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MtDNA next generation sequencing

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https://www.readbyqxmd.com/read/28928993/what-drives-embryo-development-chromosomal-normality-or-mitochondria
#1
A Bayram, I Elkhatib, A Arnanz, A Linan, F Ruiz, B Lawrenz, H M Fatemi
OBJECTIVE: To report the arrest of euploid embryos with high mtDNA content. DESIGN: A report of 2 cases. SETTING: Private fertility clinic. PATIENTS: 2 patients, 45 and 40 years old undergoing IVF treatment. INTERVENTIONS: Mature oocytes were collected and vitrified from two ovarian stimulations. Postthaw, survived mature oocytes underwent fertilization by intracytoplasmic sperm injection (ICSI)...
2017: Case Reports in Genetics
https://www.readbyqxmd.com/read/28821228/sg-adviser-mtdna-a-web-server-for-mitochondrial-dna-annotation-with-data-from-200-samples-of-a-healthy-aging-cohort
#2
Manuel Rueda, Ali Torkamani
BACKGROUND: Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians...
August 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28732215/a-method-for-next-generation-sequencing-of-paired-diagnostic-and-remission-samples-to-detect-mitochondrial-dna-mutations-associated-with-leukemia
#3
Ilaria S Pagani, Chung H Kok, Verity A Saunders, Mark B Van der Hoek, Susan L Heatley, Anthony P Schwarer, Christopher N Hahn, Timothy P Hughes, Deborah L White, David M Ross
Somatic mitochondrial DNA (mtDNA) mutations have been identified in many human cancers, including leukemia. To identify somatic mutations, it is necessary to have a control tissue from the same individual for comparison. When patients with leukemia achieve remission, the remission peripheral blood may be a suitable and easily accessible control tissue, but this approach has not previously been applied to the study of mtDNA mutations. We have developed and validated a next-generation sequencing approach for the identification of leukemia-associated mtDNA mutations in 26 chronic myeloid leukemia patients at diagnosis using either nonhematopoietic or remission blood samples as the control...
July 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28716668/incomplete-penetrance-in-mitochondrial-optic-neuropathies
#4
Leonardo Caporali, Alessandra Maresca, Mariantonietta Capristo, Valentina Del Dotto, Francesca Tagliavini, Maria Lucia Valentino, Chiara La Morgia, Valerio Carelli
Incomplete penetrance characterizes the two most frequent inherited optic neuropathies, Leber's Hereditary Optic Neuropathy (LHON) and dominant optic atrophy (DOA), due to genetic errors in the mitochondrial DNA (mtDNA) and the nuclear DNA (nDNA), respectively. For LHON, compelling evidence has accumulated on the complex interplay of mtDNA haplogroups and environmental interacting factors, whereas the nDNA remains essentially non informative. However, a compensatory mechanism of activated mitochondrial biogenesis and increased mtDNA copy number, possibly driven by a permissive nDNA background, is documented in LHON; when successful it maintains unaffected the mutation carriers, but in some individuals it might be hampered by tobacco smoking or other environmental factors, resulting in disease onset...
July 14, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28716227/mitochondrial-trna-genes-are-hotspots-for-mutations-in-a-cohort-of-patients-with-exercise-intolerance-and-mitochondrial-myopathy
#5
Yuanyuan Lu, Danhua Zhao, Sheng Yao, Shiwen Wu, Daojun Hong, Qingqing Wang, Jing Liu, Jan A M Smeitink, Yun Yuan, Zhaoxia Wang
OBJECTIVE: Mitochondrial myopathy (MM) is a relatively rare type of mitochondrial disorder characterized by predominant skeletal muscle involvement. Both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) mutations have been reported as the genetic causes of this disease. Here, we described the clinical and genetic features of a cohort of patients with MM. METHODS: We conducted a retrospective, single center study enrolling 22 patients with clinically and myopathologically diagnosed MM...
August 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28711945/the-molecular-characterization-of-porcine-egg-precursor-cells
#6
Te-Sha Tsai, Jacqueline Johnson, Yvonne White, Justin C St John
Female-factor infertility can be caused by poor oocyte quality and depleted ovarian reserves. Egg precursor cells (EPCs), isolated from the ovarian cortex, have the potential to be used to overcome female infertility. We aimed to define the origins of EPCs by analyzing their gene expression profiles and mtDNA content using a mini-pig model. We characterized FAC-sorted DDX4+-derived porcine EPCs by performing RNA-sequencing and determined that they utilize pathways important for cell cycle and proliferation, which supports the existence of adult mitotically active oogonial cells...
June 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28693754/a-comprehensive-analysis-of-mitochondrial-genes-variants-and-their-association-with-antipsychotic-induced-weight-gain
#7
Kirti Mittal, Vanessa F Gonçalves, Ricardo Harripaul, Ari B Cuperfain, Brandi Rollins, Arun K Tiwari, Clement C Zai, Malgorzata Maciukiewicz, Daniel J Müller, Marquis P Vawter, James L Kennedy
Antipsychotic Induced Weight Gain (AIWG) is a common and severe side effect of many antipsychotic medications. Mitochondria play a vital role for whole-body energy homeostasis and there is increasing evidence that antipsychotics modulate mitochondrial function. This study aimed to examine the role of variants in nuclear-encoded mitochondrial genes and the mitochondrial DNA (mtDNA) in conferring risk for AIWG. We selected 168 European-Caucasian individuals from the CATIE sample based upon meeting criteria of multiple weight measures while taking selected antipsychotics (risperidone, quetiapine or olanzapine)...
