DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals

Karina Banasik; Peter L Møller; Tanya R Techlo; Peter C Holm; G Bragi Walters; Andrés Ingason; Anders Rosengren; Palle D Rohde; Lisette J A Kogelman; David Westergaard; Troels Siggaard; Piotr J Chmura; Mona A Chalmer; Ólafur Þ Magnússon; Guðmundur Á Þórisson; Hreinn Stefánsson; Daníel F Guðbjartsson; Kári Stefánsson; Jes Olesen; Simon Winther; Morten Bøttcher; Søren Brunak; Thomas Werge; Mette Nyegaard; Thomas F Hansen

doi:10.1186/s12863-023-01132-7

DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals

Karina Banasik, Peter L Møller, Tanya R Techlo, Peter C Holm, G Bragi Walters, Andrés Ingason, Anders Rosengren, Palle D Rohde, Lisette J A Kogelman, David Westergaard, Troels Siggaard, Piotr J Chmura, Mona A Chalmer, Ólafur Þ Magnússon, Guðmundur Á Þórisson, Hreinn Stefánsson, Daníel F Guðbjartsson, Kári Stefánsson, Jes Olesen, Simon WintherMorten Bøttcher, Søren Brunak, Thomas Werge, Mette Nyegaard, Thomas F Hansen

Abstract

OBJECTIVES: Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the Danish population. Here, we present a dataset with allele counts for sequence variants (single nucleotide variants (SNVs) and indels) identified from WGS of 8,671 (5,418 females) individuals from the Danish population. The data resource is based on WGS data from three independent research projects aimed at assessing genetic risk factors for cardiovascular, psychiatric, and headache disorders. To enable the sharing of information on sequence variation in Danish individuals, we created summarized statistics on allele counts from anonymized data and made them available through the European Genome-phenome Archive (EGA, https://identifiers.org/ega.

DATASET: EGAD00001009756 ) and in a dedicated browser, DanMAC5 (available at www.danmac5.dk ). The summary level data and the DanMAC5 browser provide insight into the allelic spectrum of sequence variants segregating in the Danish population, which is important in variant interpretation.

DATA DESCRIPTION: Three WGS datasets with an average coverage of 30x were processed independently using the same quality control pipeline. Subsequently, we summarized, filtered, and merged allele counts to create a high-quality summary level dataset of sequence variants.

Originalsprog	Engelsk
Artikelnummer	30
Tidsskrift	BMC genomic data
Vol/bind	24
Udgave nummer	1
ISSN	2730-6844
DOI	https://doi.org/10.1186/s12863-023-01132-7
Status	Udgivet - 27 maj 2023

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10.1186/s12863-023-01132-7

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Banasik, K., Møller, P. L., Techlo, T. R., Holm, P. C., Walters, G. B., Ingason, A., Rosengren, A., Rohde, P. D., Kogelman, L. J. A., Westergaard, D., Siggaard, T., Chmura, P. J., Chalmer, M. A., Magnússon, Ó. Þ., Þórisson, G. Á., Stefánsson, H., Guðbjartsson, D. F., Stefánsson, K., Olesen, J., ... Hansen, T. F. (2023). DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals. BMC genomic data, 24(1), [30]. https://doi.org/10.1186/s12863-023-01132-7

Banasik, K, Møller, PL, Techlo, TR, Holm, PC, Walters, GB, Ingason, A , Rosengren, A, Rohde, PD, Kogelman, LJA, Westergaard, D, Siggaard, T, Chmura, PJ, Chalmer, MA, Magnússon, ÓÞ, Þórisson, GÁ, Stefánsson, H, Guðbjartsson, DF, Stefánsson, K, Olesen, J, Winther, S, Bøttcher, M, Brunak, S, Werge, T, Nyegaard, M & Hansen, TF 2023, 'DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals', BMC genomic data, bind 24, nr. 1, 30. https://doi.org/10.1186/s12863-023-01132-7

