Study Of Somatic Mutation In Duodenal Adenocarcinoma And Extrahepatic Cholangiocarcinoma

The advent and development of the second generation sequencing(also referred to as “the next-generation sequencing(NGS)” or “massive parallel sequencing”)is one of the most distinguished achievements in 21 st century life technology.By its enormous advance in cost,throughput and speed,NGS has redefined sequencing technology and genomics,endowing researchers with much more comprehensive resolution of human genomes.Recently,whole-genome sequencing,whole-exome sequencing and targeted sequencing have been made routines for cancer research.However,a boost of sequencing data have raised new challenges for data storage,transmission and following analysis.This dissertation starts from mutation calling,the core process of sequencing data analysis,and benchmarked multiple state-of-the-arts somatic mutation callers on whole-exome sequencing and targeted sequencing data.We also revealed the effect of different sequencing depths in mutation calling of tumor genomes.In our benchmark,MuTect outperformed other algorithms in almost every part of our evaluation,and exhibited a low rate of false-positives yet with excellent sensitivity.Mutation detection in data which have low sequencing depths lead to inferior sensitivity,but it also avoided over-representation of false candidates.We applied our pipeline to two rare yet important tumors: duodenal adenocarcinoma and extrahepatic cholangiocarcinoma.Neoplasm of small intestine is relatively rare considering its length and surface,and in duodenal adenocarcinoma the Wnt/?-catenin signalling pathway was the most affected pathways,with recurrent and mutually exclusive mutations in its core members CTNNB1 and APC.This indicate that the Wnt/?-catenin pathway is playing a vital role in the tumorigenesis of duodenal adenocarcinoma.Other recurrently mutated genes included KRAS,TP53 and BOK.Previously there have been much fewer studies in extrahepatic cholangiocarcinoma than in intrahepatic cholangiocarcinoma.We conducted whole-exome sequencing on samples from 42 extrahepatic cholangiocarcinoma patients and identified ORM1,a gene that had never been reported in cancers of digestive system,was mutated significantly in our cohort.This was confirmed by Sanger sequencing,and deserve further investigation in future research.In extrahepatic cholangiocarcinoma we revealed a mutational landscape similar to intrahepatic cholangiocarcinoma,but distinct from those in hepatocellular carcinoma or gallbladder carcinoma.In summary,this dissertation optimized current pipelines of sequencing data analysis,applied them in high-quality cancer studies and made significantly discoveries.These efforts will contribute to early diagnosis and personal therapy of these diseases in the future.