Y. Nakanuma, M. Curado, S. Franceschi, G. Gores, V. Paradis et al., Intrahepatic cholangiocarcinoma, WHO Classification of the Tumours of the Digestive System, pp.217-241, 2010.

Y. Shaib, J. Davila, K. Mcglynn, and H. El-serag, Rising incidence of intrahepatic cholangiocarcinoma in the United States: a true increase?, Journal of Hepatology, vol.40, issue.3, pp.472-479, 2004.
DOI : 10.1016/j.jhep.2003.11.030

K. Chang, J. Chang, and Y. Y. , Increasing incidence of intra-hepatic cholangiocarcinoma and its relationship to chronic viral hepatitis, J Natl Compr Canc Netw, vol.7, pp.423-430, 2009.

S. Rizvi and G. Gores, Pathogenesis, Diagnosis, and Management of Cholangiocarcinoma, Gastroenterology, vol.145, issue.6, pp.1215-1244, 2013.
DOI : 10.1053/j.gastro.2013.10.013

W. Palmer and T. Patel, Are common factors involved in the pathogenesis of primary liver cancers? A meta-analysis of risk factors for intrahepatic cholangiocarcinoma, Journal of Hepatology, vol.57, issue.1, pp.69-76, 2012.
DOI : 10.1016/j.jhep.2012.02.022

V. Cardinale, R. Semeraro, A. Torrice, M. Gatto, C. Napoli et al., Intra-hepatic and extra-hepatic cholangiocarcinoma: New insight into epidemiology and risk factors, World Journal of Gastrointestinal Oncology, vol.2, issue.11, pp.407-423, 2010.
DOI : 10.4251/wjgo.v2.i11.407

D. Sia, V. Tovar, A. Moeini, and J. Llovet, Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies, Oncogene, vol.23, issue.41, pp.4861-70, 2013.
DOI : 10.1038/onc.2012.617

J. Andersen and S. Thorgeirsson, Genetic profiling of intrahepatic cholangiocarcinoma, Current Opinion in Gastroenterology, vol.28, issue.3, pp.266-72, 2012.
DOI : 10.1097/MOG.0b013e3283523c7e

K. Ohashi, M. Tstsumi, Y. Nakajima, H. Nakano, and Y. Konishi, Ki-ras point mutations and proliferation activity in biliary tract carcinomas, British Journal of Cancer, vol.74, issue.6, pp.930-935, 1996.
DOI : 10.1038/bjc.1996.459

S. Hahn, D. Bartsch, A. Schroers, H. Galehdari, M. Becker et al., Mutations of the dpc4/smad4 gene in biliary tract carcinoma, Cancer Res, vol.58, pp.1124-1130, 1998.

A. Tannapfel, M. Benicke, A. Katalinic, D. Uhlmann, F. Köckerling et al., Frequency of p16INK4A alterations and k-ras mutations in intrahepatic cholangiocarcinoma of the liver, Gut, vol.47, issue.5, pp.721-728, 2000.
DOI : 10.1136/gut.47.5.721

K. Endo, K. Ashida, N. Miyake, and T. Terada, E-cadherin gene mutations in human intrahepatic cholangiocarcinoma, The Journal of Pathology, vol.53, issue.3, pp.310-317, 2001.
DOI : 10.1002/1096-9896(2000)9999:9999<::AID-PATH816>3.0.CO;2-K

M. Taniai, H. Higuchi, L. Burgart, and G. Gores, p16INK4a Promoter mutations are frequent in primary sclerosing cholangitis (PSC) and PSC-associated cholangiocarcinoma, Gastroenterology, vol.123, issue.4, pp.1090-1098, 2002.
DOI : 10.1053/gast.2002.36021

T. Terada, Y. Nakanuma, and A. Sirica, Immunohistochemical demonstration of MET overexpression in human intrahepatic cholangiocarcinoma and in hepatolithiasis, Human Pathology, vol.29, issue.2, pp.175-80, 1998.
DOI : 10.1016/S0046-8177(98)90229-5

K. Sugimachi, S. Aishima, K. Taguchi, S. Tanaka, M. Shimada et al., The role of overexpression and gene amplification of cyclin D1 in intrahepatic cholangiocarcinoma, Journal of Hepatology, vol.35, issue.1, pp.74-83, 2001.
DOI : 10.1016/S0168-8278(01)00079-4

Y. Ukita, M. Kato, and T. Terada, Gene amplification and mRNA and protein overexpression of c-erbB-2 (HER-2/neu) in human intrahepatic cholangiocarcinoma as detected by fluorescence in situ hybridization, in situ hybridization, and immunohistochemistry, Journal of Hepatology, vol.36, issue.6, pp.780-785, 2002.
DOI : 10.1016/S0168-8278(02)00057-0

