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Cancer Clinical Reports

Attention

These descriptions are based on the v1 Cancer Clinical Report that is automatically generated by the bioinformatics pipeline

Interpretation Portal

Description of the Cancer Clinical Report Data produced from Interpretation Portal (Interpretation Portal v2.7.0-b4. Interpretation API 2.9.1b1) |

Cancer IP - Clinical Report Data

Field Name Type Description
interpretationRequestId* string This is the entire Interpretation Request ID including CIP prefix and version number e.g.ILMN-123-1
interpretationRequestVersion int This is the version of the interpretation request identifier i.e. 1 in ILMN-123-**1**
reportingDate string
user string This will be Genomics England for the v1 Clinical Report in Cancer referrals
variants array[SmallVariant] List of small variants. Note, unlike the variants listed in the Cancer Interpreted Genome, in the Clinical Report variant list only DOMAIN 1, 2 and germline variants are shown
structuralVariants array[StructuralVariant] This list contains variants that are larger than SmallVariants. They include Copy Number Variants, Internal Tandem Duplications
chromosomalRearrangements array[ChromosomalRearrangement] List of translocations reported by the Cancer tiering pipeline
shortTandemRepeats array[ShortTandemRepeat] Always null. Short tandem repeat variants are not currently reported for cancer cases.
uniparentalDisomies array[UniparentalDisomy] Always null. UPDs are not reported in Interpretation Portal
karyotypes array[Karyotype] Always null. Karyotypes are not reported in Interpretation Portal
genomicInterpretation string Will always contain This report has been generated automatically from Genomics England automatic pipeline
additionalAnalysisPanels array[AdditionalAnalysisPanel] Always null
references array[string] Always null
referenceDatabasesVersions map[string] Always null
softwareVersions map[string] Always null 
    clinical_report_data: {
        interpretationRequestId: "ILMN-99-1",
        interpretationRequestVersion: 1
        reportingDate: "",
        user: "Genomics England",
        variants: [...],
        structuralVariants: [...],
        chromosomalRearrangements: null,
        shortTandemRepeats: null,
        uniparentalDisomies: null,
        karyotypes: null,
        genomicInterpretation: "This report has been generated automatically from Genomics England automatic pipeline",
        additionalAnalysisPanels: null,
        references: null,
        referenceDatabasesVersions: {...},
        softwareVersions: {...},
    },

Cancer IP - SmallVariant

Field Name Type Description
variantCoordinates* VariantCoordinates The variant coordinates.
variantCalls* array[VariantCall] List of variant calls across all samples under analysis for this variant
reportEvents* array[ReportEvent] The list of report events for this variant across multiple modes of inheritance and panels
variantAttributes VariantAttributes Variant attributes 
variants: [
    {
    variantCoordinates: {...}
    variantCalls: [...],
    reportEvents: [...],
    variantAttributes: {...},
    },

Cancer IP - VariantCoordinates

Field Name Type Description
chromosome string Chromosome is either 1-22, X, Y, MT or any other contig in the reference genome, no chr prefix is expected
position integer Position is 1- based
reference string Reference should never be empty or any character representing emptiness (e.g.: . or -), a VCF-like indel representation is expected
alternate string Alternate should never be empty or any character representing emptiness (e.g.: . or -), a VCF-like indel representation is expected
assembly string GRCh37 or GRCh38 
"variantCoordinates": {
  "chromosome": "1",
  "position": 9999999999,
  "reference": "A",
  "alternate": "G",
  "assembly": "GRCh38"
}

