| Column | Acceptable Values |
|---|---|
| externalid | A free text value that can be used to trace the assertion back to the originating system. |
| type | • Biological • Therapeutic • Prognostic • Diagnostic • Gene Information |
| classificationName | We recommend using the same classifications specified in the Configuration screen. Examples are as follows: For Biological: • Likely Oncogenic For Therapeutic, Prognostic, Diagnostic: • Tier 2D |
| classificationOrder | We recommend using the same classifications specified in the Configuration screen. Examples are as follows: For Biological: For Therapeutic, Prognostic, Diagnostic: When multiple classifications map to the same AMP/ASCO/CAP tier, increment the tenths value. For example, if Level 1 and Level 2 both map to Tier 1A, the classificationOrder is as follows: |
| classificationBackgroundColor | We recommend using the same classification specified in the Configuration screen. Examples are as follows: For Biological: For Therapeutic, Prognostic, Diagnostic: |
| direction | For Therapeutic: For Prognostic: |
| status | For TMB: • High • Low For MSI: • High • Stable For GIS: • High • Low |
| hrd | • Undetermined When interpreting biomarkers in a case, this information is visible for BRCA1/2 variants and GIS. |
| geneRoles | • Oncogene • Tumor Suppressor • Oncogene / Tumor Suppressor |
| summary | You can specify up to 30,000 characters. This information is included in PDF reports. |
| notes | You can specify up to 30,000 characters. This information is not included in PDF reports. |
| diseaseName | This can be found by searching for the disease using SNOMED International SNOMED CT Browser website. |
| diseaseOntology | A required field that specifies the disease ontology. We currently recommend using SNOMEDCT. |
| diseaseOntologyID | This can be found by searching for the disease using SNOMED International SNOMED CT Browser website. |
| therapy | Drug name. Multiple drug names can be specified by separating them with a pipe |. |
| biomarkerType | • Small variant • Copy number variant • Structural variant • RNA splice variant • RNA fusion variant • Genomic analysis (i.e., TMB, MSI, GIS) |
| variantType | For Copy Number Variant: For Structural Variant: |
| level | For Small variants: For Copy number variants: For Structural variants: For RNA splice variants: For RNA fusion variants: For Genomic analysis: |
| genomeBuild | • 37 • 38 |
| chromosome | • 1–22 • X • Y • MT |
| position | The VCF position. Acceptable values are within the chromosome range. |
| end | The VCF position. Acceptable values are within the chromosome range. |
| ref | The VCF reference allele. Acceptable values are combinations of A, T, C, G. |
| alt | The VCF alternate allele. Acceptable values are combinations of A, T, C, G. |
| transcriptId | Acceptable values are RefSeq and Ensembl transcript IDs, with or without the version. |
| codon | Acceptable values are a three-letter hgvsp abbreviation, including prefix “p.(“ and suffix “)” and without the amino acid change, such as p.(Val600). |
| hgvs | Acceptable values are a three-letter hgvsp abbreviation, including prefix “p.(“ and suffix “)”, such as p.(Val600Glu). |
| exon | Exon # |
| geneSymbol | NCBI gene symbol (e.g., BRAF) |
| ncbiGeneId | NCBI gene ID (e.g., 673) |
| fusionGeneSymbol | Fusion NCBI gene symbol (e.g., ALK) |
| fusionNcbiGeneID | Fusion NCBI gene ID (e.g., 238) |
| fusionPosition | Acceptable values are 0 and 1. • Without a value, the fusion directionality is unspecified, such as EML4/ALK. • If 0 is provided, the fusion is at position 0, such as [fusion gene]-[gene]. • If 1 is provided, the fusion is at position 1, such as [gene]-[fusion gene]. |
| consequence | When a consequence is specified, the assertion only matches to a case variant that has the consequence specified, such as EGFR exon 19 inframe deletion.
For small variant, gene level: For copy number variant, gene level: For RNA splice variant, exon level: |