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Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.
Gong, Binsheng; Li, Dan; Kusko, Rebecca; Novoradovskaya, Natalia; Zhang, Yifan; Wang, Shangzi; Pabón-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.
Afiliación
  • Gong B; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
  • Li D; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
  • Kusko R; Immuneering Corporation, One Broadway, 14th Floor, Cambridge, MA, 02142, USA.
  • Novoradovskaya N; Agilent Technologies, 11011 N Torrey Pines Rd, La Jolla, CA, 92037, USA.
  • Zhang Y; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
  • Wang S; Department of Information Science, University of Arkansas at Little Rock, 2801 S. Univ. Ave, Little Rock, AR, 72204, USA.
  • Pabón-Peña C; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
  • Zhang Z; Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA.
  • Lai K; Research and Development, Burning Rock Biotech, Shanghai, 201114, China.
  • Cai W; Bioinformatics, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
  • LoCoco JS; iGeneTech, 8 Shengmingyuan Rd., Zhongguancun Life Science Park, Changping District, Beijing, 100080, China.
  • Lader E; Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
  • Richmond TA; Research and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA.
  • Mittal VK; Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr, Pleasanton, CA, 94588, USA.
  • Liu LC; Thermo Fisher Scientific, 110 Miller Ave, Ann Arbor, MI, 48104, USA.
  • Johann DJ; Clinical Diagnostic Division, Thermo Fisher Scientific, 46500 Kato Rd, Fremont, CA, 94538, USA.
  • Willey JC; Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA.
  • Bushel PR; Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, 3000 Arlington Ave, Toledo, OH, 43614, USA.
  • Yu Y; National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.
  • Xu C; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
  • Chen G; Research and Development, QIAGEN Sciences Inc., Frederick, MD, 21703, USA.
  • Burgess D; Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd, Dallas, TX, 75390, USA.
  • Cawley S; Research and Development, Roche Sequencing Solutions Inc., 500 South Rosa Rd, Madison, WI, 53719, USA.
  • Giorda K; Clinical Sequencing Division, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA.
  • Haseley N; Marketing, Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA, 52241, USA.
  • Qiu F; Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
  • Wilkins K; Research and Development, Burning Rock Biotech, Shanghai, 201114, China.
  • Arib H; Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA.
  • Attwooll C; Icahn Institute and Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
  • Babson K; Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
  • Bao L; Greenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
  • Bao W; Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
  • Lucas AB; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
  • Best H; Institute of Pathology, Fudan University, Shanghai, 200032, China.
  • Bhandari A; JMP Life Sciences, SAS Institute Inc., Cary, NC, 27519, USA.
  • Bisgin H; Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA, 95051, USA.
  • Blackburn J; Departments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, 84108, USA.
  • Blomquist TM; R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT, 84108, USA.
  • Boardman L; ResearchDx, Inc., 5 Mason, Irvine, CA, 92618, USA.
  • Burgher B; Department of Computer Science, Engineering and Physics, University of Michigan-Flint, Flint, MI, 48502, USA.
  • Butler DJ; Garvan Institute of Medical Research, Sydney, NSW, Australia.
  • Chang CJ; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2010, Australia.
  • Chaubey A; Department of Pathology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA.
  • Chen T; Lucas County Coroner's Office, 2595 Arlington Ave., Toledo, OH, 43614, USA.
  • Chierici M; Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA.
  • Chin CR; OmniSeq, Inc. 700 Ellicott St, Buffalo, NY, 14203, USA.
  • Close D; Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
  • Conroy J; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
  • Cooley Coleman J; Greenwood Genetic Center, 106 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
  • Craig DJ; Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
Genome Biol ; 22(1): 109, 2021 04 16.
Article en En | MEDLINE | ID: mdl-33863344
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-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. RESULTS: 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. CONCLUSION: 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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Oncogenes / Biomarcadores de Tumor / Pruebas Genéticas / Genómica / Neoplasias Tipo de estudio: Diagnostic_studies / Guideline / Prognostic_studies Límite: Humans Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Oncogenes / Biomarcadores de Tumor / Pruebas Genéticas / Genómica / Neoplasias Tipo de estudio: Diagnostic_studies / Guideline / Prognostic_studies Límite: Humans Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido