Advances in understanding cancer genomes through second-generation sequencing

被引：791

作者：

Meyerson, Matthew ^{[1
]}

Gabriel, Stacey

Getz, Gad

机构：

[1] Dana Farber Canc Inst, Boston, MA 02115 USA

来源：

NATURE REVIEWS GENETICS | 2010年 / 11卷 / 10期

关键词：

CELL LUNG-CANCER; TYROSINE KINASE JAK2; COPY-NUMBER; ACTIVATING MUTATIONS; SOMATIC MUTATIONS; HIGH-THROUGHPUT; HUMAN BREAST; FGFR2; MUTATIONS; READ ALIGNMENT; EXON CAPTURE;

D O I：

10.1038/nrg2841

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Cancers are caused by the accumulation of genomic alterations. Therefore, analyses of cancer genome sequences and structures provide insights for understanding cancer biology, diagnosis and therapy. The application of second-generation DNA sequencing technologies (also known as next-generation sequencing) - through whole-genome, whole-exome and whole-transcriptome approaches - is allowing substantial advances in cancer genomics. These methods are facilitating an increase in the efficiency and resolution of detection of each of the principal types of somatic cancer genome alterations, including nucleotide substitutions, small insertions and deletions, copy number alterations, chromosomal rearrangements and microbial infections. This Review focuses on the methodological considerations for characterizing somatic genome alterations in cancer and the future prospects for these approaches.

引用

页码：685 / 696

页数：12

共 118 条

[1] A method and server for predicting damaging missense mutations [J].

Adzhubei, Ivan A. ;

Schmidt, Steffen ;

Peshkin, Leonid ;

Ramensky, Vasily E. ;

Gerasimova, Anna ;

Bork, Peer ;

Kondrashov, Alexey S. ;

Sunyaev, Shamil R. .

NATURE METHODS, 2010, 7 (04) :248-249

[2] Direct selection of human genomic loci by microarray hybridization [J].

Albert, Thomas J. ;

Molla, Michael N. ;

Muzny, Donna M. ;

Nazareth, Lynne ;

Wheeler, David ;

Song, Xingzhi ;

Richmond, Todd A. ;

Middle, Chris M. ;

Rodesch, Matthew J. ;

Packard, Charles J. ;

Weinstock, George M. ;

Gibbs, Richard A. .

NATURE METHODS, 2007, 4 (11) :903-905

[3] Whole exome capture in solution with 3 Gbp of data [J].

Bainbridge, Matthew N. ;

Wang, Min ;

Burgess, Daniel L. ;

Kovar, Christie ;

Rodesch, Matthew J. ;

D'Ascenzo, Mark ;

Kitzman, Jacob ;

Wu, Yuan-Qing ;

Newsham, Irene ;

Richmond, Todd A. ;

Jeddeloh, Jeffrey A. ;

Muzny, Donna ;

Albert, Thomas J. ;

Gibbs, Richard A. .

GENOME BIOLOGY, 2010, 11 (06)

[4] Acquired mutation of the tyrosine kinase JAK2 in human myeloproliferative disorders [J].

Baxter, EJ ;

Scott, LM ;

Campbell, PJ ;

East, C ;

Fourouclas, N ;

Swanton, S ;

Vassiliou, GS ;

Bench, AJ ;

Boyd, EM ;

Curtin, N ;

Scott, MA ;

Erber, WN ;

Green, AR .

LANCET, 2005, 365 (9464) :1054-1061

[5] LINE-1 Retrotransposition Activity in Human Genomes [J].

Beck, Christine R. ;

Collier, Pamela ;

Macfarlane, Catriona ;

Malig, Maika ;

Kidd, Jeffrey M. ;

Eichler, Evan E. ;

Badge, Richard M. ;

Moran, John V. .

CELL, 2010, 141 (07) :1159-U110

[6] Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[7] Integrative analysis of the melanoma transcriptome [J].

