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Copy number variants

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https://www.readbyqxmd.com/read/29346449/within-host-selection-for-faster-replicating-bacterial-symbionts
#1
Ewa Chrostek, Luis Teixeira
Wolbachia is a widespread, intracellular symbiont of arthropods, able to induce reproductive distortions and antiviral protection in insects. Wolbachia can also be pathogenic, as is the case with wMelPop, a virulent variant of the endosymbiont of Drosophila melanogaster. An extensive genomic amplification of the 20kb region encompassing eight Wolbachia genes, called Octomom, is responsible for wMelPop virulence. The Octomom copy number in wMelPop can be highly variable between individual D. melanogaster flies, even when comparing siblings arising from a single female...
2018: PloS One
https://www.readbyqxmd.com/read/29342293/genetic-analyses-in-small-for-gestational-age-newborns
#2
Susanne E Stalman, Nita Solanky, Miho Ishida, Cristina Alemán-Charlet, Sayeda Abu-Amero, Marielle Alders, Lucas Alvizi, William Baird, Charalambos Demetriou, Peter Henneman, Chela James, Lia C Knegt, Lydia J Leon, Marcel M A M Mannens, Adi N Mul, Nicole A Nibbering, Emma Peskett, Faisal I Rezwan, Carrie Ris-Stalpers, Joris A M van der Post, Gerdine A Kamp, Frans B Plötz, Jan M Wit, Philip Stanier, Gudrun E Moore, Raoul C Hennekam
Context: Small for gestational age (SGA) can be a result of fetal growth restriction, associated with perinatal morbidity and mortality. Mechanisms that control prenatal growth are poorly understood. Objective: The aim of the present study was to gain more insight into prenatal growth failure and determine an effective diagnostic approach in SGA newborns. We hypothesized that one or more CNVs and disturbed methylation and sequence variants may be present in genes known to be associated with fetal growth...
January 12, 2018: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29342233/quantumclone-clonal-assessment-of-functional-mutations-in-cancer-based-on-a-genotype-aware-method-for-clonal-reconstruction
#3
Paul Deveau, Leo Colmet Daage, Derek Oldridge, Virginie Bernard, Angela Bellini, Mathieu Chicard, Nathalie Clement, Eve Lapouble, Valerie Combaret, Anne Boland, Vincent Meyer, Jean-Francois Deleuze, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Olivier Delattre, John Maris, Gudrun Schleiermacher, Valentina Boeva
Motivation: In cancer, clonal evolution is assessed based on information coming from single nucleotide variants and copy number alterations. Nonetheless, existing methods often fail to accurately combine information from both sources to truthfully reconstruct clonal populations in a given tumor sample or in a set of tumor samples coming from the same patient. Moreover, previously published methods detect clones from a single set of variants. As a result, compromises have to be done between stringent variant filtering (reducing dispersion in variant allele frequency estimates, VAFs) and using all biologically relevant variants...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29342086/copy-number-variation-in-sox6-contributes-to-chicken-muscle-development
#4
Shudai Lin, Xiran Lin, Zihao Zhang, Mingya Jiang, Yousheng Rao, Qinghua Nie, Xiquan Zhang
Copy number variations (CNVs), which cover many functional genes, are associated with complex diseases, phenotypic diversity and traits that are economically important to raising chickens. The sex-determining region Y-box 6 (Sox6) plays a key role in fast-twitch muscle fiber differentiation of zebrafish and mice, but it is still unknown whether SOX6 plays a role in chicken skeletal muscle development. We identified two copy number polymorphisms (CNPs) which were significantly related to different traits on the genome level in chickens by AccuCopy® and CNVplex® analyses...
January 17, 2018: Genes
https://www.readbyqxmd.com/read/29341473/somatic-mosaic-deletions-involving-scn1a-cause-dravet-syndrome
#5
Tojo Nakayama, Atsushi Ishii, Takeshi Yoshida, Hirosato Nasu, Keiko Shimojima, Toshiyuki Yamamoto, Shigeo Kure, Shinichi Hirose
Somatic mosaicism in single nucleotide variants of SCN1A is known to occur in a subset of parents of children with Dravet syndrome (DS). Here, we report recurrent somatic mosaic microdeletions involving SCN1A in children diagnosed with DS. Through the evaluation of 237 affected individuals with DS who did not show SCN1A or PCHD19 mutations in prior sequencing analyzes, we identified two children with mosaic microdeletions covering the entire SCN1A region. The allele frequency of the mosaic deletions estimated by multiplex ligation-dependent probe amplification and array comparative genomic hybridization was 25-40%, which was comparable to the mosaic ratio in lymphocytes and buccal mucosa cells observed by fluorescence in situ hybridization analysis...
