Congenica Clinical Report Data
Description of the Clinical Report Data produced from Congenica DSS v2.4.0.3
Clinical Report Data¶
| Field Name | Type | Description |
|---|---|---|
| interpretationRequestId* | string | This is the interpretation request identifier (i.e. the 123; in SAP-123-1) |
| interpretationRequestVersion | int | This is the version of the interpretation request identifier (i.e. the 1; in SAP-123-1) |
| reportingDate | string | Date of this report in format YYYY-MM-DD |
| user | string | Author of this report, from Congenica this is returned as NHS.net email address of the user who is logged in |
| variants | array[SmallVariant] | List of small variants that have been flagged by users as Primary Findings in the Congenica application |
| structuralVariants | array[StructuralVariant] | List of simple structural variants (duplications, deletions, insertions, inversions, CNVs) that have been flagged by users as Primary Findings in the Congenica application |
| chromosomalRearrangements | array[ChromosomalRearrangement] | Always null. Interpretation Platform currently does not perform analysis for Chromosomal Rearrangements |
| shortTandemRepeats | array[ShortTandemRepeat] | List of STRs that have been flagged by users as Primary Findings in the Congenica application |
| uniparentalDisomies | array[UniparentalDisomy] | Always null. UPDs are not reported in Congenica application |
| karyotypes | array[Karyotype] | Always null. Karyotypes are not reported in Congenica application |
| genomicInterpretation | string | Free text comments added into the DSS application |
| additionalAnalysisPanels | array[AdditionalAnalysisPanel] | Always null. Congenica does not populate this field |
| references | array[string] | Always null. Congenica does not populate this field |
| referenceDatabasesVersions | map[string] | This map contains the versions of the different databases used in the Congenica when the Clinical Report was created. The database names are the keys and the versions are the values. |
| softwareVersions | map[string] | This map contains the versions of the different software systems used in the analysis, the keys being the software names and the versions are the values. |
"clinicalReportData": {
"interpretationRequestId": "2799",
"interpretationRequestVersion": 1,
"reportingDate": "2020-03-12",
"user": "gene.helix@nhs.net",
"variants": [
{
"variantCoordinates": {
"chromosome": "1",
"position": 9999999999,
"reference": "A",
"alternate": "G",
"assembly": "GRCh38"
},
"variantCalls": [
{
"participantId": "p11111111111",
"sampleId": "LP9000999-DNA_F99",
"zygosity": "heterozygous",
"phaseGenotype": null,
"sampleVariantAlleleFrequency": null,
"depthReference": null,
"depthAlternate": null,
"numberOfCopies": null,
"alleleOrigins": null,
"supportingReadTypes": null
}
],
"reportEvents": [
{
"reportEventId": "108658",
"phenotypes": {
"nonStandardPhenotype": [],
"standardPhenotypes": []
},
"variantConsequences": [],
"genePanel": null,
"modeOfInheritance": "na",
"genomicEntities": [
{
"type": "gene",
"ensemblId": "ENSG00000157766",
"geneSymbol": "ACAN",
"otherIds": null
}
],
"segregationPattern": null,
"penetrance": null,
"deNovoQualityScore": null,
"fullyExplainsPhenotype": false,
"groupOfVariants": null,
"eventJustification": "UAT comments 12/03/2020",
"roleInCancer": null,
"actions": null,
"score": null,
"vendorSpecificScores": null,
"variantClassification": {
"clinicalSignificance": "likely_pathogenic",
"drugResponseClassification": null,
"traitAssociation": null,
"tumorigenesisClassification": null,
"functionalEffect": null
},
"guidelineBasedVariantClassification": null,
"algorithmBasedVariantClassifications": null,
"tier": null,
"domain": null
}
],
"variantAttributes": {
"genomicChanges": null,
"cdnaChanges": null,
"proteinChanges": null,
"additionalTextualVariantAnnotations": {
"confirmation": "Passed",
"report_category": "Primary finding"
},
"references": {},
"variantIdentifiers": null,
"alleleFrequencies": null,
"additionalNumericVariantAnnotations": null,
"comments": [
"UAT comments 12/03/2020"
],
"alleleOrigins": null,
"ihp": null,
"recurrentlyReported": null,
"fdp50": null,
"others": null
}
}
],
"structuralVariants": [],
"chromosomalRearrangements": null,
"shortTandemRepeats": null,
"genomicInterpretation": "UAT comments - patient comments - 12/03/2020, UAT_12032020",
"additionalAnalysisPanels": null,
"references": [],
"referenceDatabasesVersions": {
"1000": "Phase 1 data",
"EVS": "ESP6500SI-V2 (evs.gs.washington.edu/EVS/)",
