Exome sequencing: the sweet spot before whole genomes

被引:207
作者
Teer, Jamie K. [2 ]
Mullikin, James C. [1 ]
机构
[1] NHGRI, Genome Technol Branch, NIH, Bethesda, MD 20892 USA
[2] NHGRI, Genet Dis Res Branch, NIH, Bethesda, MD 20892 USA
基金
美国国家卫生研究院;
关键词
MULTIPLEX AMPLIFICATION; HYBRID SELECTION; DNA METHYLATION; HIGH-ALTITUDE; CAPTURE; ENRICHMENT; GENE; EXONS; HYBRIDIZATION; ADAPTATION;
D O I
10.1093/hmg/ddq333
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
The development of massively parallel sequencing technologies, coupled with new massively parallel DNA enrichment technologies (genomic capture), has allowed the sequencing of targeted regions of the human genome in rapidly increasing numbers of samples. Genomic capture can target specific areas in the genome, including genes of interest and linkage regions, but this limits the study to what is already known. Exome capture allows an unbiased investigation of the complete protein-coding regions in the genome. Researchers can use exome capture to focus on a critical part of the human genome, allowing larger numbers of samples than are currently practical with whole-genome sequencing. In this review, we briefly describe some of the methodologies currently used for genomic and exome capture and highlight recent applications of this technology.
引用
收藏
页码:R145 / R151
页数:7
相关论文
共 45 条
[1]   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
[2]   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)
[3]   Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays [J].
Bau, Stephan ;
Schracke, Nadine ;
Kranzle, Marcel ;
Wu, Haiguo ;
Stahler, Peer F. ;
Hoheisel, Joerg D. ;
Beier, Markus ;
Summerer, Daniel .
ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 2009, 393 (01) :171-175
[4]   Natural selection on EPAS1 (HIF2α) associated with low hemoglobin concentration in Tibetan highlanders [J].
Beall, Cynthia M. ;
Cavalleri, Gianpiero L. ;
Deng, Libin ;
Elston, Robert C. ;
Gao, Yang ;
Knight, Jo ;
Li, Chaohua ;
Li, Jiang Chuan ;
Liang, Yu ;
McCormack, Mark ;
Montgomery, Hugh E. ;
Pan, Hao ;
Robbins, Peter A. ;
Shianna, Kevin V. ;
Tam, Siu Cheung ;
Tsering, Ngodrop ;
Veeramah, Krishna R. ;
Wang, Wei ;
Wangdui, Puchung ;
Weale, Michael E. ;
Xu, Yaomin ;
Xu, Zhe ;
Yang, Ling ;
Zaman, M. Justin ;
Zeng, Changqing ;
Zhang, Li ;
Zhang, Xianglong ;
Zhaxi, Pingcuo ;
Zheng, Yong Tang .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (25) :11459-11464
[5]   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
[6]   IFRD1 Is a Candidate Gene for SMNA on Chromosome 7q22-q23 [J].
Brkanac, Zoran ;
Spencer, David ;
Shendure, Jay ;
Robertson, Peggy D. ;
Matsushita, Mark ;
Vu, Tiffany ;
Bird, Thomas D. ;
Olson, Maynard V. ;
Raskind, Wendy H. .
AMERICAN JOURNAL OF HUMAN GENETICS, 2009, 84 (05) :692-697
[7]   Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture [J].
Burbano, Hernan A. ;
Hodges, Emily ;
Green, Richard E. ;
Briggs, Adrian W. ;
Krause, Johannes ;
Meyer, Matthias ;
Good, Jeffrey M. ;
Maricic, Tomislav ;
Johnson, Philip L. F. ;
Xuan, Zhenyu ;
Rooks, Michelle ;
Bhattacharjee, Arindam ;
Brizuela, Leonardo ;
Albert, Frank W. ;
de la Rasilla, Marco ;
Fortea, Javier ;
Rosas, Antonio ;
Lachmann, Michael ;
Hannon, Gregory J. ;
Paeaebo, Svante .
SCIENCE, 2010, 328 (5979) :723-725
[8]   Genetic diagnosis by whole exome capture and massively parallel DNA sequencing [J].
Choi, Murim ;
Scholl, Ute I. ;
Ji, Weizhen ;
Liu, Tiewen ;
Tikhonova, Irina R. ;
Zumbo, Paul ;
Nayir, Ahmet ;
Bakkaloglu, Aysin ;
Ozen, Seza ;
Sanjad, Sami ;
Nelson-Williams, Carol ;
Farhi, Anita ;
Mane, Shrikant ;
Lifton, Richard P. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (45) :19096-19101
[9]   DNA Sequence Capture and Enrichment by Microarray Followed by Next-Generation Sequencing for Targeted Resequencing: Neurofibromatosis Type 1 Gene as a Model [J].
Chou, Lan-Szu ;
Liu, C. -S. Jonathan ;
Boese, Benjamin ;
Zhang, Xinmin ;
Mao, Rong .
CLINICAL CHEMISTRY, 2010, 56 (01) :62-72
[10]   Mutation spectrum revealed by breakpoint sequencing of human germline CNVs [J].
Conrad, Donald F. ;
Bird, Christine ;
Blackburne, Ben ;
Lindsay, Sarah ;
Mamanova, Lira ;
Lee, Charles ;
Turner, Daniel J. ;
Hurles, Matthew E. .
NATURE GENETICS, 2010, 42 (05) :385-U43