Table 5.
Sample report
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Patient XY, DOB 01.01.1950, male Date of report: 07.12.2021 Ordered by: Doctor X |
|
Specimen used for NGS testing Sample ID: B2020.24987 Sample received: 01.01.2020 Specimen type: Biopsy specimen Diagnosis: Poorly differentiated lung adenocarcinoma Tumor cell content: 70% |
| Gene | Variant | Reference sequence | VAF (%) | OncoKB level/ESCAT | Drug |
|---|---|---|---|---|---|
| EGFR | P.L858R (c.2573T>G) | NM_005228.4 | 69 | 1/Tier I | Afatinib, dacomatinib, erlotinib, gefitinib, osimertinib |
| EGFR | P.T790M (c.2369C>T) | NM_005228.4 | 38 | 1/Tier I | Osimertinib |
| R1/Tier I | Afatinib, erlotinib, gefitinib | ||||
| MET | Amplification (copy number: 17) | 2/Tier I | Crizotimib |
|
Methodology Test material: Tumor DNA/RNA Gene panel: OncomineTM Comprehensive Assay v3 (ThermoFisher) (see detailed list gene). Instrument: Ion Torrent S5 platform (ThermoFisher). Data analysis: Ion Reporter Software (Filter: Oncomine Variants, 5% CI, CNV ploidy ≥ gain of 2 over normal). Reference genome: GRCh37 (hg19). Databases used for variant annotation: dsSNP, 1000 Genomes, ClinVar, COSMIC, OncoKB. Reporting: Limited to genomic alterations with level 1, 2, or R1 evidence according to OncoKB and ESCAT Therapeutic Levels of Evidence V2 classification at the time of reporting. Gene list Sequence variants (hotspot regions): AKT1, AKT2, AKT3, ALK, AR, ARAF, AXL, BRAF, BTK, CBL, CCND1, CDK4, CDK6, CHEK2, CSF1R, CTNNB1, DDR2, EGFR, ERBB2 (HER2), ERBB3, ERBB4, ERCC2, ESR1, EZH2, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, FOXL2, GATA2, GNA11, GNAQ, H3F3A, HIST1H3B, HNF1A, HRAS, IDH1, IDH2, JAK1, JAK2, JAK3, KIT, KNSTRN, KRAS, MAGOH, MAP2K1, MAP2K2, MAP2K4, MAPK1, MAX, MDM2, MED12, MET, MTOR, MYC, MYCN, MYD88, NFE2L2, NRAS, NTRK1, NTRK2, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PPP2R1A, PTPN11, RAC1, RAF1, RET, RHEB, RHOA, ROS1, SF3B1, SMAD4, SMO, SPOP, SRC, STAT3, TERT, TOP1, U2AF1, XPO1. Sequence variants (all coding regions): ARID1A, ATM, ATR, ATRX, BAP1, BRCA1, BRCA2, CDK12, CDKN1B, CDKN2A, CDKN2B, CHEK1, CREBBP, FANCA, FANCD2, FANCI, FBXW7, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, NF2, NOTCH1, NOTCH2, NOTCH3, PALB2, PIK3R1, PMS2, POLE, PTCH1, PTEN, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RB1, RNF43, SETD2, SLX4, SMARCA4, SMARCB1, STK11, TP53, TSC1, TSC2. Copy number alterations (amplification): AKT1, AKT2, AKT3, ALK, AR, AXL, BRAF, CCND1, CCND2, CCND3, CCNE1, CDK2, CDK4, CDK6, CDKN2A, CDKN2B, EGFR, ERBB2 (HER2), ESR1, FGF19, FGF3, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, IGF1R, KIT, KRAS, MDM2, MDM4, MET, MYC, MYCL, MYCN, NTRK1, NTRK2, NTRK3, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PPARG, RICTOR, TERT, TSC1, TSC2. Fusion transcripts: AKT2, ALK, AR, AXL, BRAF, BRCA1, BRCA2, CDKN2A, EGFR, ERBB2, ERBB4, ERG, ESR1, ETV1, ETV4, ETV5, FGFR1, FGFR2, FGFR3, FGR, FLT3, JAK2, KRAS, MDM4, MET, MYB, MYBL1, NF1, NOTCH1, NOTCH2, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PDGFRA, PDGFRB, PIK3CA, PRKACA, PRKACB, PPARG, PTEN, RAD51B, RAF1, RB1, RELA, RET, ROS1, RSPO2, RSPO3, TERT. |
CI, confidence interval; CNV, copy number variant; COSMIC, Catalogue of Somatic Mutations in Cancer; dsSNP, ; ESCAT, ESMO scale of clinical actionability for molecular targets; NGS, next-generation sequencing; VAF, variant allele frequency.