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MtDNA next generation sequencing

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https://www.readbyqxmd.com/read/29756269/genetic-and-clinical-features-of-chinese-patients-with-mitochondrial-ataxia-identified-by-targeted-next-generation-sequencing
#1
Hai-Lin Dong, Yin Ma, Quan-Fu Li, Yi-Chu Du, Lu Yang, Sheng Chen, Zhi-Ying Wu
AIM: To characterize the mutations in mitochondrial DNA (mtDNA) and mitochondrion-related nuclear genes (nDNA), and clinical features in Chinese patients with mitochondrial ataxia. METHODS: Targeted next-generation sequencing (NGS) technology was performed to screen the whole mtDNA sequence and nDNA genes in a cohort of 33 unrelated ataxia patients. RESULTS: A total of 5 pedigrees were finally genetically diagnosed as mitochondrial ataxia, with 3 pathogenic mutations (m...
May 13, 2018: CNS Neuroscience & Therapeutics
https://www.readbyqxmd.com/read/29752988/the-complete-mitochondrial-genome-of-parasesarma-pictum-brachyura-grapsoidea-sesarmidae-and-comparison-with-other-brachyuran-crabs
#2
Zhengfei Wang, Xuejia Shi, Yitao Tao, Qiong Wu, Yuze Bai, Huayun Guo, Dan Tang
Mitochondrial DNA (mtDNA) is an extrachromosomal genome which can provide important information for evolution and phylogenetic analysis. In this study, we assembled a complete mitogenome of a crab Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) from next generation sequencing reads at the first time. P. pictum is a mudflat crab, belonging to the Sesarmidae family (subfamily Sesarminae), which is perched on East Asia. The 15,716 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (CR)...
May 9, 2018: Genomics
https://www.readbyqxmd.com/read/29748765/de-novo-assembly-of-mitochondrial-genomes-provides-insights-into-genetic-diversity-and-molecular-evolution-in-wild-boars-and-domestic-pigs
#3
Pan Ni, Ali Akbar Bhuiyan, Jian-Hai Chen, Jingjin Li, Cheng Zhang, Shuhong Zhao, Xiaoyong Du, Hua Li, Hui Yu, Xiangdong Liu, Kui Li
Up to date, the scarcity of publicly available complete mitochondrial sequences for European wild pigs hampers deeper understanding about the genetic changes following domestication. Here, we have assembled 26 de novo mtDNA sequences of European wild boars from next generation sequencing (NGS) data and downloaded 174 complete mtDNA sequences to assess the genetic relationship, nucleotide diversity, and selection. The Bayesian consensus tree reveals the clear divergence between the European and Asian clade and a very small portion (10 out of 200 samples) of maternal introgression...
May 10, 2018: Genetica
https://www.readbyqxmd.com/read/29643477/accurate-estimation-of-5-methylcytosine-in-mammalian-mitochondrial-dna
#4
Shigeru Matsuda, Takehiro Yasukawa, Yuriko Sakaguchi, Kenji Ichiyanagi, Motoko Unoki, Kazuhito Gotoh, Kei Fukuda, Hiroyuki Sasaki, Tsutomu Suzuki, Dongchon Kang
Whilst 5-methylcytosine (5mC) is a major epigenetic mark in the nuclear DNA in mammals, whether or not mitochondrial DNA (mtDNA) receives 5mC modification remains controversial. Herein, we exhaustively analysed mouse mtDNA using three methods that are based upon different principles for detecting 5mC. Next-generation bisulfite sequencing did not give any significant signatures of methylation in mtDNAs of liver, brain and embryonic stem cells (ESCs). Also, treatment with methylated cytosine-sensitive endonuclease McrBC resulted in no substantial decrease of mtDNA band intensities in Southern hybridisation...
April 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29625556/targeted-next-generation-sequencing-with-an-extended-gene-panel-does-not-impact-variant-detection-in-mitochondrial-diseases
#5
Morgane Plutino, Annabelle Chaussenot, Cécile Rouzier, Samira Ait-El-Mkadem, Konstantina Fragaki, Véronique Paquis-Flucklinger, Sylvie Bannwarth
BACKGROUND: Since the advent of next generation sequencing (NGS), several studies have tried to evaluate the relevance of targeted gene panel sequencing and whole exome sequencing for molecular diagnosis of mitochondrial diseases. The comparison between these different strategies is extremely difficult. A recent study analysed a cohort of patients affected by a mitochondrial disease using a NGS approach based on a targeted gene panel including 132 genes. This strategy led to identify the causative mutations in 15...
