Abstract LB-226: Utilizing 486 gene assay on a NGS platform to validate guideline-adherent tumor mutational burden (TMB) module to calculate TMB

Abstract

Abstract Introduction: The quantification of TMB has emerged as a highly promising biomarker in predicting immunotherapeutic responses. The application of whole exome sequencing to measure TMB has shown to predict response to immunotherapy. Multiple studies have shown that TMB quantification using large panels are comparable to whole exome sequencing and are more practical for implementation in clinical care. The QIAseq TMB panel is a new NGS assay designed to detect genetic alterations in 486 genes, along with MSI and TMB score. Methods: The validation was guided by the joint consensus recommendation for validation of NGS assays by the AMP & CAP and NYSDOH. The validation included evaluations of precision, analytic sensitivity, analytic specificity, accuracy, reportable range, and reference range for TMB. DNA from of 60 samples which were characterized on Foundation CGP assay were used during the validation. Libraries were prepared using the QIAseq TMB panel kit and sequenced on NextSeq 550. The TMB module used for calculation of TMB in this validation was designed and developed by QIAGEN. TMB was calculated as the number of somatic mutations (SNVs and Indels only) per megabase (Mb) of the target region (1.2 Mb for QIAseq TMB panel). Results: In silico analysis using the TCGA data by QIAGEN QCI pipeline showed that the QIAseq TMB panel estimates TMB at a high level of concordance with whole exome sequencing (WES). The data show a high correlation (r2 = 0.98) between the TMB values determined using WES data and TMB using the QIAseq TMB panel data. Our validation data shows significant correlation (r2 = 0.94) among TMB values on the QIAseq panel and Foundation one CGP. Conclusions: In this validation we demonstrate that the QIAseq TMB assay can be used to reliably predict TMB across a wide range of cancer types using the QIAGEN QCI TMB module. Our lab’s experience provides an example for others that may wish to implement TMB testing by NGS on a comprehensive panel. Citation Format: PANKAJ K. AHLUWALIA, ASHIS MONDAL, SUDHA ANANTH, SALEH HENEIDI, VAMSI KOTA, RAVINDRA KOLHE. Utilizing 486 gene assay on a NGS platform to validate guideline-adherent tumor mutational burden (TMB) module to calculate TMB [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 LB-226.