"HPO": "#1248 (12 December 2017)",
"VEP": "Ensembl 90",
"GNOMAD": "gnomad 2.0.2\r\n(http://gnomad.broadinstitute.org/downloads)",
"ClinVar": "ClinVar 2019-03",
"Ensembl": "90",
"Assembly": "GRCh38",
"Decipher": "Decipher SNV 2019-07",
"Mastermind": "Mastermind SNV CVR-2 2019-06",
"DecipherCNV": "Decipher CNV 2019-07"
},
"softwareVersions": {
"congenica": "2.2.0.9"
}
}
Congenica Clinical Report - SmallVariant¶
| Field Name | Type | Description |
|---|---|---|
| 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. The 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. |
| 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, panels and |
| variantAttributes | VariantAttributes | Variant Attributes |
Congenica Clinical Report - StructuralVariant¶
| Field Name | Type | Description |
|---|---|---|
| variantType | StructuralVariantType (enumeration) | One of ins, dup, inv, amplification, deletion, dup_tandem, del_me, ins_me |
| coordinates | Coordinates | The variant coordinates. |
| leftInsSeq | string | Always null. Congenica does not populate this field |
| rightInsSeq | string | Always null. Congenica does not populate this field |
| reportEvents | array[ReportEvent] | The list of report events for this variant across multiple modes of inheritance and panels |
| variantCalls | array[VariantCall] | List of variant calls across all samples under analysis for this variant |
| variantAttributes | VariantAttributes | Variant attributes |
Congenica Clinical Report - VariantCoordinates¶
| Field Name | Type | Description |
|---|---|---|
| assembly | string | GRCh37 or GRCh38 |
| 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 |
Congenica Clinical Report - Coordinates¶
| Field Name | Type | Description | |
|---|---|---|---|
| assembly | Assembly Enum | Can either be GRCh38 or GRCh37 | |
| chromosome | string | Chromosome is either 1-22, X, Y, MT or any other contig in the reference genome, no chr prefix is expected |
|
| start | integer | Position is 1- based | |
| end | integer | Position is 1- based | |
| ciStart | null | ConfidenceInterval | Always null. rare disease tiering does not populate this field |
| ciEnd | null | ConfidenceInterval | Always null. rare disease tiering does not populate this field |
Congenica Clinical Report - ReportEvent¶
| Field Name | Type | Description |
|---|---|---|
| reportEventId* | Integer | Unique identifier for each report event, this is unique across the whole report. |
| phenotypes* | Phenotypes | List of phenotypes relevant to this report event |
| variantConsequences* | array[VariantConsequence] | Always an empty list, Congenica does not populate the list of consequences |
| genePanel | GenePanel | Always null. Congenica does not use GenePanels in the ClinicalReports |
| modeOfInheritance* | ModeOfInheritance (enumeration) | Congenica populate this as na |
| genomicEntities | array[[GenomicEntity]] | List of all of the genomic entities relevant for this report event. |
| segregationPattern | SegregationPattern (enumeration) | Always null. Congenica does not populate this field |
| penetrance | Penetrance (enumeration) | Always null. Congenica does not populate this field |
| deNovoQualityScore | float | Always null. Congenica does not populate this score in ClinicalReports |
| fullyExplainsPhenotype | boolean | True or False depending on what the user selects in the DSS |
| groupOfVariants | integer | Currently, congenica does not use this field though there is a pending change request for them to start using it to group variants (e.g. comp hets) together |
| eventJustification | string | Free text field detailing why this variant was included in the Clinical Report |
| roleInCancer | array[RoleInCancer] | Always null. Congenica does not use roleInCancer to classify variants |
| actions | Actions | Always null. Congenica does not use actions to classify variants |
| score | float | Always null. Congenica does not populate this field |
| vendorSpecificScores | map[string, float] | Always null. Congenica does not populate this field |
| variantClassification | VariantClassification | This should be populated according to the VariantClassification model according to the variant classification set in the DSS by the user interpreting the case |
| guidelineBasedVariantClassification | GuidelineBasedVariantClassification | Only set if an ACMG variant classification is performed in Congenica |
| algorithmBasedVariantClassifications | array[AlgorithmBasedVariantClassification] | Always null. Congenica does not populate this field |