April 7, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29573606/repair-of-dna-damage-caused-by-cytosine-deamination-in-mitochondrial-dna-of-forensic-case-samples
#6
Erin M Gorden, Kimberly Sturk-Andreaggi, Charla Marshall
DNA sequence damage from cytosine deamination is well documented in degraded samples, such as those from ancient and forensic contexts. This study examined the effect of a DNA repair treatment on mitochondrial DNA (mtDNA) from aged and degraded skeletal samples. DNA extracts from 21 non-probative, degraded skeletal samples (aged 50-70 years) were utilized for the analysis. A portion of each sample extract was subjected to DNA repair using a commercial repair kit, the New England BioLabs' NEBNext FFPE DNA Repair Kit (Ipswich, MA)...
February 19, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29568706/current-state-of-knowledge-on-wolbachia-infection-among-coleoptera-a-systematic-review
#7
Łukasz Kajtoch, Nela Kotásková
Background: Despite great progress in studies on Wolbachia infection in insects, the knowledge about its relations with beetle species, populations and individuals, and the effects of bacteria on these hosts, is still unsatisfactory. In this review we summarize the current state of knowledge about Wolbachia occurrence and interactions with Coleopteran hosts. Methods: An intensive search of the available literature resulted in the selection of 86 publications that describe the relevant details about Wolbachia presence among beetles...
2018: PeerJ
https://www.readbyqxmd.com/read/29538439/maternal-dna-lineages-at-the-gate-of-europe-in-the-10th-century-ad
#8
Ioana Rusu, Alessandra Modi, Stefania Vai, Elena Pilli, Cristina Mircea, Claudia Radu, Claudia Urduzia, Zeno Karl Pinter, Vitalie Bodolică, Cătălin Dobrinescu, Montserrat Hervella, Octavian Popescu, Martina Lari, David Caramelli, Beatrice Kelemen
Given the paucity of archaeogenetic data available for medieval European populations in comparison to other historical periods, the genetic landscape of this age appears as a puzzle of dispersed, small, known pieces. In particular, Southeastern Europe has been scarcely investigated to date. In this paper, we report the study of mitochondrial DNA in 10th century AD human samples from Capidava necropolis, located in Dobruja (Southeastern Romania, Southeastern Europe). This geographical region is particularly interesting because of the extensive population flux following diverse migration routes, and the complex interactions between distinct population groups during the medieval period...
2018: PloS One
https://www.readbyqxmd.com/read/29458409/mitochondrial-dysfunction-and-autism-comprehensive-genetic-analyses-of-children-with-autism-and-mtdna-deletion
#9
Noémi Ágnes Varga, Klára Pentelényi, Péter Balicza, András Gézsi, Viktória Reményi, Vivien Hársfalvi, Renáta Bencsik, Anett Illés, Csilla Prekop, Mária Judit Molnár
BACKGROUND: The etiology of autism spectrum disorders (ASD) is very heterogeneous. Mitochondrial dysfunction has been described in ASD; however, primary mitochondrial disease has been genetically proven in a small subset of patients. The main goal of the present study was to investigate correlations between mitochondrial DNA (mtDNA) changes and alterations of genes associated with mtDNA maintenance or ASD. METHODS: Sixty patients with ASD and sixty healthy individuals were screened for common mtDNA mutations...
February 20, 2018: Behavioral and Brain Functions: BBF
https://www.readbyqxmd.com/read/29410806/from-conservation-genetics-to-conservation-genomics-a-genome-wide-assessment-of-blue-whales-balaenoptera-musculus-in-australian-feeding-aggregations
#10
Catherine R M Attard, Luciano B Beheregaray, Jonathan Sandoval-Castillo, K Curt S Jenner, Peter C Gill, Micheline-Nicole M Jenner, Margaret G Morrice, Luciana M Möller
Genetic datasets of tens of markers have been superseded through next-generation sequencing technology with genome-wide datasets of thousands of markers. Genomic datasets improve our power to detect low population structure and identify adaptive divergence. The increased population-level knowledge can inform the conservation management of endangered species, such as the blue whale ( Balaenoptera musculus ). In Australia, there are two known feeding aggregations of the pygmy blue whale ( B. m. brevicauda ) which have shown no evidence of genetic structure based on a small dataset of 10 microsatellites and mtDNA...
