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E-GEOD-72220 - Application of a clinical assay for staging and prognosis of prostate cancer diagnosed in needle core biopsy specimens

Status
Released on 9 March 2016, last updated on 11 March 2016
Organism
Homo sapiens
Samples (147)
Array (1)
Protocols (5)
Description
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. 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.
Experiment type
transcription profiling by array 
Contacts
Beatrice S Knudsen, Elai Davicioni, Heesun Shin, Hyung L Kim, Imelda Tenggara, Jeffry P Simko, June M Chan, Karen Chadwich, Lucia L Lam, Matthew R Cooperberg, Mohammed Alshalalfa, Neil Fleshner, Nicholas Erho, Peter R Carroll, Theo Van Der Kwast
Citation
Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens. 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. , PMID:26945428
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-72220.idf.txt
Sample and data relationshipE-GEOD-72220.sdrf.txt
Raw data (17)Click to browse raw data
Processed data (1)E-GEOD-72220.processed.1.zip
Array designA-AFFY-143.adf.txt
Links