Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer
(A) Genomic profiles by CGH on cDNA microarrays of pancreatic (P) and bile duct (B) cancer xenografts across cytoband 18q11.2. Genes are ordered by genome position. Red indicates positive tumor/normal aCGH ratios (scale shown), and samples called gained at 18q11.2 are marked below by closed circle (gains highlighted in yellow). Genes and ESTs (IMAGE clone ID shown) on the microarray residing within the amplicon core are indicated. CTAGE1 (asterisked) was not present on the array but resides where shown. (B) Genomic profile of B291 by CGH on an Agilent ultra high-definition custom microarray tiling 18q11.2, mapped onto the UCSC genome browser (http://genome.ucsc.edu) . The amplicon peak spans two genes, GATA6 and CTAGE1. (C) Q-PCR validation of GATA6 amplification in B291. Note, hybridization measurements by CGH tend to underestimate true CNA ratios . (D) FISH validation of GATA6 amplification in the parent tumor (paraffin section) from which xenograft B291 was derived (left), and GATA6 gain in pancreatic cancer cell lines AsPC1 (center) and Panc3.27 (right). Gain is evident by the increased ratio of GATA6(red)/centromere-18(green) signals. DAPI (nuclear) counterstaining is shown in grayscale.