keyword
MENU ▼
Read by QxMD icon Read
search

MtDNA next generation sequencing

keyword
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
#1
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...
December 2, 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
#2
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...
November 28, 2016: 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
#3
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...
November 2, 2016: Gene
https://www.readbyqxmd.com/read/27814652/mtdna-the-small-workhorse-of-evolutionary-studies
#4
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
#5
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...
October 25, 2016: Fertility and Sterility
https://www.readbyqxmd.com/read/27775730/mitochondrial-diseases
#6
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
#7
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, Bert 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...
October 21, 2016: Genetics
https://www.readbyqxmd.com/read/27761019/novel-mutation-of-nd4-gene-identified-by-targeted-next-generation-sequencing-in-patient-with-leigh-syndrome
#8
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
#9
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
https://www.readbyqxmd.com/read/27659608/the-genetics-and-pathology-of-mitochondrial-disease
#10
Charlotte L Alston, Mariana C Rocha, Nichola Z Lax, Doug M Turnbull, Robert W Taylor
Mitochondria are double membrane-bound organelles that are present in all nucleated eukaryotic cells and responsible for the production of cellular energy in the form of ATP. Mitochondrial function is under dual genetic control - the 16.6 kb mitochondrial genome encoding just 37 genes with the remaining ~1300 proteins of the mitoproteome encoded by nuclear genes. Mitochondrial dysfunction can arise due to defects in either mtDNA or nuclear mitochondrial genes, and can present in childhood or adulthood in association with vast clinical heterogeneity with symptoms affecting a single organ or tissue, or multisystem involvement...
September 23, 2016: Journal of Pathology
https://www.readbyqxmd.com/read/27553902/a-study-of-the-peopling-of-greenland-using-next-generation-sequencing-of-complete-mitochondrial-genomes
#11
Maria Lopopolo, Claus Børsting, Vania Pereira, Niels Morling
OBJECTIVES: The Greenlandic population history is characterized by a number of migrations of people of various ethnicities. In this work, the analysis of the complete mtDNA genome aimed to contribute to the ongoing debate on the origin of current Greenlanders and, at the same time, to address the migration patterns in the Greenlandic population from a female inheritance demographic perspective. METHODS: We investigated the maternal genetic variation in the Greenlandic population by sequencing the whole mtDNA genome in 127 Greenlandic individuals using the Illumina MiSeq(®) platform...
December 2016: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/27436875/natural-underlying-mtdna-heteroplasmy-as-a-potential-source-of-intra-person-hipsc-variability
#12
Ester Perales-Clemente, Alexandra N Cook, Jared M Evans, Samantha Roellinger, Frank Secreto, Valentina Emmanuele, Devin Oglesbee, Vamsi K Mootha, Michio Hirano, Eric A Schon, Andre Terzic, Timothy J Nelson
Functional variability among human clones of induced pluripotent stem cells (hiPSCs) remains a limitation in assembling high-quality biorepositories. Beyond inter-person variability, the root cause of intra-person variability remains unknown. Mitochondria guide the required transition from oxidative to glycolytic metabolism in nuclear reprogramming. Moreover, mitochondria have their own genome (mitochondrial DNA [mtDNA]). Herein, we performed mtDNA next-generation sequencing (NGS) on 84 hiPSC clones derived from a cohort of 19 individuals, including mitochondrial and non-mitochondrial patients...
September 15, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27432956/reticulation-divergence-and-the-phylogeography-phylogenetics-continuum
#13
Scott V Edwards, Sally Potter, C Jonathan Schmitt, Jason G Bragg, Craig Moritz
Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels-within loci and genomes in the form of recombination and across populations and species in the form of introgression-has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era...
July 19, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27386501/deep-sequencing-of-mitochondrial-genomes-reveals-increased-mutation-load-in-friedreich-s-ataxia
#14
Angela D Bhalla, Alireza Khodadadi-Jamayran, Yanjie Li, David R Lynch, Marek Napierala
OBJECTIVE: Friedreich's ataxia (FRDA) is an autosomal recessive trinucleotide repeat expansion disorder caused by epigenetic silencing of the frataxin gene (FXN). Current research suggests that damage and variation of mitochondrial DNA (mtDNA) contribute to the molecular pathogenesis of FRDA. We sought to establish the extent of the mutation burden across the mitochondrial genome in FRDA cells and investigate the molecular mechanisms connecting FXN downregulation and the acquisition of mtDNA damage...
