title: Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.
abstract: Current genomic studies are limited by the poor availability of fresh-frozen tissue samples. Although formalin-fixed diagnostic samples are in abundance, they are seldom used in current genomic studies because of the concern of formalin-fixation artifacts. Better characterization of these artifacts will allow the use of archived clinical specimens in translational and clinical research studies. To provide a systematic analysis of formalin-fixation artifacts on Illumina sequencing, we generated 26 DNA sequencing data sets from 13 pairs of matched formalin-fixed paraffin-embedded (FFPE) and fresh-frozen (FF) tissue samples. The results indicate high rate of concordant calls between matched FF/FFPE pairs at reference and variant positions in three commonly used sequencing approaches (whole genome, whole exome, and targeted exon sequencing). Global mismatch rates and C · G > T · A substitutions were comparable between matched FF/FFPE samples, and discordant rates were low (<0.26%) in all samples. Finally, low-pass whole genome sequencing produces similar pattern of copy number alterations between FF/FFPE pairs. The results from our studies suggest the potential use of diagnostic FFPE samples for cancer genomic studies to characterize and catalog variations in cancer genomes.
authors: Illumina, Inc., San Diego, CA, USA.
authors: Sarah
authors: S
authors: Munchel
authors: Department of Bioinformatics and Biosystems Technology, University of Applied Sciences Wildau, Wildau, Germany.|Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA.
authors: Yen
authors: Y
authors: Hoang
authors: Illumina, Inc., San Diego, CA, USA.
authors: Yue
authors: Y
authors: Zhao
authors: Illumina, Inc., San Diego, CA, USA.
authors: Joseph
authors: J
authors: Cottrell
authors: Illumina, Inc., San Diego, CA, USA.
authors: Brandy
authors: B
authors: Klotzle
authors: Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
authors: Andrew K
authors: AK
authors: Godwin
authors: Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA.
authors: Devin
authors: D
authors: Koestler
authors: Department of Bioinformatics and Biosystems Technology, University of Applied Sciences Wildau, Wildau, Germany.
authors: Peter
authors: P
authors: Beyerlein
authors: Illumina, Inc., San Diego, CA, USA.
authors: Jian-Bing
authors: JB
authors: Fan
authors: Illumina, Inc., San Diego, CA, USA.
authors: Marina
authors: M
authors: Bibikova
authors: Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA.
authors: Jeremy
authors: J
authors: Chien
mesh_terms: D016477:Artifacts; D016000:Cluster Analysis; D056915:DNA Copy Number Variations; D005557:Formaldehyde; D005629:Frozen Sections / Q000379:methods* / Q000592:standards; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation; D009369:Neoplasms / Q000235:genetics*; D016612:Paraffin Embedding; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D016707:Tissue Fixation / Q000379:methods* / Q000592:standards
chemical_list: D005557:Formaldehyde
keywords: FFPE DNA; cancer genomics; copy number alterations; whole exome sequencing; whole genome sequencing