CORES: Array Core

Publications

>Background Publications

Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F and Pinkel D (1992). Comparative genomic hybridization for molecular cytogenetic analysis 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 and Albertson DG (1998). High resolution analysis of DNA copy number variation in breast cancer using comparative genomic hybridization to DNA microarrays. Nature Genetics 20: 207-211.
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 and Albertson DG (2001). Assembly of microarrays for genome-wide measurement of DNA copy number by CGH. Nature Genetics 29(3): 263-264.
A. N. Jain, T. A. Tokuyasu, A. M. Snijders, R. Segraves, D. G. Albertson, and D. Pinkel (2002). Fully automatic quantification of microarray image data. Genome Research 12: 325-332.
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 (2005). Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Research 15: 302-311.
Hamilton G, Brown N, Oseroff V, Huey B, Segraves R, Sudar D, Kumler J, Albertson D, Pinkel D (2006). A large field CCD system for quantitative imaging of microarrays. Nucleic Acids Res 34(8):e58.

>Publications by Our Users

Slavotinek AM, Moshrefi A, Davis R, Leeth E, Schaeffer GB, Burchard GE, Shaw GM, James B, Ptacek L, Pennacchio LA (2006). Array comparative genomic hybridization in patients with congenital diaphragmatic hernia: mapping of four CDH-critical regions and sequencing of candidate genes at 15q26.1-15q26.2. Eur J Hum Genet.
Misra A, Pellarin M, Hu L, Kunwar S, Perhouse M, Lamborn KR, Deen DF, Feuerstein BG (2006). Chromosome transfer experiments link regions on chromosome 7 to radiation resistance in human glioblastoma multiforme. Genes Chromosomes Cancer 45:20-30.
Leung SY, Ho C, Tu IP, Li R, So S, Chu KM, Yuen ST, Chen X (2006). Comprehensive analysis of 19q12 amplicon in human gastric cancers. Mod Pathol 19:854-863.
Lee CI, Leong SH, Png AE, Choo KW, Syn C, Lim DT, Law HY, Kon OL (2006). An isothermal method for whole genome amplification of fresh and degraded DNA for comparative genomic hybridization, genotyping and mutation detection. DNA Res 13:77-88.
Lamba JK, Chen X, Lan LB, Kim JW, Wei Wang X, Relling MV, Kazuto Y, Watkins PB, Strom S, Sun D, Schuetz JD, Schuetz EG (2006). Increased CYP3A4 copy number in TONG/HCC cells but not in DNA from other humans. Pharmacogenet Genomics 16:415-427.
Hamilton G, Brown N, Oseroff V, Huey B, Segraves R, Sudar D, Kumler J, Albertson D, Pinkel D (2006). A large field CCD system for quantitative imaging of microarrays. Nucleic Acids Res 34:e58.
Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG (2006) Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 6:96.
Wa CV, DeVries S, Chen YY, Waldman FM, Hwang ES (2005). Clinical application of array-based comparative genomic hybridization to define the relationship between multiple synchronous tumors. Mod Pathol 18:591-597.
van Duin M, van Marion R, Watson JE, Paris PL, Lapuk A, Brown N, Oseroff VV, Albertson DG, Pinkel D, de Jong P, Nacheva EP, Dinjens W, van Dekken H, Collins C (2005). Construction and application of a full-coverage, high-resolution, human chromosome 8q genomic microarray for comparative genomic hybridization. Cytometry A 63:10-19.
Snijders AM, Schmidt BL, Fridlyand J, Dekker N, Pinkel D, Jordan RC, Albertson DG (2005). Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. Oncogene 24:4232-4242.
Slavotinek A, Lee SS, Davis R, Shrit A, Leppig KA, Rhim J, Jasnosz K, Albertson D, Pinkel D (2005). Fryns syndrome phenotype caused by chromosome microdeletions at 15q26.2 and 8p23.1. J Med Genet 42:730-736.
