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10.01.2022 | Original Article

Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq

verfasst von: Hiroaki Nakanishi, Katsumi Yoneyama, Masaaki Hara, Aya Takada, Kentaro Sakai, Kazuyuki Saito

Erschienen in: International Journal of Legal Medicine | Ausgabe 2/2022

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Abstract

We tried to estimate individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq. The BAM files produced by MiSeq were viewed using Integrative Genomics Viewer (IGV) to verify mixed bases. By sorting the reads according to base type for each mixed base, partial haplotypes were determined. Then, the BAM files produced by MinKNOW were viewed using IGV. To determine haplotypes with IGV, only mixed bases determined by MiSeq were used as target bases. By sorting the reads according to base type for each target base, each contributor’s haplotype was estimated. In mixed samples from two contributors, even a haplotype with a minor contribution of 5% could be distinguished from the haplotype of the major contributor. In mixed samples of three contributors (mixture ratios of 1:1:1 and 4:2:1), each haplotype could also be distinguished. Sequences of C-stretches were determined very inaccurately in the MinION analysis. Although the analysis method was simple, each haplotype was correctly detected in all mixed samples with two or three contributors in various mixture ratios by combining MinION and MiSeq. This should be useful for identifying contributors to mixed samples.

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Titel: Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq
verfasst von: Hiroaki Nakanishi
Katsumi Yoneyama
Masaaki Hara
Aya Takada
Kentaro Sakai
Kazuyuki Saito
Publikationsdatum: 10.01.2022
Verlag: Springer Berlin Heidelberg
Erschienen in: International Journal of Legal Medicine / Ausgabe 2/2022
Print ISSN: 0937-9827
Elektronische ISSN: 1437-1596
DOI: https://doi.org/10.1007/s00414-021-02763-0

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