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

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 formal-infixation 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.
Year:
2015
Publication type:
Journal article
Journal:
OncoTarget
ISSN:
1949-2553
Number:
28
Volume:
6
Pages:
25943-25961
Language:
English
Document status:
Open access
PubListerURL:
https://publister.bib.th-wildau.de/publister/public/publication/984
Keywords:
cancer genomics; FFPE DNA; whole exome sequencing; whole genome sequencing; copy number alterations
Munchel, S., Hoang, Y., Zhao, Y., Cottrell, J., Klotzle, B., Godwin, A., et al. (2015). Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics OncoTarget. 6 (28), 25943-25961.
@article{984,
    author           = {Munchel, Sarah and Hoang, Yen and Zhao, Yue and Cottrell, Joseph and Klotzle, Brandy and Godwin, Andrew K. and Koestler, Devin and Beyerlein, Peter and Fan, Jian-Bing and Bibikova, Marina and Chien, Jeremy},
    title            = {Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics},
    journal          = {OncoTarget},
    year             = {2015},
    volume           = {6},
    number           = {28},
    pages            = {25943-25961},
    publisher        = {Impact Journals LLC},
    doi              = {10.18632/oncotarget.4671},
}


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