January 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29361782/applications-of-probe-capture-enrichment-next-generation-sequencing-for-whole-mitochondrial-genome-and-426-nuclear-snps-for-forensically-challenging-samples
#11
Shelly Y Shih, Nikhil Bose, Anna Beatriz R Gonçalves, Henry A Erlich, Cassandra D Calloway
The application of next generation sequencing (NGS) for the analysis of mitochondrial (mt) DNA, short tandem repeats (STRs), and single nucleotide polymorphism (SNPs) has demonstrated great promise for challenging forensic specimens, such as degraded, limited, and mixed samples. Target enrichment using probe capture rather than PCR amplification offers advantages for analysis of degraded DNA since two intact PCR primer sites in the template DNA molecule are not required. Furthermore, NGS software programs can help remove PCR duplicates to determine initial template copy numbers of a shotgun library...
January 22, 2018: Genes
https://www.readbyqxmd.com/read/29343773/mitochondrial-mutations-in-cholestatic-liver-disease-with-biliary-atresia
#12
Hong Koh, Gun-Seok Park, Sun-Mi Shin, Chang Eon Park, Seung Kim, Seok Joo Han, Huy Quang Pham, Jae-Ho Shin, Dong-Woo Lee
Biliary atresia (BA) results in severe bile blockage and is caused by the absence of extrahepatic ducts. Even after successful hepatic portoenterostomy, a considerable number of patients are likely to show progressive deterioration in liver function. Recent studies show that mutations in protein-coding mitochondrial DNA (mtDNA) genes and/or mitochondrial genes in nuclear DNA (nDNA) are associated with hepatocellular dysfunction. This observation led us to investigate whether hepatic dysfunctions in BA is genetically associated with mtDNA mutations...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29340697/genetic-and-clinical-evidence-of-mitochondrial-dysfunction-in-autism-spectrum-disorder-and-intellectual-disability
#13
Alba Valiente-Pallejà, Helena Torrell, Gerard Muntané, Maria J Cortés, Rafael Martínez-Leal, Nerea Abasolo, Yolanda Alonso, Elisabet Vilella, Lourdes Martorell
Clinical conditions commonly associated with mitochondrial disorders (CAMDs) are often present in autism spectrum disorders (ASD) and intellectual disability (ID). Therefore, the mitochondrial dysfunction hypothesis has been proposed as a transversal mechanism that may function in both disorders. Here, we investigated the presence of conditions associated with mitochondrial disorders and mitochondrial DNA (mtDNA) alterations in 122 subjects who presented ASD with ID (ASD group), 115 subjects who presented ID but not ASD (ID group) and 112 healthy controls (HC group)...
March 1, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29333085/next-generation-sequencing-expression-profiling-of-mitochondrial-subunits-in-men-with-klinefelter-syndrome
#14
Michele Salemi, Laura Cimino, Marika Marino, Rossella Cannarella, Rosita A Condorelli, Corrado Romano, Sandro La Vignera, Aldo E Calogero
Objectives: Klinefelter syndrome (KS) is one of the most common sex-chromosome disorders as it affects up to 1 in every 600-1000 newborn males. Men with KS carry one extra X chromosome and they usually present a 47,XXY karyotype, but less frequent variants have also been reported in literature. KS typical symptoms include tall stature, gynecomastia, broad hips, hypogonadism and absent spermatogenesis. The syndrome is also related to a wide range of cognitive deficits, among which language-based learning disabilities and verbal cognition impairment are frequently diagnosed...
