Appendix A_data format for Tumor Molecular Profiling_12.22.22_FINAL.xlsx
XLSX spreadsheet 37 KB Posted
- Attached to
- Q301--Copy of Tumor Molecular Testing Services 0004 Federal contract opportunity
- Solicitation number
- 36C10G24R0013
About this file
This document contains a template for reporting tumor molecular profiling results. The template includes tables for capturing patient information, short variants, rearrangements and fusions, copy number variants, RNA expression, additional biomarkers like microsatellite instability status and tumor mutational burden, as well as IHC results for PD-L1 and MMR proteins. Data fields cover gene symbols, gene IDs, alterations, allele fractions, reference genomes, and oncogenicity. The related federal contract opportunity is a solicitation from the Department of Veterans Affairs for tumor molecular testing services. It includes the solicitation number, title amended to reflect services, and identifies the contracting agency as the VA Headquarters.
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Patient Information ReportID/Accession Number Patient Last Name Patient First Name Patient DOB Patient MRN/SSN Diagnosis Patient Disease Stage at time of testing Date test ordered Date test reported Report Status Test/assay name Specimen Type Specimen Collection Date
Short Variants
| HGNC Gene Symbol | HGNC Gene ID | Alteration cVar (HGVS compliant) | Alteration pVar (HGVS compliant) | Transcript ID | AlterationType | Allele_Fraction | Depth of Coverage | Chromosome | Position 1 | Position 2 | Ref | Alt | Alteration detected by DNA/RNA | Alteration - Somatic or Germline? | Oncogenicity | Functional_Effect | Reference genome |
| * patient identifiers from patient tab should be included |
Rearrangements and Fusions
| HGNC Gene Symbol (for all genes involved in the fusion/rearrangement) | HGNC Gene ID (for all genes involved in the fusion/rearrangement) | Fusion supporting reads | Breakpoint 1 | Breakpoint 2 | Detected by DNA/RNA | Inframe | Protein Domains involved | Exons Involved | AlterationType | Oncogenicity | Functional_Effect | Reference genome |
| * patient identifiers from patient tab should be included |
Copy number variants HGNC Gene Symbol (for all genes involved in the fusion/rearrangement) HGNC Gene ID (for all genes involved in the fusion/rearrangement) tc={CBF712B9-57B0-4D56-8F70-027D36037EA5}: [Threaded comment]
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| delete "for all genes involved in the fusion/rearrangement" | Fold change/Copy number | Copy number - loss, amplification, equivocal | Chromosomal coordinates for copy number event | Domains involved | AlterationType | Oncogenicity | Functional_Effect | Tumor % | Reference genome |
| * patient identifiers from patient tab should be included |
RNA expression
| HGNC Gene Symbol | HGNC Gene ID | Transcript | Overexpressed/Underexpressed |
| * patient identifiers from patient tab should be included |
Other Biomarkers
| microsatelliteInstability_status | tumorMutationalBurden_tmb | bloodTumorMutationalBurden_btmb | HRD Status | Mutational Signature |
| * patient identifiers from patient tab should be included |
IHC - PDL1
PDL1_Score_Type PDL1 clone PDL1 tumorProportionScore PDL1 combinedPositiveScore PDL1 percentTumorCellStaining PDL1 percentImmuneCellStaining PDL1 result interpretation
* patient identifiers from patient tab should be included
IHC - MMR
| Protein name (HGNC Gene Symbol) | Individual protein expression result | Overall result/interpretation |
| * patient identifiers from patient tab should be included |
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