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Table. 1.

Table. 1.

Target genes evaluated by the two assays used for cfDNA analysis in this study

Mutation type Genes
Oncomine Pan-Cancer Cell-Free Assay AlphaLiquid 100 kit
SNVs, small indels AKT1, ALK, APC, AR, ARAF, BRAF, BRCA1*, BRCA2*, CHEK2, CTNNB1, DDR2, EGFR, ERBB2, ERBB3, ESR1, FBXW7, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, GNA11, GNAQ, GNAS, HRAS, IDH1, IDH2, KIT, KRAS, MAP2K1, MAP2K2, MET, MTOR, NRAS, NTRK1, NTRK3, PDGFRA, PIK3CA, PTEN, RAF1, RET, ROS1, SF3B1, SMAD4, SMO, TP53 ABL1, AKT1, AKT2, ALK, APC, AR, ARAF, ARID1A, ATM, BRAF, BRCA1, BRCA2, BTK, CBL, CCND1, CCND2, CCNE1, CD274, CDH1, CDK4, CDK6, CDKN2A, CEBPA, CSF1R, CTNNB1, DDR2, DPYD, EGFR, ERBB2, ERBB3, ESR1, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GATA3, GNA11, GNAQ, GNAS, HRAS, IDH1, IDH2, IGF1R, JAK2, JAK3, KDM6A, KDR, KEAP1, KIT, KRAS, MAP2K1, MAP2K2, MAPK1, MAPK3, MDM2, MET, MLH1, MPL, MSH2, MSH6, MTOR, MYC, MYCN, NF1, NF2, NFE2L2, NOTCH1, NPM1, NRAS, NTRK1, NTRK2, NTRK3, PDCD1LG2, PDGFRA, PDGFRB, PIK3CA, PIK3R1, PMS2, PPP2R1A, PTEN, PTPN11, RAF1, RB1, RET, RHEB, RHOA, RIT1, RNF43, ROS1, RUNX1, SETD2, SMAD4, SMO, STAG2, STK11, TCF7L2, TERT, TOP2A, TP53, TSC1, TSC2, U2AF1, UGT1A1, VHL
CNVs CCND1, CCND2, CCND3, CDK4, CDK6, EGFR, ERBB2, FGFR1, FGFR2, FGFR3, MET, MYC, MYCN* ABL1, AKT1, AKT2, ALK, APC, AR, ARAF, ARID1A, ATM, BRAF, BRCA1, BRCA2, BTK, CBL, CCND1, CCND2, CCNE1, CD274, CDH1, CDK4, CDK6, CDKN2A, CEBPA, CSF1R, CTNNB1, DDR2, DPYD, EGFR, ERBB2, ERBB3, ESR1, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GATA3, GNA11, GNAQ, GNAS, HRAS, IDH1, IDH2, IGF1R, JAK2, JAK3, KDM6A, KDR, KEAP1, KIT, KRAS, MAP2K1, MAP2K2, MAPK1, MAPK3, MDM2, MET, MLH1, MPL, MSH2, MSH6, MTOR, MYC, MYCN, NF1, NF2, NFE2L2, NOTCH1, NPM1, NRAS, NTRK1, NTRK2, NTRK3, PDCD1LG2, PDGFRA, PDGFRB, PIK3CA, PIK3R1, PMS2, PPP2R1A, PTEN, PTPN11, RAF1, RB1, RET, RHEB, RHOA, RIT1, RNF43, ROS1, RUNX1, SETD2, SMAD4, SMO, STAG2, STK11, TCF7L2, TERT, TOP2A, TP53, TSC1, TSC2, U2AF1, UGT1A1, VHL
Fusions ALK, BRAF, ERG, ETV1, FGFR1, FGFR2, FGFR3, MET, NTRK1, NTRK3, RET, ROS1 ALK, BCR, BRAF, EGFR, FGFR2, FGFR3, NTRK1, NTRK2, RET, ROS1
Exon skipping MET exon 14 skipping MET exon 14 skipping

*Genes additionally tested using Ion AmpliSeq HD Custom Panels.

Abbreviations: cfDNA, cell-free DNA; SNV, single-nucleotide variant; indel, insertion/deletion; CNV, copy number variation.

Ann Lab Med 2024;44:164~173 https://doi.org/10.3343/alm.2023.0187

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