Array-based DNA diagnostics: Let the revolution begin

被引:94
作者
Beaudet, Arthur L. [1 ]
Belmont, John W. [1 ]
机构
[1] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA
来源
ANNUAL REVIEW OF MEDICINE | 2008年 / 59卷
关键词
microarray; chromosomal imbalance; genotyping; mutation analysis; DNA sequencing;
D O I
10.1146/annurev.med.59.012907.101800
中图分类号
R-3 [医学研究方法]; R3 [基础医学];
学科分类号
1001 ;
摘要
Advances in the fabrication of DNA microarrays as well as transformations in detection chemistries have vastly increased the throughput for genotyping, DNA sequencing, and array-based copy number analysis (ABCNA). Rapid changes in technology are not only affecting research but also revolutionizing DNA diagnostics. Here we focus on the application of high-throughput ABCNA and genotyping. Targeted and genome-wide ABCNA has led to the discovery of extensive DNA copy number variation in the population and the delineation of many previously unrecognized submicroscopic chromosomal aberrations (genomic disorders). High-throughput single-nucleotide polymorphism (SNP) genotyping is being widely applied in genome-wide association studies (GWASs) with recent successes in identification of common variants that confer risk for common adult diseases. Future applications of high-throughput genotyping and array-based DNA sequencing technology will undoubtedly involve research and diagnostic analyses of rare mutations and perhaps ultimately enable full individual genome sequencing.
引用
收藏
页码:113 / 129
页数:17
相关论文
共 56 条
[31]   Genome sequencing in microfabricated high-density picolitre reactors [J].
Margulies, M ;
Egholm, M ;
Altman, WE ;
Attiya, S ;
Bader, JS ;
Bemben, LA ;
Berka, J ;
Braverman, MS ;
Chen, YJ ;
Chen, ZT ;
Dewell, SB ;
Du, L ;
Fierro, JM ;
Gomes, XV ;
Godwin, BC ;
He, W ;
Helgesen, S ;
Ho, CH ;
Irzyk, GP ;
Jando, SC ;
Alenquer, MLI ;
Jarvie, TP ;
Jirage, KB ;
Kim, JB ;
Knight, JR ;
Lanza, JR ;
Leamon, JH ;
Lefkowitz, SM ;
Lei, M ;
Li, J ;
Lohman, KL ;
Lu, H ;
Makhijani, VB ;
McDade, KE ;
McKenna, MP ;
Myers, EW ;
Nickerson, E ;
Nobile, JR ;
Plant, R ;
Puc, BP ;
Ronan, MT ;
Roth, GT ;
Sarkis, GJ ;
Simons, JF ;
Simpson, JW ;
Srinivasan, M ;
Tartaro, KR ;
Tomasz, A ;
Vogt, KA ;
Volkmer, GA .
NATURE, 2005, 437 (7057) :376-380
[32]   A common allele on chromosome 9 associated with coronary heart disease [J].
McPherson, Ruth ;
Pertsemlidis, Alexander ;
Kavaslar, Nihan ;
Stewart, Alexandre F. R. ;
Roberts, Robert ;
Cox, David R. ;
Hinds, David A. ;
Pennacchio, Len A. ;
Tybjaerg-Hansen, Anne ;
Folsom, Aaron R. ;
Boerwinkle, Eric ;
Hobbs, Helen H. ;
Cohen, Jonathan C. .
SCIENCE, 2007, 316 (5830) :1488-1491
[33]   Emerging technologies in DNA sequencing [J].
Metzker, ML .
GENOME RESEARCH, 2005, 15 (12) :1767-1776
[34]   Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility [J].
Parkes, Miles ;
Barrett, Jeffrey C. ;
Prescott, Natalie J. ;
Tremelling, Mark ;
Anderson, Carl A. ;
Fisher, Sheila A. ;
Roberts, Roland G. ;
Nimmo, Elaine R. ;
Cummings, Fraser R. ;
Soars, Dianne ;
Drummond, Hazel ;
Lees, Charlie W. ;
Khawaja, Saud A. ;
Bagnall, Richard ;
Burke, Denis A. ;
Todhunter, Catherine E. ;
Ahmad, Tariq ;
Onnie, Clive M. ;
McArdle, Wendy ;
Strachan, David ;
Bethel, Graeme ;
Bryan, Claire ;
Lewis, Cathryn M. ;
Deloukas, Panos ;
Forbes, Alastair ;
Sanderson, Jeremy ;
Jewell, Derek P. ;
Satsangi, Jack ;
Mansfield, John C. ;
Cardon, Lon ;
Mathew, Christopher G. .
NATURE GENETICS, 2007, 39 (07) :830-832
[35]   High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping [J].
Peiffer, Daniel A. ;
Le, Jennie M. ;
Steemers, Frank J. ;
Chang, Weihua ;
Jenniges, Tony ;
Garcia, Francisco ;
Haden, Kirt ;
Li, Jiangzhen ;
Shaw, Chad A. ;
Belmont, John ;
Cheung, Sau Wai ;
Shen, Richard M. ;
Barker, David L. ;
Gunderson, Kevin L. .
GENOME RESEARCH, 2006, 16 (09) :1136-1148
[36]   Global variation in copy number in the human genome [J].
Redon, Richard ;
Ishikawa, Shumpei ;
Fitch, Karen R. ;
Feuk, Lars ;
Perry, George H. ;
Andrews, T. Daniel ;
Fiegler, Heike ;
Shapero, Michael H. ;
Carson, Andrew R. ;
Chen, Wenwei ;
Cho, Eun Kyung ;
Dallaire, Stephanie ;
Freeman, Jennifer L. ;
Gonzalez, Juan R. ;
Gratacos, Monica ;
Huang, Jing ;
Kalaitzopoulos, Dimitrios ;
Komura, Daisuke ;
MacDonald, Jeffrey R. ;
Marshall, Christian R. ;
Mei, Rui ;
Montgomery, Lyndal ;
Nishimura, Kunihiro ;
Okamura, Kohji ;
Shen, Fan ;
Somerville, Martin J. ;
Tchinda, Joelle ;
Valsesia, Armand ;
Woodwark, Cara ;
Yang, Fengtang ;
Zhang, Junjun ;
Zerjal, Tatiana ;
Zhang, Jane ;
Armengol, Lluis ;
Conrad, Donald F. ;
Estivill, Xavier ;
Tyler-Smith, Chris ;
Carter, Nigel P. ;
Aburatani, Hiroyuki ;
Lee, Charles ;
Jones, Keith W. ;
Scherer, Stephen W. ;
Hurles, Matthew E. .
NATURE, 2006, 444 (7118) :444-454
[37]   Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease [J].
Rioux, JD ;
Daly, MJ ;
Silverberg, MS ;
Lindblad, K ;
Steinhart, H ;
Cohen, Z ;
Delmonte, T ;
Kocher, K ;
Miller, K ;
Guschwan, S ;
Kulbokas, EJ ;
O'Leary, S ;
Winchester, E ;
Dewar, K ;
Green, T ;
Stone, V ;
Chow, C ;
Cohen, A ;
Langelier, D ;
Lapointe, G ;
Gaudet, D ;
Faith, J ;
Branco, N ;
Bull, SB ;
McLeod, RS ;
Griffiths, AM ;
Bitton, A ;
Greenberg, GR ;
Lander, ES ;
Siminovitch, KA ;
Hudson, TJ .
NATURE GENETICS, 2001, 29 (02) :223-228
[38]   Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels [J].
