Genetic Data | PandaOmics

Genetic Data

PandaOmics extensively utilizes genetic data for the purpose of ranking drug targets and computing TargetID scores.

The Genetics tab, available for Disease and Meta-analysis pages, allows users to explore genetic variants associated with a disease of interest.

PandaOmics Manual

The Genetics page displays a list of genes carrying genetic variants, known to be associated with a disease of interest. At present, PandaOmics consolidates the following databases: ClinVar, GWAS Catalog, and IntOGen.

The following information is available for a gene:

• The number of genetic variants categorized into distinct groups: Pathogenic, Likely Pathogenic, Conflicting, Uncertain, Other
• Predicted gene role as a cancer driver: either an oncogene (gene harbors activating mutations) or tumor suppressor (gene harbors loss-of-function mutations)
• Values of several genetics-related TargetID scores, including Mutations and Mutated Sub-modules
• Gene annotation reflecting its potential as a drug target including accessibility by small molecules and antibodies, novelty, safety, availability of 3D structure, development level, target family

Genes are arranged in descending order based on the count of pathogenic variants. Clicking on a gene reveals comprehensive details about genetic variants, with the extent of information varying according to the data source.

Common genetic variant properties

include the following:

• dbSNP identifier, e.g. rs12345
• variant name, e.g. p.Gly34Phe
• variant origin: e.g. germline
• links to source databases

For ClinVar variants:

• Clinical significance (Pathogenic, Likely Pathogenic, Conflicting, Uncertain, Other)
• Variant type, specific nature of the genetic change, e.g. single nucleotide variation (SNV), insertion, deletion, copy number gain, etc.
• Values of several genetics-related TargetID scores, including Mutations and Mutated Sub-modules
• Review status, the level of review and curation that a submitted genetic variant or clinical interpretation has undergone, helping users assess the reliability of the variant's clinical significance classification, with options ranging from no assertion provided to expert panel review.

For GWAS Catalog variants:

• Variant context — synonymous, stop lost, intron, …
• p-value representing the statistical significance of the association between the variant and a particular disease or phenotype.
• Beta-coefficient or odds ratio associated with strongest SNP risk allele. Appropriate unit and increase/decrease are included for beta coefficients
• 95% confidence interval associated with strongest SNP risk allele, along with unit in the case of beta-coefficients. Unreported values are denoted by the abbreviation 'NR'