Sherr EH, Owen R, Albertson DG, Pinkel D, Cotter PD, Slavotinek AM, Hetts SW, Jeremy RJ, Schilmoeller G, Schilmoeller K, Wakahiro M, Barkovich AJ (2005). Genomic microarray analysis identifies candidate loci in patients with corpus callosum anomalies. Neurology 65:1496-1498.
Patil MA, Gutgemann I, Zhang J, Ho C, Cheung ST, Ginzinger D, Li R, Dykema KJ, So S, Fan ST, Kakar S, Furge KA, Buttner R, Chen X (2005). Array-based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for 8q gain in hepatocellular carcinoma. Carcinogenesis 26:2050-2057.
Oda K, Stokoe D, Taketani Y, McCormick F (2005). High frequency of coexistent mutations of PIK3CA and PTEN genes in endometrial carcinoma. Cancer Res 65:10669-10673.
Misra A, Pellarin M, Nigro J, Smirnov I, Moore D, Lamborn KR, Pinkel D, Albertson DG, Feuerstein BG (2005). Array comparative genomic hybridization identifies genetic subgroups in grade 4 human astrocytoma. Clin Cancer Res 11:2907-2918.
Mehta KR, Nakao K, Zuraek MB, Ruan DT, Bergsland EK, Venook AP, Moore DH, Tokuyasu TA, Jain AN, Warren RS, Terdiman JP, Waldman FM (2005). Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer. Clin Cancer Res 11:1791-1797.
Devries S, Nyante S, Korkola J, Segraves R, Nakao K, Moore D, Bae H, Wilhelm M, Hwang S, Waldman F (2005). Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. J Mol Diagn 7:65-71.
DeScipio C, Kaur M, Yaeger D, Innis JW, Spinner NB, Jackson LG, Krantz ID (2005). Chromosome rearrangements in cornelia de Lange syndrome (CdLS): report of a der(3)t(3;12)(p25.3;p13.3) in two half sibs with features of CdLS and review of reported CdLS cases with chromosome rearrangements. Am J Med Genet A 137:276-282.
Blaveri E, Brewer JL, Roydasgupta R, Fridlyand J, DeVries S, Koppie T, Pejavar S, Mehta K, Carroll P, Simko JP, Waldman FM (2005). Bladder cancer stage and outcome by array-based comparative genomic hybridization. Clin Cancer Res 11:7012-7022.
Watson JE, Doggett NA, Albertson DG, Andaya A, Chinnaiyan A, van Dekken H, Ginzinger D, Haqq C, James K, Kamkar S, Kowbel D, Pinkel D, Schmitt L, Simko JP, Volik S, Weinberg VK, Paris PL, Collins C (2004). 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. Oncogene 23:3487-3494.
Shelley Hwang E, Nyante SJ, Yi Chen Y, Moore D, DeVries S, Korkola JE, Esserman LJ, Waldman FM (2004). Clonality of lobular carcinoma in situ and synchronous invasive lobular carcinoma. Cancer 100:2562-2572.
Rubin MA, Varambally S, Beroukhim R, Tomlins SA, Rhodes DR, Paris PL, Hofer MD, Storz-Schweizer M, Kuefer R, Fletcher JA, Hsi BL, Byrne JA, Pienta KJ, Collins C, Sellers WR, Chinnaiyan AM (2004). Overexpression, amplification, and androgen regulation of TPD52 in prostate cancer. Cancer Res 64:3814-3822.
Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, Kowbel D, Brebner JH, Simko J, Watson JE, Volik S, Albertson DG, Pinkel D, Alers JC, van der Kwast TH, Vissers KJ, Schroder FH, Wildhagen MF, Febbo PG, Chinnaiyan AM, Pienta KJ, Carroll PR, Rubin MA, Collins C, van Dekken H (2004). Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet 13:1303-1313.
Nakao K, Mehta KR, Fridlyand J, Moore DH, Jain AN, Lafuente A, Wiencke JW, Terdiman JP, Waldman FM (2004). High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis 25:1345-1357.
Macoska JA, Paris P, Collins C, Andaya A, Beheshti B, Chaib H, Kant R, Begley L, MacDonald JW, Squire JA (2004). Evolution of 8p loss in transformed human prostate epithelial cells. Cancer Genet Cytogenet 154:36-43.
Kim S, Chin K, Gray JW, Bishop JM (2004). A screen for genes that suppress loss of contact inhibition: identification of ING4 as a candidate tumor suppressor gene in human cancer. Proc Natl Acad Sci U S A 101:16251-16256.

Additional Resources
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