+This track shows allele counts and frequencies from +gnomAD-Canada, the Canadian arm of the +Genome Aggregation Database. The v1.0 release aggregates whole-genome sequencing data from 10,487 +participants in the Canadian COVID-19 +HostSeq databank, a national initiative +launched in April 2020 that recruited people infected with SARS-CoV-2 together with controls from +fourteen clinical and epidemiological studies across Canada. Because the cohort was assembled to +study host susceptibility to a common infection rather than a rare genetic disease, it serves here +as a population-scale reference of Canadian genetic variation. +
++Frequencies are reported for the whole cohort and for nine genetic-ancestry groups inferred by the +gnomAD pipeline: African/African-American, Latino/Admixed-American, European (non-Finnish), +Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, South Asian, and Remaining +individuals. The release contains about 213 million variant sites. The per-variant details page +also shows the group with the highest frequency (grpmax) and the gnomAD variant-quality filter +status. +
+ ++This is a Variant Call Format (VCF) track. Hovering over a variant shows the overall allele +frequency, and clicking a variant opens a details page with the overall and per-ancestry allele +counts, allele numbers and frequencies, the dbSNP identifier, and the variant filter status. The +filter status is one of PASS, RF (failed the gnomAD random-forest +variant-quality filter), or InbreedingCoeff (excess heterozygosity); variants with zero +release allele count (AC0) are not shown. +
+ ++The data can be explored interactively with the +Table Browser or the +Data Integrator. +For programmatic access, our REST API +can be used; the track name is hostseq. +For bulk download, the VCF is available from +our download +server. The original Hail table can be downloaded from the +gnomAD-Canada portal. +
+ ++Whole-genome sequencing was performed on 10,487 HostSeq participants at three CGEn sites on the +Illumina NovaSeq 6000 platform at 30X coverage. Reads were aligned to GRCh38 with the DRAGEN +mapper (DRAGMAP v1.3.0), de-duplicated with Picard (v2.25.0) and base-quality-recalibrated with +GATK (v4.2.5.0). Per-sample SNVs and indels were called with GATK HaplotypeCaller in DRAGEN mode, +and per-sample gVCFs were joint-genotyped with GATK GenotypeGVCFs. The joint callset was then run +through the Broad Institute's gnomAD QC v3 pipeline (adapted for on-premises use at the BC Cancer +Genome Sciences Centre), which performs sample quality control, relatedness and genetic-ancestry +inference by principal-component analysis, random-forest variant filtering, and computes overall +and per-ancestry allele frequencies. Full pipeline details are in the +release README and +the HostSeq cohort reference below. +
++The release-sites Hail table (release_sites_hostseq.tar.gz, ~101 GB) was downloaded from +https://www.bcgsc.ca/gnomad/download/release_sites_hostseq.tar.gz +and read with Hail. The overall and per-ancestry +allele counts, allele numbers and frequencies were flattened from the table's freq array +into VCF INFO fields, together with the dbSNP rsID and the variant filter status, and exported as a +sites-only VCF. The source table is already biallelic-split and uses UCSC chr-prefixed contigs, so +no allele-splitting or chromosome renaming was needed. Of the 232,028,491 variant rows in the +release table, 213,382,086 with a non-zero release allele count were written; the 18,646,405 +AC0 sites (no observed allele in the high-quality release) were dropped. The source +covers the autosomes plus chrX and chrY. About 15% of the written variants (32,074,697) carry the +gnomAD RF quality-filter flag and 158,230 the InbreedingCoeff flag; the +remaining 181,149,159 are PASS. Filter-flagged variants are retained so the full release +is browsable, and can be hidden with the track's filter controls. +Processing documentation is in the +varFreqs makeDoc file; the conversion script is in +our GitHub scripts directory. +
+ ++Data were generated by the gnomAD-Canada team as part of the Canadian Genomic Data Commons (CGDC) +and the Pan-Canadian Genome Library (PCGL), using CGEn's HostSeq databank (funded by the Government +of Canada through Genome Canada, Project DACO-18). Thanks to the HostSeq participants and to the +gnomAD-Canada project leadership (Jordan Lerner-Ellis, Steven Jones and Daniel Taliun) for making +the aggregate data publicly available. Per the data providers, no attempts should be made to +relabel the gnomAD-Canada genetic-ancestry groups. +
+ ++Yoo S, Garg E, Elliott LT, Hung RJ, Halevy AR, Brooks JD, Bull SB, Gagnon F, Greenwood C, Lawless JF +et al. + +HostSeq: a Canadian whole genome sequencing and clinical data resource. +BMC Genom Data. 2023 May 2;24(1):26. +PMID: 37131148; PMC: PMC10152008 +
+ + + ++Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, +Gauthier LD et al. + +A genomic mutational constraint map using variation in 76,156 human genomes. +Nature. 2024 Jan;625(7993):92-100. +PMID: 38057664; PMC: PMC11629659 +
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