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MtDNA next generation sequencing

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https://www.readbyqxmd.com/read/28422985/revising-mtdna-haplotypes-of-the-ancient-hungarian-conquerors-with-next-generation-sequencing
#1
Endre Neparáczki, Klaudia Kocsy, Gábor Endre Tóth, Zoltán Maróti, Tibor Kalmár, Péter Bihari, István Nagy, György Pálfi, Erika Molnár, István Raskó, Tibor Török
As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination...
2017: PloS One
https://www.readbyqxmd.com/read/28419775/next-generation-sequencing-mitochondrial-dna-analysis-in-autism-spectrum-disorder
#2
Ashok Patowary, Ryan Nesbitt, Marilyn Archer, Raphael Bernier, Zoran Brkanac
Autism is a complex genetic disorder where both de-novo and inherited genetics factors play a role. Next generation sequencing approaches have been extensively used to identify rare variants associated with autism. To date, all such studies were focused on nuclear genome; thereby leaving the role of mitochondrial DNA (mtDNA) variation in autism unexplored. Recently, analytical tools have been developed to evaluate mtDNA in whole-exome data. We have analyzed the mtDNA sequence derived from whole-exome sequencing in 10 multiplex families...
April 17, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28407192/population-genetic-characterization-of-the-japanese-oak-silkmoth-antheraea-yamamai-lepidoptera-saturniidae-using-novel-microsatellite-markers-and-mitochondrial-dna-gene-sequences
#3
S R Kim, K Y Kim, J S Jeong, M J Kim, K-H Kim, K H Choi, I Kim
The Japanese oak silkmoth, Antheraea yamamai Guérin-Méneville, 1861 (Lepidoptera: Saturniidae), is an important natural resource of industrial value for silk fiber production. Owing to a lack of geographic and population genetic information, systematic domestication of An. yamamai has not been possible yet. In this study, 10 microsatellite markers developed using next-generation sequencing and two mitochondrial DNA (mtDNA) gene sequences (COI and ND4) were used to investigate the genetic variation and geographic structure of An...
April 13, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28387858/mitochondrial-dna-quantification-as-a-tool-for-embryo-viability-assessment-retrospective-analysis-of-data-from-single-euploid-blastocyst-transfers
#4
K Ravichandran, C McCaffrey, J Grifo, A Morales, M Perloe, S Munne, D Wells, E Fragouli
STUDY QUESTION: Does the amount of mitochondrial DNA (mtDNA) in blastocyst biopsy specimens have the potential to serve as a biomarker of euploid embryo implantation ability, independent of morphology? SUMMARY ANSWER: The results of this study strongly suggest that elevated mtDNA levels, above a previously defined threshold, are strongly associated with blastocyst implantation failure and represent an independent biomarker of embryo viability. WHAT IS KNOWN ALREADY: Improved methods of embryo selection are highly desirable in order to increase the efficiency of IVF treatment...
April 6, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28348369/novel-molecular-approach-to-define-pest-species-status-and-tritrophic-interactions-from-historical-bemisia-specimens
#5
W T Tay, S Elfekih, A Polaszek, L N Court, G A Evans, K H J Gordon, P J De Barro
Museum specimens represent valuable genomic resources for understanding host-endosymbiont/parasitoid evolutionary relationships, resolving species complexes and nomenclatural problems. However, museum collections suffer DNA degradation, making them challenging for molecular-based studies. Here, the mitogenomes of a single 1912 Sri Lankan Bemisia emiliae cotype puparium, and of a 1942 Japanese Bemisia puparium are characterised using a Next-Generation Sequencing approach. Whiteflies are small sap-sucking insects including B...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28273704/-clinical-and-genetic-characteristics-of-children-with-leigh-syndrome
#6
F Fang, Y Shen, D M Shen, Z M Liu, C H Ding, W C Zhang, S Z Sun, J L Lyu, T L Han, X H Wang, W H Zhang, X Y Yang, J W Li, H S Wu
Objective: To investigate the clinically and genetic characteristics of children with Leigh syndrome. Method: Patients with clinically diagnosed Leigh syndrome(LS)in the department of Neurology, Beijing Children's Hospital from January 2013 to February 2016 underwent the mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) detecting with next generation sequencing (NGS) technology. The clinical data of gene confirmed cases were retrospectively collected and analyzed. The differences in the onset age, clinical manifestations, lactic acid level and MRI results between the mtDNA variation and nDNA variation were compared and analyzed...
