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Exome sequencing of paired tumor/normal DNA samples from the eight intrahepatic cholangiocarcinoma patients

Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver malignancy after hepatocellular carcinoma, with increasing incidence worldwide. To gain new insight into the genetic basis of ICC, we performed whole-exome sequencing of paired tumor/normal DNA samples from the 8 ICC patients. The patients underwent surgical resection at the Liver Cancer Institute, Zhongshan Hospital of Fudan University. The study was approved by the Zhongshan Hospital Ethics Committee, and informed consent was obtained from each patients under Institutional Review Board protocols. Tumor tissue was analyzed by frozen section to assess neoplastic cellularity (above 80%). Normal tissue was also analyzed by frozen section to confirm the presence of only non-neoplastic tissue. The clinical information associated with these ICC tumors included sex, age, tumor size, differentiation and TNM stage. DNA libraries were prepared according to the Illumina library generation protocol version 2.3. Each sample was tagged with a custom-designed unique 4-base-long index within the Illumina adaptor, pooled, captured by TruSeq Exome Enrichment Kit and sequenced using Illumina Hiseq2000 system.