| 1. |
- Andreaggi, Kimberly, et al.
(författare)
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Complete Mitochondrial DNA Genome Variation in the Swedish Population
- 2023
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Ingår i: Genes. - : MDPI. - 2073-4425. ; 14:11, s. 1989-1989
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Tidskriftsartikel (refereegranskat)abstract
- The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies.
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| 2. |
- Sturk-Andreaggi, Kimberly, 1981-, et al.
(författare)
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Mitochondrial DNA genome variation in the Swedish population
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The development of mitochondrial genome (mitogenome) reference data for inclusion in publicly-available population databases is currently underway, and the more high-quality mitogenomes that can be generated will only enhance the statistical power of this forensically-useful locus. In order to promote mitogenome testing in Sweden, the mitochondrial DNA (mtDNA) data from the SweGen whole genome sequencing (WGS) dataset were analysed. To avoid the interference from nuclear mtDNA segments (NUMTs), a 10% frequency threshold was applied for the population analyses. In total, 934 forensic-quality mitogenome haplotypes were produced. Despite the elevated frequency threshold, 31 NUMT variants were observed in 13 lower coverage haplotypes. However, NUMT interference was minimal and localized to two hotspot regions, substantially reducing the analysis burden required at lower frequency thresholds. Almost 45% of the SweGen haplotypes belonged to haplogroup H and nearly all mitogenome haplotypes (99.1%) assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were characteristic northern Swedish (i.e., Saami) and Finnish haplogroups observe in the dataset, consistent with the nuclear DNA analyses of the SweGen data. The analysis of the complete mitogenome resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the mitogenomes generated from the SweGen WGS data provide a mitogenome reference database for Sweden as well as contribute to the global effort to increase the availability of mitogenome reference data.
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| 3. |
- Sturk-Andreaggi, Kimberly, et al.
(författare)
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The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies : Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes
- 2022
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1661-6596 .- 1422-0067. ; 23:4
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612–13,105 and 16,390–16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.
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