2. Materials and methods2.1 Samples

Peripheral blood or buccal swab samples were collected from 197 unrelated individuals residing in the Gifu Prefecture in central Japan, 80 unrelated individuals residing in Dhaka, Bangladesh, and 78 unrelated individuals living in Surabaya (eastern region of Java Island), Indonesia.

2.2 DNA extraction

Genomic DNA was extracted from blood-stained filter papers and buccal swabs using the QuickGene-810 nucleic acid isolation system (Fujifilm, Tokyo, Japan) or the QIAamp® DNA Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

2.3 PCR

The 30 INDEL markers were amplified from genomic DNA using the Investigator® DIPplex Kit (Qiagen) and a Veriti™ Thermal Cycler (Applied Biosystems, Foster City, CA, USA), according to the manufacturer’s instructions.

2.4 Typing

The amplified products were separated using capillary electrophoresis on an ABI PRISM® 310 Genetic Analyzer (Applied Biosystems). The run data were analyzed using the GeneMapper® ID Software v3.2 (Applied Biosystems).

2.5 Statistical analysis

Allele frequencies, observed heterozygosity, expected heterozygosity, polymorphic information content, power of discrimination (PD), and mean exclusion chance were calculated using the Stat40 software. A Hardy–Weinberg equilibrium (HWE) test was performed in the analyzed population using the Arlequin 3.5.2.2 software. Furthermore, population differentiation was evaluated using the Arlequin software.

3. Results and discussionAllele frequencies and forensic parameters of the 30 INDEL markers in 197 Japanese, 80 Bangladeshi, and 78 Indonesian individuals are shown in Table 1. No significant deviations from HWE were observed for the 30 INDEL markers, with the exception of HLD77 and HLD99 in the Japanese samples and HLD118 in the Bangladeshi and Indonesian samples. The highest PD value was observed for HLD77, HLD118, and HLD48 in the Japanese, Bangladeshi, and Indonesian populations, respectively. The combined PD values for the 30 INDEL markers in the Japanese, Bangladeshi, and Indonesian populations were 0.999999999983, 0.999999999999, and 0.999999999937, respectively.

Table 1Frequencies of deletion alleles and forensic parameters of 30 INDEL markers in 197 Japanese, 80 Bangladeshis and 78 Indonesians.

Ho, observed heterozygosity; He, expected heterozygosity; PIC, polymorphic information contents; DP, power of discrimination; MEC, mean exclusion chance; HWE, p-value for Hardy-Weinberg equilibrium.

A population comparison of allele frequency distributions for each of the 30 INDEL markers revealed the presence of significant differences for 14 markers (HLD45, HLD111, HLD56, HLD118, HLD93, HLD99, HLD101, HLD48, HLD122, HLD125, HLD81, HLD40, HLD128, and HLD39) between the Japanese and Bangladeshi samples, 15 markers (HLD77, HLD45, HLD131, HLD6, HLD111, HLD56, HLD118, HLD114, HLD124, HLD122, HLD125, HLD81, HLD136, HLD39, and HLD84) between the Japanese and Indonesian samples, and 12 markers (HLD131, HLD111, HLD118, HLD99, HLD101, HLD114, HLD124, HLD122, HLD40, HLD128, HLD39, and HLD84) between the Bangladeshi and Indonesian samples.

The results of the present study would be useful in forensic genetic investigations and population genetic studies.