Forensic and population genetic analyses of eighteen non-CODIS miniSTR loci in the Korean population

Multicolor-based discrimination of 21 short tandem repeats and amelogenin using four fluorescent universal primers

The aim of this study was to develop a cost-effective genotyping method using high-quality DNA for human identification. A total of 21 short tandem repeats (STRs) and amelogenin were selected, and fluorescent fragments at 22 loci were simultaneously amplified in a single-tube reaction using locus-specific primers with 24-base universal tails and four fluorescent universal primers. Several nucleotide substitutions in universal tails and fluorescent universal primers enabled the detection of specific fluorescent fragments from the 22 loci. Multiplex polymerase chain reaction (PCR) produced intense FAM-, VIC-, NED-, and PET-labeled fragments ranging from 90 to 400 bp, and these fragments were discriminated using standard capillary electrophoretic analysis. The selected 22 loci were also analyzed using two commercial kits (the AmpFLSTR Identifiler Kit and the PowerPlex ESX 17 System), and results for two loci (D19S433 and D16S539) were discordant between these kits due to mutations at the primer binding sites. All genotypes from the 100 samples were determined using 2.5 ng of DNA by our method, and the expected alleles were completely recovered. Multiplex 22-locus genotyping using four fluorescent universal primers effectively reduces the costs to less than 20% of genotyping using commercial kits, and our method would be useful to detect silent alleles from commercial kit analysis.

Association of LPHN3 rs6551665 A/G polymorphism with attention deficit and hyperactivity disorder in Korean children

Attention deficit hyperactivity disorder (ADHD) is a common and highly heritable disorder of school-age children. Its heritability was estimated at 80-90% but the genetic component underpinning this disorder remains to be disclosed. Recently, a highly consistent association between latrophilin3 (LPHN3) gene and ADHD was reported. In the present study, we examined the association between the LPHN3 rs6551665 A/G polymorphism and ADHD in Korea. The samples used in the study consisted of 150 ADHD children and 322 controls. The ADHD children were diagnosed according to DSM-IV. ADHD symptoms were evaluated with Dupaul Parent ADHD Rating Scales. LPHN3 rs6551665 SNP was determined by PCR-RFLP. Hardy-Weinberg equilibrium, genotype and allele frequency differences between the case and the control, and odds ratio were examined using the chi-square and exact tests. The LPHN3 gene locus was found to have no deviation from the Hardy-Weinberg expectation. We observed a significant association between the ADHD children and control group in genotype frequency (p=0.01) and allele frequency (p=0.02). The ADHD children appeared to have a surplus of GG genotype (OR 2.959, 95% CI 1.416-6.184, p=0.003) and G allele (OR 1.44, 95% CI 1.062-1.945, p=0.02). The association was more distinctive when analysis was confined to male samples (p=0.005), the OR of male controls and cases was 4.029 (95% CI 1.597-10.164, p=0.002) and the OR having G allele vs. A allele was 1.46 (95% CI 1.002-2.127, p=0.048). Thus our results imply that the LPHN3 rs6551665 GG genotype and G allele may provide a significant effect on the ADHD, although larger sample sizes and functional studies are necessary to further elucidate these findings.

Rapid genotyping of 25 autosomal STRs in a Japanese population using fluorescent universal primers containing locked nucleic acids

Amplification of fluorescently labeled products is one of the most popular methods for genotyping genetic variations. Two-step amplification using fluorescent universal primers simultaneously produces multiple targeted fragments labeled with fluorescent dyes, and this strategy is applicable to large-scale, cost-effective genotyping. In this study, we developed a fast PCR-based, multiple short tandem repeat (STR) genotyping method using fluorescent universal primers containing locked nucleic acids (LNAs). Four amplification reactions, each assaying six or seven markers and using 0.5-1.0 ng of genomic DNA, produced obvious Fam-labeled peaks in all 26 loci tested (25 autosomal STRs and amelogenin). The overall amplification time was 37 min. Moreover, fluorescent signals for the 25 STRs obtained from LNA-containing primers were 1.5-9.0 fold higher compared to those from non-LNA primers. Using genomic DNA from 120 Japanese individuals, 16 out of the 25 STRs had observed heterozygosity greater than 0.7. Some of these 25 STRs also had high discriminatory power, similar to that of the 13 core STRs in the Combined DNA Index System dataset. The probability of incorrectly assigning a match based on the accumulated matching probability for these 25 STRs is 1.2 × 10(-22), and their combined use can provide robust information for Japanese forensics.