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. 2020 Oct 1;8:e9908. doi: 10.7717/peerj.9908

Figure 4. Mitochondrial SNP variants associated with the specific D mtDNA haplogroup types used in this study.

Figure 4

Platelets obtained from patients were sequenced using a kit (DNeasy Blood and Tissue Kit, Qiagen, Germantown, MD), and found to be in the D mtDNA haplogroup (n = 3). The D mtDNA haplogroup is associated with individuals from Asian maternal descent. The specific variants of those in the D mtDNA haplogroup were identified and their phylogenic tree is displayed. These variants include D4a2b, D4a6, and D4d. Next Generation Sequencing (NGS) technology was used to sequence both strands of mtDNA independently in both directions. This was done to quantitate the haplogroup-defining single nucleotide polymorphisms (SNPs), private SNPs (not defining haplogroups), and low-frequency heteroplasmy SNPs across the entire mitochondrial genome. The mtDNA sequences were analyzed using HaploGrep (https://haplogrep.i-med.ac.at/) to identify the mtDNA haplogroups. SNP variants were verified using http://www.MitoMap.org, http://www.Phylotree.org, and/or http://www.hmtvar.uniba.it.