Table 1.
Overview of data types and value ranges for data elements covered by the core data model for minimum variant level data
| Class | Attribute | Value range | Example |
|---|---|---|---|
| Allele descriptive | |||
| Gene | Gene ID | Internal ID | G0002V5Z |
| Gene name | HGNC gene symbols | KRAS | |
| Chromosome | 1.. 22, X, Y | 12 | |
| Entrez gene ID | Entrez gene IDs | 3845 | |
| Ensembl gene ID | Ensembl gene IDs | ENSG00000133703 | |
| RefSeq gene ID | RefSeq gene IDs | NG_007524 | |
| Gene transript | Gene ID | Internal ID | G0002V5Z |
| Gene transcript ID | Internal ID | T0006OOW | |
| RefSeq transcript ID | RefSeq Transcript IDs | NM_033360 | |
| RefSeq protein ID | RefSeq protein IDs | NP_203524 | |
| Ensemble transcript ID | Ensemble transcript IDs | ENST00000256078 | |
| UniProt ID | UniProt IDs | P01116 | |
| Gene position | Gene ID | Internal ID | G0002V5Z |
| Genome version | Genome build IDs | GRCh37.p13 | |
| DNA position | Genomic coordinate | 12p12.1 | |
| Gene pathway | Gene ID | Internal ID | G0002V5Z |
| Pathway ID | Internal ID | P003V724 | |
| Gene pathway | Pathway ID | Internal ID | P003V724 |
| Common name | Activation of RAS in B cells | ||
| Kegg ID | Kegg IDs | map04014 | |
| Reactome ID | Reactome IDs | R-HSA-1169092 | |
| PathwayCommons ID | PathwayCommons IDs | R-HSA-1169092 | |
| Allele interpretive | |||
| Variant | Variant ID | Internal ID | V0000LBB |
| Variant type | “Single nucleotide variant (SNV)”, “multinucleotide variant (MNV)”, “insertion (INS)”, “deletion (DEL)” | SNV | |
| Variant position | Variant ID | Internal ID | V0000LBB |
| Genome version | Genome build IDs | GRCh37.p13 | |
| DNA sub. & position | HGVS genomic coordinate | NC_000012.11:g.25398284C >G | |
| Gene variant | Gene ID | Internal ID | G0002V5Z |
| Variant ID | Internal ID | V0000LBB | |
| Variant consequence | “Non-sense”, “missense”, “silent”, “frame shift”, “in-frame”, “3UTR”, “5UTR”, “splice”, “splice-region”, “intronic”, “upstream”, “downstream” | missense | |
| Gene variant transcript | Gene ID | Internal ID | G0002V5Z |
| Variant ID | Internal ID | V0000LBB | |
| Gene transcript ID | Internal ID | T0006OOW | |
| Protein sub. & Position | HGVS formatted variants | NM_033360.3(KRAS):c.35G >C (p.Gly12Ala) | |
| Protein domain | Descriptive name of protein domain | Small GTP-binding protein domain | |
| Variant consequence | “Expression”, “amplification”, “deletion”, “fusion”, “loss of function”, “missense” | missense | |
| Risk score | FATHMM, SIFT, PolyPhen | 0.98468, 0, 0.97 | |
| Somatic interpretive | |||
| Cancer type | Cancer type ID | Internal ID | C000WQFL |
| Cancer type name | NCI thesaurus | Oncotree IDs | Colorectal cancer | |
| UMLS ID | UMLS concept IDs | C1527249 | |
| HPO ID | HPO concept IDs | HP:0003003 | |
| Cancer variant | Cancer variant ID | Internal ID | CV00XBQW |
| Variant ID | Internal ID | V0000LBB | |
| Cancer type ID | Internal ID | C000WQFL | |
| Biomarker class | “Diagnostic”, “prognostic”, “predictive”, “predisposing”, “pharmacogenomic” | predictive | |
| Clinical relevance level() | “Tier 1”, “Tier 2”, “Tier 3” [8] | Tier 2 | |
| Cancer variant sample | Cancer variant ID | Internal ID | CV00XBQW |
| Sample ID | Internal ID | SXBQW0A7 | |
| Somatic classification | “Confirmed somatic”, “confirmed germline”, “unknown” | somatic | |
| Allele frequency | Allele frequency in global population | 0.00001647 | |
| Sample specimen | Sample ID | Internal ID | SXBQW0A7 |
| Tumor purity | Ratio | 0.763 | |
| TNM status | TNM values | T2N1M1 | |
| Primary / relapse | Primary || relapse | primary | |
| Cancer variant drug | Cancer variant ID | Internal ID | CV00XBQW |
| Drug ID | Internal ID | D00000Z9 | |
| Cancer variant drug effect | Cancer variant ID | Internal ID | CV00XBQW |
| Drug ID | Internal ID | D00000Z9 | |
| Effect | “Resistant”, “responsive”, “non-responsive”, “sensitive”, “reduced sensitivity”, “other” | Resistance or non-response | |
| Level of evidence | see Table 6 | C | |
| Sublevel of evidence | see Table 6 | 3A | |
| Drug | Drug ID | Internal ID | D00000Z9 |
| Substance name | FDA approved | DrugBank substance names | Panitumumab | |
| DrugBank ID | DrugBank IDs | DB01269 | |
| PharmGKB ID | PharmGKB IDs | PA162373091 | |
| FDA ID | FDA IDs | 125147 | |
| Drug mechanism | Drug ID | Internal ID | D00000Z9 |
| Molecular mechanism | Description | Binds to the epidermal growth factor receptor (EGFR) on both normal and tumor cells[...] |
Example data for evidence recording is given in Additional file 3