January 17, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29341460/intellectual-disability-and-epilepsy-due-to-the-k-l-mediated-xq28-duplication-further-evidence-of-a-distinct-dosage-dependent-phenotype
#6
David Isum Ward, Bethany A Buckley, Eyby Leon, Jullianne Diaz, Margaret Faust Galegos, Sean Hofherr, Amy Feldman Lewanda
Copy number variants of the X-chromosome are a common cause of X-linked intellectual disability in males. Duplication of the Xq28 band has been known for over a decade to be the cause of the Lubs X-linked Mental Retardation Syndrome (OMIM 300620) in males and this duplication has been narrowed to a critical region containing only the genes MECP2 and IRAK1. In 2009, four families with a distal duplication of Xq28 not including MECP2 and mediated by low-copy repeats (LCRs) designated "K" and "L" were reported with intellectual disability and epilepsy...
January 17, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29339441/allele-specific-droplet-digital-pcr-combined-with-a-next-generation-sequencing-based-algorithm-for-diagnostic-copy-number-analysis-in-genes-with-high-homology-proof-of-concept-using-stereocilin
#7
Sami S Amr, Elissa Murphy, Elizabeth Duffy, Rojeen Niazi, Jorune Balciuniene, Minjie Luo, Heidi L Rehm, Ahmad N Abou Tayoun
BACKGROUND: Copy number variants (CNVs) can substantially contribute to the pathogenic variant spectrum in several disease genes. The detection of this type of variant is complicated in genes with high homology to other genomic sequences, yet such genomics regions are more likely to lead to CNVs, making it critical to address detection in these settings. METHODS: We developed a copy number analysis approach for high homology genes/regions that consisted of next-generation sequencing (NGS)-based dosage analysis accompanied by allele-specific droplet digital PCR (ddPCR) confirmatory testing...
January 16, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29337640/molecular-determinants-of-response-to-anti-programmed-cell-death-pd-1-and-anti-programmed-death-ligand-pd-l-ligand-1-blockade-in-patients-with-non-small-cell-lung-cancer-profiled-with-targeted-next-generation-sequencing
#8
Hira Rizvi, Francisco Sanchez-Vega, Konnor La, Walid Chatila, Philip Jonsson, Darragh Halpenny, Andrew Plodkowski, Niamh Long, Jennifer L Sauter, Natasha Rekhtman, Travis Hollmann, Kurt A Schalper, Justin F Gainor, Ronglai Shen, Ai Ni, Kathryn C Arbour, Taha Merghoub, Jedd Wolchok, Alexandra Snyder, Jamie E Chaft, Mark G Kris, Charles M Rudin, Nicholas D Socci, Michael F Berger, Barry S Taylor, Ahmet Zehir, David B Solit, Maria E Arcila, Marc Ladanyi, Gregory J Riely, Nikolaus Schultz, Matthew D Hellmann
Purpose Treatment of advanced non-small-cell lung cancer with immune checkpoint inhibitors (ICIs) is characterized by durable responses and improved survival in a subset of patients. Clinically available tools to optimize use of ICIs and understand the molecular determinants of response are needed. Targeted next-generation sequencing (NGS) is increasingly routine, but its role in identifying predictors of response to ICIs is not known. Methods Detailed clinical annotation and response data were collected for patients with advanced non-small-cell lung cancer treated with anti-programmed death-1 or anti-programmed death-ligand 1 [anti-programmed cell death (PD)-1] therapy and profiled by targeted NGS (MSK-IMPACT; n = 240)...
January 16, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/29336640/novel-rnaset2-pathogenic-variants-in-an-east-asian-child-with-delayed-psychomotor-development
#9
Yan Sun, Xuyun Hu, Jiqing Song, Yanyan Hu, Caihong Liu, Guimei Li
INTRODUCTION: RNASET2 mutation has been reported in patients with cystic leukoencephalopathy without megalencephaly and the Aicardi-Goutieres syndrome. Both disorders are Mendelian mimics of congenital cytomegalovirus infection with overlapping features, including leukoencephalopathy, white matter alterations, intracranial calcification, delayed psychomotor development, intelligence disability and seizures. Only eight families with RNASET2 mutation have been previously reported. METHODS: Whole exome sequencing was performed and copy number variants were described by read-depth strategy...
