Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics

// Sarah Munchel 1, *, Yen Hoang 2, 5, *, Yue Zhao 1, Joseph Cottrell 1, Brandy Klotzle 1, Andrew K. Godwin 3, Devin Koestler 4, Peter Beyerlein 2, Jian-Bing Fan 1, Marina Bibikova 1, Jeremy Chien 5 1 Illumina, Inc. , San Diego, CA, USA 2 Department of Bioinformatics and Biosystems Technology, University of Applied Sciences Wildau, Wildau, Germany 3 Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA 4 Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS, USA 5 Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA * These authors have contributed equally to this work Correspondence to: Jeremy Chien, e-mail: jchien@kumc. edu Marina Bibikova, e-mail: mbibikova@illumina. com Jian-Bing Fan, e-mail: jianbingfan@anchordx. com Keywords: cancer genomics, FFPE DNA, whole exome sequencing, whole genome sequencing, copy number alterations Received: May 13, 2015 Accepted: July 20, 2015 Published: July 31, 2015 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.