Format

Send to

Choose Destination

See 1 citation found by title matching your search:

Exp Mol Pathol. 2015 Oct;99(2):344-53. doi: 10.1016/j.yexmp.2015.08.003. Epub 2015 Aug 8.

Genome wide DNA copy number analysis in cholangiocarcinoma using high resolution molecular inversion probe single nucleotide polymorphism assay.

Author information

1
Institute of Pathology, Charité, Universitätsmedizin Berlin, Germany; Department of Neuropathology, Charité, Universitätsmedizin Berlin, Germany.
2
Department of General, Visceral and Transplantation Surgery, Charité, Universitätsmedizin Berlin, Germany.
3
Institute of Pathology, Charité, Universitätsmedizin Berlin, Germany.
4
Department of Neuropathology, Charité, Universitätsmedizin Berlin, Germany.
5
Department of Neuropathology, Charité, Universitätsmedizin Berlin, Germany. Electronic address: arend.koch@charite.de.

Abstract

In order to study molecular similarities and differences of intrahepatic (IH-CCA) and extrahepatic (EH-CCA) cholangiocarcinoma, 24 FFPE tumor samples (13 IH-CCA, 11 EH-CCA) were analyzed for whole genome copy number variations (CNVs) using a new high-density Molecular Inversion Probe Single Nucleotide Polymorphism (MIP SNP) assay. Common in both tumor subtypes the most frequent losses were detected on chromosome 1p, 3p, 6q and 9 while gains were mostly seen in 1q, 8q as well as complete chromosome 17 and 20. Applying the statistical GISTIC (Genomic Identification of Significant Targets in Cancer) tool we identified potential novel candidate tumor suppressor- (DBC1, FHIT, PPP2R2A) and oncogenes (LYN, FGF19, GRB7, PTPN1) within these regions of chromosomal instability. Next to common aberrations in IH-CCA and EH-CCA, we additionally found significant differences in copy number variations on chromosome 3 and 14. Moreover, due to the fact that mutations in the Isocitrate dehydrogenase (IDH-1 and IDH-2) genes are more frequent in our IH-CCA than in our EH-CCA samples, we suggest that the tumor subtypes have a different molecular profile. In conclusion, new possible target genes within regions of high significant copy number aberrations were detected using a high-density Molecular Inversion Probe Single Nucleotide Polymorphism (MIP SNP) assay, which opens a future perspective of fast routine copy number and marker gene identification for gene targeted therapy.

KEYWORDS:

Cholangiocarcinoma; Copy number aberrations; ERBB2; IDH; Molecular inversion probe

PMID:
26260902
DOI:
10.1016/j.yexmp.2015.08.003
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Elsevier Science
Loading ...
Support Center