Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3.
Marcel Martin,Marcel Martin,Lars Maßhöfer,Petra Temming,Sven Rahmann,Claudia H D Metz,Norbert Bornfeld,Johannes van de Nes,Ludger Klein-Hitpass,Alan G. Hinnebusch,Bernhard Horsthemke,Dietmar R. Lohmann,Michael Zeschnigk +12 more
TLDR
Using exome sequencing, recurrent somatic mutations in EIF1AX and SF3B1 are identified occurring in uveal melanomas with disomy 3, which rarely metastasize and are associated with poor prognosis.Abstract:
Michael Zeschnigk and colleagues identify recurrent somatic mutations of EIF1AX and SF3B1 in uveal melanomas with disomy 3. The EIF1AX mutations specifically alter the N-terminal tail of the protein and were found exclusively in tumors lacking SF3B1 mutations.read more
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Integrated Genomic Analysis of Hürthle Cell Cancer Reveals Oncogenic Drivers, Recurrent Mitochondrial Mutations, and Unique Chromosomal Landscapes.
Ian Ganly,Vladimir Makarov,Shyamprasad Vasudeva Deraje,Yiyu Dong,Ed Reznik,Venkatraman E. Seshan,Gouri Nanjangud,Stephanie Eng,Promita Bose,Fengshen Kuo,Luc G. T. Morris,Iñigo Landa,Pedro Blecua Carrillo Albornoz,Nadeem Riaz,Yuri E. Nikiforov,Kepal N. Patel,Christopher B. Umbricht,Martha A. Zeiger,Electron Kebebew,Eric J. Sherman,Ronald Ghossein,James A. Fagin,Timothy A. Chan +22 more
TL;DR: A comprehensive genomic characterization of 56 primary HCC tumors that span the spectrum of tumor behavior is described and reveals unique chromosomal landscapes that involve whole-chromosomal duplications of chromosomes 5 and 7 and widespread loss of heterozygosity arising from haploidization and copy-number-neutral uniparental disomy.
Journal ArticleDOI
Alternative mRNA splicing in cancer immunotherapy
TL;DR: The promise of analysing mRNA processing events in cancer cells, with an emphasis on mRNA splicing, for the identification of potential new targets for cancer immunotherapy is discussed.
Journal ArticleDOI
Synthetic Lethal and Convergent Biological Effects of Cancer-Associated Spliceosomal Gene Mutations.
Stanley Chun-Wei Lee,Khrystyna North,Eunhee Kim,Eun Jung Jang,Esther A. Obeng,Sydney X. Lu,Bo Liu,Daichi Inoue,Akihide Yoshimi,Michelle Ki,Mirae Yeo,Xiao Jing Zhang,Min Kyung Kim,Hana Cho,Young Rock Chung,Justin Taylor,Benjamin H. Durham,Young Joon Kim,Alessandro Pastore,Sebastien Monette,James Palacino,Michael Seiler,Silvia Buonamici,Pete Smith,Benjamin L. Ebert,Benjamin L. Ebert,Robert K. Bradley,Robert K. Bradley,Omar Abdel-Wahab +28 more
TL;DR: It is reported that although different spliceosome gene mutations impart distinct effects on splicing, they are negatively selected for when co-expressed due to aberrant splicing and downregulation of regulators of hematopoietic stem cell survival and quiescence.
Journal ArticleDOI
Lack of BAP1 protein expression in uveal melanoma is associated with increased metastatic risk and has utility in routine prognostic testing
TL;DR: Absent nBAP1 protein expression is an independent survival predictor for UM patients, easily examined using immunohistochemistry.
Journal ArticleDOI
Meta-analysis in metastatic uveal melanoma to determine progression free and overall survival benchmarks: an international rare cancers initiative (IRCI) ocular melanoma study.
Leila Khoja,Leila Khoja,Eshetu G. Atenafu,Stefan Suciu,Serge Leyvraz,Takami Sato,Ernie Marshall,Ulrich Keilholz,Lisa Zimmer,Sandip Pravin Patel,Sophie Piperno-Neumann,Josep M. Piulats,Tero Kivelä,Claudia Pfoehler,Shailender Bhatia,P. Huppert,L. B. J. Van Iersel,L. de Vries,Nicolas Penel,T. Vogl,Tina Cheng,G. Fiorentini,Frédéric Mouriaux,Ahmad A. Tarhini,Poulam M. Patel,Richard D. Carvajal,Anthony M. Joshua,Anthony M. Joshua +27 more
TL;DR: In this paper, a meta-analysis using individual patient level trial data was performed to determine benchmarks of progression free survival (PFS) and overall survival (OS) for metastatic uveal melanoma (mUM).
References
More filters
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
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.
Journal ArticleDOI
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo,Eric Banks,Ryan Poplin,Kiran V. Garimella,Jared Maguire,Christopher Hartl,Anthony A. Philippakis,Anthony A. Philippakis,Anthony A. Philippakis,Guillermo del Angel,Manuel A. Rivas,Manuel A. Rivas,Matt Hanna,Aaron McKenna,Timothy Fennell,Andrew Kernytsky,Andrey Sivachenko,Kristian Cibulskis,Stacey Gabriel,David Altshuler,David Altshuler,Mark J. Daly,Mark J. Daly +22 more
TL;DR: A unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs is presented.
Journal ArticleDOI
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
TL;DR: The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution.
Journal ArticleDOI
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
TL;DR: A suite of techniques, based on ribosome profiling, are presented to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation, revealing an unanticipated complexity to mammalian proteomes.
Journal ArticleDOI
Frequent pathway mutations of splicing machinery in myelodysplasia
Kenichi Yoshida,Masashi Sanada,Yuichi Shiraishi,Daniel Nowak,Yasunobu Nagata,Ryo Yamamoto,Yusuke Sato,Aiko Sato-Otsubo,Ayana Kon,Masao Nagasaki,George Chalkidis,Yutaka Suzuki,Masashi Shiosaka,Ryoichiro Kawahata,Tomoyuki Yamaguchi,Makoto Otsu,Naoshi Obara,Mamiko Sakata-Yanagimoto,Ken Ishiyama,Hiraku Mori,Florian Nolte,Wolf-Karsten Hofmann,Shuichi Miyawaki,Sumio Sugano,Claudia Haferlach,H. Phillip Koeffler,H. Phillip Koeffler,Lee Yung Shih,Torsten Haferlach,Shigeru Chiba,Hiromitsu Nakauchi,Satoru Miyano,Seishi Ogawa +32 more
TL;DR: The results provide the first evidence indicating that genetic alterations of the major splicing components could be involved in human pathogenesis, also implicating a novel therapeutic possibility for myelodysplasia.
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