Cancer IP - ReportEvent

Field Name Type Description
domain Domain The domain the report even has been classified as by pipeline. Only present for somatic variants. Can either be DOMAIN1, DOMAIN2, DOMAIN3, NONE
tier Tier The tier assigned by the pipeline. Only present for germline variants. Can be either Null, TIER1, TIER3.
algorithmBasedVariantClassifications array[AlgorithmBasedVariantClassification] May contain details of additional algorithms
e.g.
[{
"score": None,
"classification": None
"marker": None,
"rank": None,
"algorithmName": "pharmacogenomics-cancer"}]
guidelineBasedVariantClassification GuidelineBasedVariantClassification Always null. Interpretation Portal does not use guidelineBasedVariantClassification to classify variants
variantClassification VariantClassification Always null. Interpretation Portal does not use variantClassification to classify variants
vendorSpecificScores map[string, float] Always null. Interpretation Portal does not use vendorSpecificScores to classify variants
score float Always null. Interpretation Portal does not populate this field.
actions Actions An action describes whether a variant is actionable at the variant or gene level. This decision is based on associated clinical trials, prognostic information, or known therapeutic information. The source of this information is GenomOncology Knowledge Management System. For more details please see the technical documentation in this link
roleInCancer array[RoleInCancer] This is the role played by a given variant in cancer. Potential roles are oncogene (e.g contributing to proliferation or desensitisation to apoptotic signals etc.) or tumour suppressor gene (e.g DNA repair). This data was extracted from the manually curated list of Cancer Census Genes. For more details please see the technical documentation in this link
eventJustification string Always null. Interpretation Portal does not populate this field.
groupOfVariants integer This value groups variants that together could explain the phenotype according to the mode of inheritance used. (e.g.: compound heterozygous). All the variants in the same report sharing the same value will be considered in the same group (i.e.: reported together). This value is an integer unique in the whole report. These values are only relevant within the same report.
fullyExplainsPhenotype boolean Always null. Interpretation Portal does not populate this field
penetrance Penetrance (enumeration) Always null. Cancer Tiering does not populate this field
segregationPattern SegregationPattern (enumeration) Always null. Cancer Tiering does not populate this field
modeOfInheritance* ModeOfInheritance (enumeration) Mode of inheritance reported for this report event. Always 'na' in Cancer Tiering
variantConsequences* array[VariantConsequence] List of consequence types and their SO IDs for the report event
phenotypes* Phenotypes List of phenotypes relevant to this report event. Set to a dictionary with null values for all keys in Cancer Tiering e.g.{'nonStandardPhenotype': None, 'standardPhenotypes': None}
reportEventId* Integer Unique identifier for each report event, this is unique across the whole report.
genePanel GenePanel The panel of genes to which this report corresponds
deNovoQualityScore float
genomicEntities array[GenomicEntity] List of all of the genomic entities relevant for this report event. This includes genes and transcripts in Cancer Tiering. 
    reportEvents: [
    {
    tier: null,
    score: null,
    domain: "DOMAIN1",
    actions: null,
    genePanel: null,
    penetrance: null,
    phenotypes: {...},
    roleInCancer: null,
    reportEventId: "RE2",
    genomicEntities: [...],
    groupOfVariants: null,
    modeOfInheritance: "na",
    deNovoQualityScore: null,
    eventJustification: null,
    segregationPattern: null,
    variantConsequences: [],
    vendorSpecificScores: null,
    variantClassification: null,
    fullyExplainsPhenotype: null,
    guidelineBasedVariantClassification: null,
    algorithmBasedVariantClassifications: null
    }

Cancer IP - GenomicEntity

Field Name Type Description
type* GenomicEntityType (enumeration) The type of the genomic entity.
ensemblId null string Ensembl identifier for the feature.
geneSymbol null string The HGNC gene symbol.
otherIds null array[Identifier] Others identifiers for this genomic feature. Contains data source and ID. 
"genomicEntities": [
  {
    "type": "gene",
    "ensemblId": "ENSG00000008710",
    "geneSymbol": "PKD1",
    "otherIds": null
  },

Cancer IP - VariantCall

Field Name Type Description
participantId* string Participant id
sampleId* string Sample id
zygosity* Zygosity(enumeration) Variant zygosity
phaseGenotype PhaseGenotype Always null. Interpretation Portal does not populate this field.
sampleVariantAlleleFrequency double Allele frequency for the variant allele
depthReference integer Depth for Reference Allele
depthAlternate integer Depth for Alternate Allele
numberOfCopies array[NumberOfCopies] Always null
alleleOrigins array[AlleleOrigin](https://gelreportmodels.genomicsengland.co.uk/html_schemas/org.gel.models.report.avro/6.0.1/ClinicalReport.html#/schema/schemas%2FAVPRs%2Fbuild%2FClinicalReport.avpr/org.gel.models.report.avro.AlleleOrigin) List of applicable allele origin SO terms e.g. somatic_variant or germline_variant
supportingReadTypes SupportingReadType(enumeration) Always null. 
{
sampleId: "LP900099-DNA_A09",
zygosity: "missing",
alleleOrigins: ["somatic_variant"],
participantId: "p9999999999",
phaseGenotype: null,
depthAlternate: 38,
depthReference: 44,
numberOfCopies: null,
supportingReadTypes: null,
sampleVariantAlleleFrequency: 0.46
}

