Literature DB >> 19808792

Cancer genome sequencing: a review.

Elaine R Mardis1, Richard K Wilson.   

Abstract

A genomic era of cancer studies is developing rapidly, fueled by the emergence of next-generation sequencing technologies that provide exquisite sensitivity and resolution. This article discusses several areas within cancer genomics that are being transformed by the application of new technology, and in the process are dramatically expanding our understanding of this disease. Although, we anticipate that there will be many exciting discoveries in the near future, the ultimate success of these endeavors rests on our ability to translate what is learned into better diagnosis, treatment and prevention of cancer.

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Year:  2009        PMID: 19808792      PMCID: PMC2758710          DOI: 10.1093/hmg/ddp396

Source DB:  PubMed          Journal:  Hum Mol Genet        ISSN: 0964-6906            Impact factor:   6.150


  31 in total

Review 1.  microRNAs join the p53 network--another piece in the tumour-suppression puzzle.

Authors:  Lin He; Xingyue He; Scott W Lowe; Gregory J Hannon
Journal:  Nat Rev Cancer       Date:  2007-11       Impact factor: 60.716

2.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Authors:  Heng Li; Jue Ruan; Richard Durbin
Journal:  Genome Res       Date:  2008-08-19       Impact factor: 9.043

3.  A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.

Authors:  Marc Sultan; Marcel H Schulz; Hugues Richard; Alon Magen; Andreas Klingenhoff; Matthias Scherf; Martin Seifert; Tatjana Borodina; Aleksey Soldatov; Dmitri Parkhomchuk; Dominic Schmidt; Sean O'Keeffe; Stefan Haas; Martin Vingron; Hans Lehrach; Marie-Laure Yaspo
Journal:  Science       Date:  2008-07-03       Impact factor: 47.728

4.  RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.

Authors:  John C Marioni; Christopher E Mason; Shrikant M Mane; Matthew Stephens; Yoav Gilad
Journal:  Genome Res       Date:  2008-06-11       Impact factor: 9.043

5.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

6.  Genomic profiling of microRNAs in bladder cancer: miR-129 is associated with poor outcome and promotes cell death in vitro.

Authors:  Lars Dyrskjøt; Marie S Ostenfeld; Jesper B Bramsen; Asli N Silahtaroglu; Philippe Lamy; Ramshanker Ramanathan; Niels Fristrup; Jens L Jensen; Claus L Andersen; Karsten Zieger; Sakari Kauppinen; Benedicte P Ulhøi; Jørgen Kjems; Michael Borre; Torben F Orntoft
Journal:  Cancer Res       Date:  2009-06-01       Impact factor: 12.701

7.  An integrated genomic analysis of human glioblastoma multiforme.

Authors:  D Williams Parsons; Siân Jones; Xiaosong Zhang; Jimmy Cheng-Ho Lin; Rebecca J Leary; Philipp Angenendt; Parminder Mankoo; Hannah Carter; I-Mei Siu; Gary L Gallia; Alessandro Olivi; Roger McLendon; B Ahmed Rasheed; Stephen Keir; Tatiana Nikolskaya; Yuri Nikolsky; Dana A Busam; Hanna Tekleab; Luis A Diaz; James Hartigan; Doug R Smith; Robert L Strausberg; Suely Kazue Nagahashi Marie; Sueli Mieko Oba Shinjo; Hai Yan; Gregory J Riggins; Darell D Bigner; Rachel Karchin; Nick Papadopoulos; Giovanni Parmigiani; Bert Vogelstein; Victor E Velculescu; Kenneth W Kinzler
Journal:  Science       Date:  2008-09-04       Impact factor: 47.728

8.  Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries.

Authors:  Stacia K Wyman; Rachael K Parkin; Patrick S Mitchell; Brian R Fritz; Kathy O'Briant; Andrew K Godwin; Nicole Urban; Charles W Drescher; Beatrice S Knudsen; Muneesh Tewari
Journal:  PLoS One       Date:  2009-04-23       Impact factor: 3.240

9.  Transcriptome sequencing to detect gene fusions in cancer.

Authors:  Christopher A Maher; Chandan Kumar-Sinha; Xuhong Cao; Shanker Kalyana-Sundaram; Bo Han; Xiaojun Jing; Lee Sam; Terrence Barrette; Nallasivam Palanisamy; Arul M Chinnaiyan
Journal:  Nature       Date:  2009-01-11       Impact factor: 49.962

10.  TopHat: discovering splice junctions with RNA-Seq.

Authors:  Cole Trapnell; Lior Pachter; Steven L Salzberg
Journal:  Bioinformatics       Date:  2009-03-16       Impact factor: 6.937

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  83 in total

1.  Data-independent proteomic screen identifies novel tamoxifen agonist that mediates drug resistance.

Authors:  Shawna Mae Hengel; Euan Murray; Simon Langdon; Larry Hayward; Jean O'Donoghue; Alexandre Panchaud; Ted Hupp; David R Goodlett
Journal:  J Proteome Res       Date:  2011-09-21       Impact factor: 4.466

2.  VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer.

Authors:  Jamie K Teer; Eric D Green; James C Mullikin; Leslie G Biesecker
Journal:  Bioinformatics       Date:  2011-12-30       Impact factor: 6.937

Review 3.  RNA-Seq and human complex diseases: recent accomplishments and future perspectives.

Authors:  Valerio Costa; Marianna Aprile; Roberta Esposito; Alfredo Ciccodicola
Journal:  Eur J Hum Genet       Date:  2012-06-27       Impact factor: 4.246

4.  Going small is the new big.

Authors:  Kornelia Polyak
Journal:  Nat Methods       Date:  2010-08       Impact factor: 28.547

5.  Cancer: Genomics of metastasis.

Authors:  Joe Gray
Journal:  Nature       Date:  2010-04-15       Impact factor: 49.962

Review 6.  Pathogenesis of diffuse large B cell lymphoma.

Authors:  Wing John C Chan
Journal:  Int J Hematol       Date:  2010-06-29       Impact factor: 2.490

7.  JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.

Authors:  Andrew Roth; Jiarui Ding; Ryan Morin; Anamaria Crisan; Gavin Ha; Ryan Giuliany; Ali Bashashati; Martin Hirst; Gulisa Turashvili; Arusha Oloumi; Marco A Marra; Samuel Aparicio; Sohrab P Shah
Journal:  Bioinformatics       Date:  2012-01-27       Impact factor: 6.937

8.  Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies.

Authors:  Moara Machado; Wagner Cs Magalhães; Allan Sene; Bruno Araújo; Alessandra C Faria-Campos; Stephen J Chanock; Leandro Scott; Guilherme Oliveira; Eduardo Tarazona-Santos; Maira R Rodrigues
Journal:  Investig Genet       Date:  2011-02-01

9.  Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue.

Authors:  Eric J Duncavage; Vincent Magrini; Nils Becker; Jon R Armstrong; Ryan T Demeter; Todd Wylie; Haley J Abel; John D Pfeifer
Journal:  J Mol Diagn       Date:  2011-05       Impact factor: 5.568

10.  Automated analysis of immunohistochemistry images identifies candidate location biomarkers for cancers.

Authors:  Aparna Kumar; Arvind Rao; Santosh Bhavani; Justin Y Newberg; Robert F Murphy
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-08       Impact factor: 11.205

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