Tumor mutational burden reference materials for assay standardization.

Abstract

e14746 Background: Next Generation Sequencing based assays are designed to detect genomic aberrations in a limited number of target regions. However, there is a need for accurate measurement of tumor mutational burden (TMB) as low as 4 to as high as 50. As TMB assessment is added to various targeted panels, consistent results between panels are required to advance the broad use of this biomarker. Properly designed reference materials aid measurement standardization and are required to demonstrate assay concordance. We developed reference materials that vary in TMB score, tumor content 5-50% and are prepared in FFPE format. Methods: Seven lung and two breast tumor cell lines as well as matched “normal” lymphoblastoid cell lines were expanded in cell culture. Genomic DNA (gDNA) from each cell line was extracted. Tumor/normal mixes were made by mixing DNA and by embedding cells in FFPE blocks. Whole exome sequencing (WES) results were obtained using Agilent SureSelectXT for library construction and an Illumina Novaseq for sequencing. The Friends of Cancer Research TMB consensus method for analyzing WES data was used to filter variants and calculate TMB scores. Results: The cell lines were grown at large scale to produce extractable gDNA. 100% gDNA tumor, 30% gDNA tumor mixes and 30% FFPE cell line mixes were prepared. Preliminary results show that a clinically-relevant range of TMB values ranging from 4 to 35 mutations per million bases. The several thousand mutations that were observed across the lines were found in a variety of genes, which may explain why TMB in targeted panels is influenced by the specific target regions. Also, the initial results show that 30% cell line mixes showed similar TMB results to 100% gDNA. Conclusions: Our approach with wide ranging TMB values as tumor normal mixes is flexible and can be used to test different tumors and assays. For this study we established WES as the ground truth measurement for comparison to other assay formats and obtained comparison data from other panels. This approach also allows laboratories to test additional variables including formalin fixation, sample extraction, gene panel size, target regions, sequencing depth, filtering and limits of detection.