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Cancer Tiering Interpretation Service Data

*Mandatory field

Warning

It is highly recommended to read the technical documentation for the cancer tiering available in this link where, the the algorithm is described and the gene lists used for this analysis are available.

Cancer Tiering v1.0.1 produces an Interpreted Genome with the following fields populated

Field Name Type Description
comments array[string] Always null
variants array[SmallVariant] List of small reported variants by Cancer tiering. These can be germline (derived from normal tissue/cells) or somatic An empty list will indicate the absence of reported small variants for this case.
reportUrl string Always null
karyotypes array[Karyotype] Always null. The Cancer Tiering does not perform analysis for Karyotypes.
versionControl* ReportVersionControl Cancer Tiering data is represented using version 6.0.0 of Interpreted Genome Model. More details: https://gelreportmodels.genomicsengland.co.uk/html_schemas/org.gel.models.report.avro/6.0.0/InterpretedGenome.html#/schema/org.gel.models.report.avro.InterpretedGenome
softwareVersions* map[string, string] This map contains the versions of the different software systems used in the analysis, being the software names the keys and the versions
shortTandemRepeats array[ShortTandemRepeat] Always null. The Cancer Tiering does note perform STR analysis
chromosomalRearrangements array[ChromosomalRearrangement] List of translocations reported by the Cancer tiering pipeline
interpretationService* string Fixed value. genomics_england_tiering
referenceDatabasesVersions* map[string, string] This map contains the versions of the different databases used in the analysis, being the database names the keys and the versions the values.
For a description of the data sources, please see this table. These are the expected values;
Cancer Analysis Resources: v1.11
ClinVar: 2019-06
1000 genomes project
ENSEMBL liftover
DiscovEHR: GHS Freeze 50 + GeL liftover
GoNL: Release 5 + GeL liftover
COSMIC: v89
gnomAD: 2.0.1 + GeL liftover
ENSEMBL_variation: 90_38
ENSEMBL_gene: 90_38
UK10K project: 2016-02-15 + GeL liftover
ENSEMBL_genome: 90_38
CellBase database version: 2.4.0
structuralVariants array[StructuralVariant] This list contains variants that are larger than SmallVariants. They include Copy Number Variants, Internal Tandem Duplications.
interpretationRequestVersion integer Version for the interpretation request. This will be the case version in the cipapi
interpretationRequestId* string Full id of the case in the cipapi. Generally something like: ILMN-XXXX-XX
uniparentalDisomies array[UniparentalDisomy] Always null. Cancer Tiering does not perform analysis for uniparentalDisomies 
interpreted_genome_data: {
comments: null,
variants: [...],
reportUrl: null,
karyotypes: null,
versionControl: {...},
softwareVersions: {...},
shortTandemRepeats: null,
structuralVariants: [...],
uniparentalDisomies: null,
interpretationService: "genomics_england_tiering",
interpretationRequestId: "GEL-442-1",
chromosomalRearrangements: [...],
referenceDatabasesVersions: {...},
interpretationRequestVersion: 1
},

Cancer Tiering v1.0.1 - SmallVariant

Field Name Type Description
reportEvents* array[ReportEvent] The list of report events for this variant across multiple modes of inheritance, panels and
variantCalls* array[VariantCall] List of variant calls across all samples under analysis for this variant
variantAttributes VariantAttributes A set of variant attributes
variantCoordinates* VariantCoordinates The variant coordinates. Chromosome is either 1-22, X, Y, MT or any other contig in the reference genome, no chr prefix is expected. Position is 1- based. Reference and alternate should never be empty or any character representing emptiness (e.g.: . or -), a VCF-like indel representation is expected. 
{
    variants: [
    {
    reportEvents: [...],
    variantCalls: [...],
    variantAttributes: {...},
    variantCoordinates: {...}
    },
}