September 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28677615/myopathology-of-adult-and-paediatric-mitochondrial-diseases
#8
REVIEW
Rahul Phadke
Mitochondria are dynamic organelles ubiquitously present in nucleated eukaryotic cells, subserving multiple metabolic functions, including cellular ATP generation by oxidative phosphorylation (OXPHOS). The OXPHOS machinery comprises five transmembrane respiratory chain enzyme complexes (RC). Defective OXPHOS gives rise to mitochondrial diseases (mtD). The incredible phenotypic and genetic diversity of mtD can be attributed at least in part to the RC dual genetic control (nuclear DNA (nDNA) and mitochondrial DNA (mtDNA)) and the complex interaction between the two genomes...
July 4, 2017: Journal of Clinical Medicine
https://www.readbyqxmd.com/read/28667863/a-phylogenetic-approach-for-haplotype-analysis-of-sequence-data-from-complex-mitochondrial-mixtures
#9
Samuel H Vohr, Rachel Gordon, Jordan M Eizenga, Henry A Erlich, Cassandra D Calloway, Richard E Green
Massively parallel (next-generation) sequencing provides a powerful method to analyze DNA from many different sources, including degraded and trace samples. A common challenge, however, is that many forensic samples are often known or suspected mixtures of DNA from multiple individuals. Haploid lineage markers, such as mitochondrial (mt) DNA, are useful for analysis of mixtures because, unlike nuclear genetic markers, each individual contributes a single sequence to the mixture. Deconvolution of these mixtures into the constituent mitochondrial haplotypes is challenging as typical sequence read lengths are too short to reconstruct the distinct haplotypes completely...
May 29, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28659719/somatic-mutation-analyses-in-studies-of-the-clonal-evolution-and-diagnostic-targets-of-prostate-cancer
#10
REVIEW
Dmitry S Mikhaylenko, Gennady D Efremov, Vladimir V Strelnikov, Dmitry V Zaletaev, Boris Y Alekseev
Prostate cancer (PC) is the most common uro-oncological disease in the global population and still requires a more efficient laboratory diagnosis. Point mutations of oncogenes and tumor sup-pressor genes are the most frequent molecular genetic events in carcinogenesis. The mutations are re-sponsible, to a great extent, for the clonal evolution of cancer and can be considered as primary candi-date molecular markers of PC. Using next-generation sequencing to analyze the mutations in PC, the main molecular PC subtypes were identified, which depended on the presence of fusion genes and FOXA1, CHD1, and SPOP point mutations; other driver mutations responsible for the progression of PC subclones were also characterized...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28649355/resequencing-and-comparison-of-whole-mitochondrial-genome-to-gain-insight-into-the-evolutionary-status-of-the-shennongjia-golden-snub-nosed-monkey-snj-r-roxellana
#11
Yanyun Hong, Hairui Duo, Juyun Hong, Jinyuan Yang, Shiming Liu, Lianghui Yu, Tuyong Yi
Shennongjia Rhinopithecus roxellana (SNJ R. roxellana) is the smallest geographical population of R. roxellana. The phylogenetic relationships among its genera and species and the biogeographic processes leading to their current distribution are largely unclear. To address these issues, we resequenced and obtained a new, complete mitochondrial genome of SNJ R. roxellana by next-generation sequencing and standard Sanger sequencing. We analyzed the gene composition, constructed a phylogenetic tree, inferred the divergence ages based on complete mitochondrial genome sequences, and analyzed the genetic divergence of 13 functional mtDNA genes...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28645767/assessing-the-potential-of-rad-sequencing-to-resolve-phylogenetic-relationships-within-species-radiations-the-fly-genus-chiastocheta-diptera-anthomyiidae-as-a-case-study
#12
Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic DNA markers, which have been widely used, notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies. However, with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation, phylogenies of closely related species have been resolved at a much higher detail in the last couple of years...
June 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28639102/the-clinical-and-genetic-characteristics-in-children-with-mitochondrial-disease-in-china
#13
Fang Fang, Zhimei Liu, Hezhi Fang, Jian Wu, Danmin Shen, Suzhen Sun, Changhong Ding, Tongli Han, Yun Wu, Junlan Lv, Lei Yang, Shufang Li, Jianxin Lv, Ying Shen
Mitochondrial disease was a clinically and genetically heterogeneous group of diseases, thus the diagnosis was very difficult to clinicians. Our objective was to analyze clinical and genetic characteristics of children with mitochondrial disease in China. We tested 141 candidate patients who have been suspected of mitochondrial disorders by using targeted next-generation sequencing (NGS), and summarized the clinical and genetic data of gene confirmed cases from Neurology Department, Beijing Children's Hospital, Capital Medical University from October 2012 to January 2015...
July 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28422985/revising-mtdna-haplotypes-of-the-ancient-hungarian-conquerors-with-next-generation-sequencing
#14
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
#15
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...
August 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
#16
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
#17
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...
June 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28348369/novel-molecular-approach-to-define-pest-species-status-and-tritrophic-interactions-from-historical-bemisia-specimens
#18
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
#19
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
#20
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...
September 2017: Clinics and Research in Hepatology and Gastroenterology
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