Genomes and Genes
Affiliation: University of California
- Oncogene expression and genetic background influence the frequency of DNA copy number abnormalities in mouse pancreatic islet cell carcinomasJeffrey H Hager
Department of Biochemistry, University of California at San Francisco Diabetes and Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94143, USA
Cancer Res 64:2406-10. 2004..These studies illustrate the utility of transgenic animal models for investigation of factors influencing genomic heterogeneity despite the commonalty of target cell type and initiating oncogene...
- Phase I study of intraventricular administration of rituximab in patients with recurrent CNS and intraocular lymphomaJames L Rubenstein
Division of Hematology Oncology, and the Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
J Clin Oncol 25:1350-6. 2007..We therefore conducted a phase I dose-escalation study of intrathecal rituximab monotherapy in patients with recurrent CNS non-Hodgkin's lymphoma (NHL)...
- Breast tumor copy number aberration phenotypes and genomic instabilityJane Fridlyand
Department of Epidemiology and Biostatistics, University of California San Francisco, CA 94143, USA
BMC Cancer 6:96. 2006..g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes...
- FBXW7 and DNA copy number instabilityKristin N Byrd
Cancer Research Institute, University of California San Francisco, Box 0808, San Francisco, CA 94143 0808, USA
Breast Cancer Res Treat 109:47-54. 2008..Taken together these studies suggest that FBXW7 deficiency is unlikely to contribute to the extensive copy number aberrations associated with breast and possibly other tumor types...
- Genome position and gene amplificationPavla Gajduskova
Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143 0808, USA
Genome Biol 8:R120. 2007....
- Mapping segmental and sequence variations among laboratory mice using BAC array CGHAntoine M Snijders
Cancer Research Institute, University of California San Francisco, San Francisco, California 94143, USA
Genome Res 15:302-11. 2005..1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses...
- Acquired genomic aberrations associated with methotrexate resistance vary with background genomic instabilityAntoine M Snijders
Cancer Research Institute, University of California San Francisco, San Francisco, CA, USA
Genes Chromosomes Cancer 47:71-83. 2008..On the other hand, it appears that loss of BLM function suppresses the mismatch repair mutator mechanism in mismatch repair and BLM deficient HCT116 BLM-/- cells...
- Bladder cancer stage and outcome by array-based comparative genomic hybridizationEkaterini Blaveri
Department of Laboratory Medicine, University of California San Francisco, San Francisco, California 94143 0808, USA
Clin Cancer Res 11:7012-22. 2005..The purpose of this study was to evaluate associations between measures of genomic instability and bladder cancer clinical phenotype...
- Shaping of tumor and drug-resistant genomes by instability and selectionAntoine M Snijders
Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
Oncogene 22:4370-9. 2003....
- Chromosomal instability in microsatellite-unstable and stable colon cancerKarolin Trautmann
Comprehensive Cancer Center, Department of Medicine, University of California San Francisco, San Francisco, California 94143-0808, USA
Clin Cancer Res 12:6379-85. 2006..CONCLUSION: MSI and CIN are not mutually exclusive forms of genomic instability in sporadic colon cancer, with MSI tumors also showing varying degrees of CIN...
- Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinomaAntoine M Snijders
Cancer Research Institute, University of California San Francisco, Box 0808, San Francisco, CA 94143-0808, USA
Oncogene 24:4232-42. 2005..Deregulation of these and other members of the hedgehog and notch pathways (HHIP, SMO, DLL1, NOTCH4) implicates deregulation of developmental and differentiation pathways, cell fate misspecification, in oral SCC development...
- Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3Tsui Ting Ching
The Brain Tumor Research Center, Department of Neurological Surgery and the Biomedical Sciences Program, University of California San Francisco, San Franciso, California 94143, USA
Nat Genet 37:645-51. 2005..Defects in SHANK3 seem to underlie human 22q13 deletion syndrome. Furthermore, these patterns for SHANK3 are conserved in mice and rats...
- Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinomaAntoine M Snijders
Cancer Research Institute, University of California San Francisco, San Francisco, CA, USA
Oncogene 22:4281-6. 2003..The FTC were remarkably homogeneous, with some recurrent aberrations occurring in more than 70% of samples, which suggests a stereotyped pattern of tumor evolution...
- Gene expression and angiotropism in primary CNS lymphomaJames L Rubenstein
University of California, San Francisco, Division of Hematology Oncology M1282 Box 1270, 94143, USA
Blood 107:3716-23. 2006..High expression of activated STAT6 in tumors was associated with short survival in an independent set of patients with primary CNS lymphoma who were treated with high-dose intravenous methotrexate therapy...
- Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastomaBruno M Costa
The Brain Tumor Research Center, Department of Neurological Surgery, University of California San Francisco, San Francisco, California 94158 9001, USA
Cancer Res 70:453-62. 2010..Our findings suggest a transcriptional pathway through which PI3K activates oncogenic HOXA expression with implications for mTOR or PI3K targeted therapies...
- Integration of genomic analysis and in vivo transfection to identify sprouty 2 as a candidate tumor suppressor in liver cancerSusie A Lee
Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
Hepatology 47:1200-10. 2008..In addition, we demonstrate that the integration of genomic analysis and in vivo transfection is a powerful tool to identify genes that are important during hepatic carcinogenesis...
- Differentiation of lobular versus ductal breast carcinomas by expression microarray analysisJames E Korkola
Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
Cancer Res 63:7167-75. 2003..In conclusion, specific changes in gene expression distinguish lobular from ductal breast carcinomas. These genes may be important in understanding the basis of phenotypic differences among breast cancers...
- A collection of breast cancer cell lines for the study of functionally distinct cancer subtypesRichard M Neve
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, USA
Cancer Cell 10:515-27. 2006..We show, using Trastuzumab (Herceptin) monotherapy as an example, that the system can be used to identify molecular features that predict or indicate response to targeted therapies or other physiological perturbations...
- Genomic and transcriptional aberrations linked to breast cancer pathophysiologiesKoei Chin
Comprehensive Cancer Center, 2340 Sutter Street, University of California, San Francisco, San Francisco, California 94143
Cancer Cell 10:529-41. 2006..Nine of these (FGFR1, IKBKB, ERBB2, PROCC, ADAM9, FNTA, ACACA, PNMT, and NR1D1) are considered druggable. Low-level CNAs appear to contribute to cancer progression by altering RNA and cellular metabolism...
- Deletion of chromosome 11q predicts response to anthracycline-based chemotherapy in early breast cancerJoan Climent
Division of Oncology, Center for Applied Medical Research, University of Navarra, Pamplona, and Department of Hematology and Medical Oncology, Hospital Clinico, University of Valencia, Spain
Cancer Res 67:818-26. 2007..However, these initial findings should be evaluated in randomized clinical trials...
- High-resolution genomic and expression analyses of copy number alterations in breast tumorsPeter M Haverty
Department of Bioinformatics, Genentech, Inc, South San Francisco, CA 94080, USA
Genes Chromosomes Cancer 47:530-42. 2008..This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat...
- Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancerYinghui Guan
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
Clin Cancer Res 13:5745-55. 2007..This study was designed to elucidate the role of amplification at 8q24 in the pathophysiology of ovarian and breast cancer because increased copy number at this locus is one of the most frequent genomic abnormalities in these cancers...
- Aging impacts transcriptomes but not genomes of hormone-dependent breast cancersChristina Yau
Buck Institute for Age Research, 8001 Redwood Boulevard, Novato, CA 94945, USA
Breast Cancer Res 9:R59. 2007..Except for inherited forms of breast cancer, however, there is little genetic or epigenetic understanding of the biological basis linking aging with sporadic breast cancer incidence and its clinical behavior...
- Protein biomarker identification in the CSF of patients with CNS lymphomaSushmita Roy
PPD Biomarker Discovery Sciences, LLC, Menlo Park, CA, USA
J Clin Oncol 26:96-105. 2008..Elucidation of the CSF proteome may yield insights into the pathogenesis of CNS disease. We tested the hypothesis that individual CSF proteins distinguish CNS lymphoma from benign focal brain lesions...
- Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panelKimberly J Bussey
Laboratory of Molecular Pharmacology, National Cancer Institute, Building 37, Room 5056, NIH, MSC 4255, 9000 Rockville Pike, Bethesda, MD 20892-4255, USA
Mol Cancer Ther 5:853-67. 2006..The DNA copy number database presented here will enable other investigators to explore DNA transcript-drug relationships in their own domains of research focus...
- High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridizationKentaro Nakao
Second Department of Surgery, Showa University School of Medicine, Tokyo, Japan
Carcinogenesis 25:1345-57. 2004..Array-based CGH was also able to identify DNA copy number changes in MSI-H tumors...
- Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumorsChristopher S Hackett
Department of Neurology, University of California, San Francisco, California 94143-0114, USA
Cancer Res 63:5266-73. 2003..These data demonstrate conservation of many genetic changes in murine and human neuroblastoma and suggest that further delineation of genetic abnormalities in murine tumors may identify genes important in human disease...
