Research Topics
| Jonathan PollackSummaryAffiliation: Stanford University Country: USA Publications
Research Grants
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Detail Information
Publications
Lineage-specific gene duplication and loss in human and great ape evolutionAndrew Fortna
Department of Pharmacology and Human Medical Genetics Program, University of Colorado Health Sciences Center, Denver, Colorado, USA
PLoS Biol 2:E207. 2004....- A DNA microarray survey of gene expression in normal human tissuesRadha Shyamsundar
Department of Pathology, Stanford University School of Medicine, 269 Campus Drive, CCSR 3245A, Stanford, CA 94305 5176, USA
Genome Biol 6:R22. 2005.... - A transcriptional response to Wnt protein in human embryonic carcinoma cellsJennifer Willert
Department of Developmental Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305 USA
BMC Dev Biol 2:8. 2002..Wnt signaling is implicated in many developmental decisions, including stem cell control, as well as in cancer. There are relatively few target genes known of the Wnt pathway... - Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumorsJonathan R Pollack
Departments of Pathology, Genetics, Surgery, Health Research and Policy, and Biochemistry, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 99:12963-8. 2002..These findings provide evidence that widespread DNA copy number alteration can lead directly to global deregulation of gene expression, which may contribute to the development or progression of cancer... - A perspective on DNA microarrays in pathology research and practiceJonathan R Pollack
Department of Pathology, Stanford University School of Medicine, CCSR 3245A, 269 Campus Dr, Stanford, CA 94305 5176, USA
Am J Pathol 171:375-85. 2007..This review highlights some of the key contributions of DNA microarrays to experimental pathology, focusing in the area of cancer research. Also discussed are some of the current challenges in translating utility to clinical practice... 
Genomic profiling reveals alternative genetic pathways of prostate tumorigenesisJacques Lapointe
Department of Pathology, Stanford University, Stanford, California, USA
Cancer Res 67:8504-10. 2007..The resultant molecular genetic subtypes provide a new framework for investigating prostate cancer biology and explain in part the clinical heterogeneity of the disease...- A method for calling gains and losses in array CGH dataPei Wang
Department of Statistics, Stanford University, CA, 94305, USA
Biostatistics 6:45-58. 2005..We illustrate the method using an application of CLAC on a lung cancer microarray CGH data set as well as a BAC array CGH data set of aneuploid cell strains... - Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemiaLars Bullinger
Department of Pathology, Stanford University, Stanford, Calif, USA
N Engl J Med 350:1605-16. 2004..8; 95 percent confidence interval, 2.6 to 29.3; P<0.001). CONCLUSIONS: The use of gene-expression profiling improves the molecular classification of adult AML... - Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell linesHongjuan Zhao
Department of Urology, Stanford University School of Medicine, Stanford, California, USA
Prostate 63:187-97. 2005..CONCLUSIONS: AS and AI cell lines are different in their transcriptional programs and degree of DNA copy number alterations. This dataset provides a context for the use of prostate cancer cell lines as models for clinical cancers... - Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancerMurali D Bashyam
Department of Pathology, Stanford University, Stanford, CA, USA
Neoplasia 7:556-62. 2005..Our findings suggest candidate genes and pathways, which may contribute to the development or progression of pancreatic cancer... - Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberansSabine C Linn
Departments of Pathology, Genetics, and Biochemistry, and Howard Hughes Medical Institute, Stanford University Medical Center, Stanford, California 94305, USA
Am J Pathol 163:2383-95. 2003.... - The diagnosis and management of pre-invasive breast disease: promise of new technologies in understanding pre-invasive breast lesionsStefanie S Jeffrey
Stanford University School of Medicine, Stanford, California, USA
Breast Cancer Res 5:320-8. 2003..It is expected that molecular technologies will identify breast tissue at risk for the development of unfavorable subtypes of invasive breast cancer and reveal strategies for targeted chemoprevention or eradication... - DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression dataKeyan Salari
Department of Pathology, Stanford University, Stanford, CA, USA
Bioinformatics 26:414-6. 2010.... 
