Genome-wide copy number profiling in gallbladder carcinoma - A study from north India

Gallbladder cancer (GBC) is a malignancy with poor prognosis and needs early diagnostic tools and newer therapeutics. Molecular profiling data in GBC is limited due to lack of enough high-throughput screening regarding its genetic information. The present study is carried out to determine copy number variations (CNVs), in 890 major cancer related genes in GBC patients. Eighteen histopathologically confirmed GBC cases were recruited. Tumor area was micro-dissected off from formalin fixed paraffin embedded tissue blocks having > 80% of tumor cells. DNA extraction was done by standard protocols. Copy number profiling was done by “OncoScan™ FFPE Assay Kit” (Affymetrix, CA). Data analysis was done by SNPFASST2 algorithm using Nexus Express Oncoscan software 3.0 & 7.5 (Biodiscovery, Inc., CA USA). A substantial number of CNVs detected in GBC were recurrent. Recurrent gains were at chromosome 12q14.2, 12q14.3, 20p12.1 and recurrent losses were at 4q35.1. The common genes affected in CN loss were NPP6, IRF2, CASP3, PRIMPOL, MLF1IP, CENPU, ACSL1, SLED1 in chromosome 4q35.1, whereas genes involved in CN gain were HMGA2, RPSAP52 on 12q14.3, RASSF3 gene on 12q14.2 and MACROD2 on 20p12.1. In conclusion, significant CNVs were found in GBC patients. More studies with larger sample size are suggested to validate these findings.