Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel

Methods for the analysis of mitochondrial DNA

“…The use of MPS technologies for the sequencing and analysis of mitochondrial genomes for both high quality (King et al, 2014;Parson et al, 2013;Peck et al, 2016Peck et al, , 2018Zhou et al, 2016) and compromised samples (Chaitanya et al, 2015;Parson et al, 2015;Strobl et al, 2019;Strobl, Eduardoff, Bus, Allen, & Parson, 2018) is well established in the literature. The use of MPS for mtDNA analysis also allows the detection of low-level heteroplasmy (Cho, Kim, Lee, & Lee, 2018;Holland, Makova, & McElhoe, 2018;Just et al, 2015) and mixture deconvolution (Churchill, Stoljarova, King, & Budowle, 2018;Holland, McQuillan, & O'Hanlon, 2011), further increasing the discriminatory power of the technique and expanding the range of sample types suitable for analysis.…”

“…Nucleotides in a homopolymer stretch are not detected independently, but as a cumulative change in pH, this means the platform struggles to determine the number of nucleotides in a stretch contributing to a signal. The issues with platform ability to sequence these stretches was shown to improve with new sequencing chemistries (Churchill et al, 2016; Parson et al, 2013) and the Ion Gene Studio™ S5 platform (Strobl et al, 2019; Woerner et al, 2018), but were still present.…”

“…Multiple evaluations of this panel have been carried out (Gouveia et al, 2017; Pereira, Longobardi, & Borsting, 2018; Strobl et al, 2018, 2019; Woerner et al, 2018). These studies demonstrate that the panel is able to generate consistent, concordant, and reliable mitochondrial genome haplotypes.…”

“…These studies demonstrate that the panel is able to generate consistent, concordant, and reliable mitochondrial genome haplotypes. These evaluations included compromised sample types (Gouveia et al, 2017; Pereira et al, 2018; Strobl et al, 2019).…”

“…Strobl et al (2019) carried out a wide‐scale performance evaluation of the precision ID mtDNA whole genome panel involving more than 500 samples from 24 populations (Strobl et al, 2019). The samples were selected to represent the majority of global “superhaplogroups” to determine the efficacy of the panel in amplifying a range of haplogroup motifs.…”