Genomic spectra of biliary tract cancer (original) (raw)

• Jemal, A. et al. Global cancer statistics. CA Cancer J. Clin. 61, 69–90 (2011).
  Article PubMed Google Scholar
• Patel, T. Worldwide trends in mortality from biliary tract malignancies. BMC Cancer 2, 10 (2002).
  Article PubMed PubMed Central Google Scholar
• Tyson, G.L. & El-Serag, H.B. Risk factors for cholangiocarcinoma. Hepatology 54, 173–184 (2011).
  Article CAS PubMed Google Scholar
• Rizvi, S. & Gores, G.J. Pathogenesis, diagnosis, and management of cholangiocarcinoma. Gastroenterology 145, 1215–1229 (2013).
  Article CAS PubMed Google Scholar
• Razumilava, N. & Gores, G.J. Cholangiocarcinoma. Lancet 383, 2168–2179 (2014).
  Article PubMed PubMed Central Google Scholar
• Misra, S., Chaturvedi, A., Misra, N.C. & Sharma, I.D. Carcinoma of the gallbladder. Lancet Oncol. 4, 167–176 (2003).
  Article PubMed Google Scholar
• Alexandrov, L.B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Chan-On, W. et al. Exome sequencing identifies distinct mutational patterns in liver fluke–related and non-infection-related bile duct cancers. Nat. Genet. 45, 1474–1478 (2013).
  Article CAS PubMed Google Scholar
• Li, M. et al. Whole-exome and targeted gene sequencing of gallbladder carcinoma identifies recurrent mutations in the ErbB pathway. Nat. Genet. 46, 872–876 (2014).
  Article CAS PubMed Google Scholar
• Wu, Y.M. et al. Identification of targetable FGFR gene fusions in diverse cancers. Cancer Discov. 3, 636–647 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Arai, Y. et al. Fibroblast growth factor receptor 2 tyrosine kinase fusions define a unique molecular subtype of cholangiocarcinoma. Hepatology 59, 1427–1434 (2014).
  Article CAS PubMed Google Scholar
• Honeyman, J.N. et al. Detection of a recurrent _DNAJB1_-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma. Science 343, 1010–1014 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Seshagiri, S. et al. Recurrent R-spondin fusions in colon cancer. Nature 488, 660–664 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Breast Cancer Linkage Consortium. Cancer risks in BRCA2 mutation carriers. J. Natl. Cancer Inst. 91, 1310–1316 (1999).
• Pilarski, R. et al. Expanding the clinical phenotype of hereditary BAP1 cancer predisposition syndrome, reporting three new cases. Genes Chromosom. Cancer 53, 177–182 (2014).
  Article CAS PubMed Google Scholar
• Saha, S.K. et al. Mutant IDH inhibits HNF-4α to block hepatocyte differentiation and promote biliary cancer. Nature 513, 110–114 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Totoki, Y. et al. Trans-ancestry mutational landscape of hepatocellular carcinoma genomes. Nat. Genet. 46, 1267–1273 (2014).
  Article CAS PubMed Google Scholar
• Ojesina, A.I. et al. Landscape of genomic alterations in cervical carcinomas. Nature 506, 371–375 (2014).
  Article CAS PubMed Google Scholar
• Chen, C.R., Kang, Y., Siegel, P.M. & Massagué, J. E2F4/5 and p107 as Smad cofactors linking the TGFβ receptor to c-myc repression. Cell 110, 19–32 (2002).
  Article CAS PubMed Google Scholar
• Shi, J. et al. Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation. Genes Dev. 27, 2648–2662 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Pardoll, D.M. The blockade of immune checkpoints in cancer immunotherapy. Nat. Rev. Cancer 12, 252–264 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Tumeh, P.C. et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature 515, 568–571 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Burns, M.B., Temiz, N.A. & Harris, R.S. Evidence for APOBEC3B mutagenesis in multiple human cancers. Nat. Genet. 45, 977–983 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Beuschlein, F. et al. Constitutive activation of PKA catalytic subunit in adrenal Cushing's syndrome. N. Engl. J. Med. 370, 1019–1028 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Kirschner, L.S. et al. Mutations of the gene encoding the protein kinase A type I-α regulatory subunit in patients with the Carney complex. Nat. Genet. 26, 89–92 (2000).
  Article CAS PubMed Google Scholar
• Huch, M. et al. Long-term culture of genome-stable bipotent stem cells from adult human liver. Cell 160, 299–312 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• de Visser, K.E., Eichten, A. & Coussens, L.M. Paradoxical roles of the immune system during cancer development. Nat. Rev. Cancer 6, 24–37 (2006).
  Article CAS PubMed Google Scholar
• Snyder, A. et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N. Engl. J. Med. 371, 2189–2199 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Rizvi, N.A. et al. Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer. Science 348, 124–128 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Vanneman, M. & Dranoff, G. Combining immunotherapy and targeted therapies in cancer treatment. Nat. Rev. Cancer 12, 237–251 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
  Article PubMed PubMed Central CAS Google Scholar
• Mermel, C.H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
  Article PubMed PubMed Central CAS Google Scholar
• Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557–572 (2004).
  Article PubMed Google Scholar
• Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
  Article PubMed PubMed Central CAS Google Scholar
• Lawrence, M.S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Alexandrov, L.B. et al. Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 3, 246–259 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Brunet, J.P. et al. Metagenes and molecular pattern discovery using matrix factorization. Proc. Natl. Acad. Sci. USA 101, 4164–4169 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Babur, Ö. et al. Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations. Genome Biol. 16, 45 (2015).
  Article PubMed PubMed Central CAS Google Scholar
• Leiserson, M.D., Blokh, D., Sharan, R. & Raphael, B.J. Simultaneous identification of multiple driver pathways in cancer. PLOS Comput. Biol. 9, e1003054 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Mo, Q. et al. Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc. Natl. Acad. Sci. USA 110, 4245–4250 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).
  Article CAS PubMed PubMed Central Google Scholar