A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples

PLoS One. 2017 Jan 25;12(1):e0170632. doi: 10.1371/journal.pone.0170632. eCollection 2017.

Abstract

The molecular classification of glioblastoma (GBM) based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF) tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE) tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved.

Publication types

  • Comparative Study

MeSH terms

  • Brain Neoplasms / genetics*
  • Brain Neoplasms / metabolism
  • Brain Neoplasms / pathology
  • Computational Biology
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Neoplastic*
  • Glioblastoma / genetics*
  • Glioblastoma / metabolism
  • Glioblastoma / pathology
  • High-Throughput Nucleotide Sequencing
  • Humans

Grant support

Fundació La Marató TV3, Project: 665/C/2013; CB, NdI, FA http://www.ccma.cat/tv3/marato/projectes-financats/2012/231/. Red Temática de Investigación Cooperativa en Cáncer, RD07/0020/2004 and RD12/0036/0044; MM, http://www.isciii.es/ISCIII/es/contenidos/fd-investigacion/fd-ejecucion/fd-centros-participados/centros-participados-redes-retics.shtml. Agència de Gestió d'Ajuts Universitaris i de Recerca, Departament d'Innovació, Universitats i Empresa; SGR 541; MM, http://agaur.gencat.cat/ca/beques-i-ajuts/convocatories-per-temes/Ajuts-per-donar-suport-a-les-activitats-dels-grups-de-recerca-SGR. Instituto de la Salut Carlos III; Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016; PT13/0001; AEC, http://www.isciii.es/ISCIII/es/contenidos/fd-investigacion/fd-planificacion-2/plan-estatal-investigacion-2013-16.shtml. Instituto de la Salut Carlos III; Plan Estatal de Investigación Científica y Técnica y de Innovación. Programa Estatal de Promoción del Talento y su Empleabilidad en I+D+i. Subprograma Estatal de Incorporación. 2013-2016; PTA2014-09515-I; MD, http://www.idi.mineco.gob.es/portal/site/MICINN/menuitem.791459a43fdf738d70fd325001432ea0/?vgnextoid=acf77fc6ee0f9410VgnVCM1000001d04140aRCRD&vgnextchannel=67a04939e6b42410VgnVCM1000001d04140aRCRD&vgnextfmt=formato2&id3=1af77fc6ee0f9410VgnVCM1000001d04140a. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.