Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
Authors: Gong Binsheng , Li Dan , Kusko Rebecca , Novoradovskaya Natalia , Zhang Yifan , Wang Shangzi , Pabón-Peña Carlos , Zhang Zhihong , Lai Kevin , Cai Wanshi , LoCoco Jennifer S. , Lader Eric , Richmond Todd A. , Mittal Vinay K. , Liu Liang-Chun , Johann Donald J. , Willey James C. , Bushel Pierre R. , Yu Ying , Xu Chang , Chen Guangchun , Burgess Daniel , Cawley Simon , Giorda Kristina , Haseley Nathan , Qiu Fujun , Wilkins Katherine , Arib Hanane , Attwooll Claire , Babson Kevin , Bao Longlong , Bao Wenjun , Lucas Anne Bergstrom , Best Hunter , Bhandari Ambica , Bisgin Halil , Blackburn James , Blomquist Thomas M. , Boardman Lisa , Burgher Blake , Butler Daniel J. , Chang Chia-Jung , Chaubey Alka , Chen Tao , Chierici Marco , Chin Christopher R. , Close Devin , Conroy Jeffrey , Cooley Coleman Jessica , Craig Daniel J. , Crawford Erin , del Pozo Angela , Deveson Ira W. , Duncan Daniel , Eterovic Agda Karina , Fan Xiaohui , Foox Jonathan , Furlanello Cesare , Ghosal Abhisek , Glenn Sean , Guan Meijian , Haag Christine , Hang Xinyi , Happe Scott , Hennigan Brittany , Hipp Jennifer , Hong Huixiao , Horvath Kyle , Hu Jianhong , Hung Li-Yuan , Jarosz Mirna , Kerkhof Jennifer , Kipp Benjamin , Kreil David Philip , Łabaj Paweł , Lapunzina Pablo , Li Peng , Li Quan-Zhen , Li Weihua , Li Zhiguang , Liang Yu , Liu Shaoqing , Liu Zhichao , Ma Charles , Marella Narasimha , Martín-Arenas Rubén , Megherbi Dalila B. , Meng Qingchang , Mieczkowski Piotr A. , Morrison Tom , Muzny Donna , Ning Baitang , Parsons Barbara L. , Paweletz Cloud P. , Pirooznia Mehdi , Qu Wubin , Raymond Amelia , Rindler Paul , Ringler Rebecca , Sadikovic Bekim , Scherer Andreas , Schulze Egbert , Sebra Robert , Shaknovich Rita , Shi Qiang , Shi Tieliu , Silla-Castro Juan Carlos , Smith Melissa , López Mario Solís , Song Ping , Stetson Daniel , Strahl Maya , Stuart Alan , Supplee Julianna , Szankasi Philippe , Tan Haowen , Tang Lin-ya , Tao Yonghui , Thakkar Shraddha , Thierry-Mieg Danielle , Thierry-Mieg Jean , Thodima Venkat J. , Thomas David , Tichý Boris , Tom Nikola , Garcia Elena Vallespin , Verma Suman , Walker Kimbley , Wang Charles , Wang Junwen , Wang Yexun , Wen Zhining , Wirta Valtteri , Wu Leihong , Xiao Chunlin , Xiao Wenzhong , Xu Shibei , Yang Mary , Ying Jianming , Yip Shun H. , Zhang Guangliang , Zhang Sa , Zhao Meiru , Zheng Yuanting , Zhou Xiaoyan , Mason Christopher E. , Mercer Timothy , Tong Weida , Shi Leming , Jones Wendell , Xu Joshua 
Published: April 2021

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.