó., Ólafsson, Í., et al. (2015) · Nature Communications · doi:10.1038/ncomms8975 · Cited by 173
Self-citationProgress and promise in understanding the genetic basis of common diseases
Price, A. L., Spencer, C. C. A., & Donnelly, P. (2015) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2015.1684 · Cited by 147
Variants inDENND1AAre Associated with Polycystic Ovary Syndrome in Women of European Ancestry
Welt, C. K., Styrkársdóttir, U., Ehrmann, D. A., Þorleifsson, G., Arason, G., Guðmundsson, J. A., Ober, C., Rosenfield, R. L., Saxena, R., Þorsteinsdóttir, U., et al. (2012) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2011-3478 · Cited by 170
Styrkársdóttir, U., Lund, S. H., Þorleifsson, G., Zink, F., Stefánsson, Ó. A., Sigurdsson, J. K., Juliusson, K., Bjarnadóttir, K., Sigurbjörnsdóttir, S., Jonsson, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0247-0 · Cited by 174
Self-citationHickey, J. M., Kinghorn, B. P., Tier, B., van der Werf, J. H. J., & Cleveland, M. A. (2012) · Genetics Selection Evolution · doi:10.1186/1297-9686-44-9 · Cited by 165
“The method involves simple phasing and imputation rules, long-range phasing and haplotype library imputation [16,17] as implemented in AlphaPhase1.”
A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis
Bell, S., Rigas, A. S., Magnússon, M. K., Ferkingstad, E., Allara, E., Björnsdóttir, G., Ramond, A., Sørensen, E., Halldorsson, G. H., Paul, D. S., et al. (2021) · Communications Biology · doi:10.1038/s42003-020-01575-z · Cited by 160
Self-citationA genome-wide association study yields five novel thyroid cancer risk loci
Guðmundsson, J., Þorleifsson, G., Sigurdsson, J. K., Stefánsdóttir, L., Jonasson, J. G., Gudjonsson, S. A., Gudbjartsson, D. F., Másson, G., Johannsdottir, H., Halldorsson, G. H., et al. (2017) · Nature Communications · doi:10.1038/ncomms14517 · Cited by 157
Self-citationStyrkársdóttir, U., Þorleifsson, G., Helgadottir, H. T., Bömer, N., Metrustry, S., Bierma‐Zeinstra, S., Strijbosch, A. M., Εvangelou, Ε., Hart, D. J., Beekman, M., et al. (2014) · Nature Genetics · doi:10.1038/ng.2957 · Cited by 158
Self-citationIdentification of low-frequency variants associated with gout and serum uric acid levels
Sulem, P., Gudbjartsson, D. F., Walters, G. B., Helgadottir, H. T., Helgason, A., Gudjonsson, S. A., Zanon, C., Besenbacher, S., Björnsdóttir, G., Magnússon, Ó. Þ., et al. (2011) · Nature Genetics · doi:10.1038/ng.972 · Cited by 159
“The 15,957,390 SNPs identified were then imputed into 41,675 chip-genotyped Icelanders using long-range phasin”
MethodSelf-citationA combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes
Hickey, J. M., Kinghorn, B. P., Tier, B., Wilson, J. F., Dunstan, N., & van der Werf, J. H. J. (2011) · Genetics Selection Evolution · doi:10.1186/1297-9686-43-12 · Cited by 147
“[6] in several ways to improve its robustness and ability to access more of the information contained within a dataset.”
