Daniel Pinkel, PhD

Daniel Pinkel, PhD

Professor Emeritus, Department of Laboratory Medicine, UCSF


Phone: (415) 476-3659 (voice)
Box 0808, UCSF
San Francisco, CA 94143-0808


University of Michigan, Ann Arbor, MI, B.A., 1966, Physics
University of California, San Diego, CA, Ph.D., 1974, Physics
University of California, Los Angeles, Postdoc, 1975, Medical Physics

Professional Experience

  • 1966-1974
    NSF Graduate Fellow and Research Assistant, University of California, San Diego, California. Assistant Research Physicist, University of California, San Diego, California.
  • 1975-1977
    NIH Postdoctoral Fellow, University of California, Los Angeles, California.
  • 1977-1991
    Biophysicist, Lawrence Livermore Laboratory, University of California, Livermore, California
  • 1991-1992
    Associate Professor, Laboratory Medicine, University of California - San Francisco, San Francisco, California.
  • 1992-present
    Scientist, Lawrence Berkeley National Laboratory (joint appointment)
  • 1993-2009
    Professor, Laboratory Medicine, University of California San Francisco, San Francisco, California
  • 2010-present
    Professor Emeritus, Laboratory Medicine, University of California San Francisco, San Francisco, California
  • 2006-present
    Associate Director Shared Resources, UCSF Helen Diller Family Comprehensive Cancer Center

Honors & Awards

  • Phi Beta Kappa, Sigma XI, Phi Kappa Phi
  • 2001
    Curt Stern Award, American Society of Human Genetics
  • 2008
    Team Science Award, American Association for Cancer Research