January 16, 2018: Fetal and Pediatric Pathology
https://www.readbyqxmd.com/read/29331932/cnv-biology-in-neurodevelopmental-disorders
#10
REVIEW
Toru Takumi, Kota Tamada
Copy number variants (CNVs), characterized in recent years by cutting-edge technology, add complexity to our knowledge of the human genome. CNVs contribute not only to human diversity but also to different kinds of diseases including neurodevelopmental delay, autism spectrum disorder and neuropsychiatric diseases. Interestingly, many pathogenic CNVs are shared among these diseases. Studies suggest that pathophysiology of disease may not be simply attributed to a single driver gene within a CNV but also that multifactorial effects may be important...
January 10, 2018: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/29329938/pipeline-to-gene-discovery-analysing-familial-parkinsonism-in-the-queensland-parkinson-s-project
#11
Steven R Bentley, Stephanie Bortnick, Ilaria Guella, Javed Y Fowdar, Peter A Silburn, Stephen A Wood, Matthew J Farrer, George D Mellick
INTRODUCTION: Family based study designs provide an informative resource to identify disease-causing mutations. The Queensland Parkinson's Project (QPP) has been involved in numerous genetic screening studies; however, details of the families enrolled into the register have not been comprehensively reported. This article characterises the families enrolled in the QPP and summarises monogenic forms of hereditary Parkinsonism found in the register. METHOD: The presence of pathogenic point mutations and copy number variations (CNVs) were, generally, screened in a sample of over 1000 PD patients from the total of 1725...
January 3, 2018: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/29325613/essential-tremor
#12
Lorraine N Clark, Elan D Louis
Essential tremor (ET) is one of the most common neurologic disorders, and genetic factors are thought to contribute significantly to disease etiology. There has been a relative lack of progress in understanding the genetic etiology of ET. This could reflect a number of factors, including the presence of substantial phenotypic and genotypic heterogeneity. Thus, a meticulous approach to phenotyping is important for genetic research. A lack of standardized phenotyping across studies and patient centers likely has contributed to the relative lack of success of genomewide association studies in ET...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325612/genetics-of-parkinson-disease
#13
Aloysius Domingo, Christine Klein
An understanding of the genetic etiology of Parkinson disease (PD) has become imperative for the modern-day neurologist. Although genetic forms cause only a minority of PD, the disease mechanisms they elucidate advance the understanding of idiopathic cases. Moreover, recently identified susceptibility variants contribute to complex-etiology PD and broaden the contribution of genetics beyond familial and early-onset cases. Dominantly inherited monogenic forms mimic idiopathic PD and are caused by mutations or copy number variations of SNCA, LRRK2, and VPS35...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29321673/genomic-analysis-of-family-data-reveals-additional-genetic-effects-on-intelligence-and-personality
#14
W David Hill, Ruben C Arslan, Charley Xia, Michelle Luciano, Carmen Amador, Pau Navarro, Caroline Hayward, Reka Nagy, David J Porteous, Andrew M McIntosh, Ian J Deary, Chris S Haley, Lars Penke
Pedigree-based analyses of intelligence have reported that genetic differences account for 50-80% of the phenotypic variation. For personality traits these effects are smaller, with 34-48% of the variance being explained by genetic differences. However, molecular genetic studies using unrelated individuals typically report a heritability estimate of around 30% for intelligence and between 0 and 15% for personality variables. Pedigree-based estimates and molecular genetic estimates may differ because current genotyping platforms are poor at tagging causal variants, variants with low minor allele frequency, copy number variants, and structural variants...
January 10, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29320483/microarray-analysis-in-pregnancies-with-isolated-unilateral-kidney-agenesis
#15
Lena Sagi-Dain, Idit Maya, Peleg Amir, Reches Adi, Ehud Banne, Hagit N Baris, Tenne Tamar, Amihood Singer, Shay Ben-Shachar
OBJECTIVE: To examine the risk for submicroscopic chromosomal aberrations among fetuses with apparently isolated solitary kidney. METHODS: Data acquisition was performed retrospectively by searching Israeli Ministry of Health computerized database. All cases having chromosomal microarray analysis (CMA) referred due to an indication of isolated unilateral kidney agenesis between January 2013 and September 2016 were included. Rate of clinically significant CMA findings in these pregnancies was compared to pregnancies with normal ultrasound, based on a systematic review encompassing 9792 cases and local data of 5541 pregnancies undergoing CMA due to maternal request...
