Overview
Row
Overview
SNVs/InDels
Total variants
2616
SNVs
1969
InDels
647
TIER 1 variants
0
TIER 2 variants
1
Row
Allelic support plot
Documentation
The prioritization of SNV and InDels found in the tumor sample is done according to a four-tiered structure, adopting the joint consensus recommendation by AMP/ACMG Li et al., 2017.
- TIER 1: Variants of strong clinical significance - constitutes variants linked to predictive, prognostic, or diagnostic biomarkers in the CIViC database and the Cancer Biomarkers Database that are
- Found within the same tumor type/class as specified by the user, AND
- Of strong clinical evidence (i.e. part of guidelines, validated or discovered in late clinical trials (CIViC evidence levels A/B))
- overlap between variants in the tumor sample and reported biomarkers must occur at the exact variant level or at the codon/exon level
- TIER 2: Variants of potential clinical significance - constitutes other variants linked to predictive, prognostic, or diagnostic biomarkers in the CIViC database and the Cancer Biomarkers Database that are either
- Of strong clinical evidence in other tumor types/classes than the one specified by the user, OR
- Of weak clinical evidence (early trials, case reports etc. (CIViC evidence levels C/D/E))) in the same tumor type/class as specified by the user
- overlap between variants in the tumor sample and reported biomarkers must occur at the exact variant level or at the codon/exon level
- TIER 3: Variants of uncertain clinical significance - includes other coding variants found in oncogenes or tumor suppressor genes
- Status as oncogenes and/or tumor suppressors genes are done according to the following scheme in PCGR:
- Five or more publications in the biomedical literature that suggests an oncogenic/tumor suppressor role for a given gene (as collected from the CancerMine text-mining resource), OR
- At least two publications from CancerMine that suggests an oncogenic/tumor suppressor role for a given gene AND an existing record for the same gene as a tumor suppressor/oncogene in the Network of Cancer Genes (NCG)
- Status as oncogene is ignored if a given gene has three times as much (literature evidence) support for a role as a tumor suppressor gene (and vice versa)
- Oncogenes/tumor suppressor candidates from CancerMine/NCG that are found in the curated list of false positive cancer drivers compiled by Bailey et al. (Cell, 2018) have been excluded
- Status as oncogenes and/or tumor suppressors genes are done according to the following scheme in PCGR:
- TIER 4 - includes other protein-coding variants
- NONCODING - includes other noncoding variants
Row
Global variant datatable - filters
The global variant datatable (right) can be filtered according to various criteria:
- Filtering on sequencing depth/variant allelic fraction depends on input provided by user
- Filtering performed here will only apply to the datatable and not any other visualizations presented in this page
NOTE - listing top 2000 variants
Global variant datatable
Tier 1
Row
SNVs and InDels
TIER 1
Biomarker genes
0
Biomarker variants
0
Diagnostic evidence items
0
Prognostic evidence items
0
Predictive evidence items
0
Row
Tier 1 variant evidence items - filters
- No variants of strong clinical significance found.
Tier 1 - variant evidence items
- No variants of strong clinical significance found.
