Genomics

Dataset Information

0

Pancreatic cancer_Affymetrix 100K SNP arrays


ABSTRACT: To identify genomic abnormalities characteristic of pancreatic ductal adenocarcinoma (PDAC) in vivo, a panel of 27 microdissected PDAC specimens were analyzed using high-density microarrays representing ~116 000 single nucleotide polymorphism (SNP) loci. We detected frequent gains of 1q, 2, 3, 5, 7p, 8q, 11, 14q and 17q (>78% of cases), and losses of 1p, 3p, 6, 9p, 13q, 14q, 17p and 18q (>44%). Although the results were comparable with those from array CGH, regions of those genetic changes were defined more accurately by SNP arrays. Integrating the Ensembl public data, we have generated "gene" copy number indices that facilitate the search for novel candidates involved in pancreatic carcinogenesis. Copy numbers in a subset of the genes were validated using quantitative real-time PCR. The SKAP2/SCAP2 gene (7p15.2), which belongs to the src family kinases, was most frequently (63%) amplified in our sample set and its recurrent over-expression (67%) was confirmed by reverse transcription-PCR. Furthermore, fluorescence in situ hybridization and in situ RNA hybridization analyses for this gene have demonstrated a significant correlation between DNA copy number and mRNA expression level in an independent sample set (p<0.001). These findings indicate that the dysregulation of SKAP2/SCAP2, which is mostly caused by its increased gene copy number, is likely to be associated with the development of PDAC. Keywords: pancreatic cancer; tissue microdissection; SNP array; DNA copy number; LOH

ORGANISM(S): Homo sapiens

PROVIDER: GSE7130 | GEO | 2007/10/22

SECONDARY ACCESSION(S): PRJNA98215

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
Other
Items per page:
1 - 1 of 1

Similar Datasets

2008-06-15 | E-GEOD-7130 | biostudies-arrayexpress
2010-12-16 | GSE26075 | GEO
2011-10-07 | E-GEOD-32682 | biostudies-arrayexpress
2007-07-31 | GSE8605 | GEO
2016-02-12 | GSE76456 | GEO
2008-06-15 | E-GEOD-7068 | biostudies-arrayexpress
2011-07-28 | E-TABM-1169 | biostudies-arrayexpress
2016-08-31 | GSE79187 | GEO
2015-02-27 | E-GEOD-61502 | biostudies-arrayexpress
2011-12-15 | GSE25273 | GEO