Cancer IP - VariantAttributes

Field Name Type Description
genomicChanges array[string] Always null. Cancer Tiering does not populate this field
cdnaChanges array[string] List of cdna changes. This information is calculated using cellbase (v4.7.1). Cellbase uses ENSMBL 90.
proteinChanges array[string] List of changes to amino acids. This information is calculated using cellbase (v4.7.1). Cellbase uses ENSMBL 90.
additionalTextualVariantAnnotations map[string] Contains annotations from VCFs and additional annotation.
references map[string] Always null. Cancer Tiering does not populate this field
variantIdentifiers VariantIdentifiers See table for VariantIdentifiers
alleleFrequencies array[AlleleFrequency] See table for AlleleFrequency. This field may be an empty array.
additionalNumericVariantAnnotations map[float] Contains Numerical annotations, e.g internal frequency calculations.
Expected fields:
somatic_agg_vcf_AF_FFpcrfree : Internal allele frequency; calculated using genomics england internal aggregated allele frequencies of samples prepared using an Illumina PCR-Free preparation kit and then sequenced on a HiSeq X generating 150 bp paired-end reads.
somatic_agg_vcf_AF_FFPE : Internal allele frequency; calculated using genomics england internal aggregated allele frequencies of samples prepared using an Illumina FFPE preparation kit and then sequenced on a HiSeq X generating 150 bp paired-end reads.
somatic_agg_vcf_AF_FFnano : Internal allele frequency; calculated using genomics england internal aggregated allele frequencies of samples prepared using an Illumina FFPE preparation kit and then sequenced on a HiSeq X generating 150 bp paired-end reads.
cds_length : length of the CDS for the reported gene. This information is calculated using cellbase (v4.7.1). Cellbase uses ENSEMBL 90.
GEL.GL.6628_AF : Internal allele frequency calculated using genomics england internal aggregated frequencies for germline samples.
comments array[string] Always null. Cancer Tiering does not populate this field
alleleOrigins array[AlleleOrigin] Possible value: ["germline_variant"] or ["somatic_variant"]
ihp integer Only present for indels: The number represents the largest reference interupted homopolymer length intersecting with the indel. Present in strelka2 VCFs: For more information: https://sites.google.com/site/strelkasomaticvariantcaller/home/somatic-variant-output
recurrentlyReported boolean Always null. Cancer Tiering does not populate this field.
fdp50 float A float value or null. Average tier1 number of basecalls filtered from original read depth within 50 bases. Present in strelka2 VCFs: For more information: https://sites.google.com/site/strelkasomaticvariantcaller/home/somatic-variant-output
others map[string] GEL.GL.6628_AF: Indicates if the variant is a common variant in genomics england internal aggregated frequencies. Possible Values "GE" to mark the variant.
GNOMAD_EXOMES_ALL: Indicates whether the variant is common GNOMAD exomes: Possible values "GG to indicate
pon_noise: Panel of Normal noise: Possible values: "PON" indicating that the variant is affected by noise from the Panel of Normal
end_coding_region: Indicates whether the variant in the final 10% of the coding region: Possible values: T (indicating true). The length of the CDS is extracted from cellbase (v4.7.1). Cellbase uses ENSMBL 90.
indel_noise: Indicates whether the variant is affected by Indel Noise
IHP: Whether the variant has an interrupted homopolymer length of greater than or equal to 8. Possible Values "H"
simple_repeat: Indicates whether the variant overlaps with a simple repeat. Possible values "SR"		 
variantAttributes: {
ihp: null,
fdp50: null,
others: {end_coding_region: "T"},
comments: null,
references: null,
cdnaChanges: ["ENST00000438576:c.844C>T"],
alleleOrigins: ["somatic_variant"],
genomicChanges: null,
proteinChanges: ["ENSP00000398350:p.Arg282Ter"],
alleleFrequencies: [
    {
        study: "UK10K",
        population: "ALL",
        alternateFrequency: 0.0001322402
    },
    {
        study: "UK10K",
        population: "ALSPAC",
        alternateFrequency: 0.0002594707
    }
    ],
variantIdentifiers: {dbSnpId: null, otherIds: null, cosmicIds: null,clinVarIds: null},
recurrentlyReported: null,
additionalNumericVariantAnnotations: {pon_noise: 1011,cds_length: 881},
additionalTextualVariantAnnotations: {
    AU: "38,38",
    CU: "0,0",
    DP: "83",
    GU: "44,48",
    MQ: "60.0",
    NT: "ref",
    TU: "0,0",
    FDP: "1",
    MQ0: "0",
    QSS: "79",
    SDP: "0",
    SGT: "GG->AG",
    TQSS: "1",
    SNVSB: "0.0",
    SUBDP: "0",
    QSS_NT: "79",
    SOMATIC: "true",
    TQSS_NT: "1",
    genotype: "./.",
    SomaticEVS: "19.98",
    exon_number: "ENST00000438576:2/2",
    ReadPosRankSum: "0.51",
    SomaticFisherPhred: "1011"
    }
},

Cancer IP - VariantIdentifiers

Field Name Type Description
cosmicIds null array[string] Cosmic ID for Cancer causing variants. This information is calculated using cellbase (v4.7.1). Cellbase uses cosmic v89.
clinVarIds null array[string] Clinvar ID for variant. This information is calculated using cellbase (v4.7.1). Cellbase uses clinvar data obtained in 2019-06.
dbSnpId null string Always Null
otherIds null array[Identifier] Always Null 
    {
    cosmicIds: null,
    clinVarIds: null
    dbSnpId: null, 
    otherIds: null, 
    }

Cancer IP - AlleleFrequency

Field Name Type Description
study* string The study from where this data comes from. See table.
population* string The specific population where this allele frequency belongs. See table.
alternateFrequency* float The frequency of the alternate allele 
alleleFrequencies: [
    {
        study: "UK10K",
        population: "ALL",
        alternateFrequency: 0.0001322402
    },
    {
        study: "UK10K",
        population: "ALSPAC",
        alternateFrequency: 0.0002594707
    }
    ],

Cancer IP - GenePanel

Field Name Type Description
panelIdentifier null string Panel id used
panelName null string Panel name used
panelVersion null string Panel version
source null string source is always PanelApp 
    genePanel: {
    source: "PanelApp",
    panelName: "Tumour predisposition - childhood onset",
    panelVersion: "2.5",
    panelIdentifier: "243"
    },
Last update: 2022-03-25