- Input data
- Clinical information
- Findings summary
- Mutated genes
- Fusion genes
- Structural variants
- CN altered genes
- Immune markers
- HRD genes
- Cancer genes
- Drug matching
- Addendum
The Mutated genes, Structural variants and CN altered genes sections will contain information about expression levels of the mutated genes, genes located within detected structural variants (SVs) and copy-number (CN) altered regions, respectively. Genes will be ordered by increasing variants TIER, SV score and CN value, resepctively, and then by decreasing absolute values in the Patient vs selected dataset column. Moreover, gene fusions detected in WTS data and reported in Fusion genes section will be first ordered based on the evidence from genome-based data (DNA support (gene A/B) columns).
Summary of the input data
Treatment regimen information for patient for which clinical information is available.
NOTE: for confidentiality reasons, the timeline (x-axis) projecting patient’s treatment regimens (y-axis) is set to start from 1st January 2000, but the treatments lengths are preserved.
Plot and table summarising altered genes listed across various report sections
mRNA expression levels of mutated genes (containing single nucleotide variants (SNVs) or insertions/deletions (indels)) measured in patient's sample and their average mRNA expression in samples from cancer patients (from TCGA). This section is available only for samples with available umccrise results
Prioritised fusion genes based on Arriba results and annotated with FusionGDB database. If WGS results from umccrise are available then fusion genes in the Fusion genes report section are ordered based on the evidence from genome-based data. For more information about gene fusions and methods for their detectecion and visualisation can be found here.
Fusion genes detected in transcriptome data are prioritised based on criteria ranked in the following order:
- Involvement of fusion gene(s) detected in genomic data (if Structural variants results are available)
- Detected in transcriptome data by Arriba tool
- Reported fusion event according to FusionGDB database
- Decreasing number of split reads
- Decreasing number of pair reads
- Involvement of cancer gene(s) (see Cancer genes section)
Fusion genes detected in transcriptome data are reported if at least one of the following criteria is met:
- Involvement of fusion gene(s) detected in genomic data (if Structural variants results are available)
- Reported fusion event according to FusionGDB database
- Involvement of cancer gene(s) (see Cancer genes section)
- Split reads > 1
- Pair reads > 1 and split reads > 1
Similar to Mutated genes analysis but limited to genes located within structural variants (SVs) detected by MANTA using genomic data. This section is available only for samples with available MANTA results.
Section overlaying the mRNA expression data for cancer genes with per-gene somatic copy-number (CN) data (from PURPLE) and mutation status, if available.
Similar to Mutated genes analysis but limited to genes considered to be immune markers. The immune markers used in the report are listed in PanelApp panel Immune markers for WTS report.
Similar to Mutated genes analysis but limited to genes considered to be homologous recombination deficiency (HRD) genes. The HRD genes used in the report are listed in PanelApp panel Homologous recombination deficiency (HDR) for WTS report.
Similar to analysis above, but limited to UMCCR cancer genes.
List of drugs targeting variants in detected mutated genes, fusion genes, structural variants-affected genes, CN altered genes, HRD genes and dysregulated cancer genes, which can be considered in the treatment decision making process.
This section is not displayed as default. Set the --drugs argument to TRUE to present it in the report.
Additional information, including Parameters, Reporter details and R Session information, added at the end of the report.