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

Sarah Munchel, Yen Hoang, Yue Zhao, Joseph Cottrell, Brandy Klotzle, Andrew K. Godwin, Devin Koestler, Peter Beyerlein, Jian Bing Fan, Marina Bibikova, Jeremy Chien

Research output: Contribution to journalArticle

29 Citations (Scopus)

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 formalinfixation 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.

Original languageEnglish (US)
Pages (from-to)25943-25961
Number of pages19
JournalOncotarget
Volume6
Issue number28
DOIs
StatePublished - Jan 1 2015
Externally publishedYes

Fingerprint

Genomics
Formaldehyde
Genome
Paraffin
Neoplasms
Artifacts
Exome
Translational Medical Research
DNA Sequence Analysis
Exons

Keywords

  • Cancer genomics
  • Copy number alterations
  • FFPE DNA
  • Whole exome sequencing
  • Whole genome sequencing

ASJC Scopus subject areas

  • Oncology

Cite this

Targeted or whole genome sequencing of formalin fixed tissue samples : Potential applications in cancer genomics. / Munchel, Sarah; Hoang, Yen; Zhao, Yue; Cottrell, Joseph; Klotzle, Brandy; Godwin, Andrew K.; Koestler, Devin; Beyerlein, Peter; Fan, Jian Bing; Bibikova, Marina; Chien, Jeremy.

In: Oncotarget, Vol. 6, No. 28, 01.01.2015, p. 25943-25961.

Research output: Contribution to journalArticle

Munchel, S, Hoang, Y, Zhao, Y, Cottrell, J, Klotzle, B, Godwin, AK, Koestler, D, Beyerlein, P, Fan, JB, Bibikova, M & Chien, J 2015, 'Targeted or whole genome sequencing of formalin fixed tissue samples: Potential applications in cancer genomics', Oncotarget, vol. 6, no. 28, pp. 25943-25961. https://doi.org/10.18632/oncotarget.4671
Munchel, Sarah ; Hoang, Yen ; Zhao, Yue ; Cottrell, Joseph ; Klotzle, Brandy ; Godwin, Andrew K. ; Koestler, Devin ; Beyerlein, Peter ; Fan, Jian Bing ; Bibikova, Marina ; Chien, Jeremy. / Targeted or whole genome sequencing of formalin fixed tissue samples : Potential applications in cancer genomics. In: Oncotarget. 2015 ; Vol. 6, No. 28. pp. 25943-25961.
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