Literature DB >> 19181860

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line.

Qi Zhao1, Otavia L Caballero, Samuel Levy, Brian J Stevenson, Christian Iseli, Sandro J de Souza, Pedro A Galante, Dana Busam, Margaret A Leversha, Kalyani Chadalavada, Yu-Hui Rogers, J Craig Venter, Andrew J G Simpson, Robert L Strausberg.   

Abstract

We have identified new genomic alterations in the breast cancer cell line HCC1954, using high-throughput transcriptome sequencing. With 120 Mb of cDNA sequences, we were able to identify genomic rearrangement events leading to fusions or truncations of genes including MRE11 and NSD1, genes already implicated in oncogenesis, and 7 rearrangements involving other additional genes. This approach demonstrates that high-throughput transcriptome sequencing is an effective strategy for the characterization of genomic rearrangements in cancers.

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Year:  2009        PMID： 19181860      PMCID： PMC2633215          DOI： 10.1073/pnas.0812945106

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  37 in total

1.  Chromatid cohesion defects may underlie chromosome instability in human colorectal cancers.

Authors:  Thomas D Barber; Kirk McManus; Karen W Y Yuen; Marcelo Reis; Giovanni Parmigiani; Dong Shen; Irene Barrett; Yasaman Nouhi; Forrest Spencer; Sanford Markowitz; Victor E Velculescu; Kenneth W Kinzler; Bert Vogelstein; Christoph Lengauer; Philip Hieter
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-25       Impact factor: 11.205

2.  Paired-end diTagging for transcriptome and genome analysis.

Authors:  Patrick Ng; Chia-Lin Wei; Yijun Ruan
Journal:  Curr Protoc Mol Biol       Date:  2007-07

Review 3.  Recurrent gene fusions in prostate cancer.

Authors:  Chandan Kumar-Sinha; Scott A Tomlins; Arul M Chinnaiyan
Journal:  Nat Rev Cancer       Date:  2008-06-19       Impact factor: 60.716

Review 4.  Mammalian meiotic recombination hot spots.

Authors:  Norman Arnheim; Peter Calabrese; Irene Tiemann-Boege
Journal:  Annu Rev Genet       Date:  2007       Impact factor: 16.830

5.  Multiple loci with different cancer specificities within the 8q24 gene desert.

Authors:  Maya Ghoussaini; Honglin Song; Thibaud Koessler; Ali Amin Al Olama; Zsofia Kote-Jarai; Kristy E Driver; Karen A Pooley; Susan J Ramus; Susanne Krüger Kjaer; Estrid Hogdall; Richard A DiCioccio; Alice S Whittemore; Simon A Gayther; Graham G Giles; Michelle Guy; Stephen M Edwards; Jonathan Morrison; Jenny L Donovan; Freddie C Hamdy; David P Dearnaley; Audrey T Ardern-Jones; Amanda L Hall; Lynne T O'Brien; Beatrice N Gehr-Swain; Rosemary A Wilkinson; Paul M Brown; John L Hopper; David E Neal; Paul D P Pharoah; Bruce A J Ponder; Rosalind A Eeles; Douglas F Easton; Alison M Dunning
Journal:  J Natl Cancer Inst       Date:  2008-06-24       Impact factor: 13.506

Review 6.  Tumor stroma and regulation of cancer development.

Authors:  Thea D Tlsty; Lisa M Coussens
Journal:  Annu Rev Pathol       Date:  2006       Impact factor: 23.472

7.  Transcriptome sequencing of malignant pleural mesothelioma tumors.

Authors:  David J Sugarbaker; William G Richards; Gavin J Gordon; Lingsheng Dong; Assunta De Rienzo; Gautam Maulik; Jonathan N Glickman; Lucian R Chirieac; Mor-Li Hartman; Bruce E Taillon; Lei Du; Pascal Bouffard; Stephen F Kingsmore; Neil A Miller; Andrew D Farmer; Roderick V Jensen; Steven R Gullans; Raphael Bueno
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-26       Impact factor: 11.205

8.  A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells.

Authors:  Hui Li; Jinglan Wang; Gil Mor; Jeffrey Sklar
Journal:  Science       Date:  2008-09-05       Impact factor: 47.728

9.  A common sequence motif associated with recombination hot spots and genome instability in humans.

Authors:  Simon Myers; Colin Freeman; Adam Auton; Peter Donnelly; Gil McVean
Journal:  Nat Genet       Date:  2008-09       Impact factor: 38.330

