| GONG, B.S., D. LI, R. KUSKO, N. NOVORADOVSKAYA, Y.F. ZHANG, S.Z. WANG, C. PABON-PENA, Z.H. ZHANG, K. LAI, W.S. CAI, J.S. LOCOCO, E. LADER, T.A. RICHMOND, V.K. MITTAL, L.C. LIU, D.J. JOHANN, J.C. WILLEY, P.R. BUSHEL, Y. YU, C. XU, G.C. CHEN, D. BURGESS, S. CAWLEY, K. GIORDA, N. HASELEY, F.J. QIU, K. WILKINS, H. ARIB, C. ATTWOOLL, K. BABSON, L.L. BAO, W.J. BAO, A.B. LUCAS, H. BEST, A. BHANDARI, H. BISGIN, J. BLACKBURN, T.M. BLOMQUIST, L. BOARDMAN, B. BURGHER, D.J. BUTLER, C.J. CHANG, A. CHAUBEY, T. CHEN, M. CHIERICI, C.R. CHIN, D. CLOSE, J. CONROY, J.C. COLEMAN, D.J. CRAIG, E. CRAWFORD, A. DEL POZO, I.W. DEVESON, D. DUNCAN, A.K. ETEROVIC, X.H. FAN, J. FOOX, C. FURLANELLO, A. GHOSAL, S. GLENN, M.J. GUAN, C. HAAG, X.Y. HANG, S. HAPPE, B. HENNIGAN, J. HIPP, H.X. HONG, K. HORVATH, J.H. HU, L.Y. HUNG, M. JAROSZ, J. KERKHOF, B. KIPP, D.P. KREIL, P. LAPUNZINA, P. LI, Q.Z. LI, W.H. LI, Z.G. LI, Y. LIANG, S.Q. LIU, Z.C. LIU, C. MA, N. MARELLA, R. MARTIN-ARENAS, D.B. MEGHERBI, Q.C. MENG, P.A. MIECZKOWSKI, T. MORRISON, D. MUZNY, B.T. NING, B.L. PARSONS, C.P. PAWELETZ, M. PIROOZNIA, W.B. QU, A. RAYMOND, P. RINDLER, R. RINGLER, B. SADIKOVIC, A. SCHERER, E. SCHULZE, R. SEBRA, R. SHAKNOVICH, Q. SHI, T.L. SHI, J.C. SILLA-CASTRO, M. SMITH, M.S. LOPEZ, P. SONG, D. STETSON, M. STRAHL, A. STUART, J. SUPPLEE, P. SZANKASI, H.W. TAN, L.Y. TANG, Y.H. TAO, S. THAKKAR, D. THIERRY-MIEG, J. THIERRY-MIEG, V.J. THODIMA, D. THOMAS, Boris TICHÝ, Nikola TOM, E.V. GARCIA, S. VERMA, K. WALKER, C. WANG, J.W. WANG, Y.X. WANG, Z.N. WEN, V. WIRTA, L.H. WU, C.L. XIAO, W.Z. XIAO, S.B. XU, M. YANG, J.M. YING, S.H. YIP, G.L. ZHANG, S. ZHANG, M.R. ZHAO, Y.T. ZHENG, X.Y. ZHOU, C.E. MASON, T. MERCER, W.D. TONG, L.M. SHI, W. JONES and J.S. XU. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. GENOME BIOLOGY. LONDON: BIOMED CENTRAL LTD, 2021, vol. 22, No 1, p. 109-131. ISSN 1474-760X. Available from: https://dx.doi.org/10.1186/s13059-021-02315-0. |
Other formats:
BibTeX
LaTeX
RIS
@article{1782164,
author = {Gong, B.S. and Li, D. and Kusko, R. and Novoradovskaya, N. and Zhang, Y.F. and Wang, S.Z. and PabonandPena, C. and Zhang, Z.H. and Lai, K. and Cai, W.S. and LoCoco, J.S. and Lader, E. and Richmond, T.A. and Mittal, V.K. and Liu, L.C. and Johann, D.J. and Willey, J.C. and Bushel, P.R. and Yu, Y. and Xu, C. and Chen, G.C. and Burgess, D. and Cawley, S. and Giorda, K. and Haseley, N. and Qiu, F.J. and Wilkins, K. and Arib, H. and Attwooll, C. and Babson, K. and Bao, L.L. and Bao, W.J. and Lucas, A.B. and Best, H. and Bhandari, A. and Bisgin, H. and Blackburn, J. and Blomquist, T.M. and Boardman, L. and Burgher, B. and Butler, D.J. and Chang, C.J. and Chaubey, A. and Chen, T. and Chierici, M. and Chin, C.R. and Close, D. and Conroy, J. and Coleman, J.C. and Craig, D.J. and Crawford, E. and del Pozo, A. and Deveson, I.W. and Duncan, D. and Eterovic, A.K. and Fan, X.H. and Foox, J. and Furlanello, C. and Ghosal, A. and Glenn, S. and Guan, M.J. and Haag, C. and Hang, X.Y. and Happe, S. and Hennigan, B. and Hipp, J. and Hong, H.X. and Horvath, K. and Hu, J.H. and Hung, L.Y. and Jarosz, M. and Kerkhof, J. and Kipp, B. and Kreil, D.P. and Lapunzina, P. and Li, P. and Li, Q.Z. and Li, W.H. and Li, Z.G. and Liang, Y. and Liu, S.Q. and Liu, Z.C. and Ma, C. and Marella, N. and MartinandArenas, R. and Megherbi, D.B. and Meng, Q.C. and Mieczkowski, P.A. and Morrison, T. and Muzny, D. and Ning, B.T. and Parsons, B.L. and