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. 2022 Sep 29;7(5):100570. doi: 10.1016/j.esmoop.2022.100570

Table 5.

Sample report

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.