Cancer Tiering v1.0.1 - VariantCoordinates

Field Name Type Description
assembly string Fixed Value. GRCh38
position integer Position is 1- based
alternate string Alternate should never be empty or any character representing emptiness (e.g.: . or -), a VCF-like indel representation is expected
reference string Reference should never be empty or any character representing emptiness (e.g.: . or -), a VCF-like indel representation is expected
chromosome string Chromosome is either 1-22, X, Y, MT or any other contig in the reference genome, no chr prefix is expected 
{
variantCoordinates: {
    assembly: "GRCh38",
    position: 150471550,
    alternate: "A",
    reference: "G",
    chromosome: "1"
    }
}

Cancer Tiering v1.0.1 - ReportEvent

Field Name Type Description
tier Tier The tier of variant indicates the association of the variant with the relevant condition. Possible values [TIER1, TIER3]. For a technical description of this field please see the technical documentation in this link
score float Always null. Cancer Tiering does not use score to classify variants
domain Domain The domain of the variant defines whether it is causally implicated in the disease. Possible values [DOMAIN1, DOMAIN2, DOMAIN3]. For a technical description of this field please see the technical documentation in this link
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
genePanel GenePanel The panel used to select a Tier for germline variants. For Somatic variants null value is expected.
penetrance Penetrance (enumeration) Always null. Cancer Tiering does not populate this field.
phenotypes* Phenotypes List of phenotypes relevant to this report event. Set to a dictionary with null values for all keys in Cancer Tiering
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
reportEventId* Integer Unique identifier for each report event, this is unique across the whole report.
genomicEntities array[GenomicEntity] List of all of the genomic entities relevant for this report event. This includes genes and transcripts in Cancer Tiering
groupOfVariants integer Always null. Cancer Tiering does not group variants
modeOfInheritance* ModeOfInheritance (enumeration) Mode of inheritance reported for this report event. Always na in Cancer Tiering
deNovoQualityScore float Always null. Cancer Tiering does not use deNovoQualityScore to classify variants
eventJustification string Always null.
segregationPattern SegregationPattern (enumeration) Always null. Cancer Tiering does not populate this field
variantConsequences* array[VariantConsequence] Sequence Ontology terms associated with the variant. This information is calculated using cellbase (v4.7.1). Cellbase uses ENSMBL 90 to calculate the impact of the variant in the genes.
vendorSpecificScores map[string, float] Always null. Cancer Tiering does not use to classify variants
variantClassification VariantClassification Always null. Cancer Tiering does not use variantClassification to classify variants
fullyExplainsPhenotype boolean Always null. Cancer Tiering does not populate this field
guidelineBasedVariantClassification GuidelineBasedVariantClassification Always null. Cancer Tiering does not use guidelineBasedVariantClassification to classify variants
algorithmBasedVariantClassifications array[AlgorithmBasedVariantClassification] Always null. Cancer Tiering does not use algorithmBasedVariantClassifications to classify variants 
{
reportEvents: [
    {
    tier: null,
    score: null,
    domain: "DOMAIN3",
    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 Tiering v1.0.1 - Actions

Field Name Type Description
Trial array[Trial] An array of objects representing clinical trials where the variant or gene containing the variant was covered. This data is extracted from the Genome Oncology database given that the variant is present and the associated record is a trial.
Prognosis array[Prognosis] An array of objects representing prognoses associated with the variant. This data is extracted from the Genome Oncology database given that the variant is present and the associated record contains a prognosis.
Therapy array[Therapy] An array of objects representing therapies associated with the variant. This data is extracted from the Genome Oncology database given that the variant is present and the associated record contains a therapy. 
actions: {
trials: [...],
prognosis: [...],
therapies: [...]
}