Tier 2
Row
SNVs and InDels
TIER 2
Biomarker genes
1
Biomarker variants
1
Diagnostic evidence items
0
Prognostic evidence items
0
Predictive evidence items
7
Row
Tier 2 variant evidence items - filters
Evidence items associated with variants in TIER 2 (right panel) can be interactively explored according to various criteria :
NOTE: Reported biomarkers in CIViC/CGI are mapped at different resolutions (i.e. filter Biomarker mapping). The accuracy of a match between variants in the tumor sample and the reported biomarkers will vary accordingly (highlighted by gene symbols with different color backgrounds):
- Biomarker match at the exact variant/codon level
- Biomarker match at the exon/gene level
Tier 2 - variant evidence items
Tier 3
Row
SNVs and InDels
TIER 3
Total variants
125
Variants in proto-oncogenes
36
Variants in tumor suppressor genes
78
Variants in genes with dual roles
11
Row
Tier 3 - variant filters
Variants in TIER 3 (right panel) can be interactively explored according to various criteria :
Tier 3 - variant datatable
Tier 4
Row
SNVs and InDels
TIER 4
Total variants
1601
SNVs
1150
InDels
451
Block substitutions
0
Row
Tier 4 - variant filters
Variants in TIER 4 (right panel) can be interactively explored according to various criteria :
Tier 4 - variant datatable
Noncoding
Row
SNVs and InDels
Noncoding
Total variants
889
SNVs
218
InDels
55
Block substitutions
0
Row
Noncoding - variant filters
Noncoding variants (right panel) can be interactively explored according to various criteria :
Noncoding - variant datatable
Complete biomarker set
Row
SNVs and InDels
Biomarkers
Biomarker genes
1
Biomarker variants
1
Diagnostic evidence items
0
Prognostic evidence items
0
Predictive evidence items
15
Row
All biomarker evidence items - filters
NOTE: Reported biomarkers in CIViC/CGI are mapped at different resolutions (i.e. filter Biomarker mapping). The accuracy of a match between variants in the tumor sample and the reported biomarkers will vary accordingly (highlighted by gene symbols with different color backgrounds):
- Biomarker match at the exact variant/codon level
- Biomarker match at the exon/gene level
All biomarker evidence items
Overview
Row
Overview
sCNA
Copy number gains
15
Copy number losses
30
TIER 1 biomarkers
0
TIER 2 biomarkers
1
Row
Copy number segments - filters
The following user-defined thresholds determine copy number aberrations shown here:
Copy number amplifications : Log(2) ratio >= 0.4
Homozygous deletions : Log(2) ratio <= -0.4
A total of 45 unfiltered aberration segments satisfied the above criteria.
Copy number segments
Row
Key findings
** - Proto-oncogenes subject to amplifications: 17**
** - Tumor suppressor genes subject to homozygous deletions: 2**
Documentation
Somatic copy number aberrations identified in the tumor sample are classified into two main tiers:
- TIER 1: Aberrations of strong clinical significance - constitutes amplified/lost genes linked to predictive, prognostic, or diagnostic biomarkers in the CIViC database and the Cancer Biomarkers Database that are
- Found within the same tumor type/class as specified by the user, AND
- Of strong clinical evidence (i.e. part of guidelines, validated or discovered in late clinical trials (CIViC evidence levels A/B))
- TIER 2: Aberrations of potential clinical significance - constitutes amplified/lost genes linked to predictive, prognostic, or diagnostic biomarkers in the CIViC database and the Cancer Biomarkers Database that are either
- Of strong clinical evidence in other tumor types/classes than the one specified by the user, OR
- Of weak clinical evidence (early trials, case reports etc. (CIViC evidence levels C/D/E))) in the same tumor type/class as specified by the user
Included in the report is also a complete list of all oncogenes subject to amplifications, tumor suppressor genes subject to homozygous deletions, and other drug targets subject to amplifications
- Status as oncogenes and/or tumor suppressors genes are done according to the following scheme in PCGR:
- Five or more publications in the biomedical literature that suggests an oncogenic/tumor suppressor role for a given gene (as collected from the CancerMine text-mining resource), OR
- At least two publications from CancerMine that suggests an oncogenic/tumor suppressor role for a given gene AND an existing record for the same gene as a tumor suppressor/oncogene in the Network of Cancer Genes (NCG)
- Status as oncogene is ignored if a given gene also has literature evidence support for a role as a tumor suppressor gene which is three times as large (and vice versa)
- Oncogenes/tumor suppressor candidates from CancerMine/NCG that are found in the curated list of false positive cancer drivers compiled by Bailey et al. (Cell, 2018) have been excluded
Tier 1
Row
sCNA
TIER 1
Biomarker genes
0
Biomarker aberrations
0
Diagnostic evidence items
0
Prognostic evidence items
0
Predictive evidence items
0
Row
Tier 1 variant evidence items - filters
- No somatic copy-number aberrations of strong clinical significance found.