Berger, Michael F. ;

Levin, Joshua Z. ;

Vijayendran, Krishna ;

Sivachenko, Andrey ;

Adiconis, Xian ;

Maguire, Jared ;

Johnson, Laura A. ;

Robinson, James ;

Verhaak, Roel G. ;

Sougnez, Carrie ;

Onofrio, Robert C. ;

Ziaugra, Liuda ;

Cibulskis, Kristian ;

Laine, Elisabeth ;

Barretina, Jordi ;

Winckler, Wendy ;

Fisher, David E. ;

Getz, Gad ;

Meyerson, Matthew ;

Jaffe, David B. ;

Gabriel, Stacey B. ;

Lander, Eric S. ;

Dummer, Reinhard ;

Gnirke, Andreas ;

Nusbaum, Chad ;

Garraway, Levi A. .

GENOME RESEARCH, 2010, 20 (04) :413-427

[8] Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma [J].

Beroukhim, Rameen ;

Getz, Gad ;

Nghiemphu, Leia ;

Barretina, Jordi ;

Hsueh, Teli ;

Linhart, David ;

Vivanco, Igor ;

Lee, Jeffrey C. ;

Huang, Julie H. ;

Alexander, Sethu ;

Du, Jinyan ;

Kau, Tweeny ;

Thomas, Roman K. ;

Shah, Kinial ;

Soto, Horacio ;

Perner, Sven ;

Prensner, John ;

Debiasi, Ralph M. ;

Demichelis, Francesca ;

Hatton, Charlie ;

Rubin, Mark A. ;

Garraway, Levi A. ;

Nelson, Stan F. ;

Liau, Linda ;

Mischel, Paul S. ;

Cloughesy, Tim F. ;

Meyerson, Matthew ;

Golub, Todd A. ;

Lander, Eric S. ;

Mellinghoff, Ingo K. ;

Sellers, William R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (50) :20007-20012

[9] The landscape of somatic copy-number alteration across human cancers [J].

Beroukhim, Rameen ;

Mermel, Craig H. ;

Porter, Dale ;

Wei, Guo ;

Raychaudhuri, Soumya ;

Donovan, Jerry ;

Barretina, Jordi ;

Boehm, Jesse S. ;

Dobson, Jennifer ;

Urashima, Mitsuyoshi ;

Mc Henry, Kevin T. ;

Pinchback, Reid M. ;

Ligon, Azra H. ;

Cho, Yoon-Jae ;

Haery, Leila ;

Greulich, Heidi ;

Reich, Michael ;

Winckler, Wendy ;

Lawrence, Michael S. ;

Weir, Barbara A. ;

Tanaka, Kumiko E. ;

Chiang, Derek Y. ;

Bass, Adam J. ;

Loo, Alice ;

Hoffman, Carter ;

Prensner, John ;

Liefeld, Ted ;

Gao, Qing ;

Yecies, Derek ;

Signoretti, Sabina ;

Maher, Elizabeth ;

Kaye, Frederic J. ;

Sasaki, Hidefumi ;

Tepper, Joel E. ;

Fletcher, Jonathan A. ;

Tabernero, Josep ;

Baselga, Jose ;

Tsao, Ming-Sound ;

Demichelis, Francesca ;

Rubin, Mark A. ;

Janne, Pasi A. ;

Daly, Mark J. ;

Nucera, Carmelo ;

Levine, Ross L. ;

Ebert, Benjamin L. ;

Gabriel, Stacey ;

Rustgi, Anil K. ;

Antonescu, Cristina R. ;

Ladanyi, Marc ;

Letai, Anthony .

NATURE, 2010, 463 (7283) :899-905

[10] High-resolution analysis of DNA copy number using oligonucleotide microarrays [J].

Bignell, GR ;

Huang, J ;

Greshock, J ;

Watt, S ;

Butler, A ;

West, S ;

Grigorova, M ;

Jones, KW ;

Wei, W ;

Stratton, MR ;

Futreal, PA ;

Weber, B ;

Shapero, MH ;

Wooster, R .

GENOME RESEARCH, 2004, 14 (02) :287-295

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