Application of second-generation sequencing to cancer genomics

被引：32

作者：

Robison, Keith ^{[1
]}

机构：

[1] Infin Pharmaceut Inc, Cambridge, MA 02139 USA

来源：

BRIEFINGS IN BIOINFORMATICS | 2010年 / 11卷 / 05期

关键词：

cancer; sequencing-by-synthesis; genomics; mutations; copy number variation; genomic rearrangements; HUMAN BREAST-CANCER; HIGH-THROUGHPUT; SOMATIC MUTATIONS; SHORT-READ; STRUCTURAL VARIATION; COPY-NUMBER; COMPUTATIONAL PREDICTION; DRIVER MUTATIONS; GENE FUSIONS; VARIANTS;

D O I：

10.1093/bib/bbq013

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

New generations of DNA sequencing technologies are enabling the systematic study of genetic derangement in cancers. Sequencing of cancer exomes or transcriptomes or even entire cancer genomes are now possible, though technical and economic challenges remain. Cancer samples are inherently heterogeneous and are often contaminated with normal DNA, placing additional demands on informatics tools for detecting genetic variation. However, even low coverage sequencing data can provide valuable information on genetic rearrangements, amplifications and losses in tumor genomes. Novel recurrent oncogenic mutations and fusion transcripts have been discovered with these technologies. In some sequenced cancer genomes, tens of thousands of genetic alterations have been discovered. While this enables the detailed dissection of mutation classes, it also presents a formidable informatics problem of sorting active 'driver' mutations from inactive 'passenger' mutations in order to prioritize these for further experimental characterization.

引用

页码：524 / 534

页数：11

共 93 条

[71] Probabilistic base calling of Solexa sequencing data [J].

Rougemont, Jacques ;

Amzallag, Arnaud ;

Iseli, Christian ;

Farinelli, Laurent ;

Xenarios, Ioannis ;

Naef, Felix .

BMC BIOINFORMATICS, 2008, 9 (1)

[72] Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using paired-end diTags (PETs) [J].

Ruan, Yijun ;

Ooi, Hong Sain ;

Choo, Siew Woh ;

Chiu, Kuo Ping ;

Zhao, Xiao Dong ;

Srinivasan, K. G. ;

Yao, Fei ;

Choo, Chiou Yu ;

Liu, Jun ;

Ariyaratne, Pramila ;

Bin, Wilson G. W. ;

Kuznetsov, Vladimir A. ;

Shahab, Atif ;

Sung, Wing-Kin ;

Bourque, Guillaume ;

Palanisamy, Nallasivam ;

Wei, Chia-Lin .

GENOME RESEARCH, 2007, 17 (06) :828-838

[73] Mutation patterns in cancer genomes [J].

Rubin, Alan F. ;

Green, Phil .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (51) :21766-21770

[74] Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis [J].

Schweiger, Michal R. ;

Kerick, Martin ;

Timmermann, Bernd ;

Albrecht, Marcus W. ;

Borodina, Tatjana ;

Parkhomchuk, Dmitri ;

Zatloukal, Kurt ;

Lehrach, Hans .

PLOS ONE, 2009, 4 (05)

[75] Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution [J].

Shah, Sohrab P. ;

Morin, Ryan D. ;

Khattra, Jaswinder ;

Prentice, Leah ;

Pugh, Trevor ;

Burleigh, Angela ;

Delaney, Allen ;

Gelmon, Karen ;

Guliany, Ryan ;

Senz, Janine ;

Steidl, Christian ;

Holt, Robert A. ;

Jones, Steven ;

Sun, Mark ;

Leung, Gillian ;

Moore, Richard ;

Severson, Tesa ;

Taylor, Greg A. ;

Teschendorff, Andrew E. ;

Tse, Kane ;

Turashvili, Gulisa ;

Varhol, Richard ;

Warren, Rene L. ;

Watson, Peter ;

Zhao, Yongjun ;

Caldas, Carlos ;

Huntsman, David ;

Hirst, Martin ;

Marra, Marco A. ;

Aparicio, Samuel .

NATURE, 2009, 461 (7265) :809-U67

[76] Mutation of FOXL2 in Granulosa-Cell Tumors of the Ovary [J].