Cancer Tiering v1.0.1 - VariantAttributes

Field Name Type Description
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
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.
comments array[string] Always null. Cancer Tiering does not populate this field
references map[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.
alleleOrigins array[AlleleOrigin] Possible value: [germline_variant] or [somatic_variant]
genomicChanges array[string] Always null. Cancer Tiering does not populate this field
proteinChanges array[string] List of changes to amino acids. This information is calculated using cellbase (v4.7.1). Cellbase uses ENSMBL 90.
alleleFrequencies array[AlleleFrequency] See table for AlleleFrequency. This field may be an empty array.
variantIdentifiers VariantIdentifiers See table for VariantIdentifiers
recurrentlyReported boolean Always null. Cancer Tiering does not populate this field.
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
additionalTextualVariantAnnotations map[string] Contains annotations from VCFs and additional annotation. 
variantAttributes: {
ihp: null,
fdp50: null,
others: null,
comments: null,
references: null,
cdnaChanges: ["c.141C>A"],
alleleOrigins: ["somatic_variant"],
genomicChanges: null,
proteinChanges: ["p.(Ser47Arg)"],
alleleFrequencies: null,
variantIdentifiers: {dbSnpId: null, otherIds: null, cosmicIds: null, clinVarIds: null},
recurrentlyReported: null,
additionalNumericVariantAnnotations: {pon_noise: 549, cds_length: 635, somatic_agg_vcf_AF_FFpcrfree: 0.00054945},
additionalTextualVariantAnnotations: {AU: "0,0", CU: "1,1", DP: "113", GU: "85,87", MQ: "59.56", NT: "ref", TU: "27,27", FDP: "0", MQ0: "2", QSS: "76", SDP: "0", SGT: "GG->GT", TQSS: "1", SNVSB: "0", SUBDP: "0", QSS_NT: "76", SOMATIC: "true", TQSS_NT: "1", genotype: "./.", SomaticEVS: "16.12", exon_number: "1/3", ReadPosRankSum: "-1.02", SomaticFisherPhred: "549"}
}

Cancer Tiering v1.0.1 - VariantIdentifiers

Field Name Type Description
dbSnpId null string Always Null
otherIds null array[Identifier] Always Null
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. 
variantIdentifiers: {
dbSnpId: null,
otherIds: null,
cosmicIds: null,
clinVarIds: null
}

Cancer Tiering v1.0.1 - 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: "GNOMAD_EXOMES",
population: "ALL",
alternateFrequency: 0.0000040612
},
{
study: "GNOMAD_EXOMES",
population: "NFE",
alternateFrequency: 0.0000089535
},
{
study: "GNOMAD_EXOMES",
population: "FEMALE",
alternateFrequency: 0.0000089808
}
],

Cancer Tiering v1.0.1 - VariantCall

Field Name Type Description
sampleId* string Sample id
zygosity* Zygosity(enumeration) Variant zygosity
alleleOrigins array[AlleleOrigin]; Possible value: [germline_variant] or [somatic_variant]
participantId* string Participant id
phaseGenotype PhaseGenotype Always null. Cancer Tiering does not populate this field
depthAlternate integer The read depth for the alternate allele
depthReference integer The read depth for the reference allele
numberOfCopies array[NumberOfCopies]; No of copies of the variant present in a CNV
supportingReadTypes SupportingReadType(enumeration) Always null. Cancer Tiering does not populate this field
sampleVariantAlleleFrequency double Always null. Cancer Tiering does not populate this field 
variantCalls: [
{
sampleId: "LP3000123-DNA_E12",
zygosity: "missing",
alleleOrigins: ["somatic_variant"],
participantId: "p123456789",
phaseGenotype: null,
depthAlternate: 33,
depthReference: 87,
numberOfCopies: null,
supportingReadTypes: null,
sampleVariantAlleleFrequency: 0.28
}
],

Cancer Tiering v1.0.1 - GenePanel

Field Name Type Description
source null string source is always "PanelApp
panelName null string Panel name used
panelVersion null string Panel version
panelIdentifier null string Panel id used 
 genePanel: {
source: "PanelApp",
panelName: "Adult solid tumours cancer susceptibility",
panelVersion: "2.2",
panelIdentifier: "245"
},

Cancer Tiering v1.0.1 - GenomicEntities

Field Name Type Description
type* GenomicEntityType Enum The type of the genomic entity: transcript or gene
otherIds null array[Identifier] Always null
ensemblId null string Ensembl identifier for the feature (e.g, ENST00000544455)
geneSymbol null string HGNC gene symbol e.g. LCE3C 
genomicEntities: [
{
type: "gene",
otherIds: null,
ensemblId: "ENSG00000144554",
geneSymbol: "FANCD2"
},
{
type: "transcript",
otherIds: null,
ensemblId: "ENST00000287647",
geneSymbol: "FANCD2"
}
],
Last update: 2022-03-25