Further development of multiplex single nucleotide polymorphism typing method, the DigiTag2 assay

被引:60
作者
Nishida, Nao [1 ]
Tanabe, Tetsuya
Takasu, Miwa
Suyama, Akira
Tokunaga, Katsushi
机构
[1] Univ Tokyo, Grad Sch Med, Dept Human Genet, Bunkyo Ku, Tokyo 1130033, Japan
[2] Olympus Corp, Bio Business Div, Hachioji, Tokyo 1928512, Japan
[3] Univ Tokyo, Grad Sch Arts & Sci, Dept Life Sci, Meguro Ku, Tokyo 1538902, Japan
关键词
multiplex genotyping; SNPs; mutation; oligonucleotide ligation assay;
D O I
10.1016/j.ab.2007.02.005
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
A number of single nucleotide polymorphisms (SNPs) are considered to be candidate susceptibility or resistance genetic factors for multifactorial disease. Genome-wide searches for disease susceptibility regions followed by high-resolution mapping of primary genes require cost-effective and highly reliable technology. To accomplish successful and low-cost typing for candidate SNPs, new technologies must be developed. We previously reported a multiplex SNP typing method, designated the DigiTag assay, that has the potential to analyze nearly any SNP with high accuracy and reproducibility. However, the DigiTag assay requires multiple washing steps in manipulation and uses genotyping probes modified with biotin for each target SNP. Here we describe the next version of the assay, DigiTag2, which works with simple protocols and uses unmodified genotyping probes. We investigated the feasibility of the DigiTag2 assay by genotyping 96 target SNPs spanning a 610-kb region of human chromosome 5. The DigiTag2 assay is suitable for genotyping an intermediate number of SNPs (tens to hundreds of sites) with a high conversion rate (> 90%), high accuracy, and low cost. (c) 2007 Elsevier Inc. All rights reserved.
引用
收藏
页码:78 / 85
页数:8
相关论文
共 25 条
[1]   Genomewide high-density SNP linkage analysis of 236 Japanese families supports the existence of schizophrenia susceptibility loci on chromosomes 1p, 14q, and 20p [J].
Arinami, T ;
Arinami, T ;
Ohtsuki, T ;
Ishiguro, H ;
Ujike, H ;
Tanaka, Y ;
Morita, Y ;
Mineta, M ;
Takeichi, M ;
Yamada, S ;
Imamura, A ;
Ohara, K ;
Shibuya, H ;
Ohara, K ;
Suzuki, Y ;
Muratake, T ;
Kaneko, N ;
Someya, T ;
Inada, T ;
Yoshikawa, T ;
Toyota, T ;
Yamada, K ;
Kojima, T ;
Takahashi, S ;
Osamu, O ;
Shinkai, T ;
Nakamura, M ;
Fukuzako, H ;
Hashiguchi, T ;
Niwa, S ;
Ueno, T ;
Tachikawa, H ;
Hori, T ;
Asada, T ;
Nanko, S ;
Kunugi, H ;
Hashimoto, R ;
Ozaki, N ;
Iwata, N ;
Harano, M ;
Arai, H ;
Ohnuma, T ;
Kusumi, I ;
Koyama, T ;
Yoneda, H ;
Fukumaki, Y ;
Shibata, H ;
Kaneko, S ;
Higuchi, H ;
Yasui-Furukori, N .
AMERICAN JOURNAL OF HUMAN GENETICS, 2005, 77 (06) :937-944
[3]   High-throughput multiplex SNP genotyping with MALDI-TOF mass spectrometry: Practice, problems and promise [J].
Bray, MS ;
Boerwinkle, E ;
Doris, PA .
HUMAN MUTATION, 2001, 17 (04) :296-304
[4]   Mapping complex disease loci in whole-genome association studies [J].
Carlson, CS ;
Eberle, MA ;
Kruglyak, L ;
Nickerson, DA .
NATURE, 2004, 429 (6990) :446-452
[5]   Genetic susceptibility contributes to renal and cardiovascular complications of type 2 diabetes mellitus [J].
Freedman, Barry I. ;
Bowden, Donald W. ;
Sale, Michele M. ;
Langefeld, Carl D. ;
Rich, Stephen S. .
HYPERTENSION, 2006, 48 (01) :8-13
[6]   DETECTION OF SPECIFIC POLYMERASE CHAIN-REACTION PRODUCT BY UTILIZING THE 5'-]3' EXONUCLEASE ACTIVITY OF THERMUS-AQUATICUS DNA-POLYMERASE [J].
HOLLAND, PM ;
ABRAMSON, RD ;
WATSON, R ;
GELFAND, DH .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1991, 88 (16) :7276-7280
[7]   Fidelity of DNA ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides [J].
Housby, JN ;
Southern, EM .
NUCLEIC ACIDS RESEARCH, 1998, 26 (18) :4259-4266
[8]   Genome-wide association study in esophageal cancer using GeneChip mapping 10K array [J].
Hu, N ;
Wang, CY ;
Hu, Y ;
Yang, HH ;
Giffen, C ;
Tang, ZZ ;
Han, XY ;
Goldstein, AM ;
Emmert-Buck, MR ;
Buetow, KH ;
Taylor, PR ;
Lee, MP .
CANCER RESEARCH, 2005, 65 (07) :2542-2546
[9]   Variation is the spice of life [J].
Kruglyak, L ;
Nickerson, DA .
NATURE GENETICS, 2001, 27 (03) :234-236
[10]  
Lindroos K, 2001, Nucleic Acids Res, V29, pE69, DOI 10.1093/nar/29.13.e69