BackgroundMethodResultInfluentialNew Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era
Gao, F., Chen, M., Hu, W., & Li, H. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.028233 · Cited by 155
The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes
Skov, L., Coll Macià, M., Sveinbjörnsson, G., Mafessoni, F., Lucotte, E. A., Einarsdóttir, M. S., Jonsson, H., Halldorsson, B., Gudbjartsson, D. F., Helgason, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2225-9 · Cited by 125
Self-citationCommon and low-frequency variants associated with genome-wide recombination rate
Kong, A., Þorleifsson, G., Frigge, M. L., Másson, G., Gudbjartsson, D. F., Villemoes, R., Magnúsdóttir, E., Olafsdottir, S. B., Þorsteinsdóttir, U., & Stefánsson, K. (2013) · Nature Genetics · doi:10.1038/ng.2833 · Cited by 138
Self-citationHelgason, H., Sulem, P., Duvvari, M. R., Luo, H., Þorleifsson, G., Stefánsson, H., Jónsdóttir, I., Másson, G., Gudbjartsson, D. F., Walters, G. B., et al. (2013) · Nature Genetics · doi:10.1038/ng.2740 · Cited by 141
Self-citationA missense variant in PTPN22 is a risk factor for drug-induced liver injury
Cirulli, E. T., Nicoletti, P., Abramson, K., Andrade, R. J., Bjornsson, E. S., Chalasani, N., Fontana, R. J., Hallberg, P., Li, Y. J., Lucena, M. I., et al. (2019) · Gastroenterology · doi:10.1053/j.gastro.2019.01.034 · Cited by 137
Sociotechnical safeguards for genomic data privacy
Wan, Z., Hazel, J. W., Clayton, E. W., Vorobeychik, Y., Kantarcıoğlu, M., & Malin, B. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00455-y · Cited by 148
“Due to the similarity of relatives’ genomic records, even if someone’s genomic record has never been shared or even generated, their genotypes and predispositions to certain diseases 63 can be inferred to a certain degree from their relatives’ shared genotypes 64 .”
BackgroundMapping Rare and Common Causal Alleles for Complex Human Diseases
Raychaudhuri, S. (2011) · Cell · doi:10.1016/j.cell.2011.09.011 · Cited by 136
“This approach might be most effective in isolated populations where reduced genetic diversity and founder effects make it possible to identify long-range haplotypes (Kong et al., 2008).”
BackgroundMulti-nucleotide de novo Mutations in Humans
Besenbacher, S., Sulem, P., Helgason, A., Helgason, H., Kristjansson, H., Jónasdóttir, Á., Jónasdóttir, A., Magnússon, Ó. Þ., Þorsteinsdóttir, U., Másson, G., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006315 · Cited by 129
Self-citationAccuracy of genotype imputation in sheep breeds
Hayes, B. J., Bowman, P. J., Daetwyler, H. D., Kijas, J., & van der Werf, J. H. J. (2011) · Animal Genetics · doi:10.1111/j.1365-2052.2011.02208.x · Cited by 129
Genome-wide analysis yields new loci associating with aortic valve stenosis
Helgadottir, A., Thorleifsson, G., Gretarsdottir, S., Stefansson, O. A., Tragante, V., Thorolfsdottir, R. B., Jonsdottir, I., Bjornsson, T., Steinthorsdottir, V., Verweij, N., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03252-6 · Cited by 125
Self-citationMendelian imputation of parental genotypes improves estimates of direct genetic effects
Young, A. I., Nehzati, S. M., Benonisdottir, S., Okbay, A., Jayashankar, H., Lee, C., Cesarini, D., Benjamin, D. J., Turley, P., & Kong, A. (2022) · Nature Genetics · doi:10.1038/s41588-022-01085-0 · Cited by 144
Self-citationInsights into imprinting from parent-of-origin phased methylomes and transcriptomes
Zink, F., Magnúsdóttir, D. N., Magnússon, Ó. Þ., Walker, N. J., Morris, T. J., Sigurðsson, Á., Halldorsson, G. H., Gudjonsson, S. A., Melsted, P., Ingimundardóttir, H., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0232-7 · Cited by 123
Self-citationMaximum Likelihood Estimation of Biological Relatedness from Low Coverage Sequencing Data
Lipatov, M., Sanjeev, K., Patro, R., & Veeramah, K. R. (2015) · doi:10.1101/023374 · Cited by 108
Saada, J. N., Kalantzis, G., Shyr, D., Cooper, F., Robinson, M. J., Gusev, A., & Palamara, P. F. (2020) · Nature Communications · doi:10.1038/s41467-020-19588-x · Cited by 124
Pausch, H., MacLeod, I. M., Fries, R., Emmerling, R., Bowman, P. J., Daetwyler, H. D., & Goddard, M. E. (2017) · Genetics Selection Evolution · doi:10.1186/s12711-017-0301-x · Cited by 124
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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