Tier 1 - variant evidence items
- No somatic copy-number aberrations of strong clinical significance found.
Tier 2
Row
sCNA
TIER 2
Biomarker genes
1
Biomarker aberrations
1
Diagnostic evidence items
0
Prognostic evidence items
5
Predictive evidence items
5
Row
Tier 2 variant evidence items - filters
Evidence items associated with variants in tier 1 (right panel) can be filtered according to various criteria:
Tier 2 - variant evidence items
TMB & MSI
Row
Tumor mutational burden & MSI classification
TMB/MSI status
Coding target size
34 Mb
Coding mutations
1727
TMB estimate
65.53 mut/Mb
MSI prediction
MSI - High
Row
TCGA TMB distribution
MSI evidence I
The plot below illustrates the mutational burden of indels in TCGA-BR-A4QL-01A (black dashed line) along with the distribution in TCGA samples for samples with known MSI status ( MSI.H = high microsatellite instability, MSS = microsatellite stable):
Row
MSI evidence II
The plot below illustrates the fraction of indels among all calls in TCGA-BR-A4QL-01A(black dashed line) along with the distribution in TCGA for samples with known MSI status ( MSI.H = high microsatellite instability, MSS = microsatellite stable):
Somatic mutations in MMR genes
Mutational signatures
Row
Mutational Signatures (SBS)
SIGNATURES
SNVs eligible for analysis
1969
Most dominant aetiology
Aging
Accuracy of signature fitting (%)
96.7
High confident kataegis events
0
Row
Mutational signatures - aetiology contributions
Mutational signatures - aetiologies
Row
Mutational context frequency
Genomic distribution - rainfall
Kataegis events
Trials
Row
Molecularly targeted trials
Clinical trials
Not yet recruiting
64
Recruiting
246
Enrolling by invitation
0
Active, not recruiting
81
Unknown status
61
Row
Molecularly targeted trials - filters
- Ongoing or planned clinical trials in the relevant tumor type have been retrieved from clinicaltrials.gov, focusing on the subset with molecularly targeted therapies
- Key information entities (interventions/drugs, conditions) in trial records have been mapped to established thesauri (ChEMBL, NCI Thesaurus, UMLS/MedGen)
- Results from a text-mining procedure on unstructured trial text (e.g. inclusion/exclusion criteria) attempts to highlight the presence of established molecular biomarkers in cancer and relevant therapeutic contexts.
Molecularly targeted trials
Settings & Docs
Row
Settings - sample and report
The report is generated with PCGR version 0.10.19.
Key report configuration settings:
- Genome assembly: grch37
- Minimum sequencing depth tumor (DP, SNV/InDel): 0
- Minimum allelic fraction tumor (VAF, SNV/InDel): 0
- Minimum sequencing depth control (DP, SNV/InDel): 0
- Maximum allelic fraction control (VAF, SNV/InDel): 1
- Tier system (VCF): pcgr_acmg
- Show noncoding variants: FALSE
- MSI prediction: ON
- Mutational burden estimation: ON
- TMB algorithm: all_coding
- Mutational signatures estimation: ON
- Minimum number of mutations required: 200
- All reference signatures: FALSE
- Inclusion of artefact signatures: FALSE
- Minimum tumor-type prevalence (percent) of reference signatures used for refitting: 5
- Clinical trial inclusion: ON
- Variant Effect Predictor (VEP) settings:
- Transcript set: GENCODE - basic set (v19)
