High-throughput DNA sequencing - concepts and limitations

被引：361

作者：

Kircher, Martin ^{[1
]}

Kelso, Janet ^{[1
]}

机构：

[1] Max Planck Inst Evolutionary Anthropol, Dept Evolutionary Genet, Leipzig, Germany

来源：

BIOESSAYS | 2010年 / 32卷 / 06期

关键词：

ABI/Life Technologies SOLiD; Helicos HeliScope; Illumina Genome Analyzer; Roche/454 GS FLX Titanium; Sanger capillary sequencing; GENOME SEQUENCE; FLUORESCENT NUCLEOTIDES; HYBRID SELECTION; BASE CALLER; CHIP-SEQ; GENERATION; ELECTROPHORESIS; ARRAY; READS; IDENTIFICATION;

D O I：

10.1002/bies.200900181

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Recent advances in DNA sequencing have revolutionized the field of genomics, making it possible for even single research groups to generate large amounts of sequence data very rapidly and at a substantially lower cost. These highthroughput sequencing technologies make deep transcriptome sequencing and transcript quantification, whole genome sequencing and resequencing available to many more researchers and projects. However, while the cost and time have been greatly reduced, the error profiles and limitations of the new platforms differ significantly from those of previous sequencing technologies. The selection of an appropriate sequencing platform for particular types of experiments is an important consideration, and requires a detailed understanding of the technologies available; including sources of error, error rate, as well as the speed and cost of sequencing. We review the relevant concepts and compare the issues raised by the current high-throughput DNA sequencing technologies. We analyze how future developments may overcome these limitations and what challenges remain.

引用

页码：524 / 536

页数：13

共 87 条

[1] Base dependent DNA-carbon nanotube interactions: activation enthalpies and assembly-disassembly control [J].

Albertorio, Fernando ;

Hughes, Mary E. ;

Golovchenko, Jene A. ;

Branton, Daniel .

NANOTECHNOLOGY, 2009, 20 (39)

[2] Next-generation DNA sequencing techniques [J].

Ansorge, Wilhelm J. .

NEW BIOTECHNOLOGY, 2009, 25 (04) :195-203

[3] Toward single molecule DNA sequencing:: Direct identification of ribonucleoside and deoxyribonucleoside 5′-monophosphates by using an engineered protein nanopore equipped with a molecular adapter [J].

Astier, Y ;

Braha, O ;

Bayley, H .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2006, 128 (05) :1705-1710

[4] Genome sequence data: management, storage, and visualization [J].

Batley, Jacqueline ;

Edwards, David .

BIOTECHNIQUES, 2009, 46 (05) :333-+

[5] 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

[6] Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing [J].

Blazej, Robert G. ;

Kumaresan, Palani ;

Mathies, Richard A. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (19) :7240-7245

[7] Virtual terminator nucleotides for next-generation DNA sequencing [J].

Bowers, Jayson ;

Mitchell, Judith ;

Beer, Eric ;

Buzby, Philip R. ;

Causey, Marie ;

Efcavitch, J. William ;

Jarosz, Mirna ;

Krzymanska-Olejnik, Edyta ;

Kung, Li ;

Lipson, Doron ;

Lowman, Geoffrey M. ;

Marappan, Subramanian ;

McInerney, Peter ;

Platt, Adam ;

Roy, Atanu ;

Siddiqi, Suhaib M. ;

Steinmann, Kathleen ;

Thompson, John F. .

NATURE METHODS, 2009, 6 (08) :593-U60

[8] Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA [J].

Briggs, Adrian W. ;

Stenzel, Udo ;

Meyer, Matthias ;

Krause, Johannes ;

Kircher, Martin ;

Paeaebo, Svante .

NUCLEIC ACIDS RESEARCH, 2010, 38 (06) :e87.1-e87.12

[9] Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes [J].

Briggs, Adrian W. ;

Good, Jeffrey M. ;

Green, Richard E. ;

Krause, Johannes ;

Maricic, Tomislav ;

Stenzel, Udo ;

Lalueza-Fox, Carles ;

Rudan, Pavao ;

Brajkovic, Dejana ;

Kucan, Zeljko ;

Gusic, Ivan ;

Schmitz, Ralf ;

Doronichev, Vladimir B. ;

Golovanova, Liubov V. ;

de la Rasilla, Marco ;

Fortea, Javier ;

Rosas, Antonio ;

Paeaebo, Svante .

SCIENCE, 2009, 325 (5938) :318-321

[10] De novo fragment assembly with short mate-paired reads: Does the read length matter? [J].

Chaisson, Mark J. ;

Brinza, Dumitru ;

Pevzner, Pavel A. .

GENOME RESEARCH, 2009, 19 (02) :336-346

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