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MtDNA next generation sequencing

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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
#1
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...
September 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29080494/aqme-a-forensic-mitochondrial-dna-analysis-tool-for-next-generation-sequencing-data
#2
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...
September 19, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29072135/detection-and-quantification-of-mitochondrial-dna-deletions-from-next-generation-sequence-data
#3
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
#4
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...
October 24, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/29054413/a-2-bp-deletion-in-the-mitochondrial-atp-6-gene-responsible-for-the%C3%A2-narp-neuropathy-ataxia-and-retinitis-pigmentosa-syndrome
#5
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
https://www.readbyqxmd.com/read/29050365/mitochondrial-genome-variation-and-prostate-cancer-a-review-of-the-mutational-landscape-and-application-to-clinical-management
#6
REVIEW
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
https://www.readbyqxmd.com/read/29040520/clinical-implications-of-mitochondrial-dna-quantification-on-pregnancy-outcomes-a-blinded-prospective-non-selection-study
#7
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
https://www.readbyqxmd.com/read/28969006/the-molecular-characterization-of-porcine-egg-precursor-cells
#8
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
https://www.readbyqxmd.com/read/28938736/deep-sequencing-shows-that-oocytes-are-not-prone-to-accumulate-mtdna-heteroplasmic-mutations-during-ovarian-ageing
#9
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
https://www.readbyqxmd.com/read/28928993/what-drives-embryo-development-chromosomal-normality-or-mitochondria
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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...
September 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
#19
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
#20
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
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