March 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28215537/genetic-variations-of-mitochondrial-genome-modify-risk-and-prognosis-of-hepatocellular-carcinoma-patients
#7
Cheng Chen, Yanna Ba, Deyang Li, Xiaohong Du, Xin Lia, Hai Yang, Jiaze An, Jinliang Xing, Hushan Yang, Guanglong Dong, Xu Guo
BACKGROUND: Previous studies have indicated that mitochondrial genetic variations were associated with the risk of many cancers. However, there are few reports on the association between single nucleotide polymorphisms (SNPs) or haplogroups of mitochondrial DNA (mtDNA) and the risk or prognosis of hepatocellular carcinoma (HCC). METHODS: In order to investigate the predictive and prognostic role of mtDNA SNPs and haplogroups in HCC, the mitochondrial genome of 188 HCC patients and 344 healthy controls were sequenced by next generation sequencing technology...
February 16, 2017: Clinics and Research in Hepatology and Gastroenterology
https://www.readbyqxmd.com/read/28188893/ultra-deep-next-generation-mitochondrial-genome-sequencing-reveals-widespread-heteroplasmy-in-chinese-hamster-ovary-cells
#8
Paul S Kelly, Colin Clarke, Alan Costello, Craig Monger, Justine Meiller, Heena Dhiman, Nicole Borth, Michael J Betenbaugh, Martin Clynes, Niall Barron
Recent sequencing of the Chinese hamster ovary (CHO) cell and Chinese hamster genomes has dramatically advanced our ability to understand the biology of these mammalian cell factories. In this study, we focus on the powerhouse of the CHO cell, the mitochondrion. Utilizing a high-resolution next generation sequencing approach we sequenced the Chinese hamster mitochondrial genome for the first time and surveyed the mutational landscape of CHO cell mitochondrial DNA (mtDNA). Depths of coverage ranging from ~3,319X to 8,056X enabled accurate identification of low frequency mutations (>1%), revealing that mtDNA heteroplasmy is widespread in CHO cells...
February 8, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28174739/increased-mitochondrial-genetic-diversity-in-persons-infected-with-hepatitis-c-virus
#9
David S Campo, Ha-Jung Roh, Brian L Pearlman, Daniel S Fierer, Sumathi Ramachandran, Gilberto Vaughan, Andrew Hinds, Zoya Dimitrova, Pavel Skums, Yury Khudyakov
BACKGROUND & AIMS: The host genetic environment contributes significantly to the outcomes of hepatitis C virus (HCV) infection and therapy response, but little is known about any effects of HCV infection on the host beyond any changes related to adaptive immune responses. HCV persistence is associated strongly with mitochondrial dysfunction, with liver mitochondrial DNA (mtDNA) genetic diversity linked to disease progression. METHODS: We evaluated the genetic diversity of 2 mtDNA genomic regions (hypervariable segments 1 and 2) obtained from sera of 116 persons using next-generation sequencing...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28069933/no-correlation-between-mtdna-amount-and-methylation-levels-at-the-cpg-island-of-polg-exon-2-in-wild-type-and-mutant-human-differentiated-cells
#10
Julie Steffann, Aurore Pouliet, Houda Adjal, Christine Bole, Cécile Fourrage, Jelena Martinovic, Louise Rolland-Galmiche, Agnes Rotig, Frédéric Tores, Arnold Munnich, Jean-Paul Bonnefont
BACKGROUND: While mitochondrial DNA (mtDNA) copy number is strictly regulated during differentiation and according to cell type, very little is known regarding the mechanism which accurately controls mtDNA copy number in human. Exon 2 of the human POLG gene, encoding the catalytic subunit of the mitochondrial-specific DNA polymerase gamma, contains a CpG island, highly conserved in mice and human. Changes of DNA methylation at the POLG locus have been shown to modulate mtDNA copy number during cell differentiation in both mouse and human...
