Tumor mutation burden (TMB) has been shown as a new predictive biomarker for immune checkpoint inhibitor in various cancer types. It is typically measured by processing tumor tissue with substantial input which limits its clinical utility in patients with metastatic or unresectable disease. Meanwhile, there is increasing interest in circulating tumor DNA (ctDNA) that act as a noninvasive real-time biomarker for cancer patients. Therefore, here we develop a new next generation sequencing assay that can identify patients with sufficient tumor fraction in plasma and accurately measures the TMB from blood (bTMB).
Cell free DNA (cfDNA) was extracted from plasma across four original tissue types by different tumor stages. CfDNA Assay was performed with unique molecular identifier (UMI) , sequenced on the Illumina® platforms and analyzed using an internal pipeline for variants down to 0.4%. By integrating the fragment size distribution and the clonal mutation frequency, we were able to estimate the tumor fraction per plasma sample. A bTMB score was also derived using all the coding variants on a 1.3M panel across 500+ genes. The matched TMB score is derived by the same assay using FFPE tissue.
Our assay has generated sufficient results from 1-4ml plasma for variant detection down to 0.4%. Across four tissue types by various cancer stages, our assay and pipeline yield a variant concordance of 70% between cfDNA and FFPE. Majority of mutations only found in plasma may be associated with clonal hematopoiesis in genes such as TET2, DMBT3A and etc. By combining fragment size distribution and driver mutation frequency, we were able to estimate tumor fraction in plasma. Tumor fraction in plasma is significantly associated with tumor stage that >50% of metastatic cancers and > 25% early stage lung cancers contain high tumor fraction. In patients with at least 1% tumor content, there is high correlation between bTMB measured by plasma and TMB measured by FFPE (R2=0.92).
We have developed a ctDNA assay to detect somatic variants and determine bTMB with high accuracy and precision with input as low as 10 ng of cfDNA. Our assay yield accurate measurement of TMB compared to tissue biopsy.
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T. Jiang, S. Zhang, A. Jager, S. Katz, J. Lococo, P. Le, B. Andrian, C. Zhao, D. Baker, T. Pawlowski, S. Bilke: Employee and shareholder: Illumina, Inc.