Literature DB >> 22460448

Exploring the cancer genome in the era of next-generation sequencing.

Hui Dong1, Shengyue Wang.   

Abstract

The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.

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Year:  2012        PMID: 22460448     DOI: 10.1007/s11684-012-0182-x

Source DB:  PubMed          Journal:  Front Med        ISSN: 2095-0217            Impact factor:   4.592


  40 in total

1.  Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.

Authors:  Xose S Puente; Magda Pinyol; Víctor Quesada; Laura Conde; Gonzalo R Ordóñez; Neus Villamor; Georgia Escaramis; Pedro Jares; Sílvia Beà; Marcos González-Díaz; Laia Bassaganyas; Tycho Baumann; Manel Juan; Mónica López-Guerra; Dolors Colomer; José M C Tubío; Cristina López; Alba Navarro; Cristian Tornador; Marta Aymerich; María Rozman; Jesús M Hernández; Diana A Puente; José M P Freije; Gloria Velasco; Ana Gutiérrez-Fernández; Dolors Costa; Anna Carrió; Sara Guijarro; Anna Enjuanes; Lluís Hernández; Jordi Yagüe; Pilar Nicolás; Carlos M Romeo-Casabona; Heinz Himmelbauer; Ester Castillo; Juliane C Dohm; Silvia de Sanjosé; Miguel A Piris; Enrique de Alava; Jesús San Miguel; Romina Royo; Josep L Gelpí; David Torrents; Modesto Orozco; David G Pisano; Alfonso Valencia; Roderic Guigó; Mónica Bayés; Simon Heath; Marta Gut; Peter Klatt; John Marshall; Keiran Raine; Lucy A Stebbings; P Andrew Futreal; Michael R Stratton; Peter J Campbell; Ivo Gut; Armando López-Guillermo; Xavier Estivill; Emili Montserrat; Carlos López-Otín; Elías Campo
Journal:  Nature       Date:  2011-06-05       Impact factor: 49.962

Review 2.  The MLL partial tandem duplication in acute myeloid leukaemia.

Authors:  Jorg Basecke; Jarrett T Whelan; Frank Griesinger; Fred E Bertrand
Journal:  Br J Haematol       Date:  2006-09-11       Impact factor: 6.998

3.  Use of whole-genome sequencing to diagnose a cryptic fusion oncogene.

Authors:  John S Welch; Peter Westervelt; Li Ding; David E Larson; Jeffery M Klco; Shashikant Kulkarni; John Wallis; Ken Chen; Jacqueline E Payton; Robert S Fulton; Joelle Veizer; Heather Schmidt; Tammi L Vickery; Sharon Heath; Mark A Watson; Michael H Tomasson; Daniel C Link; Timothy A Graubert; John F DiPersio; Elaine R Mardis; Timothy J Ley; Richard K Wilson
Journal:  JAMA       Date:  2011-04-20       Impact factor: 56.272

4.  A comprehensive catalogue of somatic mutations from a human cancer genome.

Authors:  Erin D Pleasance; R Keira Cheetham; Philip J Stephens; David J McBride; Sean J Humphray; Chris D Greenman; Ignacio Varela; Meng-Lay Lin; Gonzalo R Ordóñez; Graham R Bignell; Kai Ye; Julie Alipaz; Markus J Bauer; David Beare; Adam Butler; Richard J Carter; Lina Chen; Anthony J Cox; Sarah Edkins; Paula I Kokko-Gonzales; Niall A Gormley; Russell J Grocock; Christian D Haudenschild; Matthew M Hims; Terena James; Mingming Jia; Zoya Kingsbury; Catherine Leroy; John Marshall; Andrew Menzies; Laura J Mudie; Zemin Ning; Tom Royce; Ole B Schulz-Trieglaff; Anastassia Spiridou; Lucy A Stebbings; Lukasz Szajkowski; Jon Teague; David Williamson; Lynda Chin; Mark T Ross; Peter J Campbell; David R Bentley; P Andrew Futreal; Michael R Stratton
Journal:  Nature       Date:  2009-12-16       Impact factor: 49.962

5.  Genome remodelling in a basal-like breast cancer metastasis and xenograft.

Authors:  Li Ding; Matthew J Ellis; Shunqiang Li; David E Larson; Ken Chen; John W Wallis; Christopher C Harris; Michael D McLellan; Robert S Fulton; Lucinda L Fulton; Rachel M Abbott; Jeremy Hoog; David J Dooling; Daniel C Koboldt; Heather Schmidt; Joelle Kalicki; Qunyuan Zhang; Lei Chen; Ling Lin; Michael C Wendl; Joshua F McMichael; Vincent J Magrini; Lisa Cook; Sean D McGrath; Tammi L Vickery; Elizabeth Appelbaum; Katherine Deschryver; Sherri Davies; Therese Guintoli; Li Lin; Robert Crowder; Yu Tao; Jacqueline E Snider; Scott M Smith; Adam F Dukes; Gabriel E Sanderson; Craig S Pohl; Kim D Delehaunty; Catrina C Fronick; Kimberley A Pape; Jerry S Reed; Jody S Robinson; Jennifer S Hodges; William Schierding; Nathan D Dees; Dong Shen; Devin P Locke; Madeline E Wiechert; James M Eldred; Josh B Peck; Benjamin J Oberkfell; Justin T Lolofie; Feiyu Du; Amy E Hawkins; Michelle D O'Laughlin; Kelly E Bernard; Mark Cunningham; Glendoria Elliott; Mark D Mason; Dominic M Thompson; Jennifer L Ivanovich; Paul J Goodfellow; Charles M Perou; George M Weinstock; Rebecca Aft; Mark Watson; Timothy J Ley; Richard K Wilson; Elaine R Mardis
Journal:  Nature       Date:  2010-04-15       Impact factor: 49.962

