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Cancer Summary of Findings HTML report

In cancer referrals, the Summary of Findings (SoF) will be automatically produced by the Bioinformatics pipeline and is available for download in the Referral Overview page via the Summary of Findings HTML and the Supplementary Findings HTML, which are described below.

Supplementary HTML files can be downloaded from the Interpretation Portal. The coordinates for all variants presented in the supplementary HTML file are hyperlinks to access the appropriate genomic region using the IGV viewer. After following a link, a login screen for OpenCGA is presented, and after logging in, a list of files available to view in IGV is shown.

Summary of Findings HTML

This file includes information about:

  • Overview data: Patient, Tumour details, Tumour sample and Germline sample.
  • Somatic Variants
  • Structural variants (including Copy Number Variants)
  • Additional Information.

Supplementary Findings HTML

This file includes information about:

  • Overview data: Patient, Tumour details, Tumour sample, Germline sample and Sequencing quality information.
  • Description of somatic variants: Circos plot (genome-wide visualisation of somatic variants and sequencing depth), small somatic variants and structural variants (including Copy Number Variants).
  • Global analysis of somatic variants: Somatic mutation prevalence (tumour mutation burden), contextual analysis of somatic SNVs, mutational signature analysis, cluster analysis of somatic SNVs (rainfall plot), analysis of variant allele frequency (VAF) of SNVs and indels and length of indels (<50bp).
  • Analysis of germline variants: Germline analysis: variants in cancer susceptibility genes
  • Additional information
Last update: 2023-09-18