Genome-wide DNA copy number analysis in pancreatic cancer using high-density single nucleotide polymorphism arrays (original) (raw)

References

• Andersen CL, Wiuf C, Kruhoffer M, Korsgaard M, Laurberg S, Orntoft TF . (2007). Frequent occurrence of uniparental disomy in colorectal cancer. Carcinogenesis 28: 38–48.
  Article CAS PubMed Google Scholar
• Bardeesy N, DePinho RA . (2002). Pancreatic cancer biology and genetics. Nat Rev Cancer 2: 897–909.
  Article CAS PubMed Google Scholar
• Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S et al. (2004). High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 14: 287–295.
  Article CAS PubMed PubMed Central Google Scholar
• Buchholz M, Braun M, Heidenblut A, Kestler HA, Kloppel G, Schmiegel W et al. (2005). Transcriptome analysis of microdissected pancreatic intraepithelial neoplastic lesions. Oncogene 24: 6626–6636.
  Article CAS PubMed Google Scholar
• Calhoun ES, Hucl T, Gallmeier E, West KM, Arking DE, Maitra A et al. (2006). Identifying allelic loss and homozygous deletions in pancreatic cancer without matched normals using high-density single-nucleotide polymorphism arrays. Cancer Res 66: 7920–7928.
  Article CAS PubMed Google Scholar
• Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL et al. (2006). Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10: 529–541.
  Article CAS PubMed Google Scholar
• Fitzgibbon J, Smith LL, Raghavan M, Smith ML, Debernardi S, Skoulakis S et al. (2005). Association between acquired uniparental disomy and homozygous gene mutation in acute myeloid leukemias. Cancer Res 65: 9152–9154.
  Article CAS PubMed Google Scholar
• Fujita M, Sugama S, Nakai M, Takenouchi T, Wei J, Urano T et al. (2006). Alpha-synuclein stimulates differentiation of osteosarcoma cells: Relevance to downregulation of proteasome activity. J Biol Chem 282: 5736–5748.
  Article PubMed Google Scholar
• Griffin CA, Hruban RH, Morsberger LA, Ellingham T, Long PP, Jaffee EM et al. (1995). Consistent chromosome abnormalities in adenocarcinoma of the pancreas. Cancer Res 55: 2394–2399.
  CAS PubMed Google Scholar
• Harada T, Baril P, Gangeswaran R, Kelly G, Chelala C, Bhakta V et al. (2007). Identification of genetic alterations in pancreatic cancer by the combined use of tissue microdissection and array-based comparative genomic hybridisation. Br J Cancer 96: 373–382.
  Article CAS PubMed PubMed Central Google Scholar
• Harada T, Okita K, Shiraishi K, Kusano N, Furuya T, Oga A et al. (2002a). Detection of genetic alterations in pancreatic cancers by comparative genomic hybridization coupled with tissue microdissection and degenerate oligonucleotide primed polymerase chain reaction. Oncology 62: 251–258.
  Article CAS PubMed Google Scholar
• Harada T, Okita K, Shiraishi K, Kusano N, Kondoh S, Sasaki K . (2002b). Interglandular cytogenetic heterogeneity detected by comparative genomic hybridization in pancreatic cancer. Cancer Res 62: 835–839.
  CAS PubMed Google Scholar
• Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR et al. (2004). Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 1: 287–299.
  Article CAS PubMed PubMed Central Google Scholar
• Iacobuzio-Donahue CA, van der Heijden MS, Baumgartner MR, Troup WJ, Romm JM, Doheny K et al. (2004). Large-scale allelotype of pancreaticobiliary carcinoma provides quantitative estimates of genome-wide allelic loss. Cancer Res 64: 871–875.
  Article CAS PubMed Google Scholar
• Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y et al. (2004). Detection of large-scale variation in the human genome. Nat Genet 36: 949–951.
  Article CAS PubMed Google Scholar
• Janne PA, Li C, Zhao X, Girard L, Chen TH, Minna J et al. (2004). High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines. Oncogene 23: 2716–2726.