| tier | Tier | Can be either Null, NONE, TIER1, TIER2, TIER3, TIER4, TIER5, TIERA, TIERB |
| domain | Domain | Always null. Congenica does not use domain to classify variants |
{
"reportEventId": "108658",
"phenotypes": {
"nonStandardPhenotype": [],
"standardPhenotypes": []
},
"variantConsequences": [],
"genePanel": null,
"modeOfInheritance": "na",
"genomicEntities": [...],
"segregationPattern": null,
"penetrance": null,
"deNovoQualityScore": null,
"fullyExplainsPhenotype": false,
"groupOfVariants": null,
"eventJustification": "UAT comments 12/03/2020",
"roleInCancer": null,
"actions": null,
"score": null,
"vendorSpecificScores": null,
"variantClassification": {
"clinicalSignificance": "likely_pathogenic",
"drugResponseClassification": null,
"traitAssociation": null,
"tumorigenesisClassification": null,
"functionalEffect": null
},
"guidelineBasedVariantClassification": null,
"algorithmBasedVariantClassifications": null,
"tier": null,
"domain": null
}
Congenica Clinical Report - GenomicEntity¶
| Field Name | Type | Description |
|---|---|---|
| type* | GenomicEntityType (enumeration) | The type of the genomic entity. gene is the only value expected for Congenica in this field. |
| ensemblId | string | Ensembl identifier for the feature. Ensembl Ids are based on the version of Ensembl reported in referenceDatabasesVersions |
| geneSymbol | string | The HGNC gene symbol. Congenica will always populate this field with the gene symbol. Gene symbols are based on the version of Ensembl reported in referenceDatabasesVersions |
| otherIds | array[Identifier] | Always null. Congenica does not use any other identifiers. |
Congenica Clinical Report - VariantCall¶
| Field Name | Type | Description |
|---|---|---|
| participantId* | string | Participant id |
| sampleId* | string | Sample id |
| zygosity* | Zygosity(enumeration) | Variant zygosity |
| phaseGenotype | PhaseGenotype | Always null. Congenica does not populate this field |
| sampleVariantAlleleFrequency | double | Always null. Congenica does not populate this field |
| depthReference | integer | Always null. Congenica does not populate this field |
| depthAlternate | integer | Always null. Congenica does not populate this field |
| numberOfCopies | array[NumberOfCopies] | Always null. Congenica does not populate this field |
| alleleOrigins | array[AlleleOrigin] | Always null. Congenica does not populate this field |
| supportingReadTypes | SupportingReadType(enumeration) | Always null. Congenica does not populate this field |
Congenica Clinical Report - VariantAttributes¶
| Field Name | Type | Description |
|---|---|---|
| genomicChanges | array[string] | Always null. Congenica does not populate this field |
| cdnaChanges | array[string] | Always null. Congenica does not populate this field |
| proteinChanges | array[string] | Always null. Congenica does not populate this field |
| additionalTextualVariantAnnotations | map[string] | Any additional information in a free text field. Congenica uses this field to populate details about whether a variant was confirmed or not and its report category |
| references | map[string] | List of pubmed IDs entered into the DSS system |
| variantIdentifiers | VariantIdentifiers | Always null. Congenica does not populate this field |
| alleleFrequencies | array[AlleleFrequency] | Always null. Congenica does not populate this field |
| additionalNumericVariantAnnotations | map[float] | Always null. Congenica does not populate this field |
| comments | array[string] | Variant level free text interpretative comments written by the user in the Congenica application are stored here |
| alleleOrigins | array[AlleleOrigin] | Always null. Congenica does not populate this field |
| ihp | integer | Always null. Congenica does not populate this field |
| recurrentlyReported | boolean | Always null. Congenica does not populate this field |
| fdp50 | float | Always null. Congenica does not populate this field |
| others | map[string] | Always null. Congenica does not populate this field |
"variantAttributes": {
"genomicChanges": null,
"cdnaChanges": null,
"proteinChanges": null,
"additionalTextualVariantAnnotations": {
"confirmation": "Passed",
"report_category": "Primary finding"
},
"references": {},
"variantIdentifiers": null,
"alleleFrequencies": null,
"additionalNumericVariantAnnotations": null,
"comments": ["UAT comments 12/03/2020"],
"alleleOrigins": null,
"ihp": null,
"recurrentlyReported": null,
"fdp50": null,
"others": null
}
Last update:
2023-03-01