GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE70650 Query DataSets for GSE70650
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
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.
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.
Contributor(s) Luo J, Yu YP
Citation(s) 26295840
Submission date Jul 08, 2015
Last update date Nov 27, 2018
Contact name Shuchang Liu
Organization name University of Pittsburgh
Street address 130 De Soto Street
City Pittsburgh
State/province Pennsylvania
ZIP/Postal code 15261
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (273)
GSM1815552 Leukocyte 11563B
GSM1815553 Leukocyte 1199B
GSM1815554 Leukocyte 13745B
BioProject PRJNA289378

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
GSE70650_RAW.tar 7.8 Gb (http)(custom) TAR (of CEL)
GSE70650_processed_data_bloodSegment.txt.gz 1.3 Mb (ftp)(http) TXT
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap