Affiliation: University of California
- A sequence-based survey of the complex structural organization of tumor genomesBenjamin J Raphael
Department of Computer Science and Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912 1910, USA
Genome Biol 9:R59. 2008..The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes...
- Detection of recurrent rearrangement breakpoints from copy number dataAnna Ritz
Department of Computer Science, Brown University, Providence, RI, USA
BMC Bioinformatics 12:114. 2011..Typically, the interior of a recurrent CNV is examined for genes or other loci associated with a phenotype. However, in some cases, such as gene truncations and fusion genes, the target of variant lies at the boundary of the variant...
- A group of genome-based biomarkers that add to a Kattan nomogram for predicting progression in men with high-risk prostate cancerPamela L Paris
Department of Urology, Helen Diller Family Comprehensive Cancer, and Helen Diller Family Comprehensive Cancer Biostatistics Core, University of California at San Francisco, California 94143, USA
Clin Cancer Res 16:195-202. 2010..Nomograms that use clinical and pathologic variables are often used for risk prediction. Favorable outcomes exist even among men classified by nomograms as being at high risk of recurrence...
- Functional phenotyping and genotyping of circulating tumor cells from patients with castration resistant prostate cancerPamela L Paris
Department of Urology, University of California at San Francisco, San Francisco, CA 94115, USA
Cancer Lett 277:164-73. 2009..Copy number profiles for CRPC CTCs were similar to paired solid tumor DNA, and distinct from corresponding DNA from the residual CAM-depleted blood. CAM CTC enrichment may allow cellular and genetic analyses in prostate cancer...
- Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumorsPamela L Paris
Comprehensive Cancer Center, University of California at San Francisco, 94115, USA
Hum Mol Genet 13:1303-13. 2004..Moreover, comparison with an independent set of metastases revealed approximately 40 candidate markers associated with metastatic potential. Copy number aberrations at these loci may define metastatic genotypes...
- Integration of high-resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data refines common regions of loss at 16q23-qter and identifies underlying candidate tumor suppressor genes in prostate cancerJ E Vivienne Watson
Collins Lab, UCSF Comprehensive Cancer Center, University of California, 2340 Sutter Street, San Francisco, USA
Oncogene 23:3487-94. 2004....
- Evolution of 8p loss in transformed human prostate epithelial cellsJill A Macoska
Department of Urology, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109 0944, USA
Cancer Genet Cytogenet 154:36-43. 2004..Taken together, these studies illustrate a potential mechanism and functional role for 8p loss in human prostate tumorigenesis...
- Genomic profiling of hormone-naïve lymph node metastases in patients with prostate cancerPamela L Paris
Department of Urology, University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA 94115, USA
Neoplasia 8:1083-9. 2006..Matched primaries and lymph node metastases showed very similar copy number profiles that are distinct from primary tumors that fail to metastasize...
- High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarraysPamela L Paris
Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94115, USA
Am J Pathol 162:763-70. 2003..We present a straightforward protocol and demonstrate the utility of archived tissue for array comparative genomic hybridization with a 2400 element BAC array that provides high-resolution detection of both deletions and amplifications...
- High resolution oligonucleotide CGH using DNA from archived prostate tissuePamela L Paris
Department of Urology, Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94143, USA
Prostate 67:1447-55. 2007..There is an urgent need for high-resolution tools that perform well using archived tissue for biomarker discovery and tools that can translate into the clinic...
- Molecular analysis of WFDC1/ps20 gene in prostate cancerJ E Vivienne Watson
Comprehensive Cancer Center, University of California, San Francisco, California, USA
Prostate 61:192-9. 2004..It maps to chromosome 16q23.1, a region of frequent loss of heterozygosity, familial association, and genomic loss in prostate cancer. We, therefore, chose to examine WFDC1/ps20 for mutations and expression changes in prostate cancer...
- Decoding the fine-scale structure of a breast cancer genome and transcriptomeStanislav Volik
Department of Urology, and Cancer Research Institute, University of California San Francisco Comprehensive Cancer Center, San Francisco, California 94115, USA
Genome Res 16:394-404. 2006..Given these properties, ESP could play an important role in a tumor genome project...