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

  • 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.

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Author:Sarah Munchel, Yen Hoang, Yue Zhao, Joseph Cottrell, Brandy Klotzle, Andrew K. Godwin, Devin Koestler, Peter Beyerlein, Jian-Bing Fan, Marina Bibikova, Jeremy ChienORCiD
URN:urn:nbn:de:kobv:526-opus4-6307
DOI:https://doi.org/10.18632/oncotarget.4671
ISSN:1949-2553
Parent Title (English):Oncotarget
Document Type:Article
Language:English
Year of Publication:2015
Publishing Institution:Technische Hochschule Wildau
Release Date:2016/07/05
Tag:FFPE DNA; cancer genomics; copy number alteration; whole exome sequencing; whole genome sequencing
Volume:6
Issue:28
First Page:25943
Last Page:25961
Source:Munchel, S., Hoang, Y., Zhao, Y., Cottrell, J., Klotzle, B., Godwin, A., Koestler, D., Beyerlein, P., Fan, J., Bibikova, M., & Chien, J. (2015). Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics. Oncotarget, 6(28), 25943-25961. Retrieved from http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path%5B%5D=4671
Faculties an central facilities:Fachbereich Ingenieur- und Naturwissenschaften
Dewey Decimal Classification:6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 616 Krankheiten
Licence (German):Creative Commons - CC BY 3.0 - Namensnennung 3.0 Unported
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