Developing eight SNP-STR markers for DNA mixture detection

Abstract

SNP-STR marker is a compound marker constituted by a STR marker and a SNP in the flanking sequence. SNP-STR marker has been introduced to improve the discrimination power of STR markers in previous reports. Recently, some researchers have reported that SNP-STR markers performed well in detecting unbalanced DNA mixtures by designing two allele-specific primers. In this study, STR markers were selected from previously reports which had a high polymorphism in Chinese Han population. Then SNP markers with minor allele frequency (MAF) above 0.10 and locate no more than 250bp from the repeat sequence of STR markers were screened from SNP database. Based on these criteria, eight SNP-STR markers were finally selected and amplification refractory mutation system (ARMS-PCR) method was used to achieve allele-specific amplification. 20 samples were used to estimate the polymorphism of SNPs in Chinese Han population. Six of the eight loci had a high polymorphism in SNP (above 0.20) which indicated the potential of discriminating DNA mixtures. Most of the primers target minor DNA at an excess of 100-fold major DNA. However, discrimination power is not high enough using these six loci. Therefore, further studies are necessary in developing more SNP-STR markers.