DNA microarray technology. IntroductionJonathan R Pollack
Department of Pathology, Stanford University, Stanford, CA, USA
Methods Mol Biol 556:1-6. 2009..e., chromatin and transcription factor) interactions, DNA replication, and the integration of diverse genome-scale data types. Also provided is a perspective on recent advances and future directions in characterizing the physical genome...- Characterizing the physical genomeJonathan R Pollack
Department of Pathology, Stanford University School of Medicine, CCSR Building, Room 3245A, 269 Campus Drive, Stanford, California 94305 5176, USA
Nat Genet 32:515-21. 2002..Methods based on microarrays are beginning to provide a detailed picture of this physical genome, and they complement the genome-wide studies of mRNA expression profiling that have previously been so successful... - Genomic instability in breast cancer: pathogenesis and clinical implicationsKevin A Kwei
Department of Pathology, Stanford University School of Medicine, CCSR 3245A, 269 Campus Drive, Stanford, CA 94305 5176, USA
Mol Oncol 4:255-66. 2010..Future studies should clarify the pathogenesis of breast cancers with amplifier and complex-pattern genomes, and will likely identify new therapeutic opportunities... - DNA microarray and proteomic strategies for understanding alcohol actionJames M Sikela
University of Colorado at Denver and Health Sciences Center, Aurora, Colorado, USA
Alcohol Clin Exp Res 30:700-8. 2006..Kerns; and (4) Quantitative Proteomic Analysis of AC7-Modified Mice, by Kathleen J. Grant... - Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicleMaxwell Thompson
Department of Pathology, Stanford University, Stanford, California 94305 5176, USA
Prostate 68:1248-56. 2008..We hypothesized that gene-expression differences between prostate and seminal vesicle might inform mechanisms underlying the higher incidence of prostate cancer... - Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discoveryJessica Kao
Department of Pathology, Stanford University, Stanford, CA, USA
PLoS ONE 4:e6146. 2009..Here, we studied a collection of breast cancer cell lines to catalog molecular profiles and to assess their relation to breast cancer subtypes... - Development of an orthotopic model of invasive pancreatic cancer in an immunocompetent murine hostWilliam W Tseng
Department of Pathology, Stanford University, Palo Alto, California, USA
Clin Cancer Res 16:3684-95. 2010..We sought to develop an immunocompetent, orthotopic mouse model of pancreatic cancer with rapid and predictable growth kinetics... - Application of genomic technologies to human prostate cancerShijun Li
Department of Urology, Stanford University of Medicine, Stanford, California 94305-5118, USA
OMICS 10:261-75. 2006..Continued improvements in methods of tissue preparation, microarray technology and data analysis will overcome existing challenges and fuel future discoveries... - The retinoic acid synthesis gene ALDH1a2 is a candidate tumor suppressor in prostate cancerHanna Kim
Department of Pathology, Stanford University, Stanford, California 94305 5176, USA
Cancer Res 65:8118-24. 2005..Taken together, our findings implicate ALDH1a2 as a candidate tumor suppressor gene in prostate cancer and further support a role of retinoids in the prevention or treatment of prostate cancer... - Target discovery and validation in pancreatic cancerRobert M Beaty
Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
Methods Mol Biol 360:57-89. 2007.... - Challenges in developing a molecular characterization of cancerJonathan R Pollack
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
Semin Oncol 29:280-5. 2002..Here, we detail some of the challenges in developing a molecular characterization of cancer and in translating these new discoveries towards clinical utility... - Comparative genomic hybridization on mouse cDNA microarrays and its application to a murine lymphoma modelSandrine Sander
Department of Pathology, Stanford University, Stanford, CA 94305-5176, USA
Oncogene 24:6101-7. 2005.... - Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNAMarkus Bredel
Division of Oncology, Clinical Sciences Research, Stanford University School of Medicine, 269 Campus Dr, CCSR-1105, Stanford, CA 94305-5151, USA
J Mol Diagn 7:171-82. 2005..Therefore, this amplification method should lend itself to high-throughput genetic analyses of limited sources of tumor, such as fine-needle biopsies, laser-microdissected tissue, and small paraffin-embedded specimens... - Parallel analysis of gene copy number and expression using cDNA microarraysJonathan R Pollack
Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
Methods Mol Biol 224:89-97. 2003 - High-resolution array-based comparative genomic hybridization for distinguishing paraffin-embedded Spitz nevi and melanomasJeff D Harvell
Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
Diagn Mol Pathol 13:22-5. 2004.... - Gene expression profiling identifies clinically relevant subtypes of prostate cancerJacques Lapointe
Department of Pathology, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 101:811-6. 2004..Our results suggest that prostate tumors can be usefully classified according to their gene expression patterns, and these tumor subtypes may provide a basis for improved prognostication and treatment stratification... - Gene expression patterns in renal cell carcinoma assessed by complementary DNA microarrayJohn P T Higgins
Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
Am J Pathol 162:925-32. 2003..Characterization of renal cell carcinomas based on gene expression patterns provides a revised classification of these tumors and has the potential to supply significant biological and clinical insights... - A gene expression signature of genetic instability in colon cancerCraig P Giacomini
Department of Pathology, Stanford University, Stanford, CA 94305-5176, USA
Cancer Res 65:9200-5. 2005..Further, among the MSI signature genes, our findings implicate a role of elevated metallothionein expression in the clinical behavior of MSI cancers... - Comparative genomic hybridization on spotted oligonucleotide microarraysYoung H Kim
Department of Pathology, Stanford University, Stanford, CA, USA
Methods Mol Biol 556:21-32. 2009.... - Integration of diverse microarray data typesKeyan Salari
Departments of Pathology and Genetics, Stanford University, Stanford, CA, USA
Methods Mol Biol 556:205-16. 2009..This chapter will outline general approaches to microarray data integration and provide an introduction to DR-Integrator, a broadly useful analysis tool for the integration of DNA copy number and gene-expression microarray data... - RNA interference-based functional dissection of the 17q12 amplicon in breast cancer reveals contribution of coamplified genesJessica Kao
Department of Pathology, Stanford University, Stanford, California 94305, USA
Genes Chromosomes Cancer 45:761-9. 2006..Our findings validate the utility of RNAi in the functional interrogation of tumor amplicons, and provide evidence for a contribution of coamplified genes to tumor phenotypes... - Gene expression profiling in prostate cancer cells with Akt activation reveals Fra-1 as an Akt-inducible geneGunjan Tiwari
Department of Molecular Pharmacology, Stanford University and Department of Pathology, Stanford University School of Medicine, Stanford, CA
Mol Cancer Res 1:475-84. 2003..Moreover, the identification of Fra-1 as an Akt-regulated gene may have implications for the ability of Akt to transform cells since Fra-1 has been implicated in cell growth and the aggressiveness of tumors... - Interlaboratory performance of a microarray-based gene expression test to determine tissue of origin in poorly differentiated and undifferentiated cancersCatherine I Dumur
Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
J Mol Diagn 10:67-77. 2008.... - Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancerKevin A Kwei
Department of Pathology, Stanford University, Stanford, California, United States of America
PLoS Genet 4:e1000081. 2008.... - hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signatureJacques Lapointe
Department of Pathology, Stanford University, Stanford, CA 94305 51, USA
Am J Surg Pathol 32:205-9. 2008..019). Our findings identify hCAP-D3 as a new biomarker for subtype-1 tumors that improves prognostication, and reveal androgen signaling as an important biologic feature of this potentially clinically favorable molecular subtype... - Molecular characterisation of soft tissue tumours: a gene expression studyTorsten O Nielsen
Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
Lancet 359:1301-7. 2002..Large numbers of uncharacterised genes contributed to distinctions between the tumours, and some of these could be useful markers for diagnosis, have prognostic significance, or prove possible targets for treatment... - Gene copy number variation spanning 60 million years of human and primate evolutionLaura Dumas
