Estimation of the number of contributors to mixed samples of DNA by mitochondrial DNA analyses using massively parallel sequencing

• Published in: International journal of legal medicine Vol. 134; no. 1; pp. 101 - 109
• Main Authors: Nakanishi, Hiroaki, Fujii, Koji, Nakahara, Hiroaki, Mizuno, Natsuko, Sekiguchi, Kazumasa, Yoneyama, Katsumi, Hara, Masaaki, Takada, Aya, Saito, Kazuyuki
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 2020; Springer Nature B.V
• Subjects: Deoxyribonucleic acid; DNA; DNA Fingerprinting - methods; DNA Primers; DNA, Mitochondrial - analysis; Forensic Medicine; Gene Library; Gene sequencing; Genetic testing; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Medical Law; Medicine; Medicine & Public Health; Mitochondrial DNA; Original Article; Real-Time Polymerase Chain Reaction; Research Design; Sequence Analysis, DNA; Massively parallel sequencing; Mitochondrial DNA; Mixed DNA; Number of contributors
• ISSN: 0937-9827; 1437-1596
• DOI: 10.1007/s00414-019-02182-2

We evaluated whether the number of contributors to mixed DNA samples can be estimated by analyzing the D-loop of mitochondrial DNA using massively parallel sequencing. The A- (positions 16,209–16,400) and B- (positions 30–284) amplicons in hypervariable regions 1 and 2, respectively, were sequenced using MiSeq with 2 × 251 cycles. Sequence extraction and trimming were performed using CLC Genomics Workbench 11 and the number of observed haplotypes was counted for each amplicon type using Microsoft Excel. The haplotype ratios were calculated by dividing the number of counted reads of the corresponding haplotype by the total number of sequence reads. Haplotypes that were over the threshold (5%) were defined as positive haplotypes. The number of larger positive haplotypes in either of the two amplicon types was defined as the number of contributors. Samples were collected from seven individuals. Seventeen mixed samples were prepared by mixing DNA from two to five contributors at various ratios. The number of contributors was correctly estimated from almost all of the mixed samples containing equal amounts of DNA from two to five people. In mixed samples of two or three people, the minor components were detected down to a ratio of 20:1 or 8:2:1. However, heteroplasmy, base deletions, and sharing of the same haplotypes caused incorrect estimations of the number of contributors. Although this method still has room for improvement, it may be useful for estimating the number of contributors in a mixed sample, as it does not rely on forensic mathematics.