Identification of driver genes in hepatocellular carcinoma by exome sequencing.
Sean P. Cleary,William R. Jeck,Xiaobei Zhao,Kui Chen,Sara R. Selitsky,Gleb L. Savich,Ting Xu Tan,Michael C. Wu,Gad Getz,Michael S. Lawrence,Joel S. Parker,Jinyu Li,Scott Powers,Hyeja Kim,Sandra Fischer,Maha Guindi,Maha Guindi,Anand Ghanekar,Derek Y. Chiang +18 more
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TLDR
The NFE2L2‐KEAP1 and MLL pathways are recurrently mutated in multiple cohorts of HCC, with significantly affected gene families include the nucleotide‐binding domain and leucine‐rich repeat‐containing family, calcium channel subunits, and histone methyltransferases.About:
This article is published in Hepatology.The article was published on 2013-11-01 and is currently open access. It has received 272 citations till now. The article focuses on the topics: Exome & Exome sequencing.read more
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Genetic Landscape and Biomarkers of Hepatocellular Carcinoma.
Jessica Zucman-Rossi,Augusto Villanueva,Jean-Charles Nault,Jean-Charles Nault,Josep M. Llovet,Josep M. Llovet,Josep M. Llovet +6 more
TL;DR: Data from genomic profiling enabled a proposal of HCC in 2 major molecular clusters (proliferation and non Proliferation), with differential enrichment in prognostic signatures, pathway activation and tumor phenotype, which helps define some of the core deregulated pathways in HCC.
Journal ArticleDOI
Mechanisms of HBV-induced hepatocellular carcinoma
TL;DR: HBV-related HCCs may arise on non-cirrhotic livers, further supporting the notion that HBV plays a direct role in liver transformation by triggering both common and etiology specific oncogenic pathways in addition to stimulating the host immune response and driving liver chronic necro-inflammation.
Journal ArticleDOI
The Dual Roles of NRF2 in Cancer
TL;DR: In a rapidly advancing field, this review summarizes some of the known mechanisms by which NRF2 can exert its oncogenic functions, and describes the current status ofNRF2 inhibitors, providing a clear rationale for the consideration of NRF 2 as a powerful putative therapeutic target in cancer treatment.
Journal ArticleDOI
p62 links autophagy and Nrf2 signaling
TL;DR: Progress has been made in dissecting the intersection of Nrf2-Keap1-ARE and autophagy and the potential tumor-promoting role of prolonged NRF2 activation is discussed.
Journal ArticleDOI
Functions of bromodomain-containing proteins and their roles in homeostasis and cancer
TL;DR: Bromodomains can be targeted by small-molecule inhibitors, which has stimulated many translational research projects that seek to attenuate the aberrant functions of BRD-containing proteins in disease.
References
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Analysis of relative gene expression data using real-time quantitative pcr and the 2(-delta delta c(t)) method
TL;DR: The 2-Delta Delta C(T) method as mentioned in this paper was proposed to analyze the relative changes in gene expression from real-time quantitative PCR experiments, and it has been shown to be useful in the analysis of realtime, quantitative PCR data.
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Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna,Matthew Hanna,Eric Banks,Andrey Sivachenko,Kristian Cibulskis,Andrew Kernytsky,Kiran V. Garimella,David Altshuler,Stacey Gabriel,Mark J. Daly,Mark A. DePristo +10 more
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Journal ArticleDOI
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
TL;DR: The ANNOVAR tool to annotate single nucleotide variants and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP is developed.
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.
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