title: Cancer related gene alterations can be detected with next-generation sequencing analysis of bile in diffusely infiltrating type cholangiocarcinoma.
abstract: Genome-wide association study in diffusely infiltrating type cholangiocarcinoma (CC) can be limited due to the difficulty of obtaining tumor tissue. We aimed to evaluate the genomic alterations of diffusely infiltrating type CC using next-generation sequencing (NGS) of bile and to compare the variations with those of mass-forming type CC. A total of 24 bile samples obtained during endoscopic retrograde cholangiopancreatography (ERCP) and 17 surgically obtained tumor tissue samples were evaluated. Buffy coat and normal tissue samples were used as controls for a somatic mutation analysis. After extraction of genomic DNA, NGS analysis was performed for 48 cancer related genes. There were 27 men and 14 women with a mean age of 65.0±11.8years. The amount of extracted genomic DNA from 3cm(3) of bile was 66.0±84.7μg and revealed a high depth of sequencing coverage. All of the patients had genomic variations, with an average number of 19.4±2.8 and 22.3±3.3 alterations per patient from the bile and tumor tissue, respectively. After filtering process, damaging SNPs (8 sites for each type of CC) were predicted by analyzing tools, and their target genes showed relevant differences between the diffusely infiltrating and mass-forming type CC. Finally, in somatic mutation analysis, tumor-normal paired 14 tissue and 6 bile samples were analyzed, genomic alterations of EGFR, FGFR1, ABL1, PIK3CA, and CDKN2A gene were seen in the diffusely infiltrating type CC, and TP53, KRAS, APC, GNA11, ERBB4, ATM, SMAD4, BRAF, and IDH1 were altered in the mass-forming type CC group. STK11, GNAQ, RB1, KDR, and SMO genes were revealed in both groups. The NGS analysis was feasible with bile sample and diffusely infiltrating type CC revealed genetic differences compared with mass-forming type CC. Genome-wide association study could be performed using bile sample in the patients with CC undergoing ERCP and a different genetic approach for accurate diagnosis, pathogenesis study, and targeted therapy will be needed in diffusely infiltrating type CC.
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Chonbuk National University Medical School and Hospital, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea.
authors.forename: Chang Hun
authors.initials: CH
authors.lastname: Lee
authors.affiliation: Department of Medical Science, The Graduate School, Chonbuk National University, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea.
authors.forename: Hong En
authors.initials: HE
authors.lastname: Wang
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Chonbuk National University Medical School and Hospital, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea.
authors.forename: Seung Young
authors.initials: SY
authors.lastname: Seo
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Chonbuk National University Medical School and Hospital, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea.
authors.forename: Seong Hun
authors.initials: SH
authors.lastname: Kim
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Chonbuk National University Medical School and Hospital, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea.
authors.forename: In Hee
authors.initials: IH
authors.lastname: Kim
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Chonbuk National University Medical School and Hospital, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea.
authors.forename: Sang Wook
authors.initials: SW
authors.lastname: Kim
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Chonbuk National University Medical School and Hospital, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea.
authors.forename: Soo Teik
authors.initials: ST
authors.lastname: Lee
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Chonbuk National University Medical School and Hospital, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea.
authors.forename: Dae Ghon
authors.initials: DG
authors.lastname: Kim
authors.affiliation: Department of Microbiology, Chonbuk National University Medical School, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea. Electronic address: iamtom@chonbuk.ac.kr.
authors.forename: Myung Kwan
authors.initials: MK
authors.lastname: Han
authors.affiliation: Division of Gastroenterology, Department of Internal Medicine, Chonbuk National University Medical School and Hospital, Jeonju, Republic of Korea; Biomedical Research Institute, Chonbuk National University Hospital, Jeonju, Republic of Korea; Research Institute of Clinical Medicine, Chonbuk National University, Jeonju, Republic of Korea. Electronic address: solee@jbnu.ac.kr.
authors.forename: Seung Ok
authors.initials: SO
authors.lastname: Lee
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001646:Bile / Q000378:metabolism*; D018281:Cholangiocarcinoma / Q000235:genetics*; D004273:DNA, Neoplasm / Q000032:analysis; D005260:Female; D052138:Genes, Neoplasm; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012984:Software
chemical_list: D004273:DNA, Neoplasm
keywords: Bile; Cholangiocarcinoma; Next-generation sequence analysis