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| Status |
Public on Mar 09, 2016 |
| Title |
Application of a clinical assay for staging and prognosis of prostate cancer diagnosed in needle core biopsy specimens |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Molecular and genomic analysis of microscopic quantities of tumor from formalin-fixed and paraffin-embedded (FFPE) biopsies has many unique challenges. Here we evaluated the feasibility of obtaining transcriptome-wide RNA expression to measure prognostic classifiers from diagnostic prostate needle core biopsies.
158 samples from diagnostic needle core biopsies (Bx) and radical prostatectomies (RP) were collected from 33 patients at three hospitals, each patient provided up to 6 tumor and benign samples. Genome-wide transcriptomic profiles were generated using Affymetrix Human Exon arrays for comparison of gene expression alterations and prognostic signatures between the Bx and RP samples.
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| Overall design |
For 23 patients from UCSF and CSMC, six prostate tissue samples were obtained from each patient: tumor biopsy, tumor RP, benign adjacent biopsy, benign adjacent RP, and benign contralateral biopsy, and benign contralateral RP. For the 10 UHN patients only tumor biopsy and tumor RP samples were obtained. A total of 147 samples passed RNA, cDNA, and microarray quality control.
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| Contributor(s) |
Knudsen BS, Kim HL, Erho N, Shin H, Alshalalfa M, Lam LL, Tenggara I, Chadwich K, Van Der Kwast T, Fleshner N, Davicioni E, Carroll PR, Cooperberg MR, Chan JM, Simko JP |
| Citation(s) |
26945428 |
| Submission date |
Aug 20, 2015 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Elai Davicioni |
| E-mail(s) |
davicion@gmail.com
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| Phone |
6267102695
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| Organization name |
GenomeDx Biosciences
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| Street address |
10355 Science Center Dr
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| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92121 |
| Country |
USA |
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| Platforms (1) |
| GPL5175 |
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version] |
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| Samples (147)
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| Relations |
| BioProject |
PRJNA293410 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE72220_RAW.tar |
3.2 Gb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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