Human Medical Genetics Program, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045, USA
Genome Res 17:1266-77. 2007.... - Disclosure of candidate genes in acute myeloid leukemia with complex karyotypes using microarray-based molecular characterizationFrank G Rücker
Department of Neural Information Processing, University Hospital of Ulm, Ulm, Germany
J Clin Oncol 24:3887-94. 2006.... - Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancerAnna Bergamaschi
Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Oslo, Norway
Genes Chromosomes Cancer 45:1033-40. 2006..This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.. - Genomics in myeloid leukemias: an array of possibilitiesLars Bullinger
Department of Internal Medicine III, University of Ulm, Germany
Rev Clin Exp Hematol 9:E2. 2005..We expect whole genome approaches will significantly contribute to a better understanding of the pathogenesis and result in a refined molecular classification of myeloid leukemias... - A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignanciesDavid S Shames
Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
PLoS Med 3:e486. 2006.... - Gene-expression profiling identifies distinct subclasses of core binding factor acute myeloid leukemiaLars Bullinger
Department of Internal Medicine III, University of Ulm, Ulm, Germany
Blood 110:1291-300. 2007..While the leukemogenic relevance of these signatures remains to be validated, their existence nevertheless supports a prognostically relevant biologic basis for the heterogeneity observed in CBF leukemia... - Aberrant epidermal growth factor receptor signaling and enhanced sensitivity to EGFR inhibitors in lung cancerJoseph Amann
Vanderbilt Ingram Cancer Center, Nashville, TN 37232, USA
Cancer Res 65:226-35. 2005..Thus, in addition to EGFR mutations, other factors in NSCLC cells, such as high expression of ErbB family members, may constitutively activate AKT and sensitize cells to EGFR inhibitors... - Evolutionary and biomedical insights from the rhesus macaque genomeRichard A Gibbs
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
Science 316:222-34. 2007..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species... - An FLT3 gene-expression signature predicts clinical outcome in normal karyotype AMLLars Bullinger
Department of Internal Medicine III, University of Ulm, Ulm, Germany
Blood 111:4490-5. 2008..Our findings support the potential clinical utility of a gene expression-based measure of FLT3 pathway activation in AML... - An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown originRichard W Tothill
Ian Potter Centre for Cancer Genomics and Predictive Medicine, Department of Haematology and Medical Oncology, Peter MacCallum Cancer Centre, St. Andrew's Place, East Melbourne, Victoria, Australia
Cancer Res 65:4031-40. 2005..We show that the microarray SVM classifier was capable of making high confidence predictions in 11 of 13 cases. These predictions were supported by comprehensive review of the patients' clinical histories... - Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarraysJohann Y Lin
Department of Vascular Biology, The Scripps Research Institute, 10550 N, Torrey Pines Road, La Jolla, CA 92037, USA
Genome Biol 3:RESEARCH0026. 2002..Here we report experiments that establish the validity and efficacy of the methodology... - Chromosome instability leaves its markJonathan R Pollack
Nat Genet 38:973-4. 2006
Research Grants
- Gene Amplification and Deletion in Pancreatic CancerJonathan Pollack; Fiscal Year: 2007....
- Pathogenetics of a Clinically-favorable Prostate Cancer SubtypeJonathan R Pollack; Fiscal Year: 2010..Our findings may also suggest novel gene-based markers for the diagnosis of clinically- favorable tumors, leading to improved treatment stratification and clinical management of men with prostate cancer. ..
- Gene Amplification and Deletion in Pancreatic CancerJonathan Pollack; Fiscal Year: 2009..abstract_text> ..
- Pathogenetics of a Clinically-favorable Prostate Cancer SubtypeJonathan Pollack; Fiscal Year: 2009..Our findings will further our understanding of the pathogenesis of prostate cancer, and may suggest novel gene-based markers for an improved classification of prostate tumors and management of patients with prostate cancer. ..
- Role of Gene Amplification in Breast CancerJonathan Pollack; Fiscal Year: 2007..abstract_text> ..
- Gene Amplification and Deletion in Pancreatic CancerJonathan R Pollack; Fiscal Year: 2010..abstract_text> ..