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NovoPM™ Blood Tumor Mutation Burden

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Blood tumor mutation burden (bTMB) represents the total number of mutations per coding area of a tumor genome calculated through the genomic sequencing of circulating tumor DNA (ctDNA), an alternative source of diagnostic material for patients with inadequate tissue samples. The value of bTMB has been found to correlate with the efficacy of anti-PD-L1/PD-1 immunotherapies in some tumor types.

NovoPM-bTMB Algorithm

  • bTMB is calculated based on the coding DNA sequence (CDS) regions included in the NovoPM panel (approximately 1.5Mb).
  • Somatic mutations are identified with VarScan2.
  • The following mutations are excluded from the calculation of bTMB:
    • Germline mutations
    • Low frequency mutations (threshold=0.8%)
    • Known driver mutations (EGFR, MET, BRAF, PIK3CA, NF1, KRAS, and the NOTCH family genes)
    • Synonymous mutations
    • Repeat regions

NovoPM-bTMB Algorithm Validation

To analytically validate our NovoPM-bTMB algorithm, we sequenced 48 paired FFPE tumor tissue samples and ctDNA samples with NovoPM (1000X for tissue samples and 2000X for ctDNA samples). TMB and bTMB were then calculated as described above. The results showed good linear correlation (Figure 1; R2=0.7039).

Figure 1. Correlation between bTMB and TMB paired FFPE tumor tissue samples and ctDNA samples. X axis is bTMB calculated from NovoPM 2000X sequencing and Y axis is TMB calculated from NovoPM 1000X sequencing.

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