Colin C Collins
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...
- A BAC clone fingerprinting approach to the detection of human genome rearrangementsMartin Krzywinski
BC Cancer Agency Genome Sciences Centre, West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6
Genome Biol 8:R224. 2007..Our method has compelling potential for use as a whole-genome method for the identification and characterization of human genome rearrangements...
- Comprehensive genome sequence analysis of a breast cancer ampliconC Collins
University of California San Francisco Cancer Center, San Francisco, California 94143 0808, USA
Genome Res 11:1034-42. 2001....
- Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumorsGiuseppe Zardo
Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94115, USA
Nat Genet 32:453-8. 2002..Our results show that most aberrant methylation events are focal and independent of deletions, and the rare convergence of these mechanisms can pinpoint biallelic gene inactivation without the use of positional cloning...
- Chromosome arm 20q gains and other genomic alterations in colorectal cancer metastatic to liver, as analyzed by comparative genomic hybridization and fluorescence in situ hybridizationW M Korn
Cancer Center, University of California San Francisco, 94143, USA
Genes Chromosomes Cancer 25:82-90. 1999..By FISH, we identified subregions on chromosome arm 20q that are frequently involved in DNA amplifications in colorectal cancer and that may harbor candidate proto-oncogenes...
- Genome changes and gene expression in human solid tumorsJ W Gray
UCSF Cancer Center, 2340 Sutter Street, University of California San Francisco, San Francisco, CA 94143 0808, USA
Carcinogenesis 21:443-52. 2000..This review covers several commonly used large-scale genome and gene expression analysis techniques, outlines genomic approaches to gene discovery and summarizes information that has come from large-scale analyses of human solid tumors...
- Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogeneD G Albertson
1 Cancer Research Institute, University of California, San Francisco, Box 0808, San Francisco, California, USA
Nat Genet 25:144-6. 2000..The putative oncogene ZNF217 (ref. 5) mapped to one peak, and CYP24 (encoding vitamin D 24 hydroxylase), whose overexpression is likely to lead to abrogation of growth control mediated by vitamin D, mapped to the other...
- Substance abuse prevention: moving from science to policyS F Morin
AIDS Policy Research Center, University of California, San Francisco 94105, USA
Addict Behav 25:975-83. 2000..This paper suggests several direct ways in which prevention science can influence public policy and thus move prevention science to more effective substance abuse prevention policy...
- Genome sequence and splice site analysis of low-fidelity DNA polymerases H and I involved in replication of damaged DNAJ E Cleaver
UCSF Cancer Center, Box 0808, Room N431, University of California at San Francisco, San Francisco, CA 94143 0808, USA
Genomics 82:561-70. 2003..This analysis explains previous observations of tissue-specific skipping during mRNA processing, resulting in the loss of the transcription start site in exon II, in human tissues...
- The transcription factor ZNF217 is a prognostic biomarker and therapeutic target during breast cancer progressionLaurie E Littlepage
Department of Anatomy, University of California, San Francisco, CA 94143, USA
Cancer Discov 2:638-51. 2012..Because ZNF217 is amplified in numerous cancers, these results have implications for other cancers...
- DNA polymerase eta undergoes alternative splicing, protects against UV sensitivity and apoptosis, and suppresses Mre11-dependent recombinationM Thakur
UCSF Comprehensive Cancer Center, University of California, San Francisco, California 94115, USA
Genes Chromosomes Cancer 32:222-35. 2001..In normal cells, the predominant mechanism of replication of UV damage involves pol eta-dependent bypass, and Mre11-dependent recombination that acts is a secondary, backup mechanism when cells are severely depleted of pol eta...
- Biallelic inactivation of the thyroid hormone receptor beta1 gene in early stage breast cancerZheng Li
Geraldine Brush Cancer Research Institute, California Pacific Medical Center, San Francisco, California 94115, USA
Cancer Res 62:1939-43. 2002..The observation of early, frequent, and multiple mechanisms of TRbeta1 inactivation suggests a potential role for this gene in the suppression of breast tumorigenesis...
- Design considerations for array CGH to oligonucleotide arraysR A Baldocchi
University of California at San Francisco Cancer Center, San Francisco, California, USA
Cytometry A 67:129-36. 2005..However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome...
- Zf9, a Kruppel-like transcription factor up-regulated in vivo during early hepatic fibrosisV Ratziu
University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 95:9500-5. 1998..schneider cells. Our results suggest that Zf9 may be an important signal in hepatic stellate cell activation after liver injury...
- An oncogenic role for the multiple endocrine neoplasia type 1 gene in prostate cancerP L Paris
Department of Urology, University of California at San Francisco Comprehensive Cancer Center, UCSF, San Francisco, CA 94143, USA
Prostate Cancer Prostatic Dis 12:184-91. 2009..Here, we demonstrate an oncogenic role for MEN1 in prostate cancer using a variety of independent assays...
- Preliminary evaluation of prostate cancer metastatic risk biomarkersP L Paris
Comprehensive Cancer Center, University of California, San Francisco, CA 94143, USA
Int J Biol Markers 20:141-5. 2005..The classification accuracy for the Kattan nomogram was 75%. Therefore, validation of GEMCaP is warranted in a larger, appropriately designed cohort...
- Genome scanning with array CGH delineates regional alterations in mouse islet carcinomasG Hodgson
Cancer Genetics and Breast Oncology Programs, UCSF Cancer Center, University of California at San Francisco, Box 0808, San Francisco, California 94143-0808, USA
Nat Genet 29:459-64. 2001..We also show that irradiation and genetic background influence the spectrum of aberrations present in these tumors...
- Identification of a gene encoding an acyl CoA:diacylglycerol acyltransferase, a key enzyme in triacylglycerol synthesisS Cases
Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 95:13018-23. 1998..The identification of this cDNA encoding a DGAT will greatly facilitate studies of cellular glycerolipid metabolism and its regulation...
- Cloning, mapping, and in vivo localization of a human member of the PKCI-1 protein family (PRKCNH1)P M Brzoska
Department of Radiation Oncology, University of California, San Francisco, California, 94143, USA
Genomics 36:151-6. 1996..The cytoplasmic localization of hPKCI-1 is consistent with a postulated role in mediating a membrane-derived signal in response to ionizing radiation...