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Series GSE54185 Query DataSets for GSE54185
Status Public on Jan 18, 2014
Title Intratumoral heterogeneity of prostate cancers
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Copy number analyses of regionally separated intratumoral biopsies of prostate cancers.
Intratumoral heterogeneity (ITH) leads to regional biases of the mutational landscape in a single tumor and may influence the single biopsy-based clinical diagnosis and treatment decision. To evaluate the extent of ITH in unifocal prostate cancers (PCAs) that had not been sought, we analyzed multiple regional biopsies from three PCAs using DNA copy number analyses. DNA copy number showed ITH including regional biases in the presentation of a well-known driver of TMPRSS2-ERG fusion. Our analyses identified a substantial level of genetic ITH in unifocal PCAs at the genomic levels, which should be taken into account for the curation of biomarkers in the clinical setting.
Overall design Four intratumoral biopsies were obtained per tumor for three prostate cancers. Radical prostatectomy tissue from three patients with prostate cancers were obtained. Board-certified pathologists reviewed the hematoxylin&eosin stained sections and identified tumor-rich regions (> 80% purity). We selected four different areas for biopsy that were at least 5mm apart and were comprised of the most common Gleason pattern (the most common histologic patterns with minimal histologic differences). Copy number profiling was performed using Agilent 180K platform according to the manufacturer's protocol.
Contributor(s) Kim T
Citation(s) 24870262
Submission date Jan 17, 2014
Last update date Jun 07, 2014
Contact name Tae-Min Kim
Phone 82-2-2258-7753
Organization name The Catholic University of Korea, College of Medicine
Department Dept of Medical Informatics
Street address Seocho-Gu, Banpo-Dong
City Seoul
ZIP/Postal code 137-701
Country South Korea
Platforms (1)
GPL10123 Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Feature Number version)
Samples (12)
GSM1309405 Intratumoral heterogeneity of prostate cancers, patient 1, biopsy 1
GSM1309406 Intratumoral heterogeneity of prostate cancers, patient 1, biopsy 2
GSM1309407 Intratumoral heterogeneity of prostate cancers, patient 1, biopsy 3
BioProject PRJNA235387

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
GSE54185_RAW.tar 223.2 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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