10.  The genomic landscapes of human breast and colorectal cancers.

Authors:  Laura D Wood; D Williams Parsons; Siân Jones; Jimmy Lin; Tobias Sjöblom; Rebecca J Leary; Dong Shen; Simina M Boca; Thomas Barber; Janine Ptak; Natalie Silliman; Steve Szabo; Zoltan Dezso; Vadim Ustyanksky; Tatiana Nikolskaya; Yuri Nikolsky; Rachel Karchin; Paul A Wilson; Joshua S Kaminker; Zemin Zhang; Randal Croshaw; Joseph Willis; Dawn Dawson; Michail Shipitsin; James K V Willson; Saraswati Sukumar; Kornelia Polyak; Ben Ho Park; Charit L Pethiyagoda; P V Krishna Pant; Dennis G Ballinger; Andrew B Sparks; James Hartigan; Douglas R Smith; Erick Suh; Nickolas Papadopoulos; Phillip Buckhaults; Sanford D Markowitz; Giovanni Parmigiani; Kenneth W Kinzler; Victor E Velculescu; Bert Vogelstein
Journal:  Science       Date:  2007-10-11       Impact factor: 47.728
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  63 in total

Review 1.  Understanding the language of Lys36 methylation at histone H3.

Authors:  Eric J Wagner; Phillip B Carpenter
Journal:  Nat Rev Mol Cell Biol       Date:  2012-01-23       Impact factor: 94.444

Review 2.  RNA sequencing: advances, challenges and opportunities.

Authors:  Fatih Ozsolak; Patrice M Milos
Journal:  Nat Rev Genet       Date:  2010-12-30       Impact factor: 53.242

Review 3.  Histone methyltransferases: novel targets for tumor and developmental defects.

Authors:  Xin Yi; Xue-Jun Jiang; Xiao-Yan Li; Ding-Sheng Jiang
Journal:  Am J Transl Res       Date:  2015-11-15       Impact factor: 4.060

4.  Integrative analysis of the melanoma transcriptome.

Authors:  Michael F Berger; Joshua Z Levin; Krishna Vijayendran; Andrey Sivachenko; Xian Adiconis; Jared Maguire; Laura A Johnson; James Robinson; Roel G Verhaak; Carrie Sougnez; Robert C Onofrio; Liuda Ziaugra; Kristian Cibulskis; Elisabeth Laine; Jordi Barretina; Wendy Winckler; David E Fisher; Gad Getz; Matthew Meyerson; David B Jaffe; Stacey B Gabriel; Eric S Lander; Reinhard Dummer; Andreas Gnirke; Chad Nusbaum; Levi A Garraway
Journal:  Genome Res       Date:  2010-02-23       Impact factor: 9.043

5.  Chimeric transcript discovery by paired-end transcriptome sequencing.

Authors:  Christopher A Maher; Nallasivam Palanisamy; John C Brenner; Xuhong Cao; Shanker Kalyana-Sundaram; Shujun Luo; Irina Khrebtukova; Terrence R Barrette; Catherine Grasso; Jindan Yu; Robert J Lonigro; Gary Schroth; Chandan Kumar-Sinha; Arul M Chinnaiyan
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-10       Impact factor: 11.205

6.  Whole-genome cancer analysis as an approach to deeper understanding of tumour biology.

Authors:  R L Strausberg; A J G Simpson
Journal:  Br J Cancer       Date:  2009-12-22       Impact factor: 7.640

7.  Epigenetic inactivation of the Sotos overgrowth syndrome gene histone methyltransferase NSD1 in human neuroblastoma and glioma.

Authors:  María Berdasco; Santiago Ropero; Fernando Setien; Mario F Fraga; Pablo Lapunzina; Régine Losson; Miguel Alaminos; Nai-Kong Cheung; Nazneen Rahman; Manel Esteller
Journal:  Proc Natl Acad Sci U S A       Date:  2009-12-14       Impact factor: 11.205

Review 8.  The breast cancer somatic 'muta-ome': tackling the complexity.

Authors:  Andrew E Teschendorff; Carlos Caldas
Journal:  Breast Cancer Res       Date:  2009-03-30       Impact factor: 6.466

9.  Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

Authors:  Joshua Z Levin; Michael F Berger; Xian Adiconis; Peter Rogov; Alexandre Melnikov; Timothy Fennell; Chad Nusbaum; Levi A Garraway; Andreas Gnirke
Journal:  Genome Biol       Date:  2009-10-16       Impact factor: 13.583

10.  ChimerDB 2.0--a knowledgebase for fusion genes updated.

Authors:  Pora Kim; Suhyeon Yoon; Namshin Kim; Sanghyun Lee; Minjeong Ko; Haeseung Lee; Hyunjung Kang; Jaesang Kim; Sanghyuk Lee
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971
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