January 9, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/27984600/-identification-of-novel-common-mutations-among-patients-with-non-syndromic-hearing-loss-with-high-throughput-gene-capture-technology
#11
Yongan Zhou, Hongyan Zeng, Xiangshao Li, Huifang Yang, Wei Guo, Ziqi Hao, Pengli Li, Jiao Li, Xiaoli Zhao, Xiang Wang, Li Xia, Siqi Ma
OBJECTIVE: To identify novel common mutations among patients with non-syndromic hearing loss (NSHL). METHODS: High-throughput gene capture technology was used to analyze 18 patients with NSHL in whom common mutations of deafness genes including GJB2, SLC26A4, GJB3, and mtDNA were excluded. Suspected mutation was verified with Sanger sequencing. RESULTS: Next generation sequencing has identified 62 mutations in 29 genes associated with hearing loss, which included 54 missense mutations, 4 splicing mutations, 3 deletional mutations, and 1 nonsense mutation...
December 10, 2016: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/27907920/aneuploidy-detection-and-mtdna-quantification-in-bovine-embryos-with-different-cleavage-onset-using-a-next-generation-sequencing-based-protocol
#12
Miroslav Hornak, David Kubicek, Petr Broz, Pavlina Hulinska, Katerina Hanzalova, Darren Griffin, Marie Machatkova, Jiri Rubes
Bovine embryos are now routinely used in agricultural systems as a means of disseminating superior genetics worldwide, ultimately with the aim of feeding an ever-growing population. Further investigations, common for human IVF embryos, thus have priority to improve cattle IVF, as has screening for aneuploidy (abnormal chromosome number). Although the incidence and consequences of aneuploidy are well documented in human preimplantation embryos, they are less well known for the embryos of other animals. To address this, we assessed aneuploidy levels in thirty-one 2-cell bovine embryos derived from early- and late-cleaving zygotes...
2016: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/27899581/hmtdb-2016-data-update-a-better-performing-query-system-and-human-mitochondrial-dna-haplogroup-predictor
#13
Rosanna Clima, Roberto Preste, Claudia Calabrese, Maria Angela Diroma, Mariangela Santorsola, Gaetano Scioscia, Domenico Simone, Lishuang Shen, Giuseppe Gasparre, Marcella Attimonelli
The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27816474/characterization-of-complete-mitochondrial-genome-of-fives-tripe-wrasse-thalassoma-quinquevittatum-lay-bennett-1839-and-phylogenetic-analysis
#14
Kecheng Zhu, Na Wu, Xiaoxiao Sun, Huayang Guo, Nan Zhang, Shigui Jiang, Dianchang Zhang
To further supplement the genome-level features in related species, T. quinquevittatum complete mtDNA was firstly sequenced and de novo assembled by next-generation sequencing. The full-length mtDNA of T. quinquevittatum was a 16,896bp fragment, which was atypical of Labridae, with 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region (D-loop region). Additionally, the mtDNA of T. quinquevittatum exhibited characteristics of A (27.1%), T (29...
January 20, 2017: Gene
https://www.readbyqxmd.com/read/27814652/mtdna-the-small-workhorse-of-evolutionary-studies
#15
Rob Desalle, Bernd Schierwater, Heike Hadrys
The double-stranded, circular mitochondrial DNA (mtDNA), which is present in all eukaryotic life forms, was initially discovered and characterized in the last century and has been widely used in evolutionary studies. Since then, a large number of studies have taken advantage of the genetic information encoded in this genome. Because of its small size in animals (in general), the technical ease of manipulating mitochondrial genome and the dynamics of its evolutionary change, this genome has been the workhorse of evolutionary studies over the past three decades...
January 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/27793366/accurate-quantitation-of-mitochondrial-dna-reveals-uniform-levels-in-human-blastocysts-irrespective-of-ploidy-age-or-implantation-potential
#16
Andrea R Victor, Alan J Brake, Jack C Tyndall, Darren K Griffin, Christo G Zouves, Frank L Barnes, Manuel Viotti
OBJECTIVE: To accurately determine mitochondrial DNA (mtDNA) levels in human blastocysts. DESIGN: Retrospective analysis. SETTING: IVF clinic. PATIENT(S): A total of 1,396 embryos derived from 259 patients. INTERVENTION(S): Blastocyst-derived trophectoderm biopsies were tested by next-generation sequencing (NGS) and quantitative real-time polymerase chain reaction (qPCR). MAIN OUTCOME MEASURE(S): For each sample the mtDNA value was divided by the nuclear DNA value, and the result was further subjected to mathematical analysis tailored to the genetic makeup of the source embryo...
