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.

A genome-wide association study of social trust in 33,882 Danish blood donors

“…Variants displayed comparable effects on the phenotype (Supplementary Fig. 6 ), and similar minor allele frequencies that were consistent with that of other non-Finnish North-western European populations in gnomAD 36 and of a Danish genome reference panel (DanMAC5 37 ; Supplementary Table 2 ). All were in close linkage disequilibrium (LD, r 2 > 0.89) with the lead variant (rs12776883), which we focused the subsequent analyses on.…”

“…Genome-wide significant variants were filtered again for imputation quality > 0.9, genotype missingness < 0.1, and Hardy–Weinberg Equilibrium (HWE, no significant heterozygote excess at the 5% significance level). Observed MAFs were compared with those of other European populations as provided by gnomAD 36 and with a Danish reference genome panel (DanMAC5) 37 built from 8671 whole genome sequences (Supplementary Table 2 ). Data filtering, MAF calculations and tests of HWE were performed using PLINK v2.0 76 .…”

Pregnancy-Associated Bleeding and Genetics: Five Sequence Variants in the Myometrium and Progesterone Signaling Pathway are associated with postpartum hemorrhage

“…All samples were genotyped at deCODE genetics using the Illumina Infinium Global Screening array. Samples were imputed using an in-house pan-Scandinavian reference panel 28 . Association analysis was performed using software developed at deCODE genetics 29 .…”

“…Furthermore, there were strong genetic correlations with birth weight, gestational duration, and uterine fibroids. Early bleeding during pregnancy (28,898 cases and 302,894 controls) yielded no genome-wide association signals, but showed strong genetic correlation with a variety of human traits, indicative of polygenic and pleiotropic effects. Our results suggest that postpartum bleeding is related to myometrium dysregulation, whereas early bleeding is a complex trait related to underlying health and possibly socioeconomic status.…”