Selected Publications

  • Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D (1992). Comparative Genomic Hybridization: A powerful new method for cytogenetic anlaysis of solid tumors. Science 258:818-821.
  • Pinkel D, Segraves R, Sudar S, Clark S, Poole I, Kowbel D, Collins C, Kuo W-L, Chen C, Zhai Z, Dairkee S, Ljung B-M, Gray JW, Albertson DG. (1998). High resolution analysis of DNA copy number variation using comparative genomic hybridization to DNA microarrays. Nature Genetics 20:207-211.
  • Bastian BC, Kashani-Sabet M, Hamm H, Godfrey T, Moore DH, Brocker E-B, Leboit P, Pinkel D. (2000). Gene amplifications characterize acral melanoma and permit detection of occult tumor cells in the surrounding skin. Cancer Research 60: 1968-1973.
  • Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, Kowbel D, Kuo W-L, Gray JW, Pinkel D. (2000). Quantitative mapping of amplicon structure by array CGH identifies vitamin D-24 hydroxylase (CYP24) as a candidate oncogene. Nat. Genet. 25:144-146.
  • Bastian BC, LeBoit PE, Pinkel D. (2000). Mutations and copy number increase of HRASin Spitz Nevi with distinctive histopathological features. American Journal of Pathology 157:967-972.
  • Jain, AN, Tokuyasu TA, Snijders AM, Segraves R, Albertson DG, Pinkel D. (2002). Fully automatic quantification of microarray image data. Genome Research 12:325-332.
  • Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kimura K, Law S, Myambo K, Palmer J, Ylstra B, Yue JP, Gray JW, Jain AN, Pinkel D, Albertson DG. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet. 29(3):263-4.
  • Buckley PG, Pinkel D, Bastian BC, Dumanski JP (2002). A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. Hum Mol Genet 11:3221-3229.
  • Zardo G, Tiirikainen MI, Hong C, Misra A, Feuerstein BG, Volik S, Collins CC, Lamborn KR, Bollen A, Pinkel D, Albertson DG, Costello JF (2002). Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat Genet 32:453-458.
  • Locke D. P., Segraves R., Carbone L., Archidiacono N., Albertson D. G., Pinkel D., Eichler E. E. (2003). Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res. 13:347-57.
  • Snijders A., M., Fridlyand J., Mans D. A., Segraves R., Jain A. N. Pinkel D., Albertson D. G. Shaping of tumor and drug-resistant genomes by instability and selection. Oncogene 22:4370-4379.
  • Bastian BC, Olshen AB, LeBoit PE, Pinkel D (2003). Classifying melanocytic tumors based on DNA copy number changes. Am J Pathol 163 (5): 1765-1770.
  • Maldonado JL, Fridlyand J, Patel H, Jain AN, Busam K, Kagesita T, Ono T, Albertson DG, Pinkel D, Bastian BC (2003). Determinants of BRAF mutations in primary melanomas. J Natl Cancer Inst 95(24): 1878-1890.
  • Locke DP, Segraves R, Nicholls RD, Schwartz S, Pinkel D, Albertson DG, Eichler EE (2004). BAC microarray analysis of 15q11-q13 rearrangements and the impact of segmental duplications. J Med Genet 41(3):175-82.
  • Zhang X, Snijders A, Segraves R, Zhang X, Niebuhr A, Albertson D, Yang H, Gray J, Niebuhr E, Bolund L, Pinkel D. High-resolution mapping of genotype-phenotype relationships in cri du chat syndrome using array comparative genomic hybridization. Am J Hum Genet. 2005 Feb;76(2):312-26. Epub 2005 Jan 4.
  • Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao JH, Jain AN, Jones SJ, Balmain A, Pinkel D, Albertson DG. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res. 2005 Feb;15(2):302-11.
  • Snijders AM, Schmidt BL, Fridlyand J, Dekker N, Pinkel D, Jordan RC, Albertson DG. Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. Oncogene. 2005 Jun 16;24(26):4232-42.
  • Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE. Fine-scale structural variation of the human genome. Nat Genet. 2005 Jul;37(7):727-32. Epub 2005 May 15.
  • Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE. Segmental duplications and copy- number variation in the human genome. Am J Hum Genet. 2005 Jul;77(1):78-88. Epub 2005 May 25.
  • Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat Genet. 2005 Jun;37 Suppl:S11-7. Review.
  • Curtin JA, Fridlyand J, Kageshita T, Patel HN, Busam KJ, Kutzner H, Cho KH, Aiba S, Brocker EB, LeBoit PE, Pinkel D, Bastian BC. Distinct sets of genetic alterations in melanoma. N Engl J Med. 2005 Nov 17;353(20):2135-47.
  • Albertson, D.G., Snijders, A.M., Fridlyand, J., Jordan, R., Pinkel, D. and Schmidt, B.L. (2006) Genomic analysis of tumors by array comparative genomic hybridization: more is better. Cancer Res, 66, 3955-3956; author reply 3956.
  • Curtin, J.A., Busam, K., Pinkel, D. and Bastian, B.C. (2006) Somatic Activation of KIT in Distinct Subtypes of Melanomas. Journal of Clinical Oncology, 23:4340-4346
  • Fridlyand, J., Snijders, A.M., Ylstra, B., Li, H., Olshen, A., Segraves, R., Dairkee, S., Tokuyasu, T., Ljung, B.M., Jain, A.N. et al. (2006) Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer, 6, 96.
  • Hamilton, G., Brown, N., Oseroff, V., Huey, B., Segraves, R., Sudar, D., Kumler, J., Alberston, D.G. and Pinkel, D. (2006) A large field CCD system for quantitative imaging of microarrays. Nucleic Acids Res, 34, e58.
  • Landi MT, Bauer J, Pfeiffer RM, Elder DE, Hulley B, Minghetti P, Calista D, Kanetsky PA, Pinkel D, Bastian BC (2006) MC1R germline variants confer risk for BRAF-mutant melanoma. Science 313:521-522.
  • Bauer J, Curtin JA, Pinkel D, Bastian BC (2007) Congenital melanocytic nevi frequently harbor NRAS mutations but no BRAF mutations. J Invest Dermatol 127:179-182.
  • Curtin, J.A., Pinkel, D. and Bastian, B.C. (2008) Absence of PDGFRA mutations in primary melanoma. The Journal of investigative dermatology. 128:488-489.
  • Bastian, B.C. and Pinkel, D. (2008). Expanding the genetic spectrum of pigmentation. Pigment cell & melanoma research. 21:507-508.
  • North, J.P., Kageshita, T., Pinkel, D., LeBoit, P.E. and Bastian, B.C. (2008) Distribution and significance of occult intraepidermal tumor cells surrounding primary melanoma. The Journal of investigative dermatology. 128:2024-2030.
  • Viros, A., Fridlyand, J., Bauer, J., Lasithiotakis, K., Garbe, C., Pinkel, D. and Bastian, B.C. (2008) Improving melanoma classification by integrating genetic and morphologic features. PLoS medicine. 5, e120.