- Transcript pick order: canonical,appris,biotype,ccds,rank,tsl,length,mane
- Regulatory regions annotation: TRUE
Sample information:
- Tumor primary site: Esophagus/Stomach
Documentation - sequencing assay
- Assay sequencing type (VCF): WES
- Assay coding target size (VCF): 34 Mb
- Assay sequencing mode (VCF): Tumor-Control
Estimated properties on DNA cellularity and ploidy:
- Tumor purity: NA
- Tumor ploidy: NA
Documentaton - report data sources
The report generated with PCGR is based on the following underlying tools and knowledge resources:
PCGR databundle version
- 20220203
Software
- LOFTEE - Loss-Of-Function Transcript Effect Estimator (VEP plugin) (v1.0.3)
- vcfanno - Rapid annotation of VCF with other VCFs/BEDs/tabixed files (v0.3.3)
- MutationalPatterns - Comprehensive genome-wide analysis of mutational processes (v3.4.0)
- vcf2maf - VCF to MAF conversion (v1.6.21)
- Databases/datasets
- GENCODE - high quality reference gene annotation and experimental validation (release 39/19)
- dbNSFP - Database of non-synonymous functional predictions (20210406 (v4.2))
- dbMTS - Database of alterations in microRNA target sites (v1.0)
- ncER - Non-coding essential regulation score (genome-wide percentile rank) (v2)
- GERP - Genomic Evolutionary Rate Profiling (GERP) - rejected substitutions (RS) score (v1)
- Pfam - Collection of protein families/domains (2021_11 (v35.0))
- TCGA - The Cancer Genome Atlas - somatic mutations (20211029 (v31))
- ICGC-PCAWG - ICGC-Pancancer Analysis of Whole Genomes - somatic mutations (2020_01)
- TCGA-PCDM - Putative Cancer Driver Mutations based on multiple discovery approaches (2019)
- UniProtKB - Comprehensive resource of protein sequence and functional information (2021_04)
- gnomAD - Germline variant frequencies exome-wide (r2.1 (October 2018))
- COSMIC - Catalogue of somatic mutations in cancer (92)
- dbSNP - Database of short genetic variants (154)
- 1000Genomes - Germline variant frequencies genome-wide (20130502 (phase 3))
- DoCM - Database of curated mutations (release 3.2)
- CancerHotspots - A resource for statistically significant mutations in cancer (2017)
- ClinVar - Database of genomic variants of clinical significance (20220103)
- CancerMine - Literature-mined database of tumor suppressor genes/proto-oncogenes (20211106 (v42))
- OncoTree - Open-source ontology developed at MSK-CC for standardization of cancer type diagnosis (2021-11-02)
- DiseaseOntology - Standardized ontology for human disease (20220131)
- EFO - Experimental Factor Ontology (v3.38.0)
- OpenTargetsPlatform - Comprehensive and robust data integration for access to potential drug targets associated with disease (2021.11)
- ChEMBL - Manually curated database of bioactive molecules (20210701 (v29))
- KEGG - Knowledge base on the molecular interaction, reaction and relation networks (20211223)
- CIViC - Clinical interpretations of variants in cancer (20220201)
- CGI - Cancer Genome Interpreter Cancer Biomarkers Database (20180117)
Row
Documentation - report content
SNVs/InDels
The prioritization of SNV and InDels found in the tumor sample is done according to a four-tiered structure, adopting the joint consensus recommendation by AMP/ACMG Li et al., 2017.
