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 A Pockaj, David Craig, John Carpten, Daniel Von Hoff, Christine Iacobuzio-Donahue, Michael Barrett

Research output: Contribution to journalArticle

33 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere50586
JournalPLoS One
Volume7
Issue number11
DOIs
StatePublished - Nov 30 2012

Fingerprint

formalin
Paraffin
alkanes
Formaldehyde
Tissue
Exome
Tumors
Genes
Cells
Genome
sampling
genome
Flow cytometry
Biopsy
cell nucleus
oligonucleotides
Genomics
adenocarcinoma
Oligonucleotide Array Sequence Analysis
Cell Nucleus

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Holley, T., Lenkiewicz, E., Evers, L., Tembe, W., Ruiz, C., Gsponer, J. R., ... Barrett, M. (2012). Deep Clonal Profiling of Formalin Fixed Paraffin Embedded Clinical Samples. PLoS One, 7(11), [e50586]. https://doi.org/10.1371/journal.pone.0050586

Deep Clonal Profiling of Formalin Fixed Paraffin Embedded Clinical Samples. / Holley, Tara; Lenkiewicz, Elizabeth; Evers, Lisa; Tembe, Waibhav; Ruiz, Christian; Gsponer, Joel R.; Rentsch, Cyrill A.; Bubendorf, Lukas; Stapleton, Mark; Amorese, Doug; Legendre, Christophe; Cunliffe, Heather E.; McCullough, Ann E.; Pockaj, Barbara A; Craig, David; Carpten, John; Von Hoff, Daniel; Iacobuzio-Donahue, Christine; Barrett, Michael.

In: PLoS One, Vol. 7, No. 11, e50586, 30.11.2012.

Research output: Contribution to journalArticle

Holley, T, Lenkiewicz, E, Evers, L, Tembe, W, Ruiz, C, Gsponer, JR, Rentsch, CA, Bubendorf, L, Stapleton, M, Amorese, D, Legendre, C, Cunliffe, HE, McCullough, AE, Pockaj, BA, Craig, D, Carpten, J, Von Hoff, D, Iacobuzio-Donahue, C & Barrett, M 2012, 'Deep Clonal Profiling of Formalin Fixed Paraffin Embedded Clinical Samples', PLoS One, vol. 7, no. 11, e50586. https://doi.org/10.1371/journal.pone.0050586
Holley T, Lenkiewicz E, Evers L, Tembe W, Ruiz C, Gsponer JR et al. Deep Clonal Profiling of Formalin Fixed Paraffin Embedded Clinical Samples. PLoS One. 2012 Nov 30;7(11). e50586. https://doi.org/10.1371/journal.pone.0050586
Holley, Tara ; Lenkiewicz, Elizabeth ; Evers, Lisa ; Tembe, Waibhav ; Ruiz, Christian ; Gsponer, Joel R. ; Rentsch, Cyrill A. ; Bubendorf, Lukas ; Stapleton, Mark ; Amorese, Doug ; Legendre, Christophe ; Cunliffe, Heather E. ; McCullough, Ann E. ; Pockaj, Barbara A ; Craig, David ; Carpten, John ; Von Hoff, Daniel ; Iacobuzio-Donahue, Christine ; Barrett, Michael. / Deep Clonal Profiling of Formalin Fixed Paraffin Embedded Clinical Samples. In: PLoS One. 2012 ; Vol. 7, No. 11.
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