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PLoS One. 2012;7(11):e50586. doi: 10.1371/journal.pone.0050586. Epub 2012 Nov 30.

Deep clonal profiling of formalin fixed paraffin embedded clinical samples.

Author information

1
Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America.

Abstract

Formalin fixed paraffin embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas) including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.

PMID:
23226320
PMCID:
PMC3511535
DOI:
10.1371/journal.pone.0050586
[Indexed for MEDLINE]
Free PMC Article

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