Emergence of single-molecule sequencing and potential for molecular diagnostic applications

被引:7
作者
Milos, Patrice M. [1 ]
机构
[1] Helicos BioSci, Cambridge, MA 02139 USA
关键词
DNA; microbial and viral screening; nanopore; noninvasive fetal screening; quantitation; real-time DNA sequencing; RNA; sequencing by synthesis; single-molecule sequencing; tumor genome; NONINVASIVE PRENATAL-DIAGNOSIS; HYBRID SELECTION; EXON CAPTURE; DNA; GENOME; CANCER; OLIGONUCLEOTIDES; ANEUPLOIDY; MICRORNAS; BACTERIAL;
D O I
10.1586/ERM.09.50
中图分类号
R36 [病理学];
学科分类号
100104 ;
摘要
The effective demonstration of single-molecule sequencing at scale over the last several years offers the exciting opportunity for a new era in the field of molecular diagnostics. As we aim to personalize and deliver cost-effective healthcare, we must consider the need to fully integrate genomics into decision-making. We must be able to accurately and cost effectively obtain a complete genome sequence for disease diagnosis, interrogate a molecular signature from blood for therapeutic monitoring, obtain a tumor mutation profile for optimizing therapeutic choice - each molecular diagnostic measurement utilized to better inform patient care. Would a physician or molecular pathology laboratory want to utilize a PCR process in which millions of DNA copies of a patient's nucleic acid are created when an alternative approach allowing direct measurement of the nucleic acids is possible? I would suggest not! In this article we will focus on the emergence of single-molecule sequencing, the single-molecule sequencing methodologies in the marketplace or under development today, as well as the importance of these methods for molecular characterization and diagnosis of disease with the ultimate application for molecular diagnostics.
引用
收藏
页码:659 / 666
页数:8
相关论文
共 56 条
[1]   Stool DNA and occult blood testing for screen detection of colorectal neoplasia [J].
Ahlquist, David A. ;
Sargent, Daniel J. ;
Loprinzi, Charles L. ;
Levin, Theodore R. ;
Rex, Douglas K. ;
Ahnen, Dennis J. ;
Knigge, Kandice ;
Lance, Peter ;
Burgart, Lawrence J. ;
Hamilton, Stanley R. ;
Allison, James E. ;
Lawson, Michael J. ;
Devens, Mary E. ;
Harrington, Jonathan J. ;
Hillman, Shauna L. .
ANNALS OF INTERNAL MEDICINE, 2008, 149 (07) :441-W81
[2]   Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing [J].
Archer, John ;
Braverman, Michael S. ;
Taillon, Bruce E. ;
Desany, Brian ;
James, Ian ;
Harrigan, P. Richard ;
Lewis, Marilyn ;
Robertson, David L. .
AIDS, 2009, 23 (10) :1209-1218
[3]   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
[4]   Designed protein pores as components for biosensors [J].
Braha, O ;
Walker, B ;
Cheley, S ;
Kasianowicz, JJ ;
Song, LZ ;
Gouaux, JE ;
Bayley, H .
CHEMISTRY & BIOLOGY, 1997, 4 (07) :497-505
[5]   The potential and challenges of nanopore sequencing [J].
Branton, Daniel ;
Deamer, David W. ;
Marziali, Andre ;
Bayley, Hagan ;
Benner, Steven A. ;
Butler, Thomas ;
Di Ventra, Massimiliano ;
Garaj, Slaven ;
Hibbs, Andrew ;
Huang, Xiaohua ;
Jovanovich, Stevan B. ;
Krstic, Predrag S. ;
Lindsay, Stuart ;
Ling, Xinsheng Sean ;
Mastrangelo, Carlos H. ;
Meller, Amit ;
Oliver, John S. ;
Pershin, Yuriy V. ;
Ramsey, J. Michael ;
Riehn, Robert ;
Soni, Gautam V. ;
Tabard-Cossa, Vincent ;
Wanunu, Meni ;
Wiggin, Matthew ;
Schloss, Jeffery A. .
NATURE BIOTECHNOLOGY, 2008, 26 (10) :1146-1153
[6]   Sequence information can be obtained from single DNA molecules [J].
Braslavsky, I ;
Hebert, B ;
Kartalov, E ;
Quake, SR .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (07) :3960-3964
[7]   ALLPATHS: De novo assembly of whole-genome shotgun microreads [J].
Butler, Jonathan ;
MacCallum, Iain ;
Kleber, Michael ;
Shlyakhter, Ilya A. ;
Belmonte, Matthew K. ;
Lander, Eric S. ;
Nusbaum, Chad ;
Jaffe, David B. .
GENOME RESEARCH, 2008, 18 (05) :810-820
[8]   Single-molecule DNA detection with an engineered MspA protein nanopore [J].
Butler, Tom Z. ;
Pavlenok, Mikhail ;
Derrington, Ian M. ;
Niederweis, Michael ;
Gundlach, Jens H. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (52) :20647-20652
[9]   Short read fragment assembly of bacterial genomes [J].
Chaisson, Mark J. ;
Pevzner, Pavel A. .
GENOME RESEARCH, 2008, 18 (02) :324-330
[10]   Comprehensive genomic characterization defines human glioblastoma genes and core pathways [J].
Chin, L. ;
Meyerson, M. ;
Aldape, K. ;
Bigner, D. ;
Mikkelsen, T. ;
VandenBerg, S. ;
Kahn, A. ;
Penny, R. ;
Ferguson, M. L. ;
Gerhard, D. S. ;
Getz, G. ;
Brennan, C. ;
Taylor, B. S. ;
Winckler, W. ;
Park, P. ;
Ladanyi, M. ;
Hoadley, K. A. ;
Verhaak, R. G. W. ;
Hayes, D. N. ;
Spellman, Paul T. ;
Absher, D. ;
Weir, B. A. ;
Ding, L. ;
Wheeler, D. ;
Lawrence, M. S. ;
Cibulskis, K. ;
Mardis, E. ;
Zhang, Jinghui ;
Wilson, R. K. ;
Donehower, L. ;
Wheeler, D. A. ;
Purdom, E. ;
Wallis, J. ;
Laird, P. W. ;
Herman, J. G. ;
Schuebel, K. E. ;
Weisenberger, D. J. ;
Baylin, S. B. ;
Schultz, N. ;
Yao, Jun ;
Wiedemeyer, R. ;
Weinstein, J. ;
Sander, C. ;
Gibbs, R. A. ;
Gray, J. ;
Kucherlapati, R. ;
Lander, E. S. ;
Myers, R. M. ;
Perou, C. M. ;
McLendon, Roger .
NATURE, 2008, 455 (7216) :1061-1068