Saxena, Richa ;
Voight, Benjamin F. ;
Lyssenko, Valeriya ;
Burtt, Noel P. ;
de Bakker, Paul I. W. ;
Chen, Hong ;
Roix, Jeffrey J. ;
Kathiresan, Sekar ;
Hirschhorn, Joel N. ;
Daly, Mark J. ;
Hughes, Thomas E. ;
Groop, Leif ;
Altshuler, David ;
Almgren, Peter ;
Florez, Jose C. ;
Meyer, Joanne ;
Ardlie, Kristin ;
Bostroem, Kristina Bengtsson ;
Isomaa, Bo ;
Lettre, Guillaume ;
Lindblad, Ulf ;
Lyon, Helen N. ;
Melander, Olle ;
Newton-Cheh, Christopher ;
Nilsson, Peter ;
Orho-Melander, Marju ;
Rastam, Lennart ;
Speliotes, Elizabeth K. ;
Taskinen, Marja-Riitta ;
Tuomi, Tiinamaija ;
Guiducci, Candace ;
Berglund, Anna ;
Carlson, Joyce ;
Gianniny, Lauren ;
Hackett, Rachel ;
Hall, Liselotte ;
Holmkvist, Johan ;
Laurila, Esa ;
Sjoegren, Marketa ;
Sterner, Maria ;
Surti, Aarti ;
Svensson, Margareta ;
Svensson, Malin ;
Tewhey, Ryan ;
Blumenstiel, Brendan ;
Parkin, Melissa ;
DeFelice, Matthew ;
Barry, Rachel ;
Brodeur, Wendy ;
Camarata, Jody .
SCIENCE, 2007, 316 (5829) :1331-1336
[39]   A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants [J].
Scott, Laura J. ;
Mohlke, Karen L. ;
Bonnycastle, Lori L. ;
Willer, Cristen J. ;
Li, Yun ;
Duren, William L. ;
Erdos, Michael R. ;
Stringham, Heather M. ;
Chines, Peter S. ;
Jackson, Anne U. ;
Prokunina-Olsson, Ludmila ;
Ding, Chia-Jen ;
Swift, Amy J. ;
Narisu, Narisu ;
Hu, Tianle ;
Pruim, Randall ;
Xiao, Rui ;
Li, Xiao-Yi ;
Conneely, Karen N. ;
Riebow, Nancy L. ;
Sprau, Andrew G. ;
Tong, Maurine ;
White, Peggy P. ;
Hetrick, Kurt N. ;
Barnhart, Michael W. ;
Bark, Craig W. ;
Goldstein, Janet L. ;
Watkins, Lee ;
Xiang, Fang ;
Saramies, Jouko ;
Buchanan, Thomas A. ;
Watanabe, Richard M. ;
Valle, Timo T. ;
Kinnunen, Leena ;
Abecasis, Gonalo R. ;
Pugh, Elizabeth W. ;
Doheny, Kimberly F. ;
Bergman, Richard N. ;
Tuomilehto, Jaakko ;
Collins, Francis S. ;
Boehnke, Michael .
SCIENCE, 2007, 316 (5829) :1341-1345
[40]   Strong association of de novo copy number mutations with autism [J].
Sebat, Jonathan ;
Lakshmi, B. ;
Malhotra, Dheeraj ;
Troge, Jennifer ;
Lese-Martin, Christa ;
Walsh, Tom ;
Yamrom, Boris ;
Yoon, Seungtai ;
Krasnitz, Alex ;
Kendall, Jude ;
Leotta, Anthony ;
Pai, Deepa ;
Zhang, Ray ;
Lee, Yoon-Ha ;
Hicks, James ;
Spence, Sarah J. ;
Lee, Annette T. ;
Puura, Kaija ;
Lehtimaeki, Terho ;
Ledbetter, David ;
Gregersen, Peter K. ;
Bregman, Joel ;
Sutcliffe, James S. ;
Jobanputra, Vaidehi ;
Chung, Wendy ;
Warburton, Dorothy ;
King, Mary-Claire ;
Skuse, David ;
Geschwind, Daniel H. ;
Gilliam, T. Conrad ;
Ye, Kenny ;
Wigler, Michael .
SCIENCE, 2007, 316 (5823) :445-449