Explore Genetic Variation of Human Cancer Genes in DISQOVER

One of the key types of information in DISQOVER is human genetic variations and their links to genes, diseases etc. We recently integrated two new data sources: 1000 Genomes and gnomAD. These data sources include human variation and genotype data derived from a large set of human individuals.

DISQOVER is currently covering the data of a subset of 202 genes from these data sources. These are the  ‘COSMIC classic genes’ – a list of expert curated genes, that are somatically mutated and causally implicated in human cancer.

  • 1000 Genomes. The 1000 Genomes Project ran between 2008 and 2015, creating the world’s largest public catalogue of human variation and genotype data. The goal of the 1000 Genomes Project was to find genetic variants with frequencies of at least 1% in the populations studied. The project is continued by EMBL-EBI and receives funding from the Wellcome Trust.
  • gnomAD. The Genome Aggregation Database (gnomAD) is a resource developed by an international alliance of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available to the wider scientific community. The data is hosted by the Broad Institute.

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An example of such a human cancer-associated gene is RB1 a gene that encodes the protein called ‘RB Transcriptional Corepressor 1’ that acts as a tumor suppressor. In DISQOVER, RB1 is currently linked to 938 variants, 313 of which are annotated with information from gnomAD on the one hand and 113 are annotated by 1000 genomes on the other .  Moreover, 24 are classified as pathogenic variations.

You can see these results here.

With DISQOVER, genetic variation can be explored thanks to the integration and linking of several data sources like dbSNP, Clinvar, dbVar, DisGeNET, PROVEAN… and now enriched with GnomAD and 1000 genomes.

 

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