Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
Binsheng Gong, Dan Li, Rebecca Kusko, Natalia Novoradovskaya, Yifan Zhang, Shangzi Wang, Carlos Pabón-Peña, Zhihong Zhang, Kevin Lai, Wanshi Cai, Jennifer S. LoCoco, Eric Lader, Todd Richmond, Vinay Kumar Mittal, Liang-Chun Liu, Donald J. Johann, James C. Willey, Pierre R. Bushel, Ying Yu, Chang Xu, Guangchun Chen, Daniel L. Burgess, Simon Cawley, Kristina Giorda, Nathan Haseley, Fujun Qiu, Katherine Wilkins, Hanane Arib, Claire Attwooll, Kevin Babson, Longlong Bao, Wenjun Bao, Anne Bergstrom Lucas, Hunter Best, Ambica Bhandari, Halil Bişğin, James Blackburn, Thomas Blomquist, Lisa Boardman, Blake Burgher, Daniel Butler, Chia-Jung Chang, Alka Chaubey, Tao Chen, Marco Chierici, Christopher R. Chin, Devin Close, Jeffrey Conroy, Jessica A. Cooley Coleman, Daniel J. Craig, Erin L. Crawford, Ángela del Pozo, Ira W. Deveson, Daniel Duncan, Agda Karina Eterovic, Xiaohui Fan, Jonathan Foox, Cesare Furlanello, Abhisek Ghosal, Sean T. Glenn, Meijian Guan, Christine Haag, Xinyi Hang, Scott Happe, Brittany Hennigan, Jennifer Hipp, Huixiao Hong, Kyle Horvath, Taobo Hu, Li-Yuan Hung, Mirna Jarosz, Jennifer Kerkhof, Benjamin R. Kipp, David P. Kreil, Paweł P. Łabaj, Pablo Lapunzina, Peng Li, Quan‐Zhen Li, Lin Li, Zhiguang Li, Yu Liang, Shaoqing Liu, Zhichao Liu, Marie‐Aline Charles, Narasimha Marella, Rubén Martín‐Arenas, Dalila B. Megherbi, Qingchang Meng, Piotr A. Mieczkowski, Tom Morrison, Donna M. Muzny, Baitang Ning, Barbara L. Parsons, Cloud P. Paweletz, Mehdi Pirooznia, Wubin Qu, Amelia Raymond, Paul M. Rindler, Rebecca Ringler, Bekim Sadiković
Abstract
BACKGROUND: Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing. RESULTS: All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden. CONCLUSION: This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.