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| Status |
Public on Feb 09, 2017 |
| Title |
Genomic copy number variations in the genomes of leukocytes predict prostate cancer clinical outcomes |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
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| Summary |
Accurate prediction of prostate cancer clinical courses remains elusive. In this study, we performed whole genome copy number analysis on leukocytes of 273 prostate cancer patients using Affymetrix SNP6.0 chip. Copy number variations (CNV) were found across all chromosomes of the human genome. An average of 152 CNV fragments per genome was identified in the leukocytes from prostate cancer patients. The size distributions of CNV in the genome of leukocytes were highly correlative with prostate cancer aggressiveness. A prostate cancer outcome prediction model was developed based on large size ratio of CNV from the leukocyte genomes. This prediction model generated an average prediction rate of 75.2%, with sensitivity of 77.3% and specificity of 69.0% for prostate cancer recurrence. When combined with Nomogram and the status of fusion transcripts, the average prediction rate was improved to 82.5% with sensitivity of 84.8% and specificity of 78.2%. In addition, the leukocyte prediction model was 62.6% accurate in predicting short prostate specific antigen doubling time. When combined with Gleason’s grade, Nomogram and the status of fusion transcripts, the prediction model generated a correct prediction rate of 77.5% with 73.7% sensitivity and 80.1% specificity. To our knowledge, this is the first study showing that CNVs in leukocyte genomes are predictive of clinical outcomes of a human malignancy.
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| Overall design |
Prostate cancer samples were obtained from University of Pittsburgh Medical Center Tissue Bank. These samples were collected from 1998-2012. 273 buffy coat samples from prostate cancer patients were analyzed.
Among these samples, 143 samples were followed at least 90 months, 35 patients were non-recurrent for 90 months or more, 55 patients experiencing recurrence with short PSADT (PSA doubling time <4 months), and 53 patients experiencing recurrence with long PSADT (PSA doubling time >15 months) after radical prostatectomy.
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| Contributor(s) |
Luo J, Yu YP |
| Citation(s) |
26295840 |
| Submission date |
Jul 08, 2015 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Shuchang Liu |
| E-mail(s) |
silvia.shuchang.liu@gmail.com
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| Organization name |
University of Pittsburgh
|
| Street address |
130 De Soto Street
|
| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15261 |
| Country |
USA |
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| Platforms (1) |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (273)
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| Relations |
| BioProject |
PRJNA289378 |
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