Tumor mutation burden (TMB) was defined as somatic mutation counts in coding region per megabase of genome examined. Genes including TGFBR2, ACVR1B, ACVR2A, INHBA, SMAD2, SMAD3, SMAD4, IGF2, RUNX1, STAT3, TERT, and VEGFA have been reported to be the core members in the TGF-β pathway network and to act as cancer-related genes (21 (link)); they were thus selected to be included for analysis. A TGF-β pathway mutation was defined as the presence of at least one pathway gene with identified mutational types (missense mutation or truncating mutation), including nonsense mutation, nonstop mutation, frameshift insertion, frameshift deletion, and splice site mutation.
NGS-based Profiling of TGF-β Pathway Mutations
Tumor mutation burden (TMB) was defined as somatic mutation counts in coding region per megabase of genome examined. Genes including TGFBR2, ACVR1B, ACVR2A, INHBA, SMAD2, SMAD3, SMAD4, IGF2, RUNX1, STAT3, TERT, and VEGFA have been reported to be the core members in the TGF-β pathway network and to act as cancer-related genes (21 (link)); they were thus selected to be included for analysis. A TGF-β pathway mutation was defined as the presence of at least one pathway gene with identified mutational types (missense mutation or truncating mutation), including nonsense mutation, nonstop mutation, frameshift insertion, frameshift deletion, and splice site mutation.
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Variable analysis
- Not explicitly mentioned
- Tumor mutation burden (TMB) defined as somatic mutation counts in coding region per megabase of genome examined
- Presence of at least one pathway gene with identified mutational types (missense mutation or truncating mutation), including nonsense mutation, nonstop mutation, frameshift insertion, frameshift deletion, and splice site mutation
- Sample size - specimen needed to be ≥1 mm
- Tumor cell percentage - needed to be over 20%
- DNA amount - 50-200 ng of DNA extracted from the samples
- DNA fragment size - ~200 bp fragments
- Sequencing coverage - >500× coverage
- Genes included for analysis - TGFBR2, ACVR1B, ACVR2A, INHBA, SMAD2, SMAD3, SMAD4, IGF2, RUNX1, STAT3, TERT, and VEGFA
- Positive control: Not specified
- Negative control: Not specified
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