J. Andersen, . Spe-eb, B. Blechacz, I. Avital, M. Komuta et al., Genomic and Genetic Characterization of Cholangiocarcinoma Identifies Therapeutic Targets for Tyrosine Kinase Inhibitors, Gastroenterology, vol.142, issue.4, pp.1021-1052, 2012.
DOI : 10.1053/j.gastro.2011.12.005

D. Sia, Y. Hoshida, A. Villanueva, S. Roayaie, J. Ferrer et al., Integrative Molecular Analysis of Intrahepatic Cholangiocarcinoma Reveals 2 Classes That Have Different Outcomes, Gastroenterology, vol.144, issue.4, pp.829-869, 2013.
DOI : 10.1053/j.gastro.2013.01.001

Y. Jiao, T. Pawlik, R. Anders, F. Selaru, M. Streppel et al., Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas, Nature Genetics, vol.95, issue.12, pp.1470-1473, 2013.
DOI : 10.1038/nature09208

M. Borad, M. Champion, J. Egan, W. Liang, R. Fonseca et al., Integrated Genomic Characterization Reveals Novel, Therapeutically Relevant Drug Targets in FGFR and EGFR Pathways in Sporadic Intrahepatic Cholangiocarcinoma, PLoS Genetics, vol.44, issue.9, p.1004135, 2014.
DOI : 10.1371/journal.pgen.1004135.s007

D. Borger, K. Tanabe, K. Fan, H. Lopez, V. Fantin et al., Frequent Mutation of Isocitrate Dehydrogenase (IDH)1 and IDH2 in Cholangiocarcinoma Identified Through Broad-Based Tumor Genotyping, The Oncologist, vol.17, issue.1, pp.72-81, 2012.
DOI : 10.1634/theoncologist.2011-0386

B. Kipp, J. Voss, S. Kerr, B. Fritcher, E. Graham et al., Isocitrate dehydrogenase 1 and 2 mutations in cholangiocarcinoma, Human Pathology, vol.43, issue.10, pp.1552-1560, 2012.
DOI : 10.1016/j.humpath.2011.12.007

A. Zhu, D. Borger, Y. Kim, D. Cosgrove, A. Ejaz et al., Genomic Profiling of Intrahepatic Cholangiocarcinoma: Refining Prognosis and Identifying Therapeutic Targets, Annals of Surgical Oncology, vol.19, issue.12, pp.3827-3861, 2014.
DOI : 10.1245/s10434-014-3828-x

J. Voss, L. Holtegaard, S. Kerr, E. Fritcher, L. Roberts et al., Molecular profiling of cholangiocarcinoma shows potential for targeted therapy treatment decisions, Human Pathology, vol.44, issue.7, pp.1216-1238, 2013.
DOI : 10.1016/j.humpath.2012.11.006

J. Ross, K. Wang, L. Gay, R. , R. J. Jones et al., New Routes to Targeted Therapy of Intrahepatic Cholangiocarcinomas Revealed by Next-Generation Sequencing, The Oncologist, vol.19, issue.3, pp.235-277, 2014.
DOI : 10.1634/theoncologist.2013-0352

C. Ong, C. Subimerb, C. Pairojkul, S. Wongkham, I. Cutcutache et al., Exome sequencing of liver fluke???associated cholangiocarcinoma, Nature Genetics, vol.115, issue.6, pp.690-693, 2012.
DOI : 10.1186/1471-2105-11-245

W. Chan-on, M. Nairismägi, C. Ong, W. Lim, S. Dima et al., Exome sequencing identifies distinct mutational patterns in liver fluke???related and non-infection-related bile duct cancers, Nature Genetics, vol.266, issue.12, pp.1474-1482, 2013.
DOI : 10.1074/jbc.M205961200

M. Simbolo, M. Fassan, A. Ruzzenente, A. Mafficini, L. W. Corbo et al., Multigene mutational profiling of cholangiocarcinomas identifies actionable molecular subgroups, Oncotarget, vol.5, issue.9, pp.2839-52, 2014.
DOI : 10.18632/oncotarget.1943

Y. Arai, Y. Totoki, F. Hosoda, T. Shirota, N. Hama et al., Fibroblast growth factor receptor 2 tyrosine kinase fusions define a unique molecular subtype of cholangiocarcinoma, Hepatology, vol.363, issue.4, pp.1427-1461, 2014.
DOI : 10.1002/hep.26890

S. Edge, D. Byrd, C. Compton, A. Fritz, F. Greene et al., Cancer staging manual In: AJCC Cancer Staging Manual, pp.1-649, 2009.

