Test method (extracted)
5 valuesExtraction schema (list)Jev check
A list per row. The app no longer uses it for testing routes (see Testing routes); it stays here to audit the extraction.
2. No biomarker in the text (classic chemotherapy, anti-angiogenesis without biomarker gating) → biomarker_name="none", alteration_type="none", biomarker_detail="n/a", diagnostic_criterion="n/a", scoring_system="n/a", test_method=[] (empty list — no diagnostic test applies). Flag "no-biomarker" and "non-targeted-therapy".
2a. A hereditary tumour syndrome named as the population (von Hippel-Lindau disease, neurofibromatosis type 1, tuberous sclerosis complex) is a clinical diagnosis, not a biomarker: biomarker_name="none", alteration_type="none", scoring_system="n/a", test_method=[]. Put the syndrome into tumor_type (e.g. "VHL disease-associated renal cell carcinoma") and patient_eligibility, and flag "no-biomarker" but NOT "non-targeted-therapy". Record a germline biomarker only when the text names the alteration itself (e.g. "germline BRCA1/2 mutations").
7. Gene symbols uppercase (BRAF, EGFR, ERBB2). Use "PD-L1" (protein) not CD274. An HLA type is a germline genotype, never a mutation: "HLA-A*02:01-positive" → biomarker_name="HLA-A*02:01", alteration_type="overexpression", biomarker_detail="HLA-A*02:01-positive", scoring_system="n/a", test_method=["molecular"]. Hormone receptors are proteins measured by IHC: "hormone receptor-positive" → biomarker_name="HR", "oestrogen receptor-positive" → "ER", progesterone receptor → "PR"; use "ESR1" only for ESR1 mutations.
16. `test_method` is a workflow-level descriptor — what kind of pathology lab test the indication implies. Pick from:
- "IHC" — protein expression by immunohistochemistry (PD-L1, HER2 IHC, MMR proteins, ER/PR).
- "ISH" — in situ hybridization, umbrella for FISH/CISH/SISH (HER2 amplification, ALK/ROS1 fusions when ordered as FISH).
- "molecular" — any DNA/RNA assay regardless of platform: PCR, Sanger sequencing, NGS, ddPCR (mutation detection like EGFR/BRAF/KRAS, fusion detection by RNA-seq, MSI by PCR).
- "cytogenetics" — conventional karyotype / cytogenetic analysis (heme malignancies).
- "flow-cytometry" — phenotypic marker detection in heme (e.g. CD30, CD20, CD22).
Multiple values are valid when the criterion is algorithmic (HER2: ["IHC", "ISH"]). Empty list `[]` when biomarker_name="none" — no test applies.| Value | Definition (as Jev sees it) | Rows | Jev agrees | Jev answered instead |
|---|---|---|---|---|
IHC | protein expression testing by IHC (PD-L1, HER2 IHC, MMR proteins, CLDN18.2) | 144 | 84% | |
ISH | e.g. HER2 amplification by ISH | 102 | 29% | |
molecular | mutation/fusion detection, MSI by PCR | 186 | 97% | |
cytogenetics | cytogenetic analysis | 41 | 90% | |
flow-cytometry | flow cytometry marker | 18 | 100% | – |