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 A. Richmond; Vinay K. Mittal; Liang Chun Liu; Donald J. Johann; James C. Willey; Pierre R. Bushel; Ying Yu; Chang Xu; Guangchun Chen; Daniel 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 Bisgin; James Blackburn; Thomas M. Blomquist; Lisa Boardman; Blake Burgher; Daniel J. Butler; Chia Jung Chang; Alka Chaubey; Tao Chen; Marco Chierici; Christopher R. Chin; Devin Close; Jeffrey Conroy; Jessica Cooley Coleman; Daniel J. Craig; Erin Crawford; Angela del Pozo; Ira W. Deveson; Daniel Duncan; Agda Karina Eterovic; Xiaohui Fan; Jonathan Foox; Cesare Furlanello; Abhisek Ghosal; Sean Glenn; Meijian Guan; Christine Haag; Xinyi Hang; Scott Happe; Brittany Hennigan; Jennifer Hipp; Huixiao Hong; Kyle Horvath; Jianhong Hu; Li Yuan Hung; Mirna Jarosz; Jennifer Kerkhof; Benjamin Kipp; David Philip Kreil; Paweł Łabaj; Pablo Lapunzina; Peng Li; Quan Zhen Li; Weihua Li; Zhiguang Li; Yu Liang; Shaoqing Liu; Zhichao Liu; Charles Ma; Narasimha Marella; Rubén Martín-Arenas; Dalila B. Megherbi; Qingchang Meng; Piotr A. Mieczkowski; Tom Morrison; Donna Muzny; Baitang Ning; Barbara L. Parsons; Cloud P. Paweletz; Mehdi Pirooznia; Wubin Qu; Amelia Raymond; Paul Rindler; Rebecca Ringler; Bekim Sadikovic; Andreas Scherer; Egbert Schulze; Robert Sebra; Rita Shaknovich; Qiang Shi; Tieliu Shi; Juan Carlos Silla-Castro; Melissa Smith; Mario Solís López; Ping Song; Daniel Stetson; Maya Strahl; Alan Stuart; Julianna Supplee; Philippe Szankasi; Haowen Tan; Lin ya Tang; Yonghui Tao; Shraddha Thakkar; Danielle Thierry-Mieg; Jean Thierry-Mieg; Venkat J. Thodima; David Thomas; Boris Tichý; Nikola Tom; Elena Vallespin Garcia; Suman Verma; Kimbley Walker; Charles Wang; Junwen Wang; Yexun Wang; Zhining Wen; Valtteri Wirta; Leihong Wu; Chunlin Xiao; Wenzhong Xiao; Shibei Xu; Mary Yang; Jianming Ying; Shun H. Yip; Guangliang Zhang; Sa Zhang; Meiru Zhao; Yuanting Zheng; Xiaoyan Zhou; Christopher E. Mason; Timothy Mercer; Weida Tong; Leming Shi; Wendell Jones; Joshua Xu

