An efficient procedure for genotyping single nucleotide polymorphisms

Abstract

Analysis of single nucleotide polymorphisms (SNPs) has been and will be increasingly utilized in various genetic disciplines, particularly in studying genetic determinants of complex diseases. Such studies will be facilitated by rapid, simple, low cost and high throughput methodologies for SNP genotyping. One such method is reported here, named tetra-primer ARMS-PCR, which employs two primer pairs to amplify, respectively, the two different alleles of a SNP in a single PCR reaction. A computer program for designing primers was developed. Tetra-primer ARMS-PCR was combined with microplate array diagonal gel electrophoresis, gaining the advantage of high throughput for gel-based resolution of tetra-primer ARMS-PCR products. The technique was applied to analyse a number of SNPs and the results were completely consistent with those from an independent method, restriction fragment length polymorphism analysis.

Combined haplotype analysis of the interleukin-19 and -20 genes: relationship to plaque-type psoriasis

“…29 This method uses four different primers, two (the so-called inner primers) are allele specific and two (outer primers) are control primers. Primers were designed by using the program at http://cedar.genetics.soton.ac.uk/public_ html/primer1.html.…”

New genetic maps for globe artichoke and wild cardoon and their alignment with an SSR-based consensus map

“…SNP markers were directed at seven genes involved in the synthesis of caffeoylquinic acids, namely HCT, HQT, C3'H, C4H, 4CL, Acyltransf_1 and _2 (Comino et al 2007;Moglia et al 2009;Menin et al 2010). The assay was based on a tetra-primer ARMS-PCR (amplification refractory mutation system) protocol (Ye et al 2001), with the amplicons being separated by electrophoresis through 2% w/v agarose gels and visualized by ethidium bromide staining.…”

Isolation and mapping of a C3′H gene (CYP98A49) from globe artichoke, and its expression upon UV-C stress

“…SNPs genotyping was carried out with the tetra-primers ARMS-PCR method (Ye et al 2001) by using two sets of outer and inner primers (Table 1), designed using the software made available on-line (http://cedar.genetics. soton.ac.uk/public_html/primer1.html).…”