A software facilitating adapter-ligation mediated allele-specific amplification for typing multiplex single nucleotide polymorphisms
Adapter-ligation mediated allele-specific amplification (ALM-ASA) is a potential method for multiplex single nucleotide polymorphisms (SNPs) typing at an ultra low cost. Here, we describe a software, which designs allele-specific primers for ALM-ASA assay on multiplex SNPs. DNA sequences containing SNPs of interest are submitted into the software which contains various restriction enzymes for options. Based on the SNP sequence information and the selected restriction enzymes, the software is capable of automatically generating sets of information needed to perform genotyping experiments. Each set contains a suitable restriction enzyme, qualified allele-specific primers with orientations and melting temperatures, sizes of allele-specific amplicons, and gel electrophoretograms simulated according to the sizes of the allele-specific amplicons and the mobility of DNA fragments in 2％ agarose gel. As the arylamines N-Acetyltransferase 2 (NAT2) has a role in the metabolism of many clinically important substances and the NAT2 polymorphisms have been reported to be associated with a number of cancers, seven SNPs in the NAT2 gene were selected for evaluating the software. Without extra optimization, 7-plex genotyping on 127 individuals were successfully detected by using a set of allele-specific primers produced by the software. Benefiting from the software, the ALM-ASA assay is easy-to-perform, inexpensive and amenable to automation and could facilitate the large-scale genotypic analysis.
SNiPdesigner SNP NAT2 genotyping
Weipeng Wang Wenming Sun Wenjuan Wu Guohua Zhou
Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, P.R.China;School of Pharmac Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, P.R.China Huadong Research Institute for Medicine and Biotechnics, Nanjing 210002, P.R.China;Medical School, N
国际会议
The 5th International Forum on Post-genome Technologies(5IFPT)(第五届国际后基因组生命科学技术学术论坛)
苏州
英文
2007-09-10（万方平台首次上网日期，不代表论文的发表时间）