Shah, Sohrab P. ;

Koebel, Martin ;

Senz, Janine ;

Morin, Ryan D. ;

Clarke, Blaise A. ;

Wiegand, Kimberly C. ;

Leung, Gillian ;

Zayed, Abdalnasser ;

Mehl, Erika ;

Kalloger, Steve E. ;

Sun, Mark ;

Giuliany, Ryan ;

Yorida, Erika ;

Jones, Steven ;

Varhol, Richard ;

Swenerton, Kenneth D. ;

Miller, Dianne ;

Clement, Philip B. ;

Crane, Colleen ;

Madore, Jason ;

Provencher, Diane ;

Leung, Peter ;

DeFazio, Anna ;

Khattra, Jaswinder ;

Turashvili, Gulisa ;

Zhao, Yongjun ;

Zeng, Thomas ;

Glover, J. N. Mark ;

Vanderhyden, Barbara ;

Zhao, Chengquan ;

Parkinson, Christine A. ;

Jimenez-Linan, Mercedes ;

Bowtell, David D. L. ;

Mes-Masson, Anne-Marie ;

Brenton, James D. ;

Aparicio, Samuel A. ;

Boyd, Niki ;

Hirst, Martin ;

Gilks, C. Blake ;

Marra, Marco ;

Huntsman, David G. .

NEW ENGLAND JOURNAL OF MEDICINE, 2009, 360 (26) :2719-2729

[77] Complex landscapes of somatic rearrangement in human breast cancer genomes [J].

Stephens, Philip J. ;

McBride, David J. ;

Lin, Meng-Lay ;

Varela, Ignacio ;

Pleasance, Erin D. ;

Simpson, Jared T. ;

Stebbings, Lucy A. ;

Leroy, Catherine ;

Edkins, Sarah ;

Mudie, Laura J. ;

Greenman, Chris D. ;

Jia, Mingming ;

Latimer, Calli ;

Teague, Jon W. ;

Lau, King Wai ;

Burton, John ;

Quail, Michael A. ;

Swerdlow, Harold ;

Churcher, Carol ;

Natrajan, Rachael ;

Sieuwerts, Anieta M. ;

Martens, John W. M. ;

Silver, Daniel P. ;

Langerod, Anita ;

Russnes, Hege E. G. ;

Foekens, John A. ;

Reis-Filho, Jorge S. ;

van't Veer, Laura ;

Richardson, Andrea L. ;

Borresen-Dale, Anne-Lise ;

Campbell, Peter J. ;

Futreal, P. Andrew ;

Stratton, Michael R. .

NATURE, 2009, 462 (7276) :1005-U60

[78] Transcriptome sequencing of malignant pleural mesothelioma tumors [J].

Sugarbaker, David J. ;

Richards, William G. ;

Gordon, Gavin J. ;

Dong, Lingsheng ;

De Rienzo, Assunta ;

Maulik, Gautam ;

Glickman, Jonathan N. ;

Chirieac, Lucian R. ;

Hartman, Mor-Li ;

Taillon, Bruce E. ;

Du, Lei ;

Bouffard, Pascal ;

Kingsmore, Stephen F. ;

Miller, Neil A. ;

Farmer, Andrew D. ;

Jensen, Roderick V. ;

Gullans, Steven R. ;

Bueno, Raphael .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (09) :3521-3526

[79] The (non)malignancy of cancerous amino acidic substitutions [J].

Talavera, David ;

Taylor, Martin S. ;

Thornton, Janet M. .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2010, 78 (03) :518-529

[80] Microdroplet-based PCR enrichment for large-scale targeted sequencing [J].

Tewhey, Ryan ;

Warner, Jason B. ;

Nakano, Masakazu ;

Libby, Brian ;

Medkova, Martina ;

David, Patricia H. ;

Kotsopoulos, Steve K. ;

Samuels, Michael L. ;

Hutchison, J. Brian ;

Larson, Jonathan W. ;

Topol, Eric J. ;

Weiner, Michael P. ;

Harismendy, Olivier ;

Olson, Jeff ;

Link, Darren R. ;

Frazer, Kelly A. .

NATURE BIOTECHNOLOGY, 2009, 27 (11) :1025-U94

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