DANIEL D PINKEL

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc A large field CCD system for quantitative imaging of microarrays
    G Hamilton
    Comprehensive Cancer Center, University of California, San Francisco CA, USA
    Nucleic Acids Res 34:e58. 2006
  2. pmc Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer
    Mark Jesus M Magbanua
    Department of Medicine, Division of Hematology Oncology, University of California San Francisco, USA
    BMC Cancer 12:78. 2012
  3. 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
  4. 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
  5. pmc Analytical description of mutational effects in competing asexual populations
    Daniel Pinkel
    Comprehensive Cancer Center and Department of Laboratory Medicine, University of California, San Francisco, California 94143, USA
    Genetics 177:2135-49. 2007
  6. ncbi request reprint Comparative genomic hybridization
    Daniel Pinkel
    Comprehensive Cancer Center, Department of Laboratory Medicine, University of California, San Francisco, California 94143, USA
    Annu Rev Genomics Hum Genet 6:331-54. 2005
  7. ncbi request reprint Array comparative genomic hybridization and its applications in cancer
    Daniel Pinkel
    Department of Laboratory Medicine and Comprehensive Cancer Center, University of California San Francisco, Box 0808, San Francisco, California 94143, USA
    Nat Genet 37:S11-7. 2005
  8. pmc Fully automatic quantification of microarray image data
    Ajay N Jain
    Comprehensive Cancer Center, University of California, San Francisco, California 94143, USA
    Genome Res 12:325-32. 2002
  9. ncbi request reprint Interstitial deletion of chromosome 12q: genotype-phenotype correlation of two patients utilizing array comparative genomic hybridization
    Ophir D Klein
    Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California 94115, USA
    Am J Med Genet A 138:349-54. 2005
  10. ncbi request reprint Array comparative genomic hybridization identifies genetic subgroups in grade 4 human astrocytoma
    Anjan Misra
    Brain Tumor Research Center, Department of Neurosurgery, University of California San Francisco, San Francisco, California, USA
    Clin Cancer Res 11:2907-18. 2005

