Genetic analysis of 15 mtDNA SNP loci in Chinese Yi ethnic group using SNaPshot minisequencing

A combination of genome-wide association study screening and SNaPshot for detecting sex-related SNPs and genes in Cynoglossus semilaevis

Chinese tongue sole (Cynoglossus semilaevis) males and females exhibit great differences in growth rate and appearance. The species is heterogametic (ZW/ZZ) and has sex-reversed "pseudomales" that are genetically female and physiologically male. In this study, we identified eight sex-specific single nucleotide polymorphism (SNP) markers for the sex identification of C. semilaevis by using a combination of genome-wide association study (GWAS) screening and SnaPshot validation. Candidate SNPs were screened using genotyping by sequencing to perform GWAS of the differential SNPs between the sexes of C. semilaevis. The SNP loci were amplified using a multiplex PCR system and detected via SNaPshot, which enables multiplexing of up to 30-40 SNPs in a single assay and ensures high accuracy of the results. The molecular markers detected in our study were used to successfully identify normal males and pseudomales from 45 caught and 40 cultured C. semilaevis specimens. Linkage disequilibrium analysis showed that the eight SNP loci were related to each other, with a strong linkage. Moreover, we investigated the expression of prdm6 mRNA containing a missense SNP and confirmed that the gene is differentially expressed in the gonads of the different sexes of C. semilaevis; the expression of prdm6 mRNA was significantly higher in the males than in the females and pseudomales. This means prdm6 may be related to sex differentiation in C. semilaevis.

A set of 14 DIP-SNP markers to detect unbalanced DNA mixtures

Unbalanced DNA mixture is still a difficult problem for forensic practice. DIP-STRs are useful markers for detection of minor DNA but they are not widespread in the human genome and having long amplicons. In this study, we proposed a novel type of genetic marker, termed DIP-SNP. DIP-SNP refers to the combination of INDEL and SNP in less than 300bp length of human genome. The multiplex PCR and SNaPshot assay were established for 14 DIP-SNP markers in a Chinese Han population from Shanxi, China. This novel compound marker allows detection of the minor DNA contributor with sensitivity from 1:50 to 1:1000 in a DNA mixture of any gender with 1 ng-10 ng DNA template. Most of the DIP-SNP markers had a relatively high probability of informative alleles with an average I value of 0.33. In all, we proposed DIP-SNP as a novel kind of genetic marker for detection of minor contributor from unbalanced DNA mixture and established the detection method by associating the multiplex PCR and SNaPshot assay. DIP-SNP polymorphisms are promising markers for forensic or clinical mixture examination because they are shorter, widespread and higher sensitive.

Single nucleotide polymorphisms minisequencing in hypervariable regions for screening of Thais

Mitochondrial DNA (mtDNA) analysis has displayed an important role and been considered as a powerful tool in various fields of forensic science applications. Nowadays, single nucleotide polymorphisms (SNPs) on mtDNA have become additional DNA markers when conventional STR typing practically fails. mtDNA sequencing of polymerase chain reaction (PCR) products from the hypervariable region I (HVRI) and II (HVRII) is the standard method of mtDNA analysis. However, mtDNA sequencing is rather expensive, time consuming and technically complex. This study aims to develop the SNPs minisequencing for screening of Thai populations. For this purpose, sixteen SNPs that possess high discriminating power in hypervariable regions were selected. The DNA samples were obtained from 100 buccal swab samples of Thai healthy individuals. All DNA samples were extracted and were subsequently amplified by single duplex PCR technique. The duplex PCR products were genotyped by SNPs minisequencing. Based on 16 SNPs, a total of 63 haplotypes were observed of which 46 haplotypes were unique. The haplotype diversity, discriminating power and random match probability were calculated to be 0.9830, 0.9732 and 0.0268, respectively. The SNPs at 150, 199, 489, 16129, 16189, 16223, and 16304 were highly polymorphic in the studied population. Our results suggested that the SNPs minisequencing can be an alternative method of SNPs genotyping. This method can be used for an exclusion of a large number of mismatch samples and as a presumptive test prior to do confirmatory mtDNA sequencing.

Validation of Expressmarker mtDNA-SNP60: A mitochondrial SNP kit for forensic application

Expressmarker mtDNA-SNP60 kit, a 3-dye fluorescence labeling forensic mitochondrial-SNP kit, was developed and modified based on previous work. In this study, it was validated through sensitivity, precision, accuracy, reproducibility, species specificity, mixture samples, PCR-based conditions, and inhibitor studies, according to the Scientific Working Group on DNA Analysis Methods guidelines. In the sensitivity study, full profile was obtained from template DNA with the quantity ≥ 4 pg. Consistent profiles were obtained at three different laboratories, which demonstrated the reproducibility of the kit. No peak was observed in the profiles of common animal species and microorganisms demonstrating high species specificity of the kit. In the mixture study, some loci (minor contributors) were missing at 19:1 and 9:1 ratios, whereas all loci could be profiled at other ratios (4:1, 2:1, and 1:1). PCR-based studies demonstrated that there recommended PCR conditions were optimized for the kit, and there was acceptable tolerance of error. The inhibitor study indicated that the kit has varying degrees of resistance to the presence of common inhibitors. Twelve random individuals were profiled by next-generation sequencing to confirm the allele-specific PCR assay, and a consistent result was obtained. Furthermore, 520 individuals from 260 families were profiled and the results showed that all loci of the confirmed mother and child were matched. In addition, forensic population genetics parameters, including random match probability, discrimination power, and haplotype diversity, were calculated (0.0474, 0.9526, and 0.9563, respectively). Our study demonstrates that the Expressmarker mtDNA-SNP60 kit can be a useful supplementary tool for forensic application.