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Series GSE40299 Query DataSets for GSE40299
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
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.
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).
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
Submission date Aug 22, 2012
Last update date Mar 21, 2017
Contact name Michael Thomas Barrett
Phone 480-301-6736
Organization name Mayo Clinic Arizona
Department Molecular Pharmacology and Experimental Therapeutics
Street address 13400 East Shea Boulevard
City Scottsdale
State/province AZ
ZIP/Postal code 85259
Country USA
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)
Samples (23)
GSM991023 Breast PS02 1557 E3-50K
GSM991024 Breast PS02 1557 E3-50K-duplicate
GSM991025 Breast PS02 1557 E3-25K
BioProject PRJNA173438

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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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