D. Peiffer, J. Le, F. Steemers, W. Chang, T. Jenniges et al., High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping, Genome Research, vol.16, issue.9, pp.1136-1184, 2006.
DOI : 10.1101/gr.5402306

M. Pierre-jean, G. Rigaill, and P. Neuvial, Performance evaluation of DNA copy number segmentation methods, Briefings in Bioinformatics, vol.16, issue.4
DOI : 10.1093/bib/bbu026
URL : https://hal.archives-ouvertes.fr/hal-00952896

S. Gey and E. Lebarbier, Using CART to Detect Multiple Change Points in the Mean for Large Sample
URL : https://hal.archives-ouvertes.fr/hal-00327146

G. Rigaill, Pruned Dynamic Programming for Optimal Multiple Change-point Detection

J. Hartigan and P. Hartigan, The Dip Test of Unimodality, The Annals of Statistics, vol.13, issue.1, pp.70-84, 1985.
DOI : 10.1214/aos/1176346577

P. Broet, P. Tan, M. Alifano, S. Camilleri-broet, and S. Richardson, Finding exclusively deleted or amplified genomic areas in lung adenocarcinomas using a novel chromosomal pattern analysis, BMC Medical Genomics, vol.3, issue.10, p.43, 2009.
DOI : 10.1002/(SICI)1098-2264(199907)25:3<195::AID-GCC1>3.0.CO;2-8

W. Toussile and E. Gassiat, Variable selection in model-based clustering using multilocus genotype data, Advances in Data Analysis and Classification, vol.77, issue.2, pp.109-143, 2009.
DOI : 10.1007/s11634-009-0043-x

R. Team, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing, 2012.

G. Tyson and H. El-serag, Risk factors for cholangiocarcinoma, Hepatology, vol.27, issue.Suppl 2, pp.173-84, 2011.
DOI : 10.1002/hep.24351

G. Miller, N. Socci, D. Dhall, D. 'angelica, M. Dematteo et al., Genome wide analysis and clinical correlation of chromosomal and transcriptional mutations in cancers of the biliary tract, J Exp Clin Cancer Res, vol.12, pp.28-62, 2009.

S. Dachrut, S. Banthaisong, M. Sripa, A. Paeyao, C. Ho et al., Dna copy-number loss on 1p36.1 harboring runx3 with promoter hypermethylation and associated loss of runx3 expression in liver fluke-associated intrahepatic cholangiocarcinoma, Asian Pac J Cancer Prev, vol.10, pp.575-82, 2009.

R. Wu, T. Wang, and I. Shih, The emerging roles of ARID1A in tumor suppression, Cancer Biology & Therapy, vol.63, issue.6, pp.655-64, 2014.
DOI : 10.1158/2159-8290.CD-12-0076

A. Chou, C. Toon, A. Clarkson, L. Sioson, M. Houang et al., Loss of ARID1A expression in colorectal carcinoma is strongly associated with mismatch repair deficiency, Human Pathology, vol.45, issue.8, pp.1697-703, 2014.
DOI : 10.1016/j.humpath.2014.04.009

E. Samartzis, K. Gutsche, K. Dedes, D. Fink, M. Stucki et al., Loss of ARID1A expression sensitizes cancer cells to PI3K- and AKT-inhibition, Oncotarget, vol.5, issue.14, pp.5295-5325, 2014.
DOI : 10.18632/oncotarget.2092

M. Hollander, C. Maier, E. Hobbs, A. Ashmore, R. Linnoila et al., Akt1 deletion prevents lung tumorigenesis by mutant K-ras, Oncogene, vol.16, issue.15, pp.1812-1833, 2011.
DOI : 10.1016/j.cancergencyto.2009.01.009

L. Chen, T. Chan, and X. Guan, Chromosome 1q21 amplification and oncogenes in hepatocellular carcinoma, Acta Pharmacologica Sinica, vol.120, issue.9, pp.1165-71, 2010.
DOI : 10.1016/j.molcel.2009.06.011

F. Leone, G. Cavalloni, Y. Pignochino, I. Sarotto, R. Ferraris et al., Somatic Mutations of Epidermal Growth Factor Receptor in Bile Duct and Gallbladder Carcinoma, Clinical Cancer Research, vol.12, issue.6, pp.1680-1685, 2006.
DOI : 10.1158/1078-0432.CCR-05-1692

M. Miyamoto, H. Ojima, M. Iwasaki, H. Shimizu, A. Kokubu et al., Prognostic significance of overexpression of c-Met oncoprotein in cholangiocarcinoma, British Journal of Cancer, vol.8, issue.1, pp.131-139, 2011.
DOI : 10.1073/pnas.2135113100