Journal ArticleDOI
Exome sequencing identifies distinct mutational patterns in liver fluke–related and non-infection-related bile duct cancers
Waraporn Chan-on,Waraporn Chan-on,Maarja-Liisa Nairismagi,Choon Kiat Ong,Weng Khong Lim,Simona Dima,Chawalit Pairojkul,Kiat Hon Lim,John R. McPherson,Ioana Cutcutache,Hong Lee Heng,London L.P.J. Ooi,Alexander Y. F. Chung,Pierce K. H. Chow,Peng Chung Cheow,Ser Yee Lee,Su Pin Choo,Iain Beehuat Tan,Dan G. Duda,Anca Nastase,Swe Swe Myint,Bernice Huimin Wong,Anna Gan,Vikneswari Rajasegaran,Cedric Chuan Young Ng,Sanjanaa Nagarajan,Apinya Jusakul,Shenli Zhang,Priya Vohra,Willie Yu,Dachuan Huang,Paiboon Sithithaworn,Puangrat Yongvanit,Sopit Wongkham,Narong Khuntikeo,Vajaraphongsa Bhudhisawasdi,Irinel Popescu,Steven G. Rozen,Patrick Tan,Patrick Tan,Bin Tean Teh +40 more
TLDR
Functional studies demonstrated tumor suppressive functions for BAP1 and ARID1A, establishing the role of chromatin modulators in CCA pathogenesis and indicating that different causative etiologies may induce distinct somatic alterations, even within the same tumor type.Abstract:
Bin Tean Teh, Patrick Tan, Steven Rozen, Irinel Popescu and colleagues report exome sequencing of cholangiocarcinomas, including cases caused by liver fluke (Opisthorchis viverrini) infection and cases caused by non–O. viverrini etiologies. They identify recurrent somatic mutations in BAP1 and ARID1A and demonstrate different mutation patterns in liver fluke infection–related and non-infection-related cancers.read more
Citations
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Patterns of Somatic Mutation in Human Cancer Genomes
TL;DR: In this paper, the coding exons of the family of 518 protein kinases were sequenced in 210 cancers of diverse histological types to explore the nature of the information that will be derived from cancer genome sequencing.
Journal ArticleDOI
Wnt signaling in cancer.
TL;DR: Current insights into novel components of Wnt pathways are reviewed and how Wnt signaling affects maintenance of cancer stem cells, metastasis and immune control are described.
Journal ArticleDOI
Guidelines for the diagnosis and management of intrahepatic cholangiocarcinoma
John Bridgewater,Peter R. Galle,Shahid A. Khan,Josep M. Llovet,Joong-Won Park,Tushar Patel,Timothy M. Pawlik,Gregory J. Gores +7 more
TL;DR: University College, London Cancer Institute, 72 Huntley St.
Journal ArticleDOI
Cholangiocarcinoma 2020: the next horizon in mechanisms and management
Jesus M. Banales,Jesus M. Banales,Jesus M. Banales,Jose J.G. Marin,Jose J.G. Marin,Angela Lamarca,Angela Lamarca,Pedro M. Rodrigues,Shahid A. Khan,Lewis R. Roberts,Vincenzo Cardinale,Guido Carpino,Jesper B. Andersen,Chiara Braconi,Diego F. Calvisi,Maria J. Perugorria,Maria J. Perugorria,Luca Fabris,Luca Fabris,Luke Boulter,Rocio I.R. Macias,Rocio I.R. Macias,Eugenio Gaudio,Domenico Alvaro,Sergio A. Gradilone,Mario Strazzabosco,Mario Strazzabosco,Marco Marzioni,Cédric Coulouarn,Laura Fouassier,Chiara Raggi,Pietro Invernizzi,Joachim C. Mertens,Anja Moncsek,Sumera Rizvi,Julie K. Heimbach,Bas Groot Koerkamp,Jordi Bruix,Jordi Bruix,Alejandro Forner,Alejandro Forner,John Bridgewater,Juan W. Valle,Juan W. Valle,Gregory J. Gores +44 more
TL;DR: This expert Consensus Statement, endorsed by the ENS-CCA, summarizes the latest advances in CCA, including classification, genetics and treatment, and provides recommendations for CCA management and priorities across basic, translational and clinical research.
Journal ArticleDOI
Cholangiocarcinoma — evolving concepts and therapeutic strategies
TL;DR: Advances in comprehensive whole-exome and transcriptome sequencing have defined the genetic landscape of each cholangiocarcinoma subtype, and promising molecular targets for precision medicine have been identified, and are being evaluated in clinical trials, including those exploring immunotherapy.
References
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The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
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Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
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TL;DR: It is found that pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations, which defined a core set of 12 cellular signaling pathways and processes that were each genetically altered in 67 to 100% of the tumors.
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Cancer-associated IDH1 mutations produce 2-hydroxyglutarate
Lenny Dang,David W. White,Stefan Gross,Bryson D. Bennett,Mark A. Bittinger,Edward M. Driggers,Valeria Fantin,Hyun Gyung Jang,Shengfang Jin,Marie C. Keenan,Kevin Marks,Robert M. Prins,Patrick S. Ward,Katharine E. Yen,Linda M. Liau,Joshua D. Rabinowitz,Lewis C. Cantley,Craig B. Thompson,Matthew G. Vander Heiden,Matthew G. Vander Heiden,Shinsan M. Su +20 more
TL;DR: It is shown that cancer-associated IDH1 mutations result in a new ability of the enzyme to catalyse the NADPH-dependent reduction of α-ketoglutarate to R(-)-2-hydroxyglutarate (2HG), and that the excess 2HG which accumulates in vivo contributes to the formation and malignant progression of gliomas.
Related Papers (5)
Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas
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Exome sequencing of liver fluke–associated cholangiocarcinoma
Choon Kiat Ong,Chutima Subimerb,Chutima Subimerb,Chawalit Pairojkul,Sopit Wongkham,Ioana Cutcutache,Willie Yu,John R. McPherson,George E. Allen,Cedric Chuan Young Ng,Bernice Huimin Wong,Swe Swe Myint,Vikneswari Rajasegaran,Hong Lee Heng,Anna Gan,Zhi Jiang Zang,Yingting Wu,Yingting Wu,Jeanie Wu,Ming Hui Lee,Dachuan Huang,Pauline Ong,Waraporn Chan-on,Waraporn Chan-on,Yun Cao,Chao Nan Qian,Kiat Hon Lim,Aikseng Ooi,Karl Dykema,Kyle A. Furge,Veerapol Kukongviriyapan,Banchob Sripa,Chaisiri Wongkham,Puangrat Yongvanit,P. Andrew Futreal,Vajarabhongsa Bhudhisawasdi,Steve Rozen,Patrick Tan,Patrick Tan,Bin Tean Teh +39 more
Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
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