Jane Fridlyand

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Oncogene expression and genetic background influence the frequency of DNA copy number abnormalities in mouse pancreatic islet cell carcinomas
    Jeffrey 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
  2. ncbi request reprint Phase I study of intraventricular administration of rituximab in patients with recurrent CNS and intraocular lymphoma
    James 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
  3. pmc Breast tumor copy number aberration phenotypes and genomic instability
    Jane Fridlyand
    Department of Epidemiology and Biostatistics, University of California San Francisco, CA 94143, USA
    BMC Cancer 6:96. 2006
  4. ncbi request reprint FBXW7 and DNA copy number instability
    Kristin 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
  5. pmc Genome position and gene amplification
    Pavla Gajduskova
    Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143 0808, USA
    Genome Biol 8:R120. 2007
  6. pmc Mapping segmental and sequence variations among laboratory mice using BAC array CGH
    Antoine M Snijders
    Cancer Research Institute, University of California San Francisco, San Francisco, California 94143, USA
    Genome Res 15:302-11. 2005
  7. ncbi request reprint Acquired genomic aberrations associated with methotrexate resistance vary with background genomic instability
    Antoine M Snijders
    Cancer Research Institute, University of California San Francisco, San Francisco, CA, USA
    Genes Chromosomes Cancer 47:71-83. 2008
  8. ncbi request reprint Bladder cancer stage and outcome by array-based comparative genomic hybridization
    Ekaterini Blaveri
    Department of Laboratory Medicine, University of California San Francisco, San Francisco, California 94143 0808, USA
    Clin Cancer Res 11:7012-22. 2005
  9. ncbi request reprint Shaping of tumor and drug-resistant genomes by instability and selection
    Antoine M Snijders
    Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143 0808, USA
    Oncogene 22:4370-9. 2003
  10. ncbi request reprint Chromosomal instability in microsatellite-unstable and stable colon cancer
    Karolin 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

Detail Information

Publications43

  1. ncbi request reprint Oncogene expression and genetic background influence the frequency of DNA copy number abnormalities in mouse pancreatic islet cell carcinomas
    Jeffrey 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...
  2. ncbi request reprint Phase I study of intraventricular administration of rituximab in patients with recurrent CNS and intraocular lymphoma
    James 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)...
  3. pmc Breast tumor copy number aberration phenotypes and genomic instability
    Jane 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...
  4. ncbi request reprint FBXW7 and DNA copy number instability
    Kristin 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...
  5. pmc Genome position and gene amplification
    Pavla Gajduskova
    Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143 0808, USA
    Genome Biol 8:R120. 2007
    ....
  6. pmc Mapping segmental and sequence variations among laboratory mice using BAC array CGH
    Antoine 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...
  7. ncbi request reprint Acquired genomic aberrations associated with methotrexate resistance vary with background genomic instability
    Antoine 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...
  8. ncbi request reprint Bladder cancer stage and outcome by array-based comparative genomic hybridization
    Ekaterini 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...
  9. ncbi request reprint Shaping of tumor and drug-resistant genomes by instability and selection
    Antoine M Snijders
    Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143 0808, USA
    Oncogene 22:4370-9. 2003
    ....
  10. ncbi request reprint Chromosomal instability in microsatellite-unstable and stable colon cancer
    Karolin 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
    ....
  11. ncbi request reprint Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma
    Antoine 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...
  12. ncbi request reprint Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3
    Tsui 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...
  13. ncbi request reprint Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma
    Antoine 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...
  14. pmc Gene expression and angiotropism in primary CNS lymphoma
    James 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...
  15. pmc Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma
    Bruno 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...
  16. doi request reprint Integration of genomic analysis and in vivo transfection to identify sprouty 2 as a candidate tumor suppressor in liver cancer
    Susie 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...
  17. ncbi request reprint Differentiation of lobular versus ductal breast carcinomas by expression microarray analysis
    James 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...
  18. pmc A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes
    Richard 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...
  19. ncbi request reprint Genomic and transcriptional aberrations linked to breast cancer pathophysiologies
    Koei 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...
  20. ncbi request reprint Deletion of chromosome 11q predicts response to anthracycline-based chemotherapy in early breast cancer
    Joan 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...
  21. doi request reprint High-resolution genomic and expression analyses of copy number alterations in breast tumors
    Peter 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...
  22. ncbi request reprint Amplification of PVT1 contributes to the pathophysiology of ovarian and breast cancer
    Yinghui 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...
  23. pmc Aging impacts transcriptomes but not genomes of hormone-dependent breast cancers
    Christina 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...
  24. ncbi request reprint Protein biomarker identification in the CSF of patients with CNS lymphoma
    Sushmita 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...
  25. pmc Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel
    Kimberly 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...
  26. ncbi request reprint High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization
    Kentaro 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...
  27. ncbi request reprint Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors
    Christopher 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...
  28. ncbi request reprint Bagging to improve the accuracy of a clustering procedure
    Sandrine 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...
  29. ncbi request reprint Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors
    Pamela 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...
  30. ncbi request reprint Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors
    Joris A Veltman
    Cancer Center, University of California San Francisco, California 94143 0808, USA
    Cancer Res 63:2872-80. 2003
    ....
  31. pmc High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays
    Pamela 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...
  32. ncbi request reprint Genomic analysis of tumors by array comparative genomic hybridization: more is better
    Donna G Albertson
    Cancer Res 66:3955-6; author reply 3956. 2006
  33. pmc A prediction-based resampling method for estimating the number of clusters in a dataset
    Sandrine 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...
  34. pmc Improving melanoma classification by integrating genetic and morphologic features
    Amaya Viros
    Department of Dermatology, University of California San Francisco, San Francisco, California, United States of America
    PLoS Med 5:e120. 2008
    ....
  35. ncbi request reprint Tumor suppressor p16INK4A regulates polycomb-mediated DNA hypermethylation in human mammary epithelial cells
    Paul A Reynolds
    Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143 0511, USA
    J Biol Chem 281:24790-802. 2006
    ....
  36. pmc Multiple genetic loci modify susceptibility to plasmacytoma-related morbidity in E(mu)-v-abl transgenic mice
    R 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...
  37. pmc Mechanisms of cell-cycle arrest in Spitz nevi with constitutive activation of the MAP-kinase pathway
    Janet 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...
  38. ncbi request reprint Lack of germ-line promoter methylation in BRCA1-negative families with familial breast cancer
    Ying 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...
  39. ncbi request reprint Therapy-induced malignant neoplasms in Nf1 mutant mice
    Richard 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...
  40. ncbi request reprint Distinct sets of genetic alterations in melanoma
    John A Curtin
    Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143 0808, USA
    N Engl J Med 353:2135-47. 2005
    ..We hypothesized that the clinical heterogeneity is explained by genetically distinct types of melanoma with different susceptibility to ultraviolet light...
  41. ncbi request reprint A comparison study: applying segmentation to array CGH data for downstream analyses
    Hanni Willenbrock
    Center for Biological Sequence Analysis, Department of Biotechnology, Technical University of Denmark, Kgs Lyngby
    Bioinformatics 21:4084-91. 2005
    ..However, to date, no comprehensive comparison of various characteristics of these methods exists. Moreover, the segmentation results have not been utilized in downstream analyses...
  42. ncbi request reprint Chromosomal aberrations in angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma unspecified: A matrix-based CGH approach
    Christoph 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...
  43. ncbi request reprint Evaluation of whole genome amplification protocols for array and oligonucleotide CGH
    Adam 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...