Research Topics
Species | DANIEL D PINKELSummaryAffiliation: University of California Country: USA Publications
Research Grants
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Detail Information
Publications
Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancerMark 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...- 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.... - 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... - Array comparative genomic hybridization and its applications in cancerDaniel 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... - Comparative genomic hybridizationDaniel 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... - Analytical description of mutational effects in competing asexual populationsDaniel 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... - Interstitial deletion of chromosome 12q: genotype-phenotype correlation of two patients utilizing array comparative genomic hybridizationOphir 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.... - Fully automatic quantification of microarray image dataAjay 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... - Array comparative genomic hybridization identifies genetic subgroups in grade 4 human astrocytomaAnjan 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... - 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 cancerJ E Vivienne Watson
Collins Lab, UCSF Comprehensive Cancer Center, University of California, 2340 Sutter Street, San Francisco, USA
Oncogene 23:3487-94. 2004.... - Classifying melanocytic tumors based on DNA copy number changesBoris 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... - Genomic microarrays in human genetic disease and cancerDonna 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... - 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... - 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... - Detection of single clone deletions using array CGH: identification of submicroscopic deletions in the 22q11.2 deletion syndrome as a model systemTaku 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... - 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... - 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.... - Xq chromosome duplication in males: clinical, cytogenetic and array CGH characterization of a new case and reviewSabrina 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... - 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... - Somatic activation of KIT in distinct subtypes of melanomaJohn A Curtin
Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143-0808, USA
J Clin Oncol 24:4340-6. 2006..Because the majority of the KIT mutations we found in melanoma also occur in imatinib-responsive cancers of other types, imatinib may offer an immediate therapeutic benefit for a significant proportion of the global melanoma burden... - 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... - Distribution and significance of occult intraepidermal tumor cells surrounding primary melanomaJeffrey 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... - Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathwayPierre 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... - Duplication of distal 20q: clinical, cytogenetic and array CGH. Characterization of a new caseAlejandro 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... - 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... - 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... - 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... - 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... - BAC microarray-based comparative genomic hybridizationAntoine M Snijders
Comprehensive Cancer Center, University of California, San Francisco, USA
Methods Mol Biol 256:39-56. 2004 - High-efficiency microarray printer using fused-silica capillary tube printing pinsSteve M Clark
University of California San Francisco, Box 0808, San Francisco, California 94143, USA
Anal Chem 80:7639-42. 2008.... - 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.... - 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...
Research Grants
- GENOME WIDE ANALYSIS OF DNA COPY NUMBER BY ARRAYDaniel 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. ..
- Prognostic Markers for Primary Cutaneous MelanomaDaniel Pinkel; Fiscal Year: 2006....