2018: International Journal of Medical Sciences
https://www.readbyqxmd.com/read/29321868/global-mtdna-genetic-structure-and-hypothesized-invasion-history-of-a-major-pest-of-citrus-diaphorina-citri-hemiptera-liviidae
#15
Yufa Luo, Ingi Agnarsson
The Asian citrus psyllid Diaphorina citri Kuwayama is a key pest of citrus as the vector of the bacterium causing the "huanglongbing" disease (HLB). To assess the global mtDNA population genetic structure, and possible dispersal history of the pest, we investigated genetic variation at the COI gene collating newly collected samples with all previously published data. Our dataset consists of 356 colonies from 106 geographic sites worldwide. High haplotype diversity (H-mean = 0.702 ± 0.017), low nucleotide diversity (π-mean = 0...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29258879/mitochondrial-gene-order-evolution-in-mollusca-inference-of-the-ancestral-state-from-the-mtdna-of-chaetopleura-apiculata-polyplacophora-chaetopleuridae
#16
Davide Guerra, Karim Bouvet, Sophie Breton
The mitochondrial genome architecture of polyplacophorans has been usually regarded as being very ancient in comparison to all mollusks. However, even if some complete chiton mtDNAs have been recently sequenced, thorough studies of their evolution are lacking. To further expand the set of complete chiton mtDNAs and perform such analysis, we sequenced the mitochondrial genome of the Eastern beaded chiton Chaetopleura apiculata (Chaetopleuridae) using next-generation sequencing. With mitochondrial sequences from all available chiton mtDNAs, we also built a phylogeny on which we reconstructed the evolution of gene arrangement in this class...
March 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29101892/performance-evaluation-of-a-mitogenome-capture-and-illumina-sequencing-protocol-using-non-probative-case-type-skeletal-samples-implications-for-the-use-of-a-positive-control-in-a-next-generation-sequencing-procedure
#17
Charla Marshall, Kimberly Sturk-Andreaggi, Jennifer Daniels-Higginbotham, Robert Sean Oliver, Suzanne Barritt-Ross, Timothy P McMahon
Next-generation ancient DNA technologies have the potential to assist in the analysis of degraded DNA extracted from forensic specimens. Mitochondrial genome (mitogenome) sequencing, specifically, may be of benefit to samples that fail to yield forensically relevant genetic information using conventional PCR-based techniques. This report summarizes the Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory's (AFMES-AFDIL) performance evaluation of a Next-Generation Sequencing protocol for degraded and chemically treated past accounting samples...
November 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29080494/aqme-a-forensic-mitochondrial-dna-analysis-tool-for-next-generation-sequencing-data
#18
Kimberly Sturk-Andreaggi, Michelle A Peck, Cecilie Boysen, Patrick Dekker, Timothy P McMahon, Charla K Marshall
The feasibility of generating mitochondrial DNA (mtDNA) data has expanded considerably with the advent of next-generation sequencing (NGS), specifically in the generation of entire mtDNA genome (mitogenome) sequences. However, the analysis of these data has emerged as the greatest challenge to implementation in forensics. To address this need, a custom toolkit for use in the CLC Genomics Workbench (QIAGEN, Hilden, Germany) was developed through a collaborative effort between the Armed Forces Medical Examiner System - Armed Forces DNA Identification Laboratory (AFMES-AFDIL) and QIAGEN Bioinformatics...
November 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29072135/detection-and-quantification-of-mitochondrial-dna-deletions-from-next-generation-sequence-data
#19
Colleen M Bosworth, Sneha Grandhi, Meetha P Gould, Thomas LaFramboise
BACKGROUND: Chromosomal deletions represent an important class of human genetic variation. Various methods have been developed to mine "next-generation" sequencing (NGS) data to detect deletions and quantify their clonal abundances. These methods have focused almost exclusively on the nuclear genome, ignoring the mitochondrial chromosome (mtDNA). Detecting mtDNA deletions requires special care. First, the chromosome's relatively small size (16,569 bp) necessitates the ability to detect extremely focal events...
October 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29063991/mitochondrial-dna-content-is-associated-with-ploidy-status-maternal-age-and-oocyte-maturation-methods-in-mouse-blastocysts
#20
Xin Tao, Jessica N Landis, Rebecca L Krisher, Francesca E Duncan, Elena Silva, Agnieszka Lonczak, Richard T Scott, Yiping Zhan, Tinchun Chu, Richard T Scott, Nathan R Treff
PURPOSE: It was reported that mitochondrial DNA (mtDNA) was significantly increased in aneuploid human embryos compared to euploid embryos and was also associated with maternal age. In this study, we further established the mouse model of mtDNA quantitation in reproductive samples based on whole-genome amplification (WGA) and next-generation sequencing (NGS). METHODS: WGA followed by NGS-based mtDNA quantitation was first performed on 6 single- and 100-cell samples from a tumor-derived mouse cell line, which was exposed to ethidium bromide to reduce mtDNA content...
December 2017: Journal of Assisted Reproduction and Genetics
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