Reprint of: Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)

Parson, Walther; Strobl, Christina; Huber, Gabriela; Zimmermann, Bettina; Gomes, Sibylle M.; Souto, L.; Fendt, Liane; Delport, Rhena; Langit, Reina; Wootton, Sharon; Lagacé, Robert; Irwin, Jodi A.

doi:10.1016/j.fsigen.2013.09.007

Cited by 34 publications

(21 citation statements)

References 24 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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“…STS. With the utility of bench-top sequencers like Illumina MiSeq and Ion Torrent PGM (Personal Genome Machine), generation of whole mtGenome data is feasible for the application-orientated laboratory [6][7][8][9][10].…”

Section: Introductionmentioning

confidence: 99%

Whole mitochondrial genome genetic diversity in an Estonian population sample

et al. 2015

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Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25% of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7% in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85%, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99% for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions.

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“…Sequencing polymerase was added after the annealing step, and the sample was loaded onto the Ion 316 chip (Parson et al 2013;Arrach et al 2014).…”

Section: High-throughput Sequencing Of Positive Bac Clonesmentioning

confidence: 99%

Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization

Jiang

Wang

Zhang³

et al. 2015

Mar Biotechnol

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The small abalone (Haliotis diversicolor) is one of the most important aquaculture species in East Asia. To facilitate gene cloning and characterization, genome analysis, and genetic breeding of it, we constructed a large-insert bacterial artificial chromosome (BAC) library, which is an important genetic tool for advanced genetics and genomics research. The small abalone BAC library includes 92,610 clones with an average insert size of 120 Kb, equivalent to approximately 7.6× of the small abalone genome. We set up three-dimensional pools and super pools of 18,432 BAC clones for target gene screening using PCR method. To assess the approach, we screened 12 target genes in these 18,432 BAC clones and identified 16 positive BAC clones. Eight positive BAC clones were then sequenced and assembled with the next generation sequencing platform. The assembled contigs representing these 8 BAC clones spanned 928 Kb of the small abalone genome, providing the first batch of genome sequences for genome evaluation and characterization. The average GC content of small abalone genome was estimated as 40.33%. A total of 21 protein-coding genes, including 7 target genes, were annotated into the 8 BACs, which proved the feasibility of PCR screening approach with three-dimensional pools in small abalone BAC library. One hundred fifty microsatellite loci were also identified from the sequences for marker development in the future. The BAC library and clone pools provided valuable resources and tools for genetic breeding and conservation of H. diversicolor.

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Reprint of: Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM)

Cited by 34 publications

References 24 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

Whole mitochondrial genome genetic diversity in an Estonian population sample

Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization

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