Research Grants

Collaborators

Detail Information

Publications33

  1. pmc A large field CCD system for quantitative imaging of microarrays
    G Hamilton
    Comprehensive Cancer Center, University of California, San Francisco CA, USA
    Nucleic Acids Res 34:e58. 2006
    ..Resolution referred to the sample is 10 microm, sufficient for obtaining quantitative multicolor images from >30,000 array elements in an 18 mm x 18 mm square...
  2. pmc Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer
    Mark Jesus M Magbanua
    Department of Medicine, Division of Hematology Oncology, University of California San Francisco, USA
    BMC Cancer 12:78. 2012
    ..However, it is the molecular characterization of CTCs that offers insight into the biology of these tumor cells in the context of personalized treatment...
  3. 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
    ....
  4. 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...
  5. pmc Analytical description of mutational effects in competing asexual populations
    Daniel Pinkel
    Comprehensive Cancer Center and Department of Laboratory Medicine, University of California, San Francisco, California 94143, USA
    Genetics 177:2135-49. 2007
    ..Finally, experimental designs that may improve measurements of fitness distributions are suggested...
  6. ncbi request reprint Comparative genomic hybridization
    Daniel Pinkel
    Comprehensive Cancer Center, Department of Laboratory Medicine, University of California, San Francisco, California 94143, USA
    Annu Rev Genomics Hum Genet 6:331-54. 2005
    ..In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results...
  7. ncbi request reprint Array comparative genomic hybridization and its applications in cancer
    Daniel Pinkel
    Department of Laboratory Medicine and Comprehensive Cancer Center, University of California San Francisco, Box 0808, San Francisco, California 94143, USA
    Nat Genet 37:S11-7. 2005
    ..Here, we discuss the state of the art of array comparative genomic hybridization and its applications in cancer, emphasizing general concepts rather than specific results...
  8. pmc Fully automatic quantification of microarray image data
    Ajay N Jain
    Comprehensive Cancer Center, University of California, San Francisco, California 94143, USA
    Genome Res 12:325-32. 2002
    ..The software, called, runs on Windows platforms and is available free of charge for academic use...
  9. ncbi request reprint Interstitial deletion of chromosome 12q: genotype-phenotype correlation of two patients utilizing array comparative genomic hybridization
    Ophir D Klein
    Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California 94115, USA
    Am J Med Genet A 138:349-54. 2005
    ....
  10. ncbi request reprint Array comparative genomic hybridization identifies genetic subgroups in grade 4 human astrocytoma
    Anjan Misra
    Brain Tumor Research Center, Department of Neurosurgery, University of California San Francisco, San Francisco, California, USA
    Clin Cancer Res 11:2907-18. 2005
    ..The significance of these genetic groups to therapeutics needs further study...
  11. ncbi request reprint 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 cancer
    J E Vivienne Watson
    Collins Lab, UCSF Comprehensive Cancer Center, University of California, 2340 Sutter Street, San Francisco, USA
    Oncogene 23:3487-94. 2004
    ....
  12. 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...
  13. ncbi request reprint Additional patient with del(12)(q21.2q22): further evidence for a candidate region for cardio-facio-cutaneous syndrome?
    Katherine A Rauen
    Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California, USA
    Am J Med Genet 110:51-6. 2002
    ..The region 12q21.2 --> q22 remains a possible candidate region for CFC syndrome. Additional characterization of these and other CFC patients may confirm and further refine this candidate region...
  14. ncbi request reprint Genomic microarrays in human genetic disease and cancer
    Donna G Albertson
    Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143 0808, USA
    Hum Mol Genet 12:R145-52. 2003
    ..Here we discuss the performance characteristics of different array platforms and review some of the recent applications of array CGH in cancer and medical genetics...
  15. pmc Classifying melanocytic tumors based on DNA copy number changes
    Boris C Bastian
    Departments of Pathology and Dermatology, Dermatopathology Section, University of California San Francisco, San Francisco, CA 94143 0808, USA
    Am J Pathol 163:1765-70. 2003
    ..In addition, we show marked differences in the genetic make-up of melanomas that depend on anatomical location and sun-exposure pattern indicating that potential therapeutic targets might vary among melanoma types...
  16. 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...
  17. ncbi request reprint Somatic activation of KIT in distinct subtypes of melanoma
    John A Curtin
    Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143 0808, USA
    J Clin Oncol 24:4340-6. 2006
    ..This raises the question of whether other aberrations are occurring in the MAP kinase cascade in the melanoma types with infrequent mutations of BRAF and NRAS...
  18. 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...
  19. ncbi request reprint Detection of single clone deletions using array CGH: identification of submicroscopic deletions in the 22q11.2 deletion syndrome as a model system
    Taku A Tokuyasu
    Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94115, USA
    Am J Med Genet A 143:925-32. 2007
    ..We demonstrate that such technology is ideally suited for microdeletion syndromes such as 22q11.2...
  20. 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
    ....
  21. ncbi request reprint Xq chromosome duplication in males: clinical, cytogenetic and array CGH characterization of a new case and review
    Sabrina F Cheng
    Department of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, California, USA
    Am J Med Genet A 135:308-13. 2005
    ..Mental, psychomotor and growth retardation, as well as, craniofacial anomalies, muscle hypotonia, hypoplastic genitalia, cryptorchidism, feeding difficulties, and endocrine dysfunction are all significant issues in these individuals...
  22. 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...
  23. ncbi request reprint Duplication of distal 20q: clinical, cytogenetic and array CGH. Characterization of a new case
    Alejandro Iglesias
    Division of Genetics, Department of Pediatrics, Beth Israel Medical Center, New York, and Division of Medical Genetics, Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, USA
    Clin Dysmorphol 15:19-23. 2006
    ..This case further highlights the utility of array CGH in characterizing aneusomies and, in particular, for accurate breakpoint designation and quantitation of ambiguous rearrangements...
  24. pmc Distribution and significance of occult intraepidermal tumor cells surrounding primary melanoma
    Jeffrey P North
    UCSF School of Medicine, University of California, San Francisco, California, USA
    J Invest Dermatol 128:2024-30. 2008
    ..These field cells provide a plausible explanation for the tendency of certain melanoma types to recur locally despite apparently having undergone complete excision...
  25. ncbi request reprint Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway
    Pierre P Massion
    UCSF Comprehensive Cancer Center, University of California, San Francisco, California 94143 0808, USA
    Cancer Res 62:3636-40. 2002
    ..75), suggesting that these copy number increases contribute to activation of PI3K signaling in SqCas of the lung...
  26. 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...
  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 Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors
    Giuseppe 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...
  29. 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...
  30. 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
    ....
  31. doi request reprint High-efficiency microarray printer using fused-silica capillary tube printing pins
    Steve M Clark
    University of California San Francisco, Box 0808, San Francisco, California 94143, USA
    Anal Chem 80:7639-42. 2008
    ....
  32. ncbi request reprint BAC microarray-based comparative genomic hybridization
    Antoine M Snijders
    Comprehensive Cancer Center, University of California, San Francisco, USA
    Methods Mol Biol 256:39-56. 2004
  33. 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...

Research Grants9

  1. GENOME WIDE ANALYSIS OF DNA COPY NUMBER BY ARRAY
    Daniel Pinkel; Fiscal Year: 1999
    ..The combination of array CGH data with data from other sources, for example microarray measurements of mRNA expression. will provide an even more powerful window on the genetic events involved in cancer development and progression. ..
  2. GENOME WIDE ANALYSIS OF DNA COPY NUMBER BY ARRAY
    Daniel Pinkel; Fiscal Year: 1999
    ..The combination of array CGH data with data from other sources, for example microarray measurements of mRNA expression. will provide an even more powerful window on the genetic events involved in cancer development and progression. ..
  3. GENOME WIDE ANALYSIS OF DNA COPY NUMBER BY ARRAY
    Daniel Pinkel; Fiscal Year: 2000
    ..The combination of array CGH data with data from other sources, for example microarray measurements of mRNA expression. will provide an even more powerful window on the genetic events involved in cancer development and progression. ..
  4. GENOME WIDE ANALYSIS OF DNA COPY NUMBER BY ARRAY
    Daniel Pinkel; Fiscal Year: 2001
    ..The combination of array CGH data with data from other sources, for example microarray measurements of mRNA expression. will provide an even more powerful window on the genetic events involved in cancer development and progression. ..
  5. Prognostic Markers for Primary Cutaneous Melanoma
    Daniel Pinkel; Fiscal Year: 2002
    ....
  6. Prognostic Markers for Primary Cutaneous Melanoma
    Daniel Pinkel; Fiscal Year: 2003
    ....
  7. Prognostic Markers for Primary Cutaneous Melanoma
    Daniel Pinkel; Fiscal Year: 2004
    ....
  8. Prognostic Markers for Primary Cutaneous Melanoma
    Daniel Pinkel; Fiscal Year: 2005
    ....
  9. Prognostic Markers for Primary Cutaneous Melanoma
    Daniel Pinkel; Fiscal Year: 2006
    ....