Abstract 5057: Enhancing clinical applications by evaluation of sensitivity and specificity in whole exome sequencing

Abstract The cost-effectiveness of whole exome sequencing (WES) remains debated, primarily due to variability in variant calls. Evaluating the sensitivity and specificity of WES results may clarify this issue. WES was performed by three companies (AA, BB, and CC) using reference standards composed of DNA from Hydatidiform mole and individual blood at various ratios. Sensitivity was assessed by the detection rate of null-homozygote (N-H) alleles at expected variant allelic fractions, while false positive (FP) errors were counted for unexpected alleles. Sensitivity was approximately 20% for in-house results from BB and CC and around 5% for AA. Dragen analyses identified 1.34 to 1.71 times more variants, detecting over 96% of in-house variants, with sensitivity for common variants increasing to 5%. In-house FP errors varied significantly among companies (up to 13.97 times), while Dragen analyses minimized this variation. Despite Dragen showing higher FP errors for BB and CC, the increased sensitivity highlights the importance of effective bioinformatic conditions. We also assessed the potential effects of target enrichment and proposed optimal cutoff values for read depth and variant allele fraction in WES. Optimizing bioinformatic analysis based on sensitivity and specificity from reference standards can enhance variant detection and improve the clinical utility of WES. Citation Format: Chunghwan Hong, Youngbeen Moon, Hye Won Choi, Eun-Kyung Kang, Seo-Hyeon Ye, Jong-Kwang Kim, Young-Ho Kim, Hyeri Cho, Hana Choi, Dong-eun Lee, Yongdoo Choi, Tae-Min Kim, Seong Gu Heo, Namshik Han, Kyeong-Man Hong. Enhancing clinical applications by evaluation of sensitivity and specificity in whole exome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5057.