- TIER 1: Variants of strong clinical significance - constitutes variants linked to predictive, prognostic, or diagnostic biomarkers in the CIViC database and the Cancer Biomarkers Database that are
- Found within the same tumor type/class as specified by the user, AND
- Of strong clinical evidence (i.e. part of guidelines, validated or discovered in late clinical trials (CIViC evidence levels A/B))
- TIER 2: Variants of potential clinical significance - constitutes other variants linked to predictive, prognostic, or diagnostic biomarkers in the CIViC database and the Cancer Biomarkers Database that are either
- Of strong clinical evidence in other tumor types/classes than the one specified by the user, OR
- Of weak clinical evidence (early trials, case reports etc. (CIViC evidence levels C/D/E))) in the same tumor type/class as specified by the user
- TIER 3: Variants of uncertain clinical significance - includes other coding variants found in oncogenes or tumor suppressor genes
- Status as oncogenes and/or tumor suppressors genes are done according to the following scheme in PCGR:
- Five or more publications in the biomedical literature that suggests an oncogenic/tumor suppressor role for a given gene (as collected from the CancerMine text-mining resource), OR
- At least two publications from CancerMine that suggests an oncogenic/tumor suppressor role for a given gene AND an existing record for the same gene as a tumor suppressor/oncogene in the Network of Cancer Genes (NCG)
- Status as oncogene is ignored if a given gene has three times as much (literature evidence) support for a role as a tumor suppressor gene (and vice versa)
- Oncogenes/tumor suppressor candidates from CancerMine/NCG that are found in the curated list of false positive cancer drivers compiled by Bailey et al. (Cell, 2018) have been excluded
- Status as oncogenes and/or tumor suppressors genes are done according to the following scheme in PCGR:
- TIER 4 - includes other protein-coding variants
- Protein-coding refers here to variants with the following consequences:
- missense_variant
- stop_gain/stop_loss
- frameshift_variant
- inframe_insertions/inframe_deletions
- splice_donor_variant/splice_acceptor_variant
- start_loss
- NONCODING - includes other non-(protein)coding variants
A complete list of reported biomarkers that associate with variants in the tumor sample (not necessarily qualifying for assignment to TIER 1/TIER 2) is also shown in a separate section.
Somatic copy number aberrations
Somatic copy number aberrations identified in the tumor sample are classified into two main tiers:
- TIER 1: Aberrations of strong clinical significance - constitutes amplified/lost genes linked to predictive, prognostic, or diagnostic biomarkers in the CIViC database and the Cancer Biomarkers Database that are
- Found within the same tumor type/class as specified by the user, AND
- Of strong clinical evidence (i.e. part of guidelines, validated or discovered in late clinical trials (CIViC evidence levels A/B))
- overlap between variants in the tumor sample and reported biomarkers must occur at the exact variant level or at the codon/exon level
- TIER 2: Aberrations of potential clinical significance - constitutes amplified/lost genes linked to predictive, prognostic, or diagnostic biomarkers in the CIViC database and the Cancer Biomarkers Database that are either
- Of strong clinical evidence in other tumor types/classes than the one specified by the user, OR
- Of weak clinical evidence (early trials, case reports etc. (CIViC evidence levels C/D/E))) in the same tumor type/class as specified by the user
- overlap between variants in the tumor sample and reported biomarkers must occur at the exact variant level or at the codon/exon level
Included in the report is also a complete list of all oncogenes subject to amplifications, tumor suppressor genes subject to homozygous deletions, and other drug targets subject to amplifications
Mutational signatures
The set of somatic mutations observed in a tumor reflects the varied mutational processes that have been active during its life history, providing insights into the routes taken to carcinogenesis. Exogenous mutagens, such as tobacco smoke and ultraviolet light, and endogenous processes, such as APOBEC enzymatic family functional activity or DNA mismatch repair deficiency, result in characteristic patterns of mutation. Mutational signatures can have significant clinical impact in certain tumor types (Póti et al., 2019, Ma et al., 2018)
The MutationalPatterns package (Blokzijl et al., 2018) is used to estimate the relative contribution of known mutational signatures in a single tumor sample. MutationalPatterns makes an optimal reconstruction of the mutations observed in a given sample with a COSMIC’s (V3.2) reference collection of n = 78 mutational signatures (SBS, including sequencing artefacts). By default, we restrict the signatures in the reference collection to those already observed in the tumor type in question (i.e. from large-scale de novo signature extraction on ICGC-PCAWG tumor samples).
