Whole genome characterization of sequence diversity of 15,220 Icelanders

Hákon Jónsson; patrick sulem; Birte Kehr; Snædís Kristmundsdóttir; Florian Zink; Eiríkur Hjartarson; Marteinn Hardarson; Kristjan Hjorleifsson; Hannes Eggertsson; Sigurjón Axel Guðjónsson; Lucas D. Ward; Gudny Arnadottir; Einar A. Helgason; Hannes Helgason; Arnaldur Gylfason; Aðalbjörg Jónasdóttir; Áslaug Jónasdóttir; Thorunn Rafnar; Soren Besenbacher; Michael L. Frigge; Simon N. Stacey; Ólafur T. Magnússon; Unnur Þorsteinsdóttir; Gísli Másson; Augustine Kong; Bjarni Halldórsson; Agnar Helgason; Daniel Gudbjartsson; Kari Stefansson

doi:10.1038/sdata.2017.115

Whole genome characterization of sequence diversity of 15,220 Icelanders

Hákon Jónsson, patrick sulem, Birte Kehr, Snædís Kristmundsdóttir, Florian Zink, Eiríkur Hjartarson, Marteinn Hardarson, Kristjan Hjorleifsson, Hannes Eggertsson, Sigurjón Axel Guðjónsson, Lucas D. Ward, Gudny Arnadottir, Einar A. Helgason, Hannes Helgason, Arnaldur Gylfason, Aðalbjörg Jónasdóttir, Áslaug Jónasdóttir, Thorunn Rafnar, Soren Besenbacher, Michael L. FriggeSimon N. Stacey, Ólafur T. Magnússon, Unnur Þorsteinsdóttir, Gísli Másson, Augustine Kong, Bjarni Halldórsson, Agnar Helgason, Daniel Gudbjartsson, Kari Stefansson

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English
Number of pages	170115
Journal	Scientific data
Volume	4
DOIs	https://doi.org/10.1038/sdata.2017.115
Publication status	Published - 21 Sept 2017

Other keywords

DNA sequencing
Genetic variation
Haplotypes
Rare variants
DNA-rannsóknir
Erfðabreytileiki
Erfðafræði

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10.1038/sdata.2017.115

https://hdl.handle.net/20.500.11815/441

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Jónsson, H., sulem, P., Kehr, B., Kristmundsdóttir, S., Zink, F., Hjartarson, E., Hardarson, M., Hjorleifsson, K., Eggertsson, H., Guðjónsson, S. A., Ward, L. D., Arnadottir, G., Helgason, E. A., Helgason, H., Gylfason, A., Jónasdóttir, A., Jónasdóttir, Á., Rafnar, T., Besenbacher, S., ... Stefansson, K. (2017). Whole genome characterization of sequence diversity of 15,220 Icelanders. Scientific data, 4. https://doi.org/10.1038/sdata.2017.115

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abstract = "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.",

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doi = "10.1038/sdata.2017.115",

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Jónsson, H, sulem, P, Kehr, B, Kristmundsdóttir, S, Zink, F, Hjartarson, E, Hardarson, M, Hjorleifsson, K, Eggertsson, H, Guðjónsson, SA, Ward, LD, Arnadottir, G, Helgason, EA, Helgason, H, Gylfason, A, Jónasdóttir, A, Jónasdóttir, Á, Rafnar, T, Besenbacher, S, Frigge, ML, Stacey, SN, Magnússon, ÓT, Þorsteinsdóttir, U, Másson, G, Kong, A, Halldórsson, B, Helgason, A, Gudbjartsson, D & Stefansson, K 2017, 'Whole genome characterization of sequence diversity of 15,220 Icelanders', Scientific data, vol. 4. https://doi.org/10.1038/sdata.2017.115

TY - JOUR

T1 - Whole genome characterization of sequence diversity of 15,220 Icelanders

AU - Jónsson, Hákon

AU - sulem, patrick

AU - Kehr, Birte

AU - Kristmundsdóttir, Snædís

AU - Zink, Florian

AU - Hjartarson, Eiríkur

AU - Hardarson, Marteinn

AU - Hjorleifsson, Kristjan

AU - Eggertsson, Hannes

AU - Guðjónsson, Sigurjón Axel

AU - Ward, Lucas D.

AU - Arnadottir, Gudny

AU - Helgason, Einar A.

AU - Helgason, Hannes

AU - Gylfason, Arnaldur

AU - Jónasdóttir, Aðalbjörg

AU - Jónasdóttir, Áslaug

AU - Rafnar, Thorunn

AU - Besenbacher, Soren

AU - Frigge, Michael L.

AU - Stacey, Simon N.

AU - Magnússon, Ólafur T.

AU - Þorsteinsdóttir, Unnur

AU - Másson, Gísli

AU - Kong, Augustine

AU - Halldórsson, Bjarni

AU - Helgason, Agnar

AU - Gudbjartsson, Daniel

AU - Stefansson, Kari

PY - 2017/9/21

Y1 - 2017/9/21

N2 - 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.

AB - 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.

KW - DNA sequencing

KW - Genetic variation

KW - Haplotypes

KW - Rare variants

KW - DNA-rannsóknir

KW - Erfðabreytileiki

KW - Erfðafræði

KW - DNA sequencing

KW - Genetic variation

KW - Haplotypes

KW - Rare variants

KW - DNA-rannsóknir

KW - Erfðabreytileiki

KW - Erfðafræði

U2 - 10.1038/sdata.2017.115

DO - 10.1038/sdata.2017.115

M3 - Article

SN - 2052-4463

VL - 4

JO - Scientific data

JF - Scientific data

ER -

Whole genome characterization of sequence diversity of 15,220 Icelanders

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