title: Sequence variants from whole genome sequencing a large group of Icelanders.
abstract: We have accumulated considerable data on the genetic makeup of the Icelandic population by sequencing the whole genomes of 2,636 Icelanders to depth of at least 10X and by chip genotyping 101,584 more. The sequencing was done with Illumina technology. The median sequencing depth was 20X and 909 individuals were sequenced to a depth of at least 30X. We found 20 million single nucleotide polymorphisms (SNPs) and 1.5 million insertions/deletions (indels) that passed stringent quality control. Almost all the common SNPs (derived allele frequency (DAF) over 2%) that we identified in Iceland have been observed by either dbSNP (build 137) or the Exome Sequencing Project (ESP) while only 60 and 20% of rare (DAF<0.5%) SNPs and indels in coding regions, the most heavily studied parts of the genome, have been observed in the public databases. Features of our variant data, such as the transition/transversion ratio and the length distribution of indels, are similar to published reports.
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland ; School of Engineering and Natural Sciences, University of Iceland , Reykjavik 101, Iceland.
authors.forename: Daniel F
authors.initials: DF
authors.lastname: Gudbjartsson
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Sulem
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland ; School of Engineering and Natural Sciences, University of Iceland , Reykjavik 101, Iceland.
authors.forename: Hannes
authors.initials: H
authors.lastname: Helgason
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Arnaldur
authors.initials: A
authors.lastname: Gylfason
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Sigurjon A
authors.initials: SA
authors.lastname: Gudjonsson
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Florian
authors.initials: F
authors.lastname: Zink
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Asmundur
authors.initials: A
authors.lastname: Oddson
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Gisli
authors.initials: G
authors.lastname: Magnusson
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland ; Institute of Biomedical and Neural Engineering, Reykjavík University , Reykjavík 101, Iceland.
authors.forename: Bjarni V
authors.initials: BV
authors.lastname: Halldorsson
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Eirikur
authors.initials: E
authors.lastname: Hjartarson
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Gunnar Th
authors.initials: GT
authors.lastname: Sigurdsson
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland ; School of Engineering and Natural Sciences, University of Iceland , Reykjavik 101, Iceland.
authors.forename: Augustine
authors.initials: A
authors.lastname: Kong
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland ; Department of Anthropology, University of Iceland , Reykjavik 101, Iceland.
authors.forename: Agnar
authors.initials: A
authors.lastname: Helgason
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Gisli
authors.initials: G
authors.lastname: Masson
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland.
authors.forename: Olafur Th
authors.initials: OT
authors.lastname: Magnusson
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland ; Faculty of Medicine, University of Iceland , Reykjavik 101, Iceland.
authors.forename: Unnur
authors.initials: U
authors.lastname: Thorsteinsdottir
authors.affiliation: deCODE genetics/Amgen, Inc. , Reykjavik 101, Iceland ; Faculty of Medicine, University of Iceland , Reykjavik 101, Iceland.
authors.forename: Kari
authors.initials: K
authors.lastname: Stefansson
mesh_terms: D001483:Base Sequence; D005787:Gene Frequency; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D007055:Iceland; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA