Literature DB >> 21757246

Genome-wide approaches for cancer gene discovery.

Paul M Lizardi1, Matteo Forloni, Narendra Wajapeyee.   

Abstract

One of the central aims of cancer research is to identify and characterize cancer-causing alterations in cancer genomes. In recent years, unprecedented advances in genome-wide sequencing, functional genomics technologies for RNA interference screens and methods for evaluating three-dimensional chromatin organization in vivo have resulted in important discoveries regarding human cancer. The cancer-causing genes identified from these new genome-wide technologies have also provided opportunities for effective and personalized cancer therapy. In this review, we describe some of the most recent technologies for cancer gene discovery. We also provide specific examples in which these technologies have proven remarkably successful in uncovering important cancer-causing alterations.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID： 21757246      PMCID： PMC3195896          DOI： 10.1016/j.tibtech.2011.06.003

Source DB:  PubMed          Journal:  Trends Biotechnol        ISSN： 0167-7799            Impact factor:   19.536


  77 in total

1.  Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma.

Authors:  Björn Lamprecht; Korden Walter; Stephan Kreher; Raman Kumar; Michael Hummel; Dido Lenze; Karl Köchert; Mohamed Amine Bouhlel; Julia Richter; Eric Soler; Ralph Stadhouders; Korinna Jöhrens; Kathrin D Wurster; David F Callen; Michael F Harte; Maciej Giefing; Rachael Barlow; Harald Stein; Ioannis Anagnostopoulos; Martin Janz; Peter N Cockerill; Reiner Siebert; Bernd Dörken; Constanze Bonifer; Stephan Mathas
Journal:  Nat Med       Date:  2010-05-02       Impact factor: 53.440

2.  The mutation spectrum revealed by paired genome sequences from a lung cancer patient.

Authors:  William Lee; Zhaoshi Jiang; Jinfeng Liu; Peter M Haverty; Yinghui Guan; Jeremy Stinson; Peng Yue; Yan Zhang; Krishna P Pant; Deepali Bhatt; Connie Ha; Stephanie Johnson; Michael I Kennemer; Sankar Mohan; Igor Nazarenko; Colin Watanabe; Andrew B Sparks; David S Shames; Robert Gentleman; Frederic J de Sauvage; Howard Stern; Ajay Pandita; Dennis G Ballinger; Radoje Drmanac; Zora Modrusan; Somasekar Seshagiri; Zemin Zhang
Journal:  Nature       Date:  2010-05-27       Impact factor: 49.962

Review 3.  Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged.

Authors:  Charles J David; James L Manley
Journal:  Genes Dev       Date:  2010-11-01       Impact factor: 11.361

4.  Increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility.

Authors:  Song Liu
Journal:  PLoS One       Date:  2010-03-01       Impact factor: 3.240

5.  Integrative genomic profiling of human prostate cancer.

Authors:  Barry S Taylor; Nikolaus Schultz; Haley Hieronymus; Anuradha Gopalan; Yonghong Xiao; Brett S Carver; Vivek K Arora; Poorvi Kaushik; Ethan Cerami; Boris Reva; Yevgeniy Antipin; Nicholas Mitsiades; Thomas Landers; Igor Dolgalev; John E Major; Manda Wilson; Nicholas D Socci; Alex E Lash; Adriana Heguy; James A Eastham; Howard I Scher; Victor E Reuter; Peter T Scardino; Chris Sander; Charles L Sawyers; William L Gerald
Journal:  Cancer Cell       Date:  2010-06-24       Impact factor: 31.743

Review 6.  Advances in understanding cancer genomes through second-generation sequencing.

Authors:  Matthew Meyerson; Stacey Gabriel; Gad Getz
Journal:  Nat Rev Genet       Date:  2010-10       Impact factor: 53.242

7.  Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma.

Authors:  Siân Jones; Tian-Li Wang; Ie-Ming Shih; Tsui-Lien Mao; Kentaro Nakayama; Richard Roden; Ruth Glas; Dennis Slamon; Luis A Diaz; Bert Vogelstein; Kenneth W Kinzler; Victor E Velculescu; Nickolas Papadopoulos
Journal:  Science       Date:  2010-09-08       Impact factor: 47.728

8.  Loss of IGF2 imprinting is associated with abrogation of long-range intrachromosomal interactions in human cancer cells.

Authors:  Thanh H Vu; An H Nguyen; Andrew R Hoffman
Journal:  Hum Mol Genet       Date:  2009-12-16       Impact factor: 6.150

9.  A genome-wide RNA interference screen reveals an essential CREB3L2-ATF5-MCL1 survival pathway in malignant glioma with therapeutic implications.

Authors:  Zhi Sheng; Li Li; Lihua J Zhu; Thomas W Smith; Andrea Demers; Alonzo H Ross; Richard P Moser; Michael R Green
Journal:  Nat Med       Date:  2010-05-23       Impact factor: 53.440

10.  Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.

Authors:  Hugues Richard; Marcel H Schulz; Marc Sultan; Asja Nürnberger; Sabine Schrinner; Daniela Balzereit; Emilie Dagand; Axel Rasche; Hans Lehrach; Martin Vingron; Stefan A Haas; Marie-Laure Yaspo
Journal:  Nucleic Acids Res       Date:  2010-02-11       Impact factor: 16.971
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  8 in total

1.  Identification and characterization of human MIBP1 gene in glioma cell differentiation.

Authors:  Lijun Sun; Xiwen Chen; Xingnan Jin; Qiang Huang; Weilan Wang; Dashi Zhi; Defu Chen
Journal:  J Mol Neurosci       Date:  2013-10-26       Impact factor: 3.444

2.  Identification of novel direct targets of Drosophila Sine oculis and Eyes absent by integration of genome-wide data sets.

Authors:  Meng Jin; Sara Aibar; Zhongqi Ge; Rui Chen; Stein Aerts; Graeme Mardon
Journal:  Dev Biol       Date:  2016-05-10       Impact factor: 3.582

3.  Large-Scale RNA Interference Screening to Identify Transcriptional Regulators of a Tumor Suppressor Gene.

Authors:  Matteo Forloni; Thuy Ho; Lisha Sun; Narendra Wajapeyee
Journal:  Methods Mol Biol       Date:  2017

4.  Transcriptional Analysis-Based Integrative Genomics Approach to Identify Tumor-Promoting Metabolic Genes.

Authors:  Romi Gupta; Narendra Wajapeyee
Journal:  Methods Mol Biol       Date:  2017

Review 5.  Alternative splicing within the Wnt signaling pathway: role in cancer development.

Authors:  B Sumithra; Urmila Saxena; Asim Bikas Das
Journal:  Cell Oncol (Dordr)       Date:  2016-01-13       Impact factor: 6.730

6.  Multiple signatures of a disease in potential biomarker space: Getting the signatures consensus and identification of novel biomarkers.

Authors:  Ghim Siong Ow; Vladimir A Kuznetsov
Journal:  BMC Genomics       Date:  2015-06-11       Impact factor: 3.969

7.  The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells.

Authors:  Mireia Jordà; Anna Díez-Villanueva; Izaskun Mallona; Berta Martín; Sergi Lois; Víctor Barrera; Manel Esteller; Tanya Vavouri; Miguel A Peinado
Journal:  Genome Res       Date:  2016-12-20       Impact factor: 9.043

8.  Clinical, molecular- and cytogenetic analysis of a case of severe radio-sensitivity.

Authors:  K M Greulich-Bode; F Zimmermann; W-U Müller; B Pakisch; M Molls; F Würschmidt
Journal:  Curr Genomics       Date:  2012-09       Impact factor: 2.236
  8 in total

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