July 2016: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/27368088/concordance-and-reproducibility-of-a-next-generation-mtgenome-sequencing-method-for-high-quality-samples-using-the-illumina-miseq
#15
Michelle A Peck, Michael D Brandhagen, Charla Marshall, Toni M Diegoli, Jodi A Irwin, Kimberly Sturk-Andreaggi
Sanger-type sequencing (STS) of mitochondrial DNA (mtDNA), specifically the control region (CR), is routinely employed in forensics in human identification and missing persons scenarios. Yet next-generation sequencing (NGS) has the potential to overcome some of the major limitations of STS processing, permitting reasonable paths forward for full mitochondrial genome (mtGenome) sequencing, while also offering higher-throughput and higher sensitivity capabilities. To establish the accuracy and reproducibility of NGS for the development of mtDNA data, 90 DNA extracts that were previously used to generate forensic quality full mtGenomes using STS were sequenced using Nextera XT library preparation and the Illumina MiSeq...
September 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27343181/mtdna-heteroplasmy-in-monozygotic-twins-discordant-for-schizophrenia
#16
Hong Li, Rui Bi, Yu Fan, Yong Wu, Yanqing Tang, Zongchang Li, Ying He, Jun Zhou, Jinsong Tang, Xiaogang Chen, Yong-Gang Yao
Although monozygotic (MZ) twins have theoretically identical nuclear DNA sequences, there may be phenotypic differences between them caused by somatic mutations and epigenetic changes affecting each genome. In this study, we collected eight families of MZ twins discordant for schizophrenia with the aim of investigating the potential role of mitochondrial DNA (mtDNA) heteroplasmy in causing the phenotypic differences between the twin pairs. Next-generation sequencing (NGS) technology was used to screen the whole mitochondrial genome of the twin pairs and their parents...
June 24, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27315116/mitochondrial-dna-mutations-increase-in-early-stage-alzheimer-disease-and-are-inconsistent-with-oxidative-damage
#17
Jake G Hoekstra, Michael J Hipp, Thomas J Montine, Scott R Kennedy
Mitochondrial dysfunction and oxidative damage are commonly associated with early stage Alzheimer disease (AD). The accumulation of somatic mutations in mitochondrial DNA (mtDNA) has been hypothesized to be a driver of these phenotypes, but the detection of increased mutation loads has been difficult due to a lack of sensitive methods. We used an ultrasensitive next generation sequencing technique to measure the mutation load of the entire mitochondrial genome. Here, we report a significant increase in the mtDNA mutation frequency in the hippocampus of early stage AD, with the cause of these mutations being consistent with replication errors and not oxidative damage...
August 2016: Annals of Neurology
https://www.readbyqxmd.com/read/27289015/combined-hybridization-capture-and-shotgun-sequencing-for-ancient-dna-analysis-of-extinct-wild-and-domestic-dromedary-camel
#18
Elmira Mohandesan, Camilla F Speller, Joris Peters, Hans-Peter Uerpmann, Margarethe Uerpmann, Bea De Cupere, Michael Hofreiter, Pamela A Burger
The performance of hybridization capture combined with next generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multi-fold coverage in a single capture experiment...
June 11, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27259738/analysis-of-mitochondrial-control-region-using-sanger-sequencing
#19
David Ballard
The analysis of mitochondrial DNA (mtDNA) is an established forensic tool and has been used extensively to aid with both the identification of human remains and evidence recovered from scenes of crime. The biology of mtDNA confers both advantages and disadvantages when using it as a tool for identification. It benefits from a high copy number, which facilitates analysis from samples with highly degraded DNA or trace amounts of DNA, but the maternal mode of inheritance restricts its power of discrimination. With Next Generation Sequencing being used in research and some forensic casework laboratories the scope of mtDNA analysis in forensic casework may expand in the near future...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27159691/complete-sequence-of-human-mitochondrial-dna-obtained-by-combining-multiple-displacement-amplification-and-next-generation-sequencing-on-a-single-oocyte
#20
Massimo Ancora, Massimiliano Orsini, Alessia Colosimo, Maurilia Marcacci, Valentina Russo, Maria De Santo, Marco D'Aurora, Liborio Stuppia, Barbara Barboni, Cesare Cammà, Valentina Gatta
Mitochondrial DNA (mtDNA) plays a key role in the development of a competent oocyte. In this study, the complete mtDNA sequence obtained for the first time by multiple displacement amplification approach in combination with next-generation sequencing from a single human oocyte is reported (GenBank accession no. KT364276). The analysis of oocyte mitochondrial mutations could provide a better understanding of the genetic variants correlated with the oocyte quality.
February 24, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
keyword
keyword
118556
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"