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| Status |
Public on Jan 18, 2014 |
| Title |
Intratumoral heterogeneity of prostate cancers |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
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| 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.
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| 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.
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| Contributor(s) |
Kim T |
| Citation(s) |
24870262 |
| Submission date |
Jan 17, 2014 |
| Last update date |
Jun 07, 2014 |
| Contact name |
Tae-Min Kim |
| E-mail(s) |
tmkim@catholic.ac.kr
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| Phone |
82-2-2258-7753
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| Organization name |
The Catholic University of Korea, College of Medicine
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| Department |
Dept of Medical Informatics
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| Street address |
Seocho-Gu, Banpo-Dong
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| City |
Seoul |
| ZIP/Postal code |
137-701 |
| Country |
South Korea |
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| Platforms (1) |
| GPL10123 |
Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Feature Number version) |
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| Samples (12)
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| 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 |
| GSM1309408 |
Intratumoral heterogeneity of prostate cancers, patient 1, biopsy 4 |
| GSM1309409 |
Intratumoral heterogeneity of prostate cancers, patient 2, biopsy 1 |
| GSM1309410 |
Intratumoral heterogeneity of prostate cancers, patient 2, biopsy 2 |
| GSM1309411 |
Intratumoral heterogeneity of prostate cancers, patient 2, biopsy 3 |
| GSM1309412 |
Intratumoral heterogeneity of prostate cancers, patient 2, biopsy 4 |
| GSM1309413 |
Intratumoral heterogeneity of prostate cancers, patient 3, biopsy 1 |
| GSM1309414 |
Intratumoral heterogeneity of prostate cancers, patient 3, biopsy 2 |
| GSM1309415 |
Intratumoral heterogeneity of prostate cancers, patient 3, biopsy 3 |
| GSM1309416 |
Intratumoral heterogeneity of prostate cancers, patient 3, biopsy 4 |
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| Relations |
| BioProject |
PRJNA235387 |
| 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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