  Article PubMed Google Scholar
• Jemal A, Murray T, Ward E, Samuels A, Tiwari RC, Ghafoor A et al. (2005). Cancer statistics, 2005. CA Cancer J Clin 55: 10–30.
  Article PubMed Google Scholar
• Karhu R, Mahlamaki E, Kallioniemi A . (2006). Pancreatic adenocarcinoma—genetic portrait from chromosomes to microarrays. Genes Chromosomes Cancer 45: 721–730.
  Article CAS PubMed Google Scholar
• Li D, Xie K, Wolff R, Abbruzzese JL . (2004). Pancreatic cancer. Lancet 363: 1049–1057.
  Article CAS PubMed Google Scholar
• Lindblad-Toh K, Tanenbaum DM, Daly MJ, Winchester E, Lui WO, Villapakkam A et al. (2000). Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol 18: 1001–1005.
  Article CAS PubMed Google Scholar
• Lips EH, de Graaf EJ, Tollenaar RAEM, van Eijk R, Oosting J, Szuhai K et al. (2007). Single nucleotide polymorphism array analysis of chromosomal instability patterns discriminates rectal adenomas from carcinomas. J Pathol 212: 269–277.
  Article CAS PubMed Google Scholar
• McLean GW, Carragher NO, Avizienyte E, Evans J, Brunton VG, Frame MC . (2005). The role of focal-adhesion kinase in cancer—a new therapeutic opportunity. Nat Rev Cancer 5: 505–515.
  Article CAS PubMed Google Scholar
• Midorikawa Y, Yamamoto S, Ishikawa S, Kamimura N, Igarashi H, Sugimura H et al. (2006). Molecular karyotyping of human hepatocellular carcinoma using single-nucleotide polymorphism arrays. Oncogene 25: 5581–5590.
  Article CAS PubMed Google Scholar
• Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A et al. (2005). A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 65: 6071–6079.
  Article CAS PubMed Google Scholar
• Raghavan M, Lillington DM, Skoulakis S, Debernardi S, Chaplin T, Foot NJ et al. (2005). Genome-wide single nucleotide polymorphism analysis reveals frequent partial uniparental disomy due to somatic recombination in acute myeloid leukemias. Cancer Res 65: 375–378.
  CAS PubMed Google Scholar
• Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD et al. (2006). Global variation in copy number in the human genome. Nature 444: 444–454.
  Article CAS PubMed PubMed Central Google Scholar
• Ried T, Heselmeyer-Haddad K, Blegen H, Schrock E, Auer G . (1999). Genomic changes defining the genesis, progression, and malignancy potential in solid human tumors: a phenotype/genotype correlation. Genes Chromosomes Cancer 25: 195–204.
  Article CAS PubMed Google Scholar
• Saramaki OR, Porkka KP, Vessella RL, Visakorpi T . (2006). Genetic aberrations in prostate cancer by microarray analysis. Int J Cancer 119: 1322–1329.
  Article CAS PubMed Google Scholar
• Takahashi T, Yamashita H, Nagano Y, Nakamura T, Ohmori H, Avraham H et al. (2003). Identification and characterization of a novel Pyk2/related adhesion focal tyrosine kinase-associated protein that inhibits alpha-synuclein phosphorylation. J Biol Chem 278: 42225–42233.
  Article CAS PubMed Google Scholar
• Yamamoto G, Nannya Y, Kato M, Sanada M, Levine RL, Kawamata N et al. (2007). Highly sensitive method for genome-wide detection of allelic composition in nonpaired, primary tumor specimens by use of Affymetrix single-nucleotide–polymorphism genotyping microarrays. Am J Hum Genet 81: 114–126.
  Article CAS PubMed PubMed Central Google Scholar
• Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH et al. (2004). An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 64: 3060–3071.
  Article CAS PubMed Google Scholar
• Zhao X, Weir BA, LaFramboise T, Lin M, Beroukhim R, Garraway L et al. (2005). Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res 65: 5561–5570.
  Article CAS PubMed Google Scholar

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