- Bagging to improve the accuracy of a clustering procedureSandrine Dudoit
Division of Biostatistics, School of Public Health, University of California, Berkeley, 140 Earl Warren Hall, 7360, Berkeley, CA 94720 7360, USA
Bioinformatics 19:1090-9. 2003..Essential aspects of this clustering problem include identifying accurate partitions of the tumor samples into clusters and assessing the confidence of cluster assignments for individual samples...
- 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...
- Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumorsJoris A Veltman
Cancer Center, University of California-San Francisco, California 94143-0808, USA
Cancer Res 63:2872-80. 2003....
- 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...
- Genomic analysis of tumors by array comparative genomic hybridization: more is betterDonna G Albertson
Cancer Res 66:3955-6; author reply 3956. 2006
- A prediction-based resampling method for estimating the number of clusters in a datasetSandrine Dudoit
Division of Biostatistics, School of Public Health, University of California Berkeley, 140 Earl Warren Hall, Berkeley, CA 94720 7360, USA
Genome Biol 3:RESEARCH0036. 2002..Here we address the first of these problems...
- Improving melanoma classification by integrating genetic and morphologic featuresAmaya Viros
Department of Dermatology, University of California San Francisco, San Francisco, California, United States of America
PLoS Med 5:e120. 2008....
- Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cellsPaul A Reynolds
Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143 0511, USA
J Biol Chem 281:24790-802. 2006....
- Multiple genetic loci modify susceptibility to plasmacytoma-related morbidity in E(mu)-v-abl transgenic miceR C Andrew Symons
The Walter and Eliza Hall Institute of Medical Research, Post Office, Royal Melbourne Hospital, Victoria 3050, Australia
Proc Natl Acad Sci U S A 99:11299-304. 2002..Different loci influence tumor susceptibility in male and female mice. Survival in females may be largely controlled by a pair of interacting loci on chromosomes 2 and 17...
- Mechanisms of cell-cycle arrest in Spitz nevi with constitutive activation of the MAP-kinase pathwayJanet L Maldonado
Department of Dermatology, University of California, San Francisco, California 94143, USA
Am J Pathol 164:1783-7. 2004..We propose that in benign nevi with constitutive activation of the MAP-kinase pathway, p16 functions as an essential mediator of oncogene-induced senescence preventing progression to melanoma...
- Lack of germ-line promoter methylation in BRCA1-negative families with familial breast cancerYing Chen
Department of Neurological Surgery, UCSF Comprehensive Cancer Center, San Francisco, California 9443 0875, USA
Genet Test 10:281-4. 2006..Thus, epimutation is an unlikely explanation for hereditary breast cancer in women who test negative for BRCA mutations...
- Therapy-induced malignant neoplasms in Nf1 mutant miceRichard C Chao
Department of Pediatrics, University of California, San Francisco, San Francisco, California 94143, USA
Cancer Cell 8:337-48. 2005..Nf1(+/-) mice provide a tractable model for investigating the pathogenesis of common mutagen-induced cancers and for testing preventive strategies...
- Distinct sets of genetic alterations in melanomaJohn A Curtin
Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143-0808, USA
N Engl J Med 353:2135-47. 2005....
- A comparison study: applying segmentation to array CGH data for downstream analysesHanni Willenbrock
Center for Biological Sequence Analysis, Department of Biotechnology, Technical University of Denmark, Kgs. Lyngby
Bioinformatics 21:4084-91. 2005..AVAILABILITY: http://www.bioconductor.org..
- Chromosomal aberrations in angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma unspecified: A matrix-based CGH approachChristoph Thorns
Department of Pathology, German Consultation and Reference Center for Lymphomas, University Clinic Schleswig Holstein, Campus Luebeck, Luebeck, Germany
Genes Chromosomes Cancer 46:37-44. 2007..In conclusion, CGH revealed common genetic events in peripheral T-cell lymphomas as well as peculiar differences between AILT and PTCL-u...
- Evaluation of whole genome amplification protocols for array and oligonucleotide CGHAdam Hittelman
Department of Urology University of California at San Francisco Comprehensive Cancer Center, San Francisco, CA, USA
Diagn Mol Pathol 16:198-206. 2007..Quantitative analysis and clustering suggest that Sigma's whole genome amplification protocol performed best on all specimens and, moreover, worked well with a formalin-fixed, paraffin-embedded biopsy...