January 10, 2018: Pediatric Research
https://www.readbyqxmd.com/read/29317335/integrated-case-control-and-somatic-germline-interaction-analyses-of-melanoma-susceptibility-genes
#16
Yao Yu, Hao Hu, Jiun-Sheng Chen, Fulan Hu, Jerry Fowler, Paul Scheet, Hua Zhao, Chad D Huff
While a number of genes have been implicated in melanoma susceptibility, the role of protein-coding variation in melanoma development and progression remains underexplored. To better characterize the role of germline coding variation in melanoma, we conducted a whole-exome case-control and somatic-germline interaction study involving 322 skin cutaneous melanoma cases from The Cancer Genome Atlas and 3607 controls of European ancestry. We controlled for cross-platform technological stratification using XPAT and conducted gene-based association tests using VAAST 2...
January 6, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29313952/how-to-consider-rare-genetic-variants-in-personalized-drug-therapy
#17
Volker M Lauschke, Magnus Ingelman-Sundberg
Personalized drug therapy aims to optimize the efficacy of pharmacological treatments by considering genetic, pathophysiological, dietary, and environmental factors as well as comedications and compliance. A multitude of associations between the specific genetic constitution of the patient and drug pharmacokinetics and pharmacodynamics has been identified in the last decades that encompass mainly common single nucleotide variants (SNVs) and gene copy number variations (CNVs) of importance for the function of genes encoding drug-metabolizing enzymes and transporters involved in drug absorption, distribution, metabolism, and excretion (ADME)...
January 5, 2018: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/29307037/autism-spectrum-symptomatology-among-children-with-duplication-7q11-23-syndrome
#18
Bonita P Klein-Tasman, Carolyn B Mervis
Gold-standard diagnostic assessments of autism spectrum disorder (ASD) symptomatology were conducted on 63 children (mean CA: 8.81 years) with 7q11.23 duplication syndrome, one of the copy number variants identified by Sanders et al. (Neuron 70:863-885, 2011a) as associated with ASD. ASD classification rate was 39.6% for the Autism Diagnostic Interview-Revised and 25.4% for the Autism Diagnostic Observation Schedule-2 (ADOS-2). Based on these assessments combined with clinical judgment, 19.0% of children were diagnosed with ASD...
January 6, 2018: Journal of Autism and Developmental Disorders
https://www.readbyqxmd.com/read/29305854/astrocytes-in-primary-cultures-express-serine-racemase-synthesize-d-serine-and-acquire-a1-reactive-astrocyte-features
#19
Suyan Li, Yota Uno, Uwe Rudolph, Johanna Cobb, Jing Liu, Thea Anderson, Deborah Levy, Darrick T Balu, Joseph T Coyle
D-Serine is a co-agonist at forebrain N-methyl-D-aspartate receptors (NMDAR) and is synthesized by serine racemase (SR). Although D-serine and SR were originally reported to be localized to glia, recent studies have provided compelling evidence that under healthy physiologic conditions both are localized primarily in neurons. However, in pathologic conditions, reactive astrocytes can also express SR and synthesize D-serine. Since cultured astrocytes exhibit features of reactive astrocytes, we have characterized D-serine synthesis and the expression of enzymes involved in its disposition in primary glial cultures...
January 3, 2018: Biochemical Pharmacology
https://www.readbyqxmd.com/read/29305224/snpitty-an-intuitive-web-application-for-interactive-b-allele-frequency-and-copy-number-visualization-of-next-generation-sequencing-data
#20
Job van Riet, Niels M G Krol, Peggy N Atmodimedjo, Erwin Brosens, Wilfred F J van IJcken, Maurice P H M Jansen, John W M Martens, Leendert H Looijenga, Guido Jenster, Hendrikus J Dubbink, Winand N M Dinjens, Harmen J G van de Werken
Exploration and visualization of next-generation sequencing data is crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions-of-interest coupled with dynamic heuristic filtering of genetic aberrations is however lacking. Therefore, we developed the web-application SNPitty that allows interactive visualization and interrogation of variant call format (VCF) files by utilizing B-allele frequencies of single nucleotide polymorphisms and single nucleotide variants, coverage metrics and copy-numbers analysis results...
January 2, 2018: Journal of Molecular Diagnostics: JMD
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