Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population

Park, Sohyung; Cho, Sohee; Seo, Hee Jin; Lee, Ji Hyun; Kim, Moon Young; Lee, Soong Deok

doi:10.3346/jkms.2017.32.4.587

Cited by 28 publications

(23 citation statements)

References 28 publications

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“…(), Ramos et al (), nor Park, Cho, Seo, Lee, Kim, and Lee () reported any heteroplasmic hotspots; the observation being identical to the results of our study. Furthermore, the overall pattern of point heteroplasmic substitution at the level of above 10% (with a little prevalence of heteroplasmic substitution in the coding region than in the control region) in the normal colon cells reported here is similar to those observed for blood (Li et al., ; Parson et al., ; Ramos et al., ; Park et al., ) or saliva samples (Li et al., ). Nevertheless, when one takes into account the low level variants (below 10% level) from our study, the overall spectrum of heteroplasmic substitutions showed that heteroplasmy in normal colon cells hits predominantly the D‐loop region.…”

Section: Discussionsupporting

confidence: 92%

“…More importantly, the mtDNA mutational spectrum reconstructed by us for 100 normal specimens (analyzed population sample increased by 50 samples compared with our previous report, Skonieczna et al., ) is similar to that observed in healthy individuals from different populations. Indeed, different studies validated to detect the minority variant at the level of about 10%, showed that point heteroplasmy occurs in about 24%–28% of individuals (Li et al., ; Parson et al., ; Ramos et al., ; Park et al., ). Similarly, in our dataset, the 10% threshold of the minority variant detection enabled us to show heteroplasmic substitutions in 21% of normal tissue samples.…”

Section: Discussionmentioning

confidence: 99%

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Mitogenomic differences between the normal and tumor cells of colorectal cancer patients

et al. 2018

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So far, a reliable spectrum of mitochondrial DNA mutations in colorectal cancer cells is still unknown, and neither is their significance in carcinogenesis. Indeed, it remains debatable whether mtDNA mutations are "drivers" or "passengers" of colorectal carcinogenesis. Thus, we analyzed 200 mitogenomes from normal and cancer tissues of 100 colorectal cancer patients. Minority variant mutations were detected at the 1% level. We showed that somatic mutations frequently occur in colorectal cancer cells (75%) and are randomly distributed across the mitochondrial genome. Mutational signatures of somatic mitogenome mutations suggest that they might arise through nucleotide deamination due to oxidative stress. The majority of somatic mutations localized within the coding region (in positions not known from the human phylogeny) and was potentially pathogenic to cell metabolism. Further analysis suggested that the relaxation of negative selection in the mitogenomes of colorectal cancer cells may allow accumulation of somatic mutations. Thus, a shift in glucose metabolism from oxidative phosphorylation to glycolysis may create advantageous conditions for accumulation of mtDNA mutations. Considering the fact that the presence of somatic mtDNA mutations was not associated with any clinicopathological features, we suggested that mtDNA somatic mutations are "passengers" rather than the cause of colorectal carcinogenesis.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Mitogenomic differences between the normal and tumor cells of colorectal cancer patients

et al. 2018

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“…Both sites follow a 4‐mer poly‐A‐stretch (AAAA) region. Studies have suggested that it is the homopolymer stretch that lowers the efficiency of reads in this region . Low coverage in homopolymer regions of the Ion PGM™ or other MPS platforms has been described, as have high coverages in amplicons with few homopolymeric repeats .…”

Section: Resultsmentioning

confidence: 99%

“…However, the control region covers only 7% of the human mitochondrial genome and limits the resolution of matrilineal and ancestry inferences . Whole genome sequencing offers additional sequences from which mitochondrial haplogroups can be determined to the highest resolution .…”

Section: Introductionmentioning

confidence: 99%

“…Alternatively, massively parallel sequencing (MPS) can retrieve billions of ssDNA molecules, amplified from panels containing targeted or whole genome markers . Both targeted and whole genome panels have been used as in‐house methods to amplify mitochondrial genomes for sequencing . However, based on panel design, the performance of in‐house panels can be highly variable in accuracy, coverage, and strand balance.…”

Section: Introductionmentioning

confidence: 99%

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Performance of the Early Access AmpliSeq™ Mitochondrial Panel with degraded DNA samples using the Ion Torrent™ platform

2018

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The Early Access AmpliSeq™ Mitochondrial Panel amplifies whole mitochondrial genomes for phylogenetic and kinship identifications, using Ion Torrent™ technology. There is currently limited information on its performance with degraded DNA, a common occurrence in forensic samples. This study evaluated the performance of the Panel with DNA samples degraded in vitro, to mimic conditions commonly found in forensic investigations. Purified DNA from five individuals was heat-treated at five time points each (125°C for 0, 30, 60, 120, and 240 min; total n = 25). The quality of DNA was assessed via a real-time DNA assay of genomic DNA and prepared for massively parallel sequencing on the Ion Torrent™ platform. Mitochondrial sequences were obtained for all samples and had an amplicon coverage averaging between 66X to 2803X. Most amplicons (157/162) displayed high coverages (452 ± 333X), while reads with less than 100X coverage were recorded in five amplicons only (90 ± 5X). Amplicon coverage was decreased with prolonged heating. At 72% strand balance, reads were well balanced between forward and reverse strands. Using a coverage threshold of ten reads per SNP, complete sequences were recovered in all samples and resolved kinship and, haplogroup relations. Additionally, the HV1 and HV2 regions of the reference and 240-min heat-treated samples (n = 10) were Sanger-sequenced for concordance. Overall, this study demonstrates the efficacy of a novel forensic Panel that recovers high quality mitochondrial sequences from degraded DNA samples.

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Applications of Mitochondrial DNA in Forensic Science

Sinha

Rana

Kushwaha

2020

Forensic DNA Typing: Principles, Applications and Advancements

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Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population

Cited by 28 publications

References 28 publications

Mitogenomic differences between the normal and tumor cells of colorectal cancer patients

Mitogenomic differences between the normal and tumor cells of colorectal cancer patients

Performance of the Early Access AmpliSeq™ Mitochondrial Panel with degraded DNA samples using the Ion Torrent™ platform

Applications of Mitochondrial DNA in Forensic Science

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