Por favor, use este identificador para citar o enlazar este Item:http://hdl.handle.net/20.500.12105/13424
Título
Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.
Autor(es)
Gong, Binsheng | Li, Dan | Kusko, Rebecca | Novoradovskaya, Natalia | Zhang, Yifan | Wang, Shangzi | Pabon-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 CNIC | Smith, Melissa | Solis-Lopez, Mario | 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 | Tichy, Boris | Tom, Nikola | Vallespin-Garcia, Elena | 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
Fecha de publicación
2021-04
Cita
Genome Biol. 2021; 22(1):109
Idioma
Inglés
Tipo de documento
journal article
Resumen
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.
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.
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.
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