6.  A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia.

Authors:  Ulrich Steidl; Christian Steidl; Alexander Ebralidze; Björn Chapuy; Hye-Jung Han; Britta Will; Frank Rosenbauer; Annegret Becker; Katharina Wagner; Steffen Koschmieder; Susumu Kobayashi; Daniel B Costa; Thomas Schulz; Karen B O'Brien; Roel G W Verhaak; Ruud Delwel; Detlef Haase; Lorenz Trümper; Jürgen Krauter; Terumi Kohwi-Shigematsu; Frank Griesinger; Daniel G Tenen
Journal:  J Clin Invest       Date:  2007-09       Impact factor: 14.808

7.  Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: proposed guidelines for improving data collection, distribution, and integration.

Authors:  M Olivier; A Petitjean; J Teague; S Forbes; J K Dunnick; J T den Dunnen; A Langerød; J M Wilkinson; M Vihinen; R G H Cotton; P Hainaut
Journal:  Hum Mutat       Date:  2009-03       Impact factor: 4.878

8.  Genome-wide association studies in cancer.

Authors:  Douglas F Easton; Rosalind A Eeles
Journal:  Hum Mol Genet       Date:  2008-10-15       Impact factor: 6.150

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.  A small-cell lung cancer genome with complex signatures of tobacco exposure.

Authors:  Erin D Pleasance; Philip J Stephens; Sarah O'Meara; David J McBride; Alison Meynert; David Jones; Meng-Lay Lin; David Beare; King Wai Lau; Chris Greenman; Ignacio Varela; Serena Nik-Zainal; Helen R Davies; Gonzalo R Ordoñez; Laura J Mudie; Calli Latimer; Sarah Edkins; Lucy Stebbings; Lina Chen; Mingming Jia; Catherine Leroy; John Marshall; Andrew Menzies; Adam Butler; Jon W Teague; Jonathon Mangion; Yongming A Sun; Stephen F McLaughlin; Heather E Peckham; Eric F Tsung; Gina L Costa; Clarence C Lee; John D Minna; Adi Gazdar; Ewan Birney; Michael D Rhodes; Kevin J McKernan; Michael R Stratton; P Andrew Futreal; Peter J Campbell
Journal:  Nature       Date:  2009-12-16       Impact factor: 49.962

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  8 in total

Review 1.  Genomic characterization of esophageal squamous cell carcinoma: Insights from next-generation sequencing.

Authors:  Yasushi Sasaki; Miyuki Tamura; Ryota Koyama; Takafumi Nakagaki; Yasushi Adachi; Takashi Tokino
Journal:  World J Gastroenterol       Date:  2016-02-21       Impact factor: 5.742

2.  Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment.

Authors:  Elena Garralda; Keren Paz; Pedro P López-Casas; Siân Jones; Amanda Katz; Lisa M Kann; Fernando López-Rios; Francesca Sarno; Fátima Al-Shahrour; David Vasquez; Elizabeth Bruckheimer; Samuel V Angiuoli; Antonio Calles; Luis A Diaz; Victor E Velculescu; Alfonso Valencia; David Sidransky; Manuel Hidalgo
Journal:  Clin Cancer Res       Date:  2014-03-14       Impact factor: 12.531

3.  Deleterious mutations in esophageal carcinoma cuniculatum detected by next generation sequencing.

Authors:  Feng Yin; Kai Wang; Ming Hu; Petr Starostik; Kimberly J Newsom; Xiuli Liu
Journal:  Int J Clin Exp Pathol       Date:  2022-01-15

4.  Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples.

Authors:  Stefan Graw; Richard Meier; Kay Minn; Clark Bloomer; Andrew K Godwin; Brooke Fridley; Anda Vlad; Peter Beyerlein; Jeremy Chien
Journal:  Sci Rep       Date:  2015-07-23       Impact factor: 4.379

5.  Design and implementation of a randomized controlled trial of genomic counseling for patients with chronic disease.

Authors:  Kevin Sweet; Erynn S Gordon; Amy C Sturm; Tara J Schmidlen; Kandamurugu Manickam; Amanda Ewart Toland; Margaret A Keller; Catharine B Stack; J Felipe García-España; Mark Bellafante; Neeraj Tayal; Peter Embi; Philip Binkley; Ray E Hershberger; Wolfgang Sadee; Michael Christman; Clay Marsh
Journal:  J Pers Med       Date:  2014-01-08

6.  A ceRNA approach may unveil unexpected contributors to deletion syndromes, the model of 5q- syndrome.

Authors:  Walter Arancio; Swonild Ilenia Genovese; Lucia Bongiovanni; Claudio Tripodo
Journal:  Oncoscience       Date:  2015-11-11

7.  DNA qualification workflow for next generation sequencing of histopathological samples.

Authors:  Michele Simbolo; Marisa Gottardi; Vincenzo Corbo; Matteo Fassan; Andrea Mafficini; Giorgio Malpeli; Rita T Lawlor; Aldo Scarpa
Journal:  PLoS One       Date:  2013-06-06       Impact factor: 3.240

8.  Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.

Authors:  Sarah Munchel; Yen Hoang; Yue Zhao; Joseph Cottrell; Brandy Klotzle; Andrew K Godwin; Devin Koestler; Peter Beyerlein; Jian-Bing Fan; Marina Bibikova; Jeremy Chien
Journal:  Oncotarget       Date:  2015-09-22
  8 in total

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