TY - JOUR
T1 - Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
AU - SEQC2 Oncopanel Sequencing Working Group
AU - Deveson, Ira W.
AU - Gong, Binsheng
AU - Lai, Kevin
AU - LoCoco, Jennifer S.
AU - Richmond, Todd A.
AU - Schageman, Jeoffrey
AU - Zhang, Zhihong
AU - Novoradovskaya, Natalia
AU - Willey, James C.
AU - Jones, Wendell
AU - Kusko, Rebecca
AU - Chen, Guangchun
AU - Madala, Bindu Swapna
AU - Blackburn, James
AU - Stevanovski, Igor
AU - Bhandari, Ambica
AU - Close, Devin
AU - Conroy, Jeffrey
AU - Hubank, Michael
AU - Marella, Narasimha
AU - Mieczkowski, Piotr A.
AU - Qiu, Fujun
AU - Sebra, Robert
AU - Stetson, Daniel
AU - Sun, Lihyun
AU - Szankasi, Philippe
AU - Tan, Haowen
AU - Tang, Lin ya
AU - Arib, Hanane
AU - Best, Hunter
AU - Burgher, Blake
AU - Bushel, Pierre R.
AU - Casey, Fergal
AU - Cawley, Simon
AU - Chang, Chia Jung
AU - Choi, Jonathan
AU - Dinis, Jorge
AU - Duncan, Daniel
AU - Eterovic, Agda Karina
AU - Feng, Liang
AU - Ghosal, Abhisek
AU - Giorda, Kristina
AU - Glenn, Sean
AU - Happe, Scott
AU - Haseley, Nathan
AU - Horvath, Kyle
AU - Hung, Li Yuan
AU - Jarosz, Mirna
AU - Kushwaha, Garima
AU - Li, Quan Zhen
N1 - Publisher Copyright:
© 2021, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.
PY - 2021/9
Y1 - 2021/9
N2 - Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.
AB - Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.
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U2 - 10.1038/s41587-021-00857-z
DO - 10.1038/s41587-021-00857-z
M3 - Article
C2 - 33846644
AN - SCOPUS:85104365330
SN - 1087-0156
VL - 39
SP - 1115
EP - 1128
JO - Nature biotechnology
JF - Nature biotechnology
IS - 9
ER -