January 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/27775730/mitochondrial-diseases
#17
REVIEW
Gráinne S Gorman, Patrick F Chinnery, Salvatore DiMauro, Michio Hirano, Yasutoshi Koga, Robert McFarland, Anu Suomalainen, David R Thorburn, Massimo Zeviani, Douglass M Turnbull
Mitochondrial diseases are a group of genetic disorders that are characterized by defects in oxidative phosphorylation and caused by mutations in genes in the nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) that encode structural mitochondrial proteins or proteins involved in mitochondrial function. Mitochondrial diseases are the most common group of inherited metabolic disorders and are among the most common forms of inherited neurological disorders. One of the challenges of mitochondrial diseases is the marked clinical variation seen in patients, which can delay diagnosis...
October 20, 2016: Nature Reviews. Disease Primers
https://www.readbyqxmd.com/read/27770035/replication-errors-made-during-oogenesis-lead-to-detectable-de-novo-mtdna-mutations-in-zebrafish-oocytes-with-a-low-mtdna-copy-number
#18
Auke B C Otten, Alphons P M Stassen, Michiel Adriaens, Mike Gerards, Richard G J Dohmen, Adriana J Timmer, Sabina J V Vanherle, Rick Kamps, Iris B W Boesten, Jo M Vanoevelen, Marc Muller, Hubert J M Smeets
Of all pathogenic mitochondrial DNA (mtDNA) mutations in humans, ∼25% is de novo, although the occurrence in oocytes has never been directly assessed. We used next-generation sequencing to detect point mutations directly in the mtDNA of 3-15 individual mature oocytes and three somatic tissues from eight zebrafish females. Various statistical and biological filters allowed reliable detection of de novo variants with heteroplasmy ≥1.5%. In total, we detected 38 de novo base substitutions, but no insertions or deletions...
December 2016: Genetics
https://www.readbyqxmd.com/read/27761019/novel-mutation-of-nd4-gene-identified-by-targeted-next-generation-sequencing-in-patient-with-leigh-syndrome
#19
Bing Xu, Xiyuan Li, Miaomiao Du, Chao Zhou, Hezhi Fang, Jianxin Lyu, Yanling Yang
By using next-generation sequencing targeted to MitoExome including the entire mtDNA and exons of 1033 genes encoding the mitochondrial proteome, we described here a novel m.11240C>T mutation in the mitochondrial ND4 gene from a patient with Leigh syndrome. High mutant loads of m.11240C>T were detected in blood, urinary epithelium, oral mucosal epithelium cells, and skin fibroblasts of the patient. Decreased mitochondrial complex I activity was found in transmitochondrial cybrids containing the m.11240C>T mutation with biochemical analysis...
October 20, 2016: Journal of Human Genetics
https://www.readbyqxmd.com/read/27705925/mutational-load-of-the-mitochondrial-genome-predicts-pathological-features-and-biochemical-recurrence-in-prostate-cancer
#20
Anton M F Kalsbeek, Eva F K Chan, Judith Grogan, Desiree C Petersen, Weerachai Jaratlerdsiri, Ruta Gupta, Ruth J Lyons, Anne-Maree Haynes, Lisa G Horvath, James G Kench, Phillip D Stricker, Vanessa M Hayes
Prostate cancer management is complicated by extreme disease heterogeneity, which is further limited by availability of prognostic biomarkers. Recognition of prostate cancer as a genetic disease has prompted a focus on the nuclear genome for biomarker discovery, with little attention given to the mitochondrial genome. While it is evident that mitochondrial DNA (mtDNA) mutations are acquired during prostate tumorigenesis, no study has evaluated the prognostic value of mtDNA variation. Here we used next-generation sequencing to interrogate the mitochondrial genomes from prostate tissue biopsies and matched blood of 115 men having undergone a radical prostatectomy for which there was a mean of 107 months clinical follow-up...
October 5, 2016: Aging
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