RT Journal Article
SR Electronic
T1 Whole-genome sequencing of an advanced case of small-cell gallbladder neuroendocrine carcinoma
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 052316
DO 10.1101/052316
A1 Maolan Li
A1 Fatao Liu
A1 Yijian Zhang
A1 Xiangsong Wu
A1 Wenguang Wu
A1 Xu-An Wang
A1 Shuai Zhao
A1 Shibo Liu
A1 Haibin Liang
A1 Fei Zhang
A1 Yuan Gao
A1 Shanshan Xiang
A1 Huaifeng Li
A1 Wei Lu
A1 Hao Weng
A1 Jiasheng Mu
A1 Yijun Shu
A1 Runfa Bao
A1 Lin Jiang
A1 Yunping Hu
A1 Wei Gong
A1 Yun Zhang
A1 Tieliang Ma
A1 Kai Zhang
A1 Yun Liu
A1 Yingbin Liu
YR 2016
UL http://biorxiv.org/content/early/2016/05/09/052316.abstract
AB The majority of gallbladder cancer cases are discovered at later stages, which frequently leads to poor prognoses. Small-cell gallbladder neuroendocrine carcinoma (GB-SCNEC) is a relatively rare histological type of gallbladder cancer, and its survival rate is exceptionally low because of its greater malignant potential. In addition, the genomic landscape of GB-SCNEC is rarely considered in treatment decisions. We performed whole-genome sequencing on an advanced case of GB-SCNEC. By analyzing the whole-genome sequencing data of the primary cancer tissue (76.29X coverage), lymphatic metastatic cancer tissue (73.92X coverage) and matched non-cancerous tissue (35.73X coverage), we identified approximately 900 high-quality somatic single nucleotide variants (SNVs), 109 of which were shared by both the primary and metastatic tumor tissues. Somatic non-synonymous coding variations with damaging impact in HMCN1 and CDH10 were observed in both the primary and metastatic tissue specimens. A pathway analysis of the genes mapped to the SNVs revealed gene enrichment associated with axon guidance, ERBB signaling, sulfur metabolism and calcium signaling. Furthermore, we identified 20 chromosomal rearrangements that included 11 deletions, 4 tandem duplications and 5 inversions that mapped to known genes. Two gene fusions, NCAM2-SGCZ and BTG3-CCDC40 were also discovered and validated by Sanger sequencing. Additionally, we identified genome-wide copy number variations and microsatellite instability. In this study, we identified novel biological markers of GB-SCNEC that may serve as valuable prognostic factors or indicators of treatment response in patients with GB-SCNEC with lymphatic metastasis.