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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.
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 |
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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 |