doi:10.1186/s13059-021-02315-0

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 A. Richmond, Vinay K. Mittal, Liang Chun Liu, Donald J. Johann, James C. Willey, Pierre R. Bushel, Ying Yu, Chang XuGuangchun Chen, Daniel 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 Bisgin, James Blackburn, Thomas M. Blomquist, Lisa Boardman, Blake Burgher, Daniel J. Butler, Chia Jung Chang, Alka Chaubey, Tao Chen, Marco Chierici, Christopher R. Chin, Devin Close, Jeffrey Conroy, Jessica Cooley Coleman, Daniel J. Craig, Erin Crawford, Angela del Pozo, Ira W. Deveson, Daniel Duncan, Agda Karina Eterovic, Xiaohui Fan, Jonathan Foox, Cesare Furlanello, Abhisek Ghosal, Sean Glenn, Meijian Guan, Christine Haag, Xinyi Hang, Scott Happe, Brittany Hennigan, Jennifer Hipp, Huixiao Hong, Kyle Horvath, Jianhong Hu, Li Yuan Hung, Mirna Jarosz, Jennifer Kerkhof, Benjamin Kipp, David Philip Kreil, Paweł Łabaj, Pablo Lapunzina, Peng Li, Quan Zhen Li, Weihua Li, Zhiguang Li, Yu Liang, Shaoqing Liu, Zhichao Liu, Charles Ma, Narasimha Marella, Rubén Martín-Arenas, Dalila B. Megherbi, Qingchang Meng, Piotr A. Mieczkowski, Tom Morrison, Donna Muzny, Baitang Ning, Barbara L. Parsons, Cloud P. Paweletz, Mehdi Pirooznia, Wubin Qu, Amelia Raymond, Paul Rindler, Rebecca Ringler, Bekim Sadikovic, Andreas Scherer, Egbert Schulze, Robert Sebra, Rita Shaknovich, Qiang Shi, Tieliu Shi, Juan Carlos Silla-Castro, Melissa Smith, Mario Solís López, Ping Song, Daniel Stetson, Maya Strahl, Alan Stuart, Julianna Supplee, Philippe Szankasi, Haowen Tan, Lin ya Tang, Yonghui Tao, Shraddha Thakkar, Danielle Thierry-Mieg, Jean Thierry-Mieg, Venkat J. Thodima, David Thomas, Boris Tichý, Nikola Tom, Elena Vallespin Garcia, Suman Verma, Kimbley Walker, Charles Wang, Junwen Wang, Yexun Wang, Zhining Wen, Valtteri Wirta, Leihong Wu, Chunlin Xiao, Wenzhong Xiao, Shibei Xu, Mary Yang, Jianming Ying, Shun H. Yip, Guangliang Zhang, Sa Zhang, Meiru Zhao, Yuanting Zheng, Xiaoyan Zhou, Christopher E. Mason, Timothy Mercer, Weida Tong, Leming Shi, Wendell Jones, Joshua Xu

Research output: Contribution to journal › Article › peer-review

Original language	English
Article number	109
Journal	Genome Biology
Volume	22
Issue number	1
DOIs	https://doi.org/10.1186/s13059-021-02315-0
State	Published - Apr 16 2021

ASJC Scopus Subject Areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

Keywords

Analytical performance
Molecular diagnostics
Oncopanel sequencing
Precision medicine
Reproducibility
Target enrichment
Reproducibility of Results
Humans
Genomics/methods
Biomarkers, Tumor
DNA Copy Number Variations
Genetic Testing/methods
Neoplasms/diagnosis
Sensitivity and Specificity
Polymorphism, Single Nucleotide
Mutation
Molecular Diagnostic Techniques/methods
Oncogenes

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10.1186/s13059-021-02315-0

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Gong, B., Li, D., Kusko, R., Novoradovskaya, N., Zhang, Y., Wang, S., Pabón-Peña, C., Zhang, Z., Lai, K., Cai, W., 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, J. (2021). Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biology, 22(1), Article 109. https://doi.org/10.1186/s13059-021-02315-0

