Large-scale whole-genome sequencing of the Icelandic population
Abstract
Here we describe the insights gained from sequencing the whole genomes of 2,636 Icelanders to a median depth of 20×. We found 20 million SNPs and 1.5 million insertions-deletions (indels). We describe the density and frequency spectra of sequence variants in relation to their functional annotation, gene position, pathway and conservation score. We demonstrate an excess of homozygosity and rare protein-coding variants in Iceland. We imputed these variants into 104,220 individuals down to a minor allele frequency of 0.1% and found a recessive frameshift mutation in MYL4 that causes early-onset atrial fibrillation, several mutations in ABCB4 that increase risk of liver diseases and an intronic variant in GNAS associating with increased thyroid-stimulating hormone levels when maternally inherited. These data provide a study design that can be used to determine how variation in the sequence of the human genome gives rise to human diversity.
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The transition:transversion mutation ratio for missense mutations observed in large-scale genomic analyses is 2.3.
“we used the transition:transversion mutation ratio as a figure of merit, and compared this figure to a value of 2.3, which is the ratio for missense mutations observed in large-scale genomic analyses [34,35].”
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Self-citation
- Authors
- Gudbjartsson, D. F., Helgason, H., Gudjonsson, S. A., Zink, F., Oddson, A., Gylfason, A., Besenbacher, S., Magnusson, G., Halldorsson, B. V., Hjartarson, E., Sigurdsson, G. T., Stacey, S. N., Frigge, M. L., Holm, H., Saemundsdottir, J., Helgadottir, H. T., Johannsdottir, H., Sigfusson, G., Thorgeirsson, G., Sverrisson, J. T., Gretarsdottir, S., Walters, G. B., Rafnar, T., Thjodleifsson, B., Bjornsson, E. S., Olafsson, S., Thorarinsdottir, H., Steingrimsdottir, T., Gudmundsdottir, T. S., Theodors, A., Jonasson, J. G., Sigurdsson, A., Bjornsdottir, G., Jonsson, J. J., Thorarensen, O., Ludvigsson, P., Gudbjartsson, H., Eyjolfsson, G. I., Sigurdardottir, O., Olafsson, I., Arnar, D. O., Magnusson, O. T., Kong, A., Masson, G., Thorsteinsdottir, U., Helgason, A., Sulem, P., & Stefansson, K.
- Affiliations
- deCODE Genetics (Iceland) (IS)
- University of Iceland (IS)
- National University Hospital of Iceland (IS)
- Corresponding author
- Gudbjartsson, Daniel F
- ORCID
- Venue
- Nature Genetics
- Published
- 2015-03-25
- Volume
- 47
- Issue
- 5
- Pages
- 435-444
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W1990139627
- Cited by
- 791
- References
- 80
- Citations by year
- 2026: 30 · 2025: 43 · 2024: 54 · 2023: 66 · 2022: 73 · 2021: 83 · 2020: 63 · 2019: 75 · 2018: 87 · 2017: 95 · 2016: 71 · 2015: 49 · 2014: 1
- FWCI
- 68.31
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Hirsla (Landspítali University Hospital) (submittedVersion)
- Funders
- Villum Fonden (00007278)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- whole genome sequencing, Icelandic population, isolated populations, genetic variation, population structure, homozygosity, rare variants, variant imputation, atrial fibrillation, ABCB4, liver disease, GNAS, thyroid-stimulating hormone, maternally inherited variant, human genetic variation
- MeSH terms
- Aged, Aged, 80 and over, Atrial Fibrillation, Chromogranins, Female, Gene Frequency, Hearing Loss, Sensorineural, Humans, Iceland, Liver Diseases, Male, Middle Aged, Bulbar Palsy, Progressive, Risk, Thyrotropin, Genome, Human, Frameshift Mutation, Sequence Analysis, DNA, ATP Binding Cassette Transporter, Subfamily B, Myosin Light Chains, GTP-Binding Protein alpha Subunits, Gs, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Receptors, G-Protein-Coupled, INDEL Mutation, Genome-Wide Association Study, Phylogeography, Molecular Sequence Annotation
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