Sequencing arrays for screening multiple genes associated with early-onset human retinal degenerations on a high-throughput platform

被引:50
作者
Mandal, MNA
Heckenlively, JR
Burch, T
Chen, LC
Vasireddy, V
Koenekoop, RK
Sieving, PA
Ayyagari, R
机构
[1] Univ Michigan, Dept Ophthalmol & Visual Sci, Ann Arbor, MI 48105 USA
[2] McGill Univ, Ctr Hlth, MTL Childrens Hosp, McGill Ocular Genet Lab, Montreal, PQ, Canada
[3] NEI, NIH, Bethesda, MD 20892 USA
关键词
D O I
10.1167/iovs.05-0007
中图分类号
R77 [眼科学];
学科分类号
100212 ;
摘要
PURPOSE. To develop and apply microarray-based resequencing technology to detect sequence alterations in multiple autosomal recessive retinal disease genes on a single high-throughput platform. METHODS. Oligonucleotides corresponding to both strands of the target exons and the flanking intron sequences of 29,214 bp from 11 genes associated with autosomal recessive retinitis pigmentosa (arRP) were tiled on 20 x 25-mu m microarrays (arRP-I arrays). A total of 155 exons were amplified from 35 arRP patient DNA samples, with each sample being sequenced on an arRP-I chip by hybridization. RESULTS. With the arRP-I arrays, 97.6% of the tiled sequence were determined with more than 99% accuracy and reproducibility. Of the 2.4% unread sequence, 89.5% involved stretches of G or C. In analyzing the 903,140-bp sequence from the 35 patient samples, 506 sequence changes have been detected in which 386 are previously reported alterations, and 120 are novel. In addition to four known causative mutations, six novel sequence changes that are potentially pathogenic were observed. Additional analysis is needed to determine whether these changes are responsible for arRP in these patients. CONCLUSIONS. The use of microarray for sequencing is a novel approach, and the arRP-I chip is the first successful application of this technology for determining sequence alteration in multiple disease-related genes. These arrays can be used for high-throughput genotyping of patients with relevant retinal conditions. In addition, these arrays offer a unique opportunity to interrogate complex patterns of inheritance due to the involvement of more one gene by screening multiple genes on a single platform.
引用
收藏
页码:3355 / 3362
页数:8
相关论文
共 39 条
[1]   Gene therapy restores vision in a canine model of childhood blindness [J].
Acland, GM ;
Aguirre, GD ;
Ray, J ;
Zhang, Q ;
Aleman, TS ;
Cideciyan, AV ;
Pearce-Kelling, SE ;
Anand, V ;
Zeng, Y ;
Maguire, AM ;
Jacobson, SG ;
Hauswirth, WW ;
Bennett, J .
NATURE GENETICS, 2001, 28 (01) :92-95
[2]  
AlMaghtheh M, 1996, AM J HUM GENET, V59, P864
[3]   Heterozygous mutations in BBS1, BBS2 and BBS6 have a potential epistatic effect on Bardet-Biedl patients with two mutations at a second BBS locus [J].
Badano, JL ;
Kim, JC ;
Hoskins, BE ;
Lewis, RA ;
Ansley, SJ ;
Cutler, DJ ;
Castellan, C ;
Beales, PL ;
Leroux, MR ;
Katsanis, N .
HUMAN MOLECULAR GENETICS, 2003, 12 (14) :1651-1659
[4]  
Briggs CE, 2001, INVEST OPHTH VIS SCI, V42, P2229
[5]   Autosomal recessive retinitis pigmentosa and cone-rod dystrophy caused by splice site mutations in the Stargardt's disease gene ABCR [J].
Cremers, FPM ;
van De Pol, DJR ;
van Driel, M ;
den Hollander, AI ;
van Haren, FJJ ;
Knoers, NVAM ;
Tijmes, N ;
Bergen, AAB ;
Rohrschneider, K ;
Blankenagel, A ;
Pinckers, AJLG ;
Deutman, AF ;
Hoyng, CB .
HUMAN MOLECULAR GENETICS, 1998, 7 (03) :355-362
[6]   High-throughput variation detection and genotyping using microarrays [J].
Cutler, DJ ;
Zwick, ME ;
Carrasquillo, MM ;
Yohn, CT ;
Tobin, KP ;
Kashuk, C ;
Mathews, DJ ;
Shah, NA ;
Eichler, EE ;
Warrington, JA ;
Chakravarti, A .
GENOME RESEARCH, 2001, 11 (11) :1913-1925
[7]  
DAIGER SP, 2004, RETINAL DYSTROPHIES, P17
[8]   SEQUENCING BY HYBRIDIZATION - TOWARDS AN AUTOMATED SEQUENCING OF ONE MILLION M13 CLONES ARRAYED ON MEMBRANES [J].
DRMANAC, R ;
DRMANAC, S ;
LABAT, I ;
CRKVENJAKOV, R ;
VICENTIC, A ;
GEMMELL, A .
ELECTROPHORESIS, 1992, 13 (08) :566-573
[9]   MUTATIONS IN THE GENE ENCODING THE ALPHA-SUBUNIT OF THE ROD CGMP-GATED CHANNEL IN AUTOSOMAL RECESSIVE RETINITIS-PIGMENTOSA [J].
DRYJA, TP ;
FINN, JT ;
PENG, YW ;
MCGEE, TL ;
BERSON, EL ;
YAU, KW .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (22) :10177-10181
[10]   MUTATIONS WITHIN THE RHODOPSIN GENE IN PATIENTS WITH AUTOSOMAL DOMINANT RETINITIS-PIGMENTOSA [J].
DRYJA, TP ;
MCGEE, TL ;
HAHN, LB ;
COWLEY, GS ;
OLSSON, JE ;
REICHEL, E ;
SANDBERG, MA ;
BERSON, EL .
NEW ENGLAND JOURNAL OF MEDICINE, 1990, 323 (19) :1302-1307