Gong, B, Li, D, Kusko, R, Novoradovskaya, N, Zhang, Y, Wang, S, Pabón-Peña, C, Zhang, Z, Lai, K, Cai, W, LoCoco, JS, Lader, E, Richmond, TA, Mittal, VK, Liu, LC, Johann, DJ, Willey, JC, Bushel, PR, Yu, Y, Xu, C, Chen, G, Burgess, D, Cawley, S, Giorda, K, Haseley, N, Qiu, F, Wilkins, K, Arib, H, Attwooll, C, Babson, K, Bao, L, Bao, W, Lucas, AB, Best, H, Bhandari, A, Bisgin, H, Blackburn, J, Blomquist, TM, Boardman, L, Burgher, B, Butler, DJ, Chang, CJ, Chaubey, A, Chen, T, Chierici, M, Chin, CR, Close, D, Conroy, J, Coleman, JC, Craig, DJ, Crawford, E, del Pozo, A, Deveson, IW, Duncan, D, Eterovic, AK, Fan, X, Foox, J, Furlanello, C, Ghosal, A, Glenn, S, Guan, M, Haag, C, Hang, X, Happe, S, Hennigan, B, Hipp, J, Hong, H, Horvath, K, Hu, J, Hung, LY, Jarosz, M, Kerkhof, J, Kipp, B, Kreil, DP, Łabaj, P, Lapunzina, P, Li, P, Li, QZ, Li, W, Li, Z, Liang, Y, Liu, S, Liu, Z, Ma, C, Marella, N, Martín-Arenas, R, Megherbi, DB, Meng, Q, Mieczkowski, PA, Morrison, T, Muzny, D, Ning, B, Parsons, BL, Paweletz, CP, Pirooznia, M, Qu, W, Raymond, A, Rindler, P, Ringler, R, Sadikovic, B, Scherer, A, Schulze, E, Sebra, R, Shaknovich, R, Shi, Q, Shi, T, Silla-Castro, JC, Smith, M, López, MS, Song, P, Stetson, D, Strahl, M, Stuart, A, Supplee, J, Szankasi, P, Tan, H, Tang, LY, Tao, Y, Thakkar, S, Thierry-Mieg, D, Thierry-Mieg, J, Thodima, VJ, Thomas, D, Tichý, B, Tom, N, Garcia, EV, Verma, S, Walker, K, Wang, C, Wang, J, Wang, Y, Wen, Z, Wirta, V, Wu, L, Xiao, C, Xiao, W, Xu, S, Yang, M, Ying, J, Yip, SH, Zhang, G, Zhang, S, Zhao, M, Zheng, Y, Zhou, X, Mason, CE, Mercer, T, Tong, W, Shi, L, Jones, W & Xu, J 2021, 'Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions', Genome Biology, vol. 22, no. 1, 109. https://doi.org/10.1186/s13059-021-02315-0

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title = "Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions",

keywords = "Analytical performance, Molecular diagnostics, Oncopanel sequencing, Precision medicine, Reproducibility, Target enrichment, Reproducibility of Results, Humans, Genomics/methods, Biomarkers, Tumor, DNA Copy Number Variations, Genetic Testing/methods, Neoplasms/diagnosis, Sensitivity and Specificity, Polymorphism, Single Nucleotide, Mutation, Molecular Diagnostic Techniques/methods, Oncogenes",

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

note = "Publisher Copyright: {\textcopyright} 2021, The Author(s).",

year = "2021",

month = apr,

day = "16",

doi = "10.1186/s13059-021-02315-0",

language = "English",

volume = "22",

journal = "Genome Biology",

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T1 - Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

AU - Gong, Binsheng

AU - Li, Dan

AU - Kusko, Rebecca

AU - Novoradovskaya, Natalia

AU - Zhang, Yifan

AU - Wang, Shangzi

AU - Pabón-Peña, Carlos

AU - Zhang, Zhihong

AU - Lai, Kevin

AU - Cai, Wanshi

AU - LoCoco, Jennifer S.

AU - Lader, Eric

AU - Richmond, Todd A.

AU - Mittal, Vinay K.

AU - Liu, Liang Chun

AU - Johann, Donald J.

AU - Willey, James C.

AU - Bushel, Pierre R.

AU - Yu, Ying

AU - Xu, Chang

AU - Chen, Guangchun

AU - Burgess, Daniel

AU - Cawley, Simon

AU - Giorda, Kristina

AU - Haseley, Nathan

AU - Qiu, Fujun

AU - Wilkins, Katherine

AU - Arib, Hanane

AU - Attwooll, Claire

AU - Babson, Kevin

AU - Bao, Longlong

AU - Bao, Wenjun

AU - Lucas, Anne Bergstrom

AU - Best, Hunter

AU - Bhandari, Ambica

AU - Bisgin, Halil

AU - Blackburn, James

AU - Blomquist, Thomas M.

AU - Boardman, Lisa

AU - Burgher, Blake

AU - Butler, Daniel J.

AU - Chang, Chia Jung

AU - Chaubey, Alka

AU - Chen, Tao

AU - Chierici, Marco

AU - Chin, Christopher R.

AU - Close, Devin

AU - Conroy, Jeffrey

AU - Coleman, Jessica Cooley

AU - Craig, Daniel J.

