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| Status |
Public on Dec 31, 2012 |
| Title |
Deep Clonal Profiling of Formalin-Fixed Paraffin-Embedded Clinical Samples |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
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.
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| Overall design |
A total of 23 test samples were each hybridized with a pooled 46,XX commercial reference (Promega catalog# G1521, Madison, WI). Twenty-two of the test samples included flow-sorted fresh frozen and formalin-fixed paraffin-embedded tumor samples. The tissues included pancreatic adenocarcinomas, breast carcinomas, small cell carcinoma of the ovary, glioblastoma, and bladder carcinoma. The last test sample was a pancreatic adenocarcinoma cell line (A10-74).
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| Contributor(s) |
Holley T, Lenkiewicz E, Evers L, Tembe W, Ruiz C, Gsponder J, Bubendorf L, Stapleton M, Amorese D, Legendre C, Cunliffe HE, McCullough AE, Pockaj B, Craig D, Carpten J, Von Hoff D, Iacobuzio-Donahue C, Barrett MT |
| Citation(s) |
23226320 |
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| Submission date |
Aug 22, 2012 |
| Last update date |
Mar 21, 2017 |
| Contact name |
Michael Thomas Barrett |
| E-mail(s) |
barrett.michael@mayo.edu
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| Phone |
480-301-6736
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| Organization name |
Mayo Clinic Arizona
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| Department |
Molecular Pharmacology and Experimental Therapeutics
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| Street address |
13400 East Shea Boulevard
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| City |
Scottsdale |
| State/province |
AZ |
| ZIP/Postal code |
85259 |
| Country |
USA |
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| Platforms (2) |
| GPL9777 |
Agilent-021850 SurePrint G3 Human CGH Microarray (Feature Number version) |
| GPL10123 |
Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Feature Number version) |
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| Samples (23)
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| Relations |
| BioProject |
PRJNA173438 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40299_RAW.tar |
970.9 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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