Deep Clonal Profiling of Formalin Fixed Paraffin Embedded Clinical Samples

Tara Holley, Elizabeth Lenkiewicz, Lisa Evers, Waibhav Tembe, Christian Ruiz, Joel R. Gsponer, Cyrill A. Rentsch, Lukas Bubendorf, Mark Stapleton, Doug Amorese, Christophe Legendre, Heather E. Cunliffe, Ann E. McCullough, Barbara Pockaj, David Craig, John Carpten, Daniel Von Hoff, Christine Iacobuzio-Donahue, Michael T. Barrett

Research output: Contribution to journalArticlepeer-review

38 Scopus citations


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.

Original languageEnglish (US)
Article numbere50586
JournalPloS one
Issue number11
StatePublished - Nov 30 2012
Externally publishedYes

ASJC Scopus subject areas

  • General


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