Paweletz, C.P. and Pirooznia, M. and Qu, W.B. and Raymond, A. and Rindler, P. and Ringler, R. and Sadikovic, B. and Scherer, A. and Schulze, E. and Sebra, R. and Shaknovich, R. and Shi, Q. and Shi, T.L. and SillaandCastro, J.C. and Smith, M. and Lopez, M.S. and Song, P. and Stetson, D. and Strahl, M. and Stuart, A. and Supplee, J. and Szankasi, P. and Tan, H.W. and Tang, L.Y. and Tao, Y.H. and Thakkar, S. and ThierryandMieg, D. and ThierryandMieg, J. and Thodima, V.J. and Thomas, D. and Tichý, Boris and Tom, Nikola and Garcia, E.V. and Verma, S. and Walker, K. and Wang, C. and Wang, J.W. and Wang, Y.X. and Wen, Z.N. and Wirta, V. and Wu, L.H. and Xiao, C.L. and Xiao, W.Z. and Xu, S.B. and Yang, M. and Ying, J.M. and Yip, S.H. and Zhang, G.L. and Zhang, S. and Zhao, M.R. and Zheng, Y.T. and Zhou, X.Y. and Mason, C.E. and Mercer, T. and Tong, W.D. and Shi, L.M. and Jones, W. and Xu, J.S.},
article_location = {LONDON},
article_number = {1},
doi = {http://dx.doi.org/10.1186/s13059-021-02315-0},
keywords = {Oncopanel sequencing; Target enrichment; Molecular diagnostics; Reproducibility; Analytical performance; Precision medicine},
language = {eng},
issn = {1474-760X},
journal = {GENOME BIOLOGY},
title = {Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions},
url = {https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-021-02315-0.pdf},
volume = {22},
year = {2021}
}
TY - JOUR
ID - 1782164
AU - Gong, B.S. - Li, D. - Kusko, R. - Novoradovskaya, N. - Zhang, Y.F. - Wang, S.Z. - Pabon-Pena, C. - Zhang, Z.H. - Lai, K. - Cai, W.S. - LoCoco, J.S. - Lader, E. - Richmond, T.A. - Mittal, V.K. - Liu, L.C. - Johann, D.J. - Willey, J.C. - Bushel, P.R. - Yu, Y. - Xu, C. - Chen, G.C. - Burgess, D. - Cawley, S. - Giorda, K. - Haseley, N. - Qiu, F.J. - Wilkins, K. - Arib, H. - Attwooll, C. - Babson, K. - Bao, L.L. - Bao, W.J. - Lucas, A.B. - Best, H. - Bhandari, A. - Bisgin, H. - Blackburn, J. - Blomquist, T.M. - Boardman, L. - Burgher, B. - Butler, D.J. - Chang, C.J. - Chaubey, A. - Chen, T. - Chierici, M. - Chin, C.R. - Close, D. - Conroy, J. - Coleman, J.C. - Craig, D.J. - Crawford, E. - del Pozo, A. - Deveson, I.W. - Duncan, D. - Eterovic, A.K. - Fan, X.H. - Foox, J. - Furlanello, C. - Ghosal, A. - Glenn, S. - Guan, M.J. - Haag, C. - Hang, X.Y. - Happe, S. - Hennigan, B. - Hipp, J. - Hong, H.X. - Horvath, K. - Hu, J.H. - Hung, L.Y. - Jarosz, M. - Kerkhof, J. - Kipp, B. - Kreil, D.P. - Lapunzina, P. - Li, P. - Li, Q.Z. - Li, W.H. - Li, Z.G. - Liang, Y. - Liu, S.Q. - Liu, Z.C. - Ma, C. - Marella, N. - Martin-Arenas, R. - Megherbi, D.B. - Meng, Q.C. - Mieczkowski, P.A. - Morrison, T. - Muzny, D. - Ning, B.T. - Parsons, B.L. - Paweletz, C.P. - Pirooznia, M. - Qu, W.B. - Raymond, A. - Rindler, P. - Ringler, R. - Sadikovic, B. - Scherer, A. - Schulze, E. - Sebra, R. - Shaknovich, R. - Shi, Q. - Shi, T.L. - Silla-Castro, J.C. - Smith, M. - Lopez, M.S. - Song, P. - Stetson, D. - Strahl, M. - Stuart, A. - Supplee, J. - Szankasi, P. - Tan, H.W. - Tang, L.Y. - Tao, Y.H. - Thakkar, S. - Thierry-Mieg, D. - Thierry-Mieg, J. - Thodima, V.J. - Thomas, D. - Tichý, Boris - Tom, Nikola - Garcia, E.V. - Verma, S. - Walker, K. - Wang, C. - Wang, J.W. - Wang, Y.X. - Wen, Z.N. - Wirta, V. - Wu, L.H. - Xiao, C.L. - Xiao, W.Z. - Xu, S.B. - Yang, M. - Ying, J.M. - Yip, S.H. - Zhang, G.L. - Zhang, S. - Zhao, M.R. - Zheng, Y.T. - Zhou, X.Y. - Mason, C.E. - Mercer, T. - Tong, W.D. - Shi, L.M. - Jones, W. - Xu, J.S.
PY - 2021
TI - Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
JF - GENOME BIOLOGY
VL - 22
IS - 1
SP - 109
EP - 109
PB - BIOMED CENTRAL LTD
SN - 1474760X
KW - Oncopanel sequencing
KW - Target enrichment
KW - Molecular diagnostics
KW - Reproducibility
KW - Analytical performance
KW - Precision medicine
UR - https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-021-02315-0.pdf
N2 - BackgroundTargeted 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.ResultsAll 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.ConclusionThis 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.
ER -
GONG, B.S., D. LI, R. KUSKO, N. NOVORADOVSKAYA, Y.F. ZHANG, S.Z. WANG, C. PABON-PENA, Z.H. ZHANG, K. LAI, W.S. CAI, J.S. LOCOCO, E. LADER, T.A. RICHMOND, V.K. MITTAL, L.C. LIU, D.J. JOHANN, J.C. WILLEY, P.R. BUSHEL, Y. YU, C. XU, G.C. CHEN, D. BURGESS, S. CAWLEY, K. GIORDA, N. HASELEY, F.J. QIU, K. WILKINS, H. ARIB, C. ATTWOOLL, K. BABSON, L.L. BAO, W.J. BAO, A.B. LUCAS, H. BEST, A. BHANDARI, H. BISGIN, J. BLACKBURN, T.M. BLOMQUIST, L. BOARDMAN, B. BURGHER, D.J. BUTLER, C.J. CHANG, A. CHAUBEY, T. CHEN, M. CHIERICI, C.R. CHIN, D. CLOSE, J. CONROY, J.C. COLEMAN, D.J. CRAIG, E. CRAWFORD, A. DEL POZO, I.W. DEVESON, D. DUNCAN, A.K. ETEROVIC, X.H. FAN, J. FOOX, C. FURLANELLO, A. GHOSAL, S. GLENN, M.J. GUAN, C. HAAG, X.Y. HANG, S. HAPPE, B. HENNIGAN, J. HIPP, H.X. HONG, K. HORVATH, J.H. HU, L.Y. HUNG, M. JAROSZ, J. KERKHOF, B. KIPP, D.P. KREIL, P. LAPUNZINA, P. LI, Q.Z. LI, W.H. LI, Z.G. LI, Y. LIANG, S.Q. LIU, Z.C. LIU, C. MA, N. MARELLA, R. MARTIN-ARENAS, D.B. MEGHERBI, Q.C. MENG, P.A. MIECZKOWSKI, T. MORRISON, D. MUZNY, B.T. NING, B.L. PARSONS, C.P. PAWELETZ, M. PIROOZNIA, W.B. QU, A. RAYMOND, P. RINDLER, R. RINGLER, B. SADIKOVIC, A. SCHERER, E. SCHULZE, R. SEBRA, R. SHAKNOVICH, Q. SHI, T.L. SHI, J.C. SILLA-CASTRO, M. SMITH, M.S. LOPEZ, P. SONG, D. STETSON, M. STRAHL, A. STUART, J. SUPPLEE, P. SZANKASI, H.W. TAN, L.Y. TANG, Y.H. TAO, S. THAKKAR, D. THIERRY-MIEG, J. THIERRY-MIEG, V.J. THODIMA, D. THOMAS, Boris TICHÝ, Nikola TOM, E.V. GARCIA, S. VERMA, K. WALKER, C. WANG, J.W. WANG, Y.X. WANG, Z.N. WEN, V. WIRTA, L.H. WU, C.L. XIAO, W.Z. XIAO, S.B. XU, M. YANG, J.M. YING, S.H. YIP, G.L. ZHANG, S. ZHANG, M.R. ZHAO, Y.T. ZHENG, X.Y. ZHOU, C.E. MASON, T. MERCER, W.D. TONG, L.M. SHI, W. JONES and J.S. XU. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. \textit{GENOME BIOLOGY}. LONDON: BIOMED CENTRAL LTD, 2021, vol.~22, No~1, p.~109-131. ISSN~1474-760X. Available from: https://dx.doi.org/10.1186/s13059-021-02315-0.
|
