title: Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancer.
abstract: Pancreatic cancer, the fourth leading cause of cancer death in the United States, is frequently associated with the amplification and deletion of specific oncogenes and tumor-suppressor genes (TSGs), respectively. To identify such novel alterations and to discover the underlying genes, we performed comparative genomic hybridization on a set of 22 human pancreatic cancer cell lines, using cDNA microarrays measuring approximately 26,000 human genes (thereby providing an average mapping resolution of <60 kb). To define the subset of amplified and deleted genes with correspondingly altered expression, we also profiled mRNA levels in parallel using the same cDNA microarray platform. In total, we identified 14 high-level amplifications (38-4934 kb in size) and 15 homozygous deletions (46-725 kb). We discovered novel localized amplicons, suggesting previously unrecognized candidate oncogenes at 6p21, 7q21 (SMURF1, TRRAP), 11q22 (BIRC2, BIRC3), 12p12, 14q24 (TGFB3), 17q12, and 19q13. Likewise, we identified novel polymerase chain reaction-validated homozygous deletions indicating new candidate TSGs at 6q25, 8p23, 8p22 (TUSC3), 9q33 (TNC, TNFSF15), 10q22, 10q24 (CHUK), 11p15 (DKK3), 16q23, 18q23, 21q22 (PRDM15, ANKRD3), and Xp11. Our findings suggest candidate genes and pathways, which may contribute to the development or progression of pancreatic cancer.
authors.affiliation: Department of Pathology, Stanford University, Stanford, CA, USA.
authors.forename: Murali D
authors.initials: MD
authors.lastname: Bashyam
authors.forename: Ryan
authors.initials: R
authors.lastname: Bair
authors.forename: Young H
authors.initials: YH
authors.lastname: Kim
authors.forename: Pei
authors.initials: P
authors.lastname: Wang
authors.forename: Tina
authors.initials: T
authors.lastname: Hernandez-Boussard
authors.forename: Collins A
authors.initials: CA
authors.lastname: Karikari
authors.forename: Robert
authors.initials: R
authors.lastname: Tibshirani
authors.forename: Anirban
authors.initials: A
authors.lastname: Maitra
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Pollack
mesh_terms: D045744:Cell Line, Tumor; D004247:DNA / Q000235:genetics* / Q000378:metabolism; D018076:DNA, Complementary / Q000378:metabolism; D018450:Disease Progression; D017353:Gene Deletion; D015972:Gene Expression Regulation, Neoplastic; D005821:Genetic Techniques; D006720:Homozygote; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010190:Pancreatic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology*; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger; D004247:DNA