The short tandem repeat (STR) and single nucleotide polymorphisms (SNP) are widely distributed in human genomes. SNP-STR, a compound genetic marker combining a STR locus with tightly linked SNPs, is more informative than any single polymorphism. The amplification refractory mutation system (ARMS) can allow DNA sample with specific base (e.g., SNP) amplify successfully, which avoids the common PCR bias in the analyses of mixtures. This study aims at enriching the rs25768-D5S818 (D5S818, from U.S. Core Loci) primers obtained in the previous study to develop a forensic SNP-STRs multiplex. Two SNP-STRs (rs2246512-D10S1248 and rs9531308-D13S317) were screened from the UCSC genome browser. Two forward SNP allele-specific primers labelled with different fluorescent dyes for each SNP-STR marker were designed with the ARMS, and a common reverse primer was designed near the 3 0 region of STR. The amplicons of the three SNP-STRs were profiled via Genetic Analyzer ABI 3130. The sensitivity and specificity of the multiplex were confirmed by using the standard DNA (9947A). The SNP-STR genotype of minor component (0.05 ng) in the artificial extremely unbalanced two DNA mixture (ratio 1:40) was detected.

The existence of cell-free fetal (cff) DNA in maternal plasma through the process of pregnancy, makes it possible to do noninvasive paternity test for a woman who got pregnant as a result of a sexual assault. However, the cff DNA in a high background of maternal DNA could not be easily detected. The SNP-STR markers, developed for analyzing the minor component in a two-man unbalanced mixture, were used for noninvasive paternity identification during pregnancy. Six SNP-STR loci, rs4847015-D1S1656, rs6736691-D2S1338, rs25768-D5S818, rs7786079-D7S820, rs2246512-D10S1248, rs11642858-D16S539, were screened based on autosomal STRs of Expanded U.S. Core Loci, and the corresponding primers were designed by amplification refractory mutation system (ARMS) method. The primers for every loci consisted of two forward primers targeting the genotype of SNP and one reverse primer, and each forward primer was amplified with the reverse one respectively. The amplicons of the six loci were all less than 210 bp. The cff DNA of plasma samples from ten pregnant women at 16 to 22-week was detected using the informative makers selected from the analysis of maternal and biological paternal DNA by SNP-STR PCR. The results demonstrate the availability of SNP-STR in the noninvasive paternity test.

A B S T R A C TWith the advantages of lower mutation rates and improved analysis of the degraded or aged samples, single nucleotide polymorphism (SNP) markers has been considered as supplementary to the STRs. Consequently, a robust, simple and cost effective technique for SNP typing is essential to analyze a large number of SNPs. Ligase detection reaction (LDR) could detect a SNP on CE platform through the ability of DNA ligase which can seal the nick junction formed by oligonucleotides hybridized to the flank region of target SNP. Here we purposed a prestudy to set up a 8 Y-SNPs (M9, M74, M35, M95, M110, M89, M13, M20) multiplex panel for forensic application through PCR-ligase detection reaction (LDR) system. Primers of 8 loci were designed for multiplexed PCR. According to the sequence around the SNP site, three LDR probes were designed for each SNP including one common fluorescent labeled probe and two allele specific probes different in size with mismatching bases at the 3' end. PCR-LDR products were profiled through ABI3130 Genetic Analyzer. A set of 8 Y-SNP could be profiled through two multiplexed PCR and two multiplexed LDR. Even though the number of markers in the current system is limited, when fully developed, it can easily be multiplied more SNPs and yield a greater power of discrimination. Our study indicated that the PCR-LDR could provide a robust, simple and cost effective multiplexed SNP typing method for forensic cases in the future.