Whole genome characterization of sequence diversity of 15,220 Icelanders

• Published in: Scientific data Vol. 4; no. 1; p. 170115
• Main Authors: Jónsson, Hákon, Sulem, Patrick, Kehr, Birte, Kristmundsdottir, Snaedis, Zink, Florian, Hjartarson, Eirikur, Hardarson, Marteinn T., Hjorleifsson, Kristjan E., Eggertsson, Hannes P., Gudjonsson, Sigurjon Axel, Ward, Lucas D., Arnadottir, Gudny A., Helgason, Einar A., Helgason, Hannes, Gylfason, Arnaldur, Jonasdottir, Adalbjorg, Jonasdottir, Aslaug, Rafnar, Thorunn, Besenbacher, Soren, Frigge, Michael L., Stacey, Simon N., Magnusson, Olafur Th, Thorsteinsdottir, Unnur, Masson, Gisli, Kong, Augustine, Halldorsson, Bjarni V., Helgason, Agnar, Gudbjartsson, Daniel F., Stefansson, Kari
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21.09.2017; Nature Publishing Group
• Subjects: 631/1647/514/1948; 631/208/457/649/2219; 631/208/726/649; 631/208/728; Data Descriptor; Genetic disorders; Genome, Human; Genomes; Humanities and Social Sciences; Humans; Iceland; INDEL Mutation; multidisciplinary; Mutation; Nucleotide sequence; Polymorphism, Single Nucleotide; Population genetics; Science; Single-nucleotide polymorphism
• ISSN: 2052-4463; 2052-4463
• DOI: 10.1038/sdata.2017.115

Understanding of sequence diversity is the cornerstone of analysis of genetic disorders, population genetics, and evolutionary biology. Here, we present an update of our sequencing set to 15,220 Icelanders who we sequenced to an average genome-wide coverage of 34X. We identified 39,020,168 autosomal variants passing GATK filters: 31,079,378 SNPs and 7,940,790 indels. Calling de novo mutations (DNMs) is a formidable challenge given the high false positive rate in sequencing datasets relative to the mutation rate. Here we addressed this issue by using segregation of alleles in three-generation families. Using this transmission assay, we controlled the false positive rate and identified 108,778 high quality DNMs. Furthermore, we used our extended family structure and read pair tracing of DNMs to a panel of phased SNPs, to determine the parent of origin of 42,961 DNMs. Design Type(s) individual genetic characteristics comparison design • population genetics analysis objective Measurement Type(s) genetic sequence variation analysis Technology Type(s) whole genome sequencing Factor Type(s) Sample Characteristic(s) Homo sapiens • whole blood • buccal epithelium Machine-accessible metadata file describing the reported data (ISA-Tab format)