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abstract = "OBJECTIVES: Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the Danish population. Here, we present a dataset with allele counts for sequence variants (single nucleotide variants (SNVs) and indels) identified from WGS of 8,671 (5,418 females) individuals from the Danish population. The data resource is based on WGS data from three independent research projects aimed at assessing genetic risk factors for cardiovascular, psychiatric, and headache disorders. To enable the sharing of information on sequence variation in Danish individuals, we created summarized statistics on allele counts from anonymized data and made them available through the European Genome-phenome Archive (EGA, https://identifiers.org/ega.DATASET: EGAD00001009756 ) and in a dedicated browser, DanMAC5 (available at www.danmac5.dk ). The summary level data and the DanMAC5 browser provide insight into the allelic spectrum of sequence variants segregating in the Danish population, which is important in variant interpretation.DATA DESCRIPTION: Three WGS datasets with an average coverage of 30x were processed independently using the same quality control pipeline. Subsequently, we summarized, filtered, and merged allele counts to create a high-quality summary level dataset of sequence variants.",

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T2 - a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals

AU - Banasik, Karina

AU - Møller, Peter L

AU - Techlo, Tanya R

AU - Holm, Peter C

AU - Walters, G Bragi

AU - Ingason, Andrés

AU - Rosengren, Anders

AU - Rohde, Palle D

AU - Kogelman, Lisette J A

AU - Westergaard, David

AU - Siggaard, Troels

AU - Chmura, Piotr J

AU - Chalmer, Mona A

AU - Magnússon, Ólafur Þ

AU - Þórisson, Guðmundur Á

AU - Stefánsson, Hreinn

AU - Guðbjartsson, Daníel F

AU - Stefánsson, Kári

AU - Olesen, Jes

AU - Winther, Simon

AU - Bøttcher, Morten

AU - Brunak, Søren

AU - Werge, Thomas

AU - Nyegaard, Mette

AU - Hansen, Thomas F

PY - 2023/5/27

Y1 - 2023/5/27

N2 - OBJECTIVES: Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the Danish population. Here, we present a dataset with allele counts for sequence variants (single nucleotide variants (SNVs) and indels) identified from WGS of 8,671 (5,418 females) individuals from the Danish population. The data resource is based on WGS data from three independent research projects aimed at assessing genetic risk factors for cardiovascular, psychiatric, and headache disorders. To enable the sharing of information on sequence variation in Danish individuals, we created summarized statistics on allele counts from anonymized data and made them available through the European Genome-phenome Archive (EGA, https://identifiers.org/ega.DATASET: EGAD00001009756 ) and in a dedicated browser, DanMAC5 (available at www.danmac5.dk ). The summary level data and the DanMAC5 browser provide insight into the allelic spectrum of sequence variants segregating in the Danish population, which is important in variant interpretation.DATA DESCRIPTION: Three WGS datasets with an average coverage of 30x were processed independently using the same quality control pipeline. Subsequently, we summarized, filtered, and merged allele counts to create a high-quality summary level dataset of sequence variants.

AB - OBJECTIVES: Allele counts of sequence variants obtained by whole genome sequencing (WGS) often play a central role in interpreting the results of genetic and genomic research. However, such variant counts are not readily available for individuals in the Danish population. Here, we present a dataset with allele counts for sequence variants (single nucleotide variants (SNVs) and indels) identified from WGS of 8,671 (5,418 females) individuals from the Danish population. The data resource is based on WGS data from three independent research projects aimed at assessing genetic risk factors for cardiovascular, psychiatric, and headache disorders. To enable the sharing of information on sequence variation in Danish individuals, we created summarized statistics on allele counts from anonymized data and made them available through the European Genome-phenome Archive (EGA, https://identifiers.org/ega.DATASET: EGAD00001009756 ) and in a dedicated browser, DanMAC5 (available at www.danmac5.dk ). The summary level data and the DanMAC5 browser provide insight into the allelic spectrum of sequence variants segregating in the Danish population, which is important in variant interpretation.DATA DESCRIPTION: Three WGS datasets with an average coverage of 30x were processed independently using the same quality control pipeline. Subsequently, we summarized, filtered, and merged allele counts to create a high-quality summary level dataset of sequence variants.

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KW - Humans

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KW - Whole Genome Sequencing/methods

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DO - 10.1186/s12863-023-01132-7

M3 - Journal article

C2 - 37244984

VL - 24

JO - BMC genomic data

JF - BMC genomic data

SN - 2730-6844

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DanMAC5: a browser of aggregated sequence variants from 8,671 whole genome sequenced Danish individuals

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