Specifically, for tumors of type Esophagus/Stomach , mutational signature reconstruction is limited to the following reference collection:- SBS1 - Aging
- SBS2 - AID/APOBEC
- SBS3 - HR deficiency
- SBS5 - Unknown
- SBS13 - AID/APOBEC
- SBS15 - MMR deficiency
- SBS17a - Unknown
- SBS17b - Unknown
- SBS18 - ROS damage
- SBS20 - POLD1/MMR deficiency
- SBS40 - Unknown
- SBS90 - Duocarmycin
- SBS93 - Unknown
The accuracy of signature fitting (highlighted in value box) reflects how well the mutational profile can be reconstructed with signatures from the reference collection. Reconstructions with fitting accuracy below 90% should be interpreted with caution.
Tumor mutational burden (TMB)
Tumor mutational load or mutational burden is a measure of the number of mutations within a tumor genome, defined as the total number of mutations per coding area of a tumour genome. TMB may serve as a proxy for determining the number of neoantigens per tumor, which in turn may have implications for response to immunotherapy. For estimation of TMB, PCGR employs two different algorithms (one to be chosen by the user):
- all_coding: the same approach as was outlined in a recently published large-scale study of TMB (Chalmers et al., 2017), i.e. counting all somatic base substitutions and indels in the protein-coding regions of the sequencing assay, including synonymous alterations.
- nonsyn: non-synonymous variants only, i.e. as employed by Fernandez et al., 2019
Numbers obtained with 1) or 2) is next divided by the coding target size of the sequencing assay.
MSI classification
Microsatellite instability (MSI) is the result of impaired DNA mismatch repair and constitutes a cellular phenotype of clinical significance in many cancer types, most prominently colorectal cancers, stomach cancers, endometrial cancers, and ovarian cancers (Cortes-Ciriano et al., 2017). We have built a statistical MSI classifier from somatic mutation profiles that separates MSI.H (MSI-high) from MSS (MS stable) tumors. The MSI classifier was trained using 999 exome-sequenced TCGA tumor samples with known MSI status (i.e. assayed from mononucleotide markers), and obtained a positive predictive value of 100% and a negative predictive value of 99.4% on an independent test set of 427 samples. Details of the MSI classification approach can be found here.
Note that the MSI classifier is applied only for WGS/WES tumor-control sequencing assays.
Kataegis
Kataegis describes a pattern of localized hypermutations identified in some cancer genomes, in which a large number of highly-patterned basepair mutations occur in a small region of DNA (ref Wikipedia). Kataegis is prevalently seen among breast cancer patients, and it also exists in lung cancers, cervical, head and neck, and bladder cancers, as shown in the results from tracing APOBEC mutation signatures (ref Wikipedia). PCGR implements the kataegis detection algorithm outlined in the KataegisPortal R package, applied in the study by Yin et al. (2020).
Explanation of key columns in the resulting table of potential kataegis events:
- weight.C>X: proportion of C>X mutations
- confidence: confidence degree of potential kataegis events (range: 0 to 3)
- 0 - a hypermutation with weight.C>X < 0.8;
- 1 - one hypermutation with weight.C>X >= 0.8 in a chromosome;
- 2 - two hypermutations with weight.C>X >= 0.8 in a chromosome;
- 3 - high confidence with three or more hypermutations with weight.C>X >= 0.8 in a chromosome)
Germline findings
For PCGR reports that are fueled with CPSR report contents (JSON), we here list the main findings from the CPSR report, i.e. the collection of Pathogenic/Likely Pathogenic/VUS variants (ClinVar and novel CPSR-classified variants). We also show whether any of the query variants are associated with established biomarker evidence items with respect to cancer predisposition, prognosis, therapeutic regimens etc.
Clinical trials
Each report is provided with a list of trials for the tumor type in question, where we limit the trials listed to ongoing or forthcoming trials with a “molecular focus” (presence of molecular biomarkers in inclusion criteria, targeted drugs as interventions etc.). Recognition of biomarkers in trials is conducted through an in-house text mining procedure.
Note that the trials have currently not been subject to any matching with respect to the molecular profile of the tumor, trials are thus basically unprioritized, and have to be explored interactively by the user in order to discover relevant trials.