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

Figure 3. Mitochondrial SNP variants associated with the A and B mtDNA haplogroups used in this study.

Figure 3

Platelets obtained from patients were sequenced using a kit (DNeasy Blood and Tissue Kit, Qiagen, Germantown, MD), and found to be in the A or B mtDNA haplogroups (n = 4). (A) The A mtDNA haplogroup is associated with individuals from Hispanic maternal descent. The specific variants of those in the A mtDNA haplogroup were identified and their phylogenic tree is displayed. These variants include A2 and A2w. (B) The B mtDNA haplogroup is also associated with individuals from Hispanic maternal descent. The specific variants of those in the B mtDNA haplogroup were identified and their phylogenic tree is displayed. These variants include B and B2a. 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.