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Mitochondrial DNA Mutations and Aging
Published in Sara C. Zapico, Mechanisms Linking Aging, Diseases and Biological Age Estimation, 2017
Rebecca Gordon, Sara C. Zapico
As described above, human mtDNA is highly polymorphic. On the basis of certain SNPs present in mtDNA, which are well established and widely distributed, the human population can be divided into haplogroups (Malhi et al. 2003). Analysis of these polymorphisms from a wide range of human populations have revealed sets of ancestral mutations that define these haplogroups that have common ancestry and, because of uniparental inheritance, evolve independently from each other. Each of these haplogroups is defined by specific sets of associated mutations, thus allowing for a quick and precise classification of the mtDNA molecules within a certain population (De Benedictis et al. 1999). These associated mutations were suggested to affect coupling efficiency of the ETC enabling adaptation to life in different climatic conditions (Wallace 2005).
Ascaris
Published in Dongyou Liu, Handbook of Foodborne Diseases, 2018
Stefano D'Amelio, Viliam Snabel, Serena Cavallero
A comprehensive review on the genetic variation at regional and global scales and implications on epidemiological and transmission patterns was provided.30 These authors state that no molecular markers have been so far able to give a clear-cut definition of species boundaries in Ascaris, as no fixed differences have been observed. Although a strong genetic structuring related to host affiliation has been observed at local scale, such a scenario seems to be groundless at global scale, with degree of genetic differentiation seemingly mostly reliant on geography.31 Local-scale analyses of Ascaris roundworms have often shown contrasting results, for instance, a tree where the two clusters A and B depicted a strong influence of host affiliation, in analyzing samples from Guatemala.25 In contrast, networks where the character host affiliation is clearly paraphyletic were described in China32 and in Brazil.33 Although revealing some clustering differences according to host preference, shared haplotypes between African and Asian locations and between worms of human and pig origin were identified. The phylogenetic tree and the parsimony network then provided,20 based on samples from the two hosts and from different geographic areas, described a more complex situation with a cross-linked relationships among haplotypes, with no clear geographical or host-affiliation criteria to be obviously relevant in shaping haplogroups. In this study, molecular variance analysis underlined that accumulation of genetic variability is predominant at the individual and population level rather than at the level of groups, defined on geography or host affiliation.
Use of Mitochondrial Donation
Published in Botros Rizk, Yakoub Khalaf, Controversies in Assisted Reproduction, 2020
The most contentious elements of MD from the perspective of safety and efficacy appear to be the risks that (a) carried-over pathogenic mtDNA might persist in the child at dangerous levels—perhaps due to a phenomenon analogous to the reversion seen in vitro; or that (b) mitonuclear interactions may be disrupted (see the section “Mitochondrial Donation: Preclinical Assessments of Safety and Efficacy in Human Research Embryos”). The expert panel reporting to the HFEA recommended that prenatal testing be offered to women who become pregnant following MD, as an acknowledgment of the risk of (a) and recommended that haplogroup/haplotype matching be considered due to (b). Moreover, given the additional risks associated with any first-in-human intervention, it is also recommended that MD be offered only to women for whom PGD is not a viable option, that is, for women who have consistently high levels of abnormal mtDNA in their oocytes. Like PGD, MD should currently be viewed as a risk-reduction strategy in these women, rather than a guaranteed way of preventing transmission of mitochondrial disease. These techniques require further refinements as they unfold in the clinic, the most significant of which would be to find a way to completely eliminate carryover of pathogenic mtDNA (36). This would eliminate any possibility of reversion and also avoid establishing significant heteroplasmy in MD offspring, which some reports, mostly based on experiments in mouse inbred strains, suggest should be avoided (21,37,38). But, given the strength of their desire to have genetically related children free of mitochondrial disease, and the possibility that some might simply risk the lottery of continued “natural” reproduction, the existing risks of MD were considered likely to be acceptable to some women.
Phylogenetic analyses of 41 Y-STRs and machine learning-based haplogroup prediction in the Qingdao Han population from Shandong province, Eastern China
Published in Annals of Human Biology, 2023
Guang-Yao Fan, De-Zhi Jiang, Yao-Heng Jiang, Wei Song, Ying-Yun He, Nixon Austin Wuo
The k-nearest neighbour (kNN) is a non-parametric supervised learning method which is helpful for both regression and classification (Altman 1992). Many prior studies mentioned its potential for allocating each haplogroup based on the Y-STR haplotype (Song et al. 2019b; Yin et al. 2022). Its availability had already been validated by a recent study (Fan 2022). In order to further enhance the predictive performance of the kNN model, a substantial training dataset was adopted for analysis using the “knn” package under the statistical environment R (Zhang 2016). The developed kNN predictor includes 23 common Y-STR loci and corresponding Y haplogroups from 3,248 Han males (Lang et al. 2019; Song et al. 2019a; Yin et al. 2020, 2022; Zhang et al. 2020). The algorithms were implemented using the R script available on GitHub (https://github.com/fanyoyo1983/knn-Y-haplogroup.git). Meanwhile, multi-copy loci and copy number variation (CNV) were excluded in the ML. The specificity and sensitivity of the kNN predictor for each predicted haplogroup were measured and performance was also shown in a confusion matrix.
Gene flow and phylogenetic analyses of paternal lineages in the Yi-Luo valley using Y-STR genetic markers
Published in Annals of Human Biology, 2021
Guang-Yao Fan, Dan-Lu Song, Hai-Ying Jin, Xing-Kai Zheng
Based on Y-STR loci information, each haplotype was assigned with a Y-linked haplogroup with the highest probability value by the Nevgen Y-DNA Haplogroup Predictor. To guarantee enough accuracy of the assignments, we only retained 1,102 Y-haplogroups assignments with probability assignment values over 70% (Supplementary Table S5). Their nomenclature complied with the guidelines of the International Society of Genetic Genealogy (ISSOG: https://isogg.org/tree). Finally, we constructed a phylogenetic network based on median-joining. The list of predicted haplogroups is shown in Supplementary Table S5. Six major haplogroups (C2, N1a2, O1a1, O1b1, O2a1, and O2a2) existed among the Yi-Luo valley population (Supplementary Table S6). The first three common haplogroups of the population were O2a2, C2, and O2a1, which represented 47.1% (519/1,102), 14.6% (161/1,102), and 12.5% (138/1,102), respectively. The complete haplogroups for each population of the Yi-Luo valley are shown in Supplementary Table S6. The Y-chromosome haplogroups and their frequency distribution in the populations of the Yi-Luo valley are noted in Supplementary Figure S3.
Differential mitochondrial genome in patients with Rheumatoid Arthritis
Published in Autoimmunity, 2021
Kumar Sagar Jaiswal, Shweta Khanna, Arup Ghosh, Prasanta Padhan, Sunil Kumar Raghav, Bhawna Gupta
Using the mtDNA sequence, we can determine the haplogroups using the mutation signature and comparing them with the HapMap data. In order to find the contribution of mtDNA haplogroup-specific mutations with the occurrence of RA, we performed a haplogroup analysis of RA samples and corresponding controls. A total of 23 RA and 17 HC samples were sequenced and all samples were combined into a resulting rooted tree which includes all related polymorphisms relative to the rCRS. In the sequenced 40 samples, 35 distinct haplogroups were observed. All samples were found to belong to four haplogroups M, N, R and U (Supplementary Figure S2). After the assignment of samples to haplogroups, the prevalence of each haplogroup was determined in each group. The population sequenced have a high frequency of haplogroup M lineage in both RA and HC groups.