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, respectively, 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).
Clinical information
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.
Mutated genes
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.
Fusion genes
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. More information about
gene fusions and methods for their detection and visualisation can be
found in the fusions dir.
Prioritisation
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
- 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)
Filtering
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 SV 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
Structural variants
Similar to Mutated genes analysis but limited to genes located within SVs detected by Manta using genomic data. This section is available only for samples with available Manta results.
CN altered genes
Section overlaying the mRNA expression data for cancer genes with per-gene somatic copy-number (CN) data (from PURPLE) and mutation status, if available.
Immune markers
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.
HRD genes
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.
Drug matching
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.
Note
This section is not displayed as default. Set the
--drugs argument to TRUE to present it in the
report.