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MtDNA next generation sequencing

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
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
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Genetic datasets of tens of markers have been superseded through next-generation sequencing technology with genome-wide datasets of thousands of markers.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
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
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
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
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
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
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...
December 16, 2017: Molecular Phylogenetics and Evolution
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
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
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
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
Patrick Mordel, Stéphane Schaeffer, Quentin Dupas, Marie-Alice Laville, Marion Gérard, Françoise Chapon, S Allouche
Mitochondrial (mt) DNA-associated NARP (neurogenic muscle weakness, ataxia, and retinitis pigmentosa) syndrome is due to mutation in the MT-ATP6 gene. We report the case of a 18-year-old man who presented with deafness, a myoclonic epilepsy, muscle weakness since the age of 10 and further developed a retinitis pigmentosa and ataxia. The whole mtDNA analysis by next-generation sequencing revealed the presence of the 2 bp microdeletion m.9127-9128 del AT in the ATP6 gene at 82% heteroplasmy in muscle and to a lower load in blood (10-20%) and fibroblasts (50%)...
December 9, 2017: Biochemical and Biophysical Research Communications
Anton M F Kalsbeek, Eva K F Chan, Niall M Corcoran, Christopher M Hovens, Vanessa M Hayes
Prostate cancer is a genetic disease. While next generation sequencing has allowed for the emergence of molecular taxonomy, classification is restricted to the nuclear genome. Mutations within the maternally inherited mitochondrial genome are known to impact cancer pathogenesis, as a result of disturbances in energy metabolism and apoptosis. With a higher mutation rate, limited repair and increased copy number compared to the nuclear genome, the clinical relevance of mitochondrial DNA (mtDNA) variation requires deeper exploration...
September 19, 2017: Oncotarget
Elpida Fragouli, Caroline McCaffrey, Krithika Ravichandran, Katharina Spath, James A Grifo, Santiago Munné, Dagan Wells
STUDY QUESTION: Can quantification of mitochondrial DNA (mtDNA) in trophectoderm (TE) biopsy samples provide information concerning the viability of a blastocyst, potentially enhancing embryo selection and improving IVF treatment outcomes? SUMMARY ANSWER: This study demonstrated that euploid blastocysts of good morphology, but with high mtDNA levels had a greatly reduced implantation potential. WHAT IS KNOWN ALREADY: Better methods of embryo selection leading to IVF outcome improvement are necessary, as the transfer of chromosomally normal embryos of high morphological grade cannot guarantee the establishment of an ongoing pregnancy...
November 1, 2017: Human Reproduction
Te-Sha Tsai, Jacqueline Johnson, Yvonne White, Justin C 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...
September 8, 2017: Oncotarget
L Boucret, C Bris, V Seegers, D Goudenège, V Desquiret-Dumas, M Domin-Bernhard, V Ferré-L'Hotellier, P E Bouet, P Descamps, P Reynier, V Procaccio, P May-Panloup
STUDY QUESTION: Does ovarian ageing increase the number of heteroplasmic mitochondrial DNA (mtDNA) point mutations in oocytes? SUMMARY ANSWER: Our results suggest that oocytes are not subject to the accumulation of mtDNA point mutations during ovarian ageing. WHAT IS KNOWN ALREADY: Ageing is associated with the alteration of mtDNA integrity in various tissues. Primary oocytes, present in the ovary since embryonic life, may accumulate mtDNA mutations during the process of ovarian ageing...
October 1, 2017: Human Reproduction
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
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
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