AU - Crawford, Erin

AU - del Pozo, Angela

AU - Deveson, Ira W.

AU - Duncan, Daniel

AU - Eterovic, Agda Karina

AU - Fan, Xiaohui

AU - Foox, Jonathan

AU - Furlanello, Cesare

AU - Ghosal, Abhisek

AU - Glenn, Sean

AU - Guan, Meijian

AU - Haag, Christine

AU - Hang, Xinyi

AU - Happe, Scott

AU - Hennigan, Brittany

AU - Hipp, Jennifer

AU - Hong, Huixiao

AU - Horvath, Kyle

AU - Hu, Jianhong

AU - Hung, Li Yuan

AU - Jarosz, Mirna

AU - Kerkhof, Jennifer

AU - Kipp, Benjamin

AU - Kreil, David Philip

AU - Łabaj, Paweł

AU - Lapunzina, Pablo

AU - Li, Peng

AU - Li, Quan Zhen

AU - Li, Weihua

AU - Li, Zhiguang

AU - Liang, Yu

AU - Liu, Shaoqing

AU - Liu, Zhichao

AU - Ma, Charles

AU - Marella, Narasimha

AU - Martín-Arenas, Rubén

AU - Megherbi, Dalila B.

AU - Meng, Qingchang

AU - Mieczkowski, Piotr A.

AU - Morrison, Tom

AU - Muzny, Donna

AU - Ning, Baitang

AU - Parsons, Barbara L.

AU - Paweletz, Cloud P.

AU - Pirooznia, Mehdi

AU - Qu, Wubin

AU - Raymond, Amelia

AU - Rindler, Paul

AU - Ringler, Rebecca

AU - Sadikovic, Bekim

AU - Scherer, Andreas

AU - Schulze, Egbert

AU - Sebra, Robert

AU - Shaknovich, Rita

AU - Shi, Qiang

AU - Shi, Tieliu

AU - Silla-Castro, Juan Carlos

AU - Smith, Melissa

AU - López, Mario Solís

AU - Song, Ping

AU - Stetson, Daniel

AU - Strahl, Maya

AU - Stuart, Alan

AU - Supplee, Julianna

AU - Szankasi, Philippe

AU - Tan, Haowen

AU - Tang, Lin ya

AU - Tao, Yonghui

AU - Thakkar, Shraddha

AU - Thierry-Mieg, Danielle

AU - Thierry-Mieg, Jean

AU - Thodima, Venkat J.

AU - Thomas, David

AU - Tichý, Boris

AU - Tom, Nikola

AU - Garcia, Elena Vallespin

AU - Verma, Suman

AU - Walker, Kimbley

AU - Wang, Charles

AU - Wang, Junwen

AU - Wang, Yexun

AU - Wen, Zhining

AU - Wirta, Valtteri

AU - Wu, Leihong

AU - Xiao, Chunlin

AU - Xiao, Wenzhong

AU - Xu, Shibei

AU - Yang, Mary

AU - Ying, Jianming

AU - Yip, Shun H.

AU - Zhang, Guangliang

AU - Zhang, Sa

AU - Zhao, Meiru

AU - Zheng, Yuanting

AU - Zhou, Xiaoyan

AU - Mason, Christopher E.

AU - Mercer, Timothy

AU - Tong, Weida

AU - Shi, Leming

AU - Jones, Wendell

AU - Xu, Joshua

PY - 2021/4/16

Y1 - 2021/4/16

KW - Analytical performance

KW - Molecular diagnostics

KW - Oncopanel sequencing

KW - Precision medicine

KW - Reproducibility

KW - Target enrichment

KW - Reproducibility of Results

KW - Humans

KW - Genomics/methods

KW - Biomarkers, Tumor

KW - DNA Copy Number Variations

KW - Genetic Testing/methods

KW - Neoplasms/diagnosis

KW - Sensitivity and Specificity

KW - Polymorphism, Single Nucleotide

KW - Mutation

KW - Molecular Diagnostic Techniques/methods

KW - Oncogenes

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JO - Genome Biology

JF - Genome Biology

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ER -

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

ASJC Scopus Subject Areas

Keywords

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