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

Autor: 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

Publikováno v: Genome Biology, Vol 22, Iss 1, Pp 1-23 (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-l

Externí odkaz: https://doaj.org/article/c5365bb671514dddbb3d5b324f62ed28

SWI/SNF chromatin remodeling complex alterations in meningioma

Autor: Margaret Pain, Joshua B. Bederson, Melissa Umphlett, Yayoi Kinoshita, Michael J. Donovan, John W. Rutland, Joshua Loewenstern, Mary Fowkes, Raj K. Shrivastava, Hanane Arib, Corey M. Gill, Russell B. McBride, Robert Sebra

Publikováno v: Journal of Cancer Research and Clinical Oncology. 147:3431-3440

While SWI/SNF chromatin remodeling complex alterations occur in approximately 20% of cancer, the frequency and potential impact on clinical outcomes in meningiomas remains to be comprehensively elucidated. A large series of 255 meningiomas from a sin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a53c736fd216637a84ff8e1468751f4a
https://doi.org/10.1007/s00432-021-03586-7

NF2 mutation status and tumor mutational burden correlate with immune cell infiltration in meningiomas

Autor: Joshua Loewenstern, Robert Sebra, Margaret Pain, Melissa Umphlett, Mary Fowkes, Joshua B. Bederson, John W. Rutland, Russell B. McBride, Yayoi Kinoshita, Michael J. Donovan, Raj K. Shrivastava, Hanane Arib, Corey M. Gill

Publikováno v: Cancer Immunology, Immunotherapy. 70:169-176

The tumor microenvironment is an emerging biomarker of underlying genomic heterogeneity and response to immunotherapy-based treatment regimens in solid malignancies. How tumor mutational burden influences the density, distribution, and presence of a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a5bdb70b3687224a7456f90fd75bfe13
https://doi.org/10.1007/s00262-020-02671-z

Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples

Autor: Mary Qu Yang, Dominiak N, Daniel Stetson, Rebecca Kusko, Hanane Arib, Yin L, Zhang Z, Robert Sebra, Daniel J. Craig, Todd Richmond, Natalia Novoradovskaya, Vinay K. Mittal, James C. Willey, Yaqin Zhang, Joshua Xu, Will Xiao, Leming Shi, Jennifer A. Hipp, Amelia Raymond, Weida Tong, Qiu F, Wendell D. Jones, Nikola Tom, Donald J. Johann, Dan Li, Tom Morrison, Melissa Smith, Christopher E. Mason, Jennifer S. LoCoco, Farkas Dh, Brock Je, Jiyoun Yeo, Thomas M. Blomquist, E.L. Crawford, Binsheng Gong

Clinical laboratories routinely use formalin-fixed paraffin-embedded (FFPE) tissue or cell block cytology samples in oncology panel sequencing to identify mutations that can predict patient response to targeted therapy. To understand the technical er

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::8e88fa5befa151c526a2db9a08258111
https://doi.org/10.1101/2021.04.06.438687

SWI/SNF Chromatin Remodeling Complex Alterations in Meningioma

Autor: Russell B. McBride, Raj K. Shrivastava, Yayoi Kinoshita, Hanane Arib, Mary Fowkes, Corey M Gil, Margaret Pain, Joshua B. Bederson, Melissa Umphlett, Joshua Loewenstern, John W. Rutland, Robert Sebra, Michael J. Donovan

Publikováno v: Neurosurgery. 67

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1e5fbd98ff4cef6de6a52ac9dc438012
https://doi.org/10.1093/neuros/nyaa447_817