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Copy number alteration burden predicts prostate cancer relapse: Agilent 1M aCGH data for human primary prostate cancer samples

UID: 11158

Author(s): Hieronymus, Haley, Schultz, Nikolaus D.*, Taylor, Barry Stephen*, Sawyers, Charles L.* * MSK affiliated

Description
Summary from GEO:

"Prostate cancer is the most common malignancy in men. Yet, the modest benefit of treatment highlights the unmet need for prognostic biomarkers in prostate cancer (1). Few large prostate oncogenome resources currently exist that combine the molecular and clinical outcome data necessary for prognostic discovery. To determine the extent to which genomic aberrations reflect the risk of prostate cancer-specific outcomes, we profiled more than 100 primary prostate cancers with long-term follow-up for genome-wide copy number alterations (CNA). We also updated the long-term clinical outcome (median 8 years) of an additional independent cohort of 181 primary prostate cancers that we previously profiled for CNA and expression changes (2). Together, we found that CNA burden across the genome, defined as the percent of the tumor genome affected by CNA, is prognostic for recurrence and metastasis in these two cohorts. This prognostic significance of CNA is independent of Gleason grade, a major existing histopathological prognostic variable in prostate cancer. Moreover, in intermediate-risk Gleason 7 prostate cancers that show a wide range of outcomes, CNA burden is also prognostic for biochemical recurrence, independent of prostate-specific antigen or nomogram score. CNA burden therefore has the potential to stratify patients by their risk of recurrence in an otherwise intermediate risk subpopulation. We further demonstrate that CNA burden can be established in diagnostic FFPE needle biopsies using low-input whole genome sequencing. Together, this work highlights the potential of oncogenomics to identify useful and clinically amenable prognostic factors that may inform prostate cancer outcome and treatment."

Overall design from GEO:

"Human prostate samples were profiled on Agilent 1M aCGH arrays per manufacturer's instructions. A pooled reference normal DNA was used as the reference."
Subject of Study
Homo sapiens
Subject(s)
Biomarkers, Tumor
Genomics
Neoplasm Metastasis
Prostatic Neoplasms
Recurrence
Access via GEO


Accession #: GSE54691

Access via BioProject


Accession #: PRJNA237482

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus and BioProject databases provide open access to these files.
Associated Publications
Hieronymus H, Schultz N, Gopalan A, Carver B, Chang M, Xiao Y, Heguy A, Huberman K, Bernstein M, Assel M, Murali R, Vickers A, Scardino P, Sander C, Reuter V, Taylor B, Sawyers C. Copy number alteration burden predicts prostate cancer relapse. Proceedings of the National Academy of Sciences of the United States of America. 2014; 111(30):11139-11144.
Equipment Used
Agilent-021529 Human CGH Whole Genome Microarray 1x1M (G4447A)

Array Comparative genomic hybridization (CGH) has been developed as a molecular test for chromosomal analysis

Dataset Format(s)
TAR, TXT
Dataset Size
25 GB
Data Catalog Record Updated
2024-02-16