keyword
MENU ▼
Read by QxMD icon Read
search

mitochondrial copy number detect

keyword
https://www.readbyqxmd.com/read/28914264/comprehensive-use-of-extended-exome-analysis-improves-diagnostic-yield-in-rare-disease-a-retrospective-survey-in-1-059-cases
#1
Gaber Bergant, Ales Maver, Luca Lovrecic, Goran Čuturilo, Alenka Hodzic, Borut Peterlin
PurposeWe sought to determine the analytical sensitivity of several extended exome variation analysis approaches in terms of their contribution to diagnostic yield and their clinical feasibility.MethodsWe retrospectively analyzed the results of genetic testing in 1,059 distinct cases referred for exome sequencing to our institution. In these, we routinely employed extended exome analysis approaches in addition to basic variant analysis, including (i) copy-number variation (CNV) detection, (ii) nonconsensus splice defect detection, (ii) genomic breakpoint detection, (iv) homozygosity mapping, and (v) mitochondrial variant analysis...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28910489/nucleoside-nucleotide-reverse-transcriptase-inhibitors-attenuate-angiogenesis-and-lymphangiogenesis-by-impairing-receptor-tyrosine-kinases-signalling-in-endothelial-cells
#2
Lin Song, Sha Ding, Zhen Ge, Xiaolong Zhu, Cong Qiu, Yuewen Wang, Enyin Lai, Weijun Yang, Yi Sun, Samson A Chow, Luyang Yu
BACKGROUND AND PURPOSE: Cardiovascular disease associated with antiretroviral therapy (ART) has become a major clinical challenge for HIV-positive patients. However, the role of ART in blood vessel growth is largely unknown. Here, we examined an integral component of ART, nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs), and investigated their effects on key microvascular functions, including angiogenesis and lymphangiogenesis. EXPERIMENTAL APPROACH: The angiogenesis/lymphangiogenesis capability of endothelial cells (ECs) was evaluated using migration, proliferation and tube formation assays in vitro, and mouse ear and Matrigel plug assays in vivo...
September 14, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28851493/evaluation-of-quantitative-ftd-pneumocystis-jirovecii-kit-for-pneumocystis-infection-diagnosis
#3
Gautier Hoarau, Solène Le Gal, Patricia Zunic, Patrice Poubeau, Emmanuel Antok, Julien Jaubert, Gilles Nevez, Sandrine Picot
We evaluated the Fast track Diagnostics (FTD) Pneumocystis PCR kit, targeting the mitochondrial large subunit ribosomal RNA gene (mtLSU rRNA) of Pneumocystis jirovecii (P. jirovecii). A hundred and thirty-three patients were prospectively enrolled. Respiratory specimens were examined using both microscopy and the PCR assay. Twenty-six patients led to P. jirovecii detection. Fourteen patients presented with Pneumocystis pneumonia (PCP) whereas 12 patients were considered to be colonized. The median copy numbers in bronchoalveolar lavage fluid were significantly different in the PCP and colonization groups (1...
August 9, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28818680/clinical-validation-of-copy-number-variant-detection-from-targeted-next-generation-sequencing-panels
#4
Jennifer Kerkhof, Laila C Schenkel, Jack Reilly, Sheri McRobbie, Erfan Aref-Eshghi, Alan Stuart, C Anthony Rupar, Paul Adams, Robert A Hegele, Hanxin Lin, David Rodenhiser, Joan Knoll, Peter J Ainsworth, Bekim Sadikovic
Next-generation sequencing (NGS) technology has rapidly replaced Sanger sequencing in the assessment of sequence variations in clinical genetics laboratories. One major limitation of current NGS approaches is the ability to detect copy number variations (CNVs) greater than approximately 50bp. Since these represent a major mutational burden in many genetic disorders, parallel CNV assessment using alternate supplemental methods, along with the NGS analysis, is normally required resulting in increased labor, costs, and turnaround times...
August 14, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28810700/a-single-mini-barcode-test-to-screen-for-australian-mammalian-predators-from-environmental-samples
#5
Elodie Modave, Anna J MacDonald, Stephen D Sarre
Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28807237/mitochondrial-dysfunctions-in-bladder-cancer-exploring-their-role-as-disease-markers-and-potential-therapeutic-targets
#6
REVIEW
Antonella Cormio, Francesca Sanguedolce, Clara Musicco, Vito Pesce, Giuseppe Calò, Pantaleo Bufo, Giuseppe Carrieri, Luigi Cormio
Bladder cancer (BC) is a major cause of mortality worldwide as it currently lacks fully reliable markers of disease outcome and effective molecular targets for therapy. Mitochondria play a key role in cell metabolism but the role of mitochondrial dysfunctions in BC has been scarcely investigated. In this review, we explored current evidence for the potential role of mitochondrial DNA (mtDNA) alterations (point mutations and copy number) as disease markers in BC. Some germline mtDNA mutations detectable in blood could represent a non-invasive tool to predict the risk of developing BC...
September 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28803790/utility-of-the-cytochrome-c-oxidase-subunit-i-gene-for-the-diagnosis-of-toxoplasmosis-using-pcr
#7
Xue Feng, Kazumi Norose, Kexin Li, Kenji Hikosaka
Toxoplasmosis is caused by the protozoan parasite Toxoplasma gondii, which belongs to the phylum Apicomplexa. Since this parasite causes severe clinical symptoms in immunocompromised patients, early diagnosis of toxoplasmosis is essential. PCR is currently used for early diagnosis, but there is no consensus regarding the most effective method for amplifying Toxoplasma DNA. In this study, we considered the utility of the cytochrome c subunit I (cox1) gene, which is encoded in the mitochondrial DNA of this parasite, as a novel target of PCR for the diagnosis of toxoplasmosis...
August 10, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28767123/complete-mitochondrial-genome-of-the-lappet-moth-kunugia-undans-lepidoptera-lasiocampidae-genomic-comparisons-among-macroheteroceran-superfamilies
#8
Min Jee Kim, Jun Seong Jeong, Jong Seok Kim, Su Yeon Jeong, Iksoo Kim
The mitochondrial genome (mitogenome) characteristics of the monotypic Lasiocampoidea are largely unknown, because only limited number of mitogenomes is available from this superfamily. In this study, we sequenced the complete mitogenome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae) and compared it to those of Lasiocampoidea and macroheteroceran superfamilies (59 species in six superfamilies). The 15,570-bp K. undans genome had one additional trnR that was located between trnA and trnN loci and this feature was unique in Macroheterocera, including Lasiocampoidea...
July 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28722338/hdr-del-a-tool-based-on-hamming-distance-for-prioritizing-pathogenic-chromosomal-deletions-in-exome-sequencing
#9
Atsuko Imai, Masakazu Kohda, Kaori Kobayashi, Tomoko Hirata, Yasushi Sakata, Kei Murayama, Akira Ohtake, Yasushi Okazaki, Akihiro Nakaya, Jurg Ott
High-density oligonucleotide arrays have been widely used to detect pathogenic chromosomal deletions. In addition to high-density oligonucleotide arrays, programs using whole exome sequencing have become available for estimating copy number variations using depth of coverage. Here we propose a new statistical method, HDR-del, to prioritize pathogenic chromosomal deletions based on Hamming distance in exome sequencing. In vcf (Variant Call Format) files generated from exome sequencing, hemizygous chromosomal deletion regions lack heterozygous variants and lead to apparent long runs of homozygosity (ROH)...
July 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28677739/protein-profiling-and-functional-analysis-of-liver-mitochondria-from-rats-with-nonalcoholic-steatohepatitis
#10
Yanting You, Yuxing Zhang, Yuanyuan Lu, Keke Hu, Xiaohu Qu, Yongzhag Liu, Bin Lu, Liqin Jin
Mitochondrial dysfunction is closely associated with the pathogenesis of nonalcoholic steatohepatitis (NASH). The aim of the present study was to comprehensively determine mitochondrial abnormalities in NASH by detecting the proteomics in liver mitochondria in a NASH rat model, which was induced for 16 weeks by the provision of a high fat and high cholesterol diet (HFD). Serum parameters, including triglycerides, total cholesterol, low‑density lipoprotein cholesterol and high‑density lipoprotein cholesterol were determined, and hematoxylin and eosin staining of liver tissues was examined to evaluate the NASH rat model...
September 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28659721/mtdna-as-a-cancer-marker-a-finally-closed-chapter
#11
REVIEW
Elmar Kirches
Sequence alterations of the mitochondrial DNA (mtDNA) have been identified in many tu-mor types. Their nature is not entirely clear. Somatic mutation or shifts of heteroplasmic mtDNA vari-ants may play a role. These sequence alterations exhibit a sufficient frequency in all tumor types investi-gated thus far to justify their use as a tumor marker. This statement is supported by the high copy num-ber of mtDNA, which facilitates the detection of aberrant tumor-derived DNA in bodily fluids. This will be of special interest in tumors, which release a relatively high number of cells into bodily fluids, which are easily accessible, most strikingly in urinary bladder carcinoma...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28652445/increased-copy-number-variation-of-mtdna-in-an-array-based-digital-pcr-assay-predicts-ulcerative-colitis-associated-colorectal-cancer
#12
Toshiaki Tanaka, Takashi Kobunai, Yoko Yamamoto, Koji Murono, Kensuke Otani, Koji Yasuda, Takeshi Nishikawa, Tomomichi Kiyomatsu, Kazushige Kawai, Keisuke Hata, Hiroaki Nozawa, Soichiro Ishihara, Toshiaki Watanabe
AIM: Mitochondrial dysfunction plays a central role in carcinogenesis in numerous cancer-related diseases. We examined the copy number variation of mitochondrial DNA (mtDNA) and the expression of energy-producing genes in relation to ulcerative colitis (UC)-associated carcinogenesis. MATERIALS AND METHODS: We studied 17 patients with UC-associated adenocarcinoma (UC-Ca) and 16 without UC-associated adenocarcinoma (UC-nonCa). The copy number of mtDNA in non-dysplastic mucosa in both groups was quantified by an array-based digital polymerase chain reaction (PCR) assay...
July 2017: In Vivo
https://www.readbyqxmd.com/read/28551263/identification-of-a-chicken-gallus-gallus-endogenous-reference-gene-actb-and-its-application-in-meat-adulteration
#13
Wenjin Xiang, Ying Shang, Qin Wang, Yuancong Xu, Pengyu Zhu, Kunlun Huang, Wentao Xu
The genes commonly used to determine meat species are mainly mitochondrial, but the copy numbers of such genes are high, meaning they cannot be accurately quantified. In this paper, for the first time, the chromosomal gene Actb was selected as an endogenous reference gene for chicken species. It was assayed in four different chicken varieties and 16 other species using both qualitative and quantitative PCR. No amplification of the Actb gene was found in species other than chicken and no allelic variations were detected in chicken...
November 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28507561/deletion-extents-are-not-the-cause-of-clinical-variability-in-22q11-2-deletion-syndrome-does-the-interaction-between-dgcr8-and-mirna-cnvs-play-a-major-role
#14
Veronica Bertini, Alessia Azzarà, Annalisa Legitimo, Roberta Milone, Roberta Battini, Rita Consolini, Angelo Valetto
In humans, the most common genomic disorder is the hemizygous deletion of the chromosome 22q11.2 region, that results in the "22q11.2 deletion syndrome" (22q11.2DS). A peculiarity of 22q11.2DS is its great phenotypic variability that makes this pathology a classic example of a syndrome with variable expressivity and incomplete penetrance. The reasons for this variability have not been elucidated yet, and the molecular substrates underlying the different clinical features of 22q11.2DS are still debated. A cohort of 21 patients has been analyzed by array CGH in order to detect some of the genetic differences that may influence this variability...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28497457/mitochondrial-dna-copy-number-variation-as-a-potential-predictor-of-renal-cell-carcinoma
#15
Eman T Elsayed, Mohamed M Hashad, Iman E Elgohary
BACKGROUND: Peripheral blood mitochondrial DNA (mtDNA) copy number alteration has been suggested as a risk factor for several types of cancer. The aim of the present study was to assess the role of peripheral blood mtDNA copy number variation as a noninvasive biomarker in the prediction and early detection of renal cell carcinoma (RCC) in a cohort of Egyptian patients. METHODS: Quantitative real-time polymerase chain reaction (qPCR) was used to measure peripheral blood mtDNA copy numbers in 57 patients with newly diagnosed, early-stage localized RCC and 60 age- and sex-matched healthy individuals as a control group...
May 10, 2017: International Journal of Biological Markers
https://www.readbyqxmd.com/read/28489755/kennedy-disease-with-difficulty-in-differential-diagnosis-a-case-report
#16
Yating Chen, Peng Luo, Zhongli Li, Hengping Hu, Duobin Wu, Tingting Xu, Xingzuo Wang, Haiting Xie
RATIONALE: Kennedy disease (KD) is also known as spinal bulbar muscular dystrophy. As KD has similar symptoms with most neuromuscular diseases, so it is difficult to make a rapid diagnosis clinically. PATIENT CONCERNS: We report a case of a 43-year-old male with progressive limb proximal weakness without family history. Physical examination showed gynecomastia, erectile dysfunction, bilateral tendon reflex and quadriceps weakness, and tongue muscle atrophy. DIAGNOSES: Laboratory examination found increased creatine kinase, impaired glucose tolerance, and abnormal lactic acid values...
May 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28441938/mitors-a-method-for-high-throughput-sensitive-and-accurate-detection-of-mitochondrial-dna-heteroplasmy
#17
Julien Marquis, Gregory Lefebvre, Yiannis A I Kourmpetis, Mohamed Kassam, Frédéric Ronga, Umberto De Marchi, Andreas Wiederkehr, Patrick Descombes
BACKGROUND: Mitochondrial dysfunction is linked to numerous pathological states, in particular related to metabolism, brain health and ageing. Nuclear encoded gene polymorphisms implicated in mitochondrial functions can be analyzed in the context of classical genome wide association studies. By contrast, mitochondrial DNA (mtDNA) variants are more challenging to identify and analyze for several reasons. First, contrary to the diploid nuclear genome, each cell carries several hundred copies of the circular mitochondrial genome...
April 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28438607/obesity-exposed-oocytes-accumulate-and-transmit-damaged-mitochondria-due-to-an-inability-to-activate-mitophagy
#18
Anna L Boudoures, Jessica Saben, Andrea Drury, Suzanne Scheaffer, Zeel Modi, Wendy Zhang, Kelle H Moley
Mitochondria are the most prominent organelle in the oocyte. Somatic cells maintain a healthy population of mitochondria by degrading damaged mitochondria via mitophagy, a specialized autophagy pathway. However, evidence from previous work investigating the more general macroautophagy pathway in oocytes suggests that mitophagy may not be active in the oocyte. This would leave the vast numbers of mitochondria - poised to be inherited by the offspring - vulnerable to damage. Here we test the hypothesis that inactive mitophagy in the oocyte underlies maternal transmission of dysfunctional mitochondria...
June 1, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28424544/association-of-genetic-variations-in-the-mitochondrial-dna-control-region-with-presbycusis
#19
Masoumeh Falah, Mohammad Farhadi, Seyed Kamran Kamrava, Saeid Mahmoudian, Ahmad Daneshi, Maryam Balali, Alimohamad Asghari, Massoud Houshmand
BACKGROUND: The prominent role of mitochondria in the generation of reactive oxygen species, cell death, and energy production contributes to the importance of this organelle in the intracellular mechanism underlying the progression of the common sensory disorder of the elderly, presbycusis. Reduced mitochondrial DNA (mtDNA) gene expression and coding region variation have frequently been reported as being associated with the development of presbycusis. The mtDNA control region regulates gene expression and replication of the genome of this organelle...
2017: Clinical Interventions in Aging
https://www.readbyqxmd.com/read/28406926/high-resolution-respirometry-of-fine-needle-muscle-biopsies-in-pre-manifest-huntington-s-disease-expansion-mutation-carriers-shows-normal-mitochondrial-respiratory-function
#20
Eva Buck, Martina Zügel, Uwe Schumann, Tamara Merz, Anja M Gumpp, Anke Witting, Jürgen M Steinacker, G Bernhard Landwehrmeyer, Patrick Weydt, Enrico Calzia, Katrin S Lindenberg
Alterations in mitochondrial respiration are an important hallmark of Huntington's disease (HD), one of the most common monogenetic causes of neurodegeneration. The ubiquitous expression of the disease causing mutant huntingtin gene raises the prospect that mitochondrial respiratory deficits can be detected in skeletal muscle. While this tissue is readily accessible in humans, transgenic animal models offer the opportunity to cross-validate findings and allow for comparisons across organs, including the brain...
2017: PloS One
keyword
keyword
106983
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"