Korean J Leg Med.  2013 Nov;37(4):183-190. 10.7580/kjlm.2013.37.4.183.

Rapid and Simple Screening of Mitochondrial DNA in Koreans by the Analysis of Highly Variable Control Region SNPs

• Kim EH
• Shin KJ
• Kim HY
• Park SJ
• Yang WI
• Lee HY

• KMID: 1928014
• DOI: http://doi.org/10.7580/kjlm.2013.37.4.183

Abstract

Human mitochondrial DNA (mtDNA) is generally used to identify highly degraded forensic samples, particularly when the extracted DNA is not sufficient for nuclear DNA analysis. However, direct sequencing, the most widely used mtDNA analysis method, is laborious and time-consuming, and precludes the simultaneous analysis of many samples. Here, we describe a rapid and simple screening method for mtDNA analysis in Koreans using single base extension (SBE) methods. Sixteen highly polymorphic mtDNA SNPs from the control region were selected, and a multiplex SBE system was constructed to analyze them. Because the developed system consists of two duplex PCRs, which produce small amplicons with fewer than 270 bp, it works well with highly degraded samples such as old skeletal remains. Using this multiplex SBE system, 145 different haplotypes were expected to be observed from 593 unrelated Koreans. Seventy-three haplotypes were expected to be observed only once, and the most frequent haplotype was expected to occur 80 times. Since the mean number of pairwise differences was estimated to be 4.55, the developed system could be useful to exclude samples that do not match evidence and reference samples. Therefore, the multiplex SBE system used in this study will be a useful tool to analyze many samples simultaneously and to efficiently screen out non-matching mtDNA sequences in forensic casework.

Keyword

Mitochondria DNA; Control region; Single nucleotide polymorphism; Single base extension; Koreans

MeSH Terms

Asian Continental Ancestry Group
DNA
DNA, Mitochondrial*
Haplotypes
Humans
Mass Screening*
Methods
Polymerase Chain Reaction
Polymorphism, Single Nucleotide*
DNA
DNA, Mitochondrial

Figure

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  Fig. 1. Multiplex SBE genotyping of various Korean mtDNA samples (a-c). Results for multiplex SBE I were shown on the left, and the results for multiplex SBE II were shown on the right.

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  Fig. 2. Electropherograms of multiplex SBE using degraded DNA obtained from old skeletal remains (a-d). Results for multiplex SBE I were shown on the left, and the results for multiplex SBE II were shown on the right.

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