Nucleic Acids Research, 2002, Vol. 30, No. 14 e70
© 2002 Oxford University Press
Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system
Department of Medical Sciences, Uppsala University, 75185 Uppsala, Sweden
*To whom correspondence should be addressed at: Molecular Medicine, Entrance 70, Third Floor, Research Department 2, Uppsala University Hospital, 75187 Uppsala, Sweden. Tel: +46 18 6112959; Fax: +46 18 6112519; Email: ann-christine.syvanen{at}medsci.uu.se
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
We selected 125 candidate single nucleotide polymorphisms (SNPs) in genes belonging to the human type 1 interferon (IFN) gene family and the genes coding for proteins in the main type 1 IFN signalling pathway by screening databases and by in silico comparison of DNA sequences. Using quantitative analysis of pooled DNA samples by solid-phase mini-sequencing, we found that only 20% of the candidate SNPs were polymorphic in the Finnish and Swedish populations. To allow more effective validation of candidate SNPs, we developed a four-colour microarray-based mini-sequencing assay for multiplex, quantitative allele frequency determination in pooled DNA samples. We used cyclic mini-sequencing reactions with primers carrying 5'-tag sequences, followed by capture of the products on microarrays by hybridisation to complementary tag oligonucleotides. Standard curves prepared from mixtures of known amounts of SNP alleles demonstrate the applicability of the system to quantitative analysis, and showed that for about half of the tested SNPs the limit of detection for the minority allele was below 5%. The microarray-based genotyping system established here is universally applicable for genotyping and quantification of any SNP, and the validated system for SNPs in type 1 IFN-related genes should find many applications in genetic studies of this important immunoregulatory pathway.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. Chavan, K. Joshi, and B. Patwardhan DNA Microarrays in Herbal Drug Research Evid. Based Complement. Altern. Med., December 1, 2006; 3(4): 447 - 457. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Hu, H.-Y. Wang, D. M. Greenawalt, M. A. Azaro, M. Luo, I. V. Tereshchenko, X. Cui, Q. Yang, R. Gao, L. Shen, et al. AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays Nucleic Acids Res., October 18, 2006; 34(17): e116 - e116. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-C. Yang, Y.-J. Liang, M.-C. Huang, L.-H. Li, C.-H. Lin, J.-Y. Wu, Y.-T. Chen, and C.S.J. Fann A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments Nucleic Acids Res., September 10, 2006; 34(15): e106 - e106. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Milani, M. Fredriksson, and A.-C. Syvanen Detection of Alternatively Spliced Transcripts in Leukemia Cell Lines by Minisequencing on Microarrays Clin. Chem., February 1, 2006; 52(2): 202 - 211. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-H. Park, I.-J. Kim, H. C. Kang, Y. Shin, H.-W. Park, S.-G. Jang, J.-L. Ku, S.-B. Lim, S.-Y. Jeong, and J.-G. Park Oligonucleotide Microarray-Based Mutation Detection of the K-ras Gene in Colorectal Cancers with Use of Competitive DNA Hybridization Clin. Chem., September 1, 2004; 50(9): 1688 - 1691. [Full Text] [PDF]
|
|
|
|
 |
|
 A. Forche, P. T. Magee, B. B. Magee, and G. May Genome-Wide Single-Nucleotide Polymorphism Map for Candida albicans Eukaryot. Cell, June 1, 2004; 3(3): 705 - 714. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Lovmar, M. Fredriksson, U. Liljedahl, S. Sigurdsson, and A.-C. Syvanen Quantitative evaluation by minisequencing and microarrays reveals accurate multiplexed SNP genotyping of whole genome amplified DNA Nucleic Acids Res., November 1, 2003; 31(21): e129 - e129. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Flavell, V. N. Bolshakov, A. Booth, R. Jing, J. Russell, T. H. N. Ellis, and P. Isaac A microarray-based high throughput molecular marker genotyping method: the tagged microarray marker (TAM) approach Nucleic Acids Res., October 1, 2003; 31(19): e115 - e115. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Baner, A. Isaksson, E. Waldenstrom, J. Jarvius, U. Landegren, and M. Nilsson Parallel gene analysis with allele-specific padlock probes and tag microarrays Nucleic Acids Res., September 1, 2003; 31(17): e103 - e103. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Shmulevich, J. Astola, D. Cogdell, S. R. Hamilton, and W. Zhang Data extraction from composite oligonucleotide microarrays Nucleic Acids Res., April 1, 2003; 31(7): e36 - e36. [Abstract] [Full Text] [PDF]
|
|