Elsevier

Legal Medicine

Volume 17, Issue 6, November 2015, Pages 467-470
Legal Medicine

Short Communication
Analysis of 30 insertion–deletion polymorphisms in the Japanese population using the Investigator DIPplex® kit

https://doi.org/10.1016/j.legalmed.2015.10.002Get rights and content

Highlights

  • Analysis of INDELs in Japanese population by Investigator DIPplex kit was performed.

  • This system must be useful for personal identity in Japanese subjects.

  • This system may be useful for the analysis of the degrade DNA samples.

Abstract

Allele frequencies and forensic parameters for 30 insertion–deletion polymorphisms (INDELs) were investigated in a sample of 251 unrelated Japanese individuals using the Investigator DIPplex® kit (QIAGEN). The frequency distributions showed no deviations from Hardy–Weinberg equilibrium expectations. The combined powers of discrimination and match probability for the 30 INDELs were 0.9999999998 and 2.67 × 10−11, respectively. To assess the effectiveness of the kit in typing degraded DNA, an ancient bone sample of a Jomon skeleton was analyzed; most of 30 INDELs and amelogenin were typed successfully. We concluded that the kit offers considerable potential for personal identification from degraded DNA samples due to the small amplicon length and high degree of polymorphisms.

Introduction

Recent forensic interest has focused on insertion–deletion polymorphisms (INDELs or DIPs) for personal identification. Several authors have reported population genetic data for INDELs since the development of the first commercial kit (QIAGEN, Hilden, Germany) [1], [2], [3], [4], [5], [6], [7], [8], [9], [10]. The kit can be used for typing 30 INDELs, and is designed to generate amplicons of less than 160 bp, with the optimal amount of DNA is set low volume (0.2–0.5 ng) according to the manual. Therefore, this technique may be capable of efficiently analyzing degraded samples. In this study, we investigated data obtained from a Japanese population for the 30 INDELs using the commercially available kit, and the allelic frequencies among the Japanese population data were compared with those of other populations. In addition, to assess the effectiveness of the kit in analyzing degraded DNA, we analyzed an ancient bone sample of a Jomon skeleton.

Section snippets

Population

This study was approved by the ethics committee of Shinshu University. With informed consent, we collected samples from 251 unrelated, healthy, adult Japanese individuals (154 males and 97 females). The Jomon skeleton, which was discovered at the Shimekake site in Nagano, Japan, was used as the highly degraded DNA sample. This skeleton is estimated to belong to the Jomon period, approximately 3,300–2,200 years ago [11].

DNA extraction

DNA was extracted from blood or buccal mucosa cells using the QIAamp DNA

Results and discussion

Table 1 shows the allele frequencies and forensic statistical parameters of 30 INDELs in the Japanese population. The genotype frequency distributions showed no significant deviation from HWE by an exact test (p = 0.0017, after Bonferroni’s correction for multiple testing). Ho values ranged from 0.1474 (HLD 118) to 0.5538 (HLD 136), with a mean value of 0.422. The PD values ranged from 0.258 (HLD 118) to 0.623 (HLD 56), and 24 of the 30 INDELs showed PD values greater than 0.5. The combined PD

Access of data

Available upon request to [email protected].

References (13)

There are more references available in the full text version of this article.

Cited by (12)

  • Diallelic Markers: INDELs and INNULs

    2022, Forensic Genetic Approaches for Identification of Human Skeletal Remains: Challenges, Best Practices, and Emerging Technologies
  • Genetic polymorphisms of 30 insertion/deletion markers in the populations of Japan, Bangladesh, and Indonesia

    2019, Forensic Science International: Genetics Supplement Series
    Citation Excerpt :

    Several studies have reported the population data of 30 insertion/deletion (INDEL) markers; however, few of these reports pertain to Asian populations, with the exception of Taiwanese [1], Bangladeshi [2], Korean [3,4], Chinese [5,6], and Japanese [7] populations.

  • Evaluation of 30 insertion/deletion polymorphisms as forensic markers in the Kuwaiti population

    2019, Forensic Science International: Genetics Supplement Series
    Citation Excerpt :

    Fig. 1 shows there was a clear signal of genetic differentiation between the populations, suggesting there is genetic structuring between populations, in agreement with the PCA analysis. To determine how genetically distant the Kuwaiti population is compared to other global populations, PCA was carried out using DIPplex marker allele frequencies from 27 different global populations [2–17], including Kuwait. This revealed five distinct clusters representing different continents, namely Asia, Europe, South America, Africa and the Middle East region (Supplementary Fig. 2).

  • A comprehensive exploration of the genetic legacy and forensic features of Afghanistan and Pakistan Mongolian-descent Hazara

    2019, Forensic Science International: Genetics
    Citation Excerpt :

    We used the ddH2O as the negative control sample and 9947A cell line as the positive control sample in each batch of amplification and capillary electrophoresis. To comprehensively and deeply dissect the genetic structure and reconstruct the phylogenetic relationship between the Hazara and worldwide human populations, we employed four different datasets (namely DatasetⅠ, DatasetⅡ, DatasetⅢ, and DatasetⅣ) [10–12,14–49]. We first merged our newly genotyped data with previously published data to form the first set of data.

  • Applicability of the SNPforID 52-plex panel for human identification and ancestry evaluation in a Brazilian population sample by next-generation sequencing

    2019, Forensic Science International: Genetics
    Citation Excerpt :

    Studies using the Investigator DIPplex set of INDELs revealed lower informativeness, which is consistent with its lower number of markers. Analysis performed in Brazil [11], Japan [12], Poland and Taiwan [13] resulted in match probabilities of 3.4 × 10−13, 2.67 × 10−11, 7.98 × 10−14 and 1.22 × 10−11, respectively. The match probabilities obtained with these INDELs are at least five degrees of magnitude lower than the ones estimated by Sanchez’s group [8] using the 52-plex kit.

View all citing articles on Scopus
View full text