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https://www.readbyqxmd.com/read/28917518/genome-stability-of-programmed-stem-cell-products
#1
REVIEW
Ulrich Martin
Inherited and acquired genomic abnormalities are known to cause genetic diseases and contribute to cancer formation. Recent studies demonstrated a substantial mutational load in mouse and human embryonic and induced pluripotent stem cells (ESCs and iPSCs). Single nucleotide variants, copy number variations, and larger chromosomal abnormalities may influence the differentiation capacity of pluripotent stem cells and the functionality of their derivatives in disease modelling and drug screening, and are considered a serious risk for cellular therapies based on ESC or iPSC derivatives...
September 13, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/28915599/copy-number-variations-of-circulating-cell-free-dna-in-urothelial-carcinoma-of-the-bladder-patients-treated-with-radical-cystectomy-a-prospective-study
#2
Armin Soave, Felix K-H Chun, Timo Hillebrand, Michael Rink, Lars Weisbach, Bettina Steinbach, Margit Fisch, Klaus Pantel, Heidi Schwarzenbach
The aim of the present study was to establish a rapid profiling method using multiplex ligation-dependent probe amplification (MLPA) and characterize copy number variations (CNV) in circulating, cell-free DNA (cfDNA) in 85 urothelial carcinoma of the bladder (UCB) patients treated with radical cystectomy (RC). MLPA was tested for the use of cfDNA extracted from serum and plasma by various commercial extraction kits. Eighteen probes served as reference to control denaturation, ligation and amplification efficiency...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28914499/copy-number-variants-of-ras-mapk-pathway-genes-in-patients-with-isolated-cryptorchidism
#3
F Rodríguez, C Vallejos, F Giraudo, N Unanue, M I Hernández, P Godoy, S Célis, R Martín-Arenas, M Palomares-Bralo, K E Heath, M T López, F Cassorla
Cryptorchidism is the most common congenital disorder in boys, but the cause for most cases remains unknown. Patients with Noonan Syndrome are characterized by a typical face, growth retardation, congenital heart defects, learning disabilities and cryptorchidism. Copy number variations of Ras/MAPK pathway genes are unusual in patients with several clinical features of Noonan Syndrome; however, they have not been studied in patients with only one feature of this condition, such as cryptorchidism. Our aim was to determine whether patients with isolated cryptorchidism exhibit Ras/MAPK pathway gene copy number variations (CNVs)...
September 2017: Andrology
https://www.readbyqxmd.com/read/28914269/looking-beyond-the-exome-a-phenotype-first-approach-to-molecular-diagnostic-resolution-in-rare-and-undiagnosed-diseases
#4
Loren D M Pena, Yong-Hui Jiang, Kelly Schoch, Rebecca C Spillmann, Nicole Walley, Nicholas Stong, Sarah Rapisardo Horn, Jennifer A Sullivan, Allyn McConkie-Rosell, Sujay Kansagra, Edward C Smith, Mays El-Dairi, Jane Bellet, Martha Ann Keels, Joan Jasien, Peter G Kranz, Richard Noel, Shashi K Nagaraj, Robert K Lark, Daniel S G Wechsler, Daniela Del Gaudio, Marco L Leung, Laura G Hendon, Collette C Parker, Kelly L Jones, David B Goldstein, Vandana Shashi
PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
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
#5
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/28911203/mutations-of-conserved-non-coding-elements-of-pitx2-in-patients-with-ocular-dysgenesis-and-developmental-glaucoma
#6
Meredith E Protas, Eric Weh, Tim Footz, Jay Kasberger, Scott C Baraban, Alex V Levin, L Jay Katz, Robert Ritch, Michael A Walter, Elena V Semina, Douglas B Gould
Mutations in FOXC1 and PITX2 constitute the most common causes of ocular anterior segment dysgenesis (ASD), and confer a high risk for secondary glaucoma. The genetic causes underlying ASD in approximately half of patients remain unknown, despite many of them being screened by whole exome sequencing. Here, we performed whole genome sequencing on DNA from two affected individuals from a family with dominantly inherited ASD and glaucoma to identify a 748-kb deletion in a gene desert that contains conserved putative PITX2 regulatory elements...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28904201/heterogeneity-of-the-epstein-barr-virus-major-internal-repeat-reveals-evolutionary-mechanisms-of-ebv-and-a-functional-defect-in-the-prototype-ebv-strain-b95-8
#7
Mohammed Ba Abdullah, Richard Palermo, Anne Palser, Nicholas E Grayson, Paul Kellam, Samantha Correia, Agnieszka Szymula, Rob White
Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified both through co-evolution with its host, and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging, because of the large number and length of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat of EBV (IR1 or BamW repeats) from over 70 strains...
September 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28900073/-molecular-mechanisms-of-hiv-1-genetic-diversity
#8
D V Sosin, N A Tchurikov
High genetic diversity of HIV-1 is the main factor behind the fact that HIV infection is widespread and difficult to treat. Although a limited number (or only one) of virus particles enters the blood upon infection, the particles are replicated in infected cells and rapidly produce new genetic variants that are resistant to the host immune system and antiretroviral drugs. This circumstance hampers the development of anti-HIV-1 vaccines and requires new antiretroviral drugs to be designed. The cause of the high variation of HIV-1 is related to the properties of its reverse transcriptase, which is error prone and often makes mistakes when transcribing virus RNA...
July 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28892071/a-novel-rare-variant-r292h-in-rtn4r-affects-growth-cone-formation-and-possibly-contributes-to-schizophrenia-susceptibility
#9
H Kimura, Y Fujita, T Kawabata, K Ishizuka, C Wang, Y Iwayama, Y Okahisa, I Kushima, M Morikawa, Y Uno, T Okada, M Ikeda, T Inada, A Branko, D Mori, T Yoshikawa, N Iwata, H Nakamura, T Yamashita, N Ozaki
Reticulon 4 receptor (RTN4R) plays an essential role in regulating axonal regeneration and plasticity in the central nervous system through the activation of rho kinase, and is located within chromosome 22q11.2, a region that is known to be a hotspot for schizophrenia (SCZ) and autism spectrum disorder (ASD). Recently, rare variants such as copy-number variants and single-nucleotide variants have been a focus of research because of their large effect size associated with increased susceptibility to SCZ and ASD and the possibility of elucidating the pathophysiology of mental disorder through functional analysis of the discovered rare variants...
August 22, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28889126/chromosomal-microarray-analysis-in-fetuses-with-growth-restriction-and-normal-karyotype-a-systematic-review-and-meta-analysis
#10
Antoni Borrell, Maribel Grande, Montse Pauta, Laia Rodriguez-Revenga, Francesc Figueras
OBJECTIVE: To perform a systematic review of the literature and a meta-analysis to estimate the incremental yield of chromosomal microarray analysis (CMA) over karyotyping in fetal growth restriction (FGR). METHODS: This was a systematic review conducted in accordance with the PRISMA criteria. All articles identified in PubMed, Ovid Medline, and ISI Web of Knowledge (Web of Science) from January 2009 to November 2016 describing pathogenic copy number variants (CNVs) in fetuses with growth restriction were included...
September 9, 2017: Fetal Diagnosis and Therapy
https://www.readbyqxmd.com/read/28887889/the-genetic-basis-for-most-patients-with-pustular-skin-disease-remains-elusive
#11
R Mössner, D Wilsmann-Theis, V Oji, P Gkogkolou, S Löhr, P Schulz, A Körber, J Christoph-Prinz, R Renner, K Schäkel, L Vogelsang, K-P Peters, S Philipp, K Reich, H Ständer, A Jacobi, A Weyergraf, K Kingo, S Kõks, S Gerdes, K Steinz, T Schill, K G Griewank, M Müller, S Frey, L Ebertsch, S Uebe, M Sticherling, H Sticht, U Hüffmeier
BACKGROUND: Rare variants in the genes IL36RN, CARD14 and AP1S3 have been identified to cause/ contribute to pustular skin diseases, primarily generalized pustular psoriasis (GPP). OBJECTIVES: To better understand the disease-relevance of these genes, we screened our cohorts of patients with pustular skin diseases (primarily GPP and palmoplantar pustular psoriasis [PPP]) for coding changes in these three genes. Carriers of single heterozygous IL36RN mutations were screened for a second mutation in IL36RN...
August 5, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/28886095/reduced-slc1a1-expression-is-associated-with-neuroinflammation-and-impaired-sensorimotor-gating-and-cognitive-performance-in-mice-implications-for-schizophrenia
#12
Parisa Afshari, Wei-Dong Yao, Frank A Middleton
We previously reported a 84-Kb hemi-deletion copy number variant at the SLC1A1 gene locus that reduces its expression and appeared causally linked to schizophrenia. In this report, we characterize the in vivo and in vitro consequences of reduced expression of Slc1a1 in mice. Heterozygous (HET) Slc1a1+/- mice, which more closely model the hemi-deletion we found in human subjects, were examined in a series of behavioral, anatomical and biochemical assays. Knockout (KO) mice were also included in the behavioral studies for comparative purposes...
2017: PloS One
https://www.readbyqxmd.com/read/28882788/efficient-detection-of-chromosome-imbalances-and-exome-single-nucleotide-variants-using-targeted-sequencing-in-the-clinical-setting
#13
Darine Villela, Silvia Souza da Costa, Angela M Vianna-Morgante, Ana C V Krepischi, Carla Rosenberg
We evaluated an approach to detect copy number variants (CNVs) and single nucleotide changes (SNVs), using a clinically focused exome panel complemented with a backbone and SNP probes that allows for genome-wide copy number changes and copy-neutral absence of heterozygosity (AOH) calls; this approach potentially substitutes the use of chromosomal microarray testing and sequencing into a single test. A panel of 16 DNA samples with known alterations ranging from megabase-scale CNVs to single base modifications were used as positive controls for sequencing data analysis...
September 4, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28882566/genetic-variations-in-ugt2b28-ugt2b17-ugt2b15-genes-and-the-risk-of-prostate-cancer-a-case-control-study
#14
Mohsen Habibi, Reza Mirfakhraie, Maryam Khani, Azadeh Rakhshan, Eznollah Azargashb, Farkhondeh Pouresmaeili
Glucuronidation is a major pathway for elimination of exogenous and endogenous compounds such as environmental carcinogens and androgens from the body. This biochemical pathway is mediated by enzymes called uridine diphosphoglucuronosyltransferases (UGTs). Null (del/del) genes polymorphisms in UGT2B17, and UGT2B28 and D85Y single-nucleotide polymorphism (SNP) of UGT2B15 have been reported to increase the risk of prostate cancer. The goal of this study was to determine the association of mentioned genetic variants with the risk of prostate cancer...
September 4, 2017: Gene
https://www.readbyqxmd.com/read/28882180/high-performance-of-targeted-next-generation-sequencing-on-variance-detection-in-clinical-tumor-specimens-in-comparison-with-current-conventional-methods
#15
Dan Su, Dadong Zhang, Kaiyan Chen, Jing Lu, Junzhou Wu, Xinkai Cao, Lisha Ying, Qihuang Jin, Yizhou Ye, Zhenghua Xie, Lei Xiong, Weimin Mao, Fugen Li
BACKGROUND: Next generation sequencing (NGS) is being increasingly applied for assisting cancer molecular diagnosis. However, it is still needed to validate NGS accuracy on detection of DNA alternations based on a large number of clinical samples, especially for DNA rearrangements and copy number variations (CNVs). This study is to set up basic parameters of targeted NGS for clinical diagnosis and to understand advantage of targeted NGS in comparison with the conventional methods of molecular diagnosis...
September 7, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28878743/characterization-of-the-copy-number-and-variants-of-deformed-wing-virus-dwv-in-the-pairs-of-honey-bee-pupa-and-infesting-varroa-destructor-or-tropilaelaps-mercedesae
#16
Yunfei Wu, Xiaofeng Dong, Tatsuhiko Kadowaki
Recent honey bee colony losses, particularly during the winter, have been shown to be associated with the presence of both ectoparasitic mites and Deformed Wing Virus (DWV). Whilst the role of Varroa destructor mites as a viral vector is well established, the role of Tropilaelaps mercedesae mites in viral transmission has not been fully investigated. In this study, we tested the effects that V. destructor and T. mercedesae infestation have on fluctuation of the DWV copy number and alteration of the virus variants in honey bees by characterizing individual pupae and their infesting mites...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28877932/detection-and-genomic-characterization-of-a-mammary-like-adenocarcinoma
#17
Jasleen K Grewal, Peter Eirew, Martin Jones, Kenrry Chiu, Basile Tessier-Cloutier, Anthony N Karnezis, Aly Karsan, Andy Mungall, Chen Zhou, Stephen Yip, Anna V Tinker, Janessa Laskin, Marco Marra, Steven J M Jones
Whole-genome and transcriptome sequencing were performed to identify potential therapeutic strategies in the absence of viable treatment options for a patient initially diagnosed with vulvar adenocarcinoma. Genomic events were prioritized by comparison against variant distributions in the TCGA pan-cancer dataset, and complemented with detailed transcriptome sequencing and copy number analysis. These findings were considered against published scientific literature in order to evaluate the functional effects of potentially relevant genomic events...
September 6, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28874442/use-of-next-generation-sequencing-to-detect-ldlr-gene-copy-number-variation-in-familial-hypercholesterolemia
#18
Michael A Iacocca, Jian Wang, Jacqueline S Dron, John F Robinson, Adam D McIntyre, Henian Cao, Robert A Hegele
Familial hypercholesterolemia (FH) is a heritable condition of severely elevated LDL cholesterol, caused predominantly by autosomal codominant mutations in the LDL receptor gene (LDLR). In providing a molecular diagnosis for FH, the current procedure often includes targeted next-generation sequencing (NGS) panels for the detection of small-scale DNA variants, followed by multiplex ligation-dependent probe amplification (MLPA) in LDLR for the detection of whole-exon copy number variants (CNVs). The latter is essential as ~10% of FH cases are attributed to CNVs in LDLR; accounting for them decreases false negative findings...
September 5, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28871548/studying-individual-plant-aox-gene-functionality-in-early-growth-regulation-a-new-approach
#19
Birgit Arnholdt-Schmitt, Vinod Kumar Patil
AOX1 and AOX2 genes are thought to play different physiological roles. Whereas AOX1 is typically expected to associate to stress and growth responses, AOX2 was more often found to be linked to development and housekeeping functions. However, this view is questioned by several adverse observations. For example, co-regulated expression for DcAOX1 and DcAOX2a genes was recently reported during growth induction in carrot (Daucus carota L.). Early expression peaks for both genes during the lag phase of growth coincided with a critical time point for biomass prediction, a result achieved by applying calorespirometry...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28871546/a-driving-bioinformatics-approach-to-explore-co-regulation-of-aox-gene-family-members-during-growth-and-development
#20
José Hélio Costa, Birgit Arnholdt-Schmitt
The alternative oxidase (AOX) gene family is a hot candidate for functional marker development that could help plant breeding on yield stability through more robust plants based on multi-stress tolerance. However, there is missing knowledge on the interplay between gene family members that might interfere with the efficiency of marker development. It is common view that AOX1 and AOX2 have different physiological roles. Nevertheless, both family member groups act in terms of molecular-biochemical function as "typical" alternative oxidases and co-regulation of AOX1 and AOX2 had been reported...
2017: Methods in Molecular Biology
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