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

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

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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.

Original language	English
Article number	30
Journal	BMC genomic data
Volume	24
Issue number	1
Number of pages	4
ISSN	2730-6844
DOIs	https://doi.org/10.1186/s12863-023-01132-7
Publication status	Published - 27 May 2023

Bibliographical note

Keywords

Denmark
Female
Genome
Genomics
Humans
Polymorphism, Single Nucleotide/genetics
Whole Genome Sequencing/methods
Minor allele counts
Whole genome sequencing
Sequence variants
Browser
Variant interpretation

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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), Article 30. https://doi.org/10.1186/s12863-023-01132-7

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

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.",

keywords = "Denmark, Female, Genome, Genomics, Humans, Polymorphism, Single Nucleotide/genetics, Whole Genome Sequencing/methods, Minor allele counts, Whole genome sequencing, Sequence variants, Browser, Variant interpretation",

author = "Karina Banasik and M{\o}ller, {Peter L} and Techlo, {Tanya R} and Holm, {Peter C} and Walters, {G Bragi} and Andr{\'e}s Ingason and Anders Rosengren and Rohde, {Palle D} and Kogelman, {Lisette J A} and David Westergaard and Troels Siggaard and Chmura, {Piotr J} and Chalmer, {Mona A} and Magn{\'u}sson, {{\'O}lafur {\TH}} and {\TH}{\'o}risson, {Gu{\dh}mundur {\'A}} and Hreinn Stef{\'a}nsson and Gu{\dh}bjartsson, {Dan{\'i}el F} and K{\'a}ri Stef{\'a}nsson and Jes Olesen and Simon Winther and Morten B{\o}ttcher and S{\o}ren Brunak and Thomas Werge and Mette Nyegaard and Hansen, {Thomas F}",

note = "{\textcopyright} 2023. The Author(s).",

year = "2023",

month = may,

day = "27",

doi = "10.1186/s12863-023-01132-7",

language = "English",

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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, vol. 24, no. 1, 30. https://doi.org/10.1186/s12863-023-01132-7

TY - JOUR

T1 - DanMAC5

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 - Female

KW - Genome

KW - Genomics

KW - Humans

KW - Polymorphism, Single Nucleotide/genetics

KW - Whole Genome Sequencing/methods

KW - Minor allele counts

KW - Whole genome sequencing

KW - Sequence variants

KW - Browser

KW - Variant interpretation

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U2 - 10.1186/s12863-023-01132-7

DO - 10.1186/s12863-023-01132-7

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SN - 2730-6844

VL - 24

JO - BMC genomic data

JF - BMC genomic data

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

Abstract

Bibliographical note

Keywords

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