Dataset Information

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.

SUBMITTER: Banasik K

PROVIDER: S-EPMC10225079 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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Publications

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

Banasik Karina K Møller Peter L PL Techlo Tanya R TR Holm Peter C PC Walters G Bragi GB Ingason Andrés A Rosengren Anders A Rohde Palle D PD Kogelman Lisette J A LJA Westergaard David D Siggaard Troels T Chmura Piotr J PJ Chalmer Mona A MA Magnússon Ólafur Þ ÓÞ Þórisson Guðmundur Á GÁ Stefánsson Hreinn H Guðbjartsson Daníel F DF Stefánsson Kári K Olesen Jes J Winther Simon S Bøttcher Morten M Brunak Søren S Werge Thomas T Nyegaard Mette M Hansen Thomas F TF

BMC genomic data 20230527 1

<h4>Objectives</h4>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 ...[more]

PMID: 37244984

Similar Datasets

Project description:BackgroundStructural variants (SVs) are chromosomal segments that differ between genomes, such as deletions, duplications, insertions, inversions and translocations. The genomics revolution enabled the discovery of sub-microscopic SVs via array and whole-genome sequencing (WGS) data, paving the way to unravel the functional impact of SVs. Recent human expression QTL mapping studies demonstrated that SVs play a disproportionally large role in altering gene expression, underlining the importance of including SVs in genetic analyses. Therefore, this study aimed to generate and explore a high-quality bovine SV catalogue exploiting a unique cattle family cohort data (total 266 samples, forming 127 trios).ResultsWe curated 13,731 SVs segregating in the population, consisting of 12,201 deletions, 1,509 duplications, and 21 multi-allelic CNVs (> 50-bp). Of these, we validated a subset of copy number variants (CNVs) utilising a direct genotyping approach in an independent cohort, indicating that at least 62% of the CNVs are true variants, segregating in the population. Among gene-disrupting SVs, we prioritised two likely high impact duplications, encompassing ORM1 and POPDC3 genes, respectively. Liver expression QTL mapping results revealed that these duplications are likely causing altered gene expression, confirming the functional importance of SVs. Although most of the accurately genotyped CNVs are tagged by single nucleotide polymorphisms (SNPs) ascertained in WGS data, most CNVs were not captured by individual SNPs obtained from a 50K genotyping array.ConclusionWe generated a high-quality SV catalogue exploiting unique whole genome sequenced bovine family cohort data. Two high impact duplications upregulating the ORM1 and POPDC3 are putative candidates for postpartum feed intake and hoof health traits, thus warranting further investigation. Generally, CNVs were in low LD with SNPs on the 50K array. Hence, it remains crucial to incorporate CNVs via means other than tagging SNPs, such as investigation of tagging haplotypes, direct imputation of CNVs, or direct genotyping as done in the current study. The SV catalogue and the custom genotyping array generated in the current study will serve as valuable resources accelerating utilisation of full spectrum of genetic variants in bovine genomes.

Dataset Information

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

Objectives

Dataset

Data description

Publications

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

Similar Datasets

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