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https://www.readbyqxmd.com/read/28224622/slc2a3-single-nucleotide-polymorphism-and-duplication-influence-cognitive-processing-and-population-specific-risk-for-attention-deficit-hyperactivity-disorder
#1
Sören Merker, Andreas Reif, Georg C Ziegler, Heike Weber, Ute Mayer, Ann-Christine Ehlis, Annette Conzelmann, Stefan Johansson, Clemens Müller-Reible, Indrajit Nanda, Thomas Haaf, Reinhard Ullmann, Marcel Romanos, Andreas J Fallgatter, Paul Pauli, Tatyana Strekalova, Charline Jansch, Alejandro Arias Vasquez, Jan Haavik, Marta Ribasés, Josep Antoni Ramos-Quiroga, Jan K Buitelaar, Barbara Franke, Klaus-Peter Lesch
BACKGROUND: Attention-deficit/hyperactivity disorder (ADHD) is a common, highly heritable neurodevelopmental disorder with profound cognitive, behavioral, and psychosocial impairments with persistence across the life cycle. Our initial genome-wide screening approach for copy number variants (CNVs) in ADHD implicated a duplication of SLC2A3, encoding glucose transporter-3 (GLUT3). GLUT3 plays a critical role in cerebral glucose metabolism, providing energy for the activity of neurons, which, in turn, moderates the excitatory-inhibitory balance impacting both brain development and activity-dependent neural plasticity...
February 22, 2017: Journal of Child Psychology and Psychiatry, and Allied Disciplines
https://www.readbyqxmd.com/read/28221368/no-evidence-for-the-presence-of-genetic-variants-predisposing-to-psychotic-disorders-on-the-non-deleted-22q11-2-allele-of-vcfs-patients
#2
M Guipponi, F Santoni, M Schneider, C Gehrig, X B Bustillo, W R Kates, B Morrow, M Armando, S Vicari, F Sloan-Béna, M Gagnebin, V Shashi, S R Hooper, S Eliez, S E Antonarakis
The velo-cardio-facial syndrome (VCFS) is caused by hemizygous deletions on chromosome 22q11.2. The VCFS phenotype is complex and characterized by frequent occurrence of neuropsychiatric symptoms with up to 25-30% of cases suffering from psychotic disorders compared with only ~1% in the general population (odds ratio≈20-25). This makes the 22q11.2 deletion one of the most prominent risk factors for schizophrenia. However, its penetrance for neuropsychiatric phenotypes is incomplete suggesting that additional risk factors are required for disease development...
February 21, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28220983/clinical-and-molecular-cytogenetic-analyses-of-four-families-with-1q21-1-microdeletion-or-microduplication
#3
Hong-Dan Wang, Lin Liu, Dong Wu, Tao Li, Cun-Ying Cui, Lian-Zhong Zhang, Cheng-Zeng Wang
BACKGROUND: Little information is available regarding penetrance of the 1q21.1 copy number variants (CNVs). We explored the clinical significance of 1q21.1 microdeletion or microduplication. METHODS: In four families, chromosome karyotype was analyzed using G-banding karyotype analysis technology, CNVs were detected using array-comparative genomic hybridization (aCGH), and then quantitative polymerase chain reaction (qPCR) was used to validate candidate CNVs. Sequence signature in the breakpoint region was analyzed using UCSC databases...
February 21, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28218758/variant-aware-saturating-mutagenesis-using-multiple-cas9-nucleases-identifies-regulatory-elements-at-trait-associated-loci
#4
Matthew C Canver, Samuