When genomic information is ingested and made available in the Cohort Browser, variants can be annotated using NCBI's dbSNP and Ensembl's gnomAD. The specific versions of each are provided during the ingestion process and allows the ingestion process to create a set of tables optimized for cohort creation through the Cohort Browser.
Accessing the Locus Details Page
In the Cohort Browser, various annotation data (e.g. gene name, consequence, rsID) are already available for both cohort creation and for quick cohort interrogation. To access more detailed information, in the variant section of the Cohort Browser, simply clickthelocation in the allele table and the locus detail’s page will open in a new tab.
An example using synthetic UKB data shows how clicking a locus launches a locus details page.
Locus Details Page Subsections
The page is split into 3 sections, all pre-calculated during ingestion of the dataset. The sections start with a summary of the locus, including the genotype frequencies for the datasets at the locus and then there's a detailed breakdown of annotations by allele.
An example of a location detail pane.
This pane shows quickly summary information for the locus in relation to the dataset. It shows the chromosome and starting position, the frequency of both the reference allele and the no-calls, and it shows the sum total of alleles available.
Synthetic genotype distribution of a dataset
The genotypes section allows users to see a detailed breakdown of the various genotypes in the dataset. Given order is not preserved, which means a C/A and A/C will count in the same bucket so only half of the crosstab is populated. Note that these genotypes are for the dataset as a whole at the specific location, and are not specific to the selected cohort.
Sample annotation information for the 13:32,332,383 C>A allele
Each allele available in the dataset is split up to show various information that was pulled from dbSNP and gnomAD during ingestion. If an rsID or AffyID was available, it is shown along with a link to its NCBI's dbSNP page. Additionally, the allele type, dataset frequency, and gnomAD frequency are shown for easy reference. Further information about the allele is broken down based on the different transcripts available. Columns in this section can very based on the annotation resources used.