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Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples.
Zhang, Yifan; Blomquist, Thomas M; Kusko, Rebecca; Stetson, Daniel; Zhang, Zhihong; Yin, Lihui; Sebra, Robert; Gong, Binsheng; Lococo, Jennifer S; Mittal, Vinay K; Novoradovskaya, Natalia; Yeo, Ji-Youn; Dominiak, Nicole; Hipp, Jennifer; Raymond, Amelia; Qiu, Fujun; Arib, Hanane; Smith, Melissa L; Brock, Jay E; Farkas, Daniel H; Craig, Daniel J; Crawford, Erin L; Li, Dan; Morrison, Tom; Tom, Nikola; Xiao, Wenzhong; Yang, Mary; Mason, Christopher E; Richmond, Todd A; Jones, Wendell; Johann, Donald J; Shi, Leming; Tong, Weida; Willey, James C; Xu, Joshua.
Afiliación
  • Zhang Y; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
  • Blomquist TM; (Formerly) Department of Pathology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA.
  • Kusko R; Lucas County Coroner's Office, 2595 Arlington Ave, Toledo, OH, 43614, USA.
  • Stetson D; Immuneering Corporation, 245 Main St, Cambridge, MA, 02142, USA.
  • Zhang Z; Astrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA.
  • Yin L; Research and Development, Burning Rock Biotech, Shanghai, 201114, China.
  • Sebra R; (Formerly) Pathology and Laboratory Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.
  • Gong B; Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
  • Lococo JS; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
  • Mittal VK; Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
  • Novoradovskaya N; Thermo Fisher Scientific, 110 Miller Ave, Ann Arbor, MI, 48104, USA.
  • Yeo JY; Agilent Technologies, 11011 N Torrey Pines Rd, La Jolla, CA, 92037, USA.
  • Dominiak N; Department of Pathology, University of Toledo, 3000 Arlington Ave, Toledo, OH, 43614, USA.
  • Hipp J; Department of Pathology, University of Toledo, 3000 Arlington Ave, Toledo, OH, 43614, USA.
  • Raymond A; Department of Pathology, Strata Oncology, Inc., Ann Arbor, MI, 48103, USA.
  • Qiu F; Astrazeneca Pharmaceuticals, 35 Gatehouse Dr, Waltham, MA, 02451, USA.
  • Arib H; Research and Development, Burning Rock Biotech, Shanghai, 201114, China.
  • Smith ML; Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
  • Brock JE; Icahn Institute and Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, New York, NY, 10029, USA.
  • Farkas DH; Pathology and Laboratory Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.
  • Craig DJ; Pathology and Laboratory Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.
  • Crawford EL; Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA.
  • Li D; Department of Medicine, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH, 43614, USA.
  • Morrison T; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
  • Tom N; Accugenomics, Inc., 1410 Commonwealth Drive, Suite 105, Wilmington, NC, 20403, USA.
  • Xiao W; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
  • Yang M; EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081 HZ, Amsterdam, The Netherlands.
  • Mason CE; Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
  • Richmond TA; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
  • Jones W; Department of Information Science, University of Arkansas at Little Rock, 2801 S. Univ. Ave, Little Rock, AR, 72204, USA.
  • Johann DJ; Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
  • Shi L; Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr, Pleasanton, CA, 94588, USA.
  • Tong W; Q2 Solutions - EA Genomics, 5927 S Miami Blvd, Morrisville, NC, 27560, USA.
  • Willey JC; Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR, 72205, USA.
  • Xu J; State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.
Genome Biol ; 23(1): 141, 2022 06 29.
Article en En | MEDLINE | ID: mdl-35768876
ABSTRACT

BACKGROUND:

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 error due to FFPE processing, a robustly characterized diploid cell line was used to create FFPE samples with four different pre-tissue processing formalin fixation times. A total of 96 FFPE sections were then distributed to different laboratories for targeted sequencing analysis by four oncopanels, and variants resulting from technical error were identified.

RESULTS:

Tissue sections that fail more frequently show low cellularity, lower than recommended library preparation DNA input, or target sequencing depth. Importantly, sections from block surfaces are more likely to show FFPE-specific errors, akin to "edge effects" seen in histology, while the inner samples display no quality degradation related to fixation time.

CONCLUSIONS:

To assure reliable results, we recommend avoiding the block surface portion and restricting mutation detection to genomic regions of high confidence.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Secuenciación de Nucleótidos de Alto Rendimiento / Formaldehído Límite: Humans Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Secuenciación de Nucleótidos de Alto Rendimiento / Formaldehído Límite: Humans Idioma: En Revista: Genome Biol Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos