Abstract 1701: Improvement of tumor mutation burden measurement by removal of deaminated bases in FFPE DNA

Abstract

Tumor mutation burden (TMB) is a positive predictive factor for response to immune-checkpoint inhibitors in certain types of cancer. The Oncomine™ Tumor Mutation Load Assay, a 1.7Mb targeted next generation sequencing (NGS) panel, measures TMB and detects mutations in 409 cancer genes. The TMB values obtained using targeted sequencing are positively correlated with TMB measured by whole exome sequencing in NSCLC, colorectal, endometrial and gastric cancers. TMB from these tumor samples are correlated with other phenotypes associated with genomic instability, specifically microsatellite instability (MSI) and mutations involved in mismatch repair and cancer related genes. Analysis of the Oncomine™ TML Assay results with Torrent Suite and Ion Reporter software uniquely measures the degree of deamination of cytosines to uracils in fixed tissues. FFPE preservation methods can lead to significant cytosine deamination of the isolated DNA, resulting in decreased sequencing quality. In these samples, uracils are propagated as thymines and result in false C>T substitutions. To minimize the influence that excess deamination has on TMB results, we have incorporated a UDG enzyme treatment to eliminate damaged targets and improve usable TMB values of DNA from damaged FFPE tumor tissue. The Oncomine™ TML assay for TMB on Ion GeneStudio™ S5 in conjunction with MSI detection is informative and potentially predictive for the use of checkpoint inhibitors in multiple cancer types. Citation Format: Warren Tom, Ruchi Chaudhary, Vinay Mittal, Dinesh Cyanam, Iris Casuga, Elaine Wong-Ho, Rob Bennett, Fiona Hyland, Seth Sadis, Janice Au-Young. Improvement of tumor mutation burden measurement by removal of deaminated bases in FFPE DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1701.

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“…Additionally, deamination that occurs in FFPE samples was a significant issue in our cohort when using the OTML panel. This could be reduced by implementing an enzymatic deamination repair using UDG, confirming previously reported results [29]. For future studies, we would therefore recommend that one generally includes the UDG-treatment when using the OTML panel for TMB assessment to overcome FFPE-related artefacts [30,31].…”