title: Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples.
abstract: Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples.
authors.affiliation: 1] Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas, 66160 Kansas City, USA [2] Department of Bioinformatics and Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Graw
authors.affiliation: 1] Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas, 66160 Kansas City, USA [2] Department of Bioinformatics and Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
authors.forename: Richard
authors.initials: R
authors.lastname: Meier
authors.affiliation: Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas, 66160 Kansas City, USA.
authors.forename: Kay
authors.initials: K
authors.lastname: Minn
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas, 66160 Kansas City, USA.
authors.forename: Clark
authors.initials: C
authors.lastname: Bloomer
authors.affiliation: Genome Sequencing Facility, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas, 66160 Kansas City, USA.
authors.forename: Andrew K
authors.initials: AK
authors.lastname: Godwin
authors.affiliation: Department of Biostatistics, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas, 66160 Kansas City, USA.
authors.forename: Brooke
authors.initials: B
authors.lastname: Fridley
authors.affiliation: Department of Obstetrics, Gynecology &Reproductive Sciences, University of Pittsburgh, 4200 Fifth Ave, Pennsylvania, 15260 Pittsburgh, USA.
authors.forename: Anda
authors.initials: A
authors.lastname: Vlad
authors.affiliation: Department of Bioinformatics and Biosystems Technology, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
authors.forename: Peter
authors.initials: P
authors.lastname: Beyerlein
authors.affiliation: Department of Cancer Biology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas, 66160 Kansas City, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Chien
mesh_terms: D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D005260:Female; D005404:Fixatives / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods*; D052138:Genes, Neoplasm / Q000235:genetics*; D020022:Genetic Predisposition to Disease / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D010051:Ovarian Neoplasms / Q000175:diagnosis / Q000235:genetics*; D012334:RNA, Neoplasm / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*; D014021:Tissue Preservation / Q000379:methods
chemical_list: D005404:Fixatives; D012334:RNA, Neoplasm; D005557:Formaldehyde