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.
Note
Variant filtering for reported variants in tumour first cases in DSS may differ from that in HTMLs: in these cases, we apply both somatic and germline prioritisation algorithms to all variants with GEL internal population germline allele frequency under 2%, so all such variants will appear on the DSS. In the HTMLs and CSV tables, all variants with either GEL internal or gnomAD population germline allele frequency over 1% and no potential effect on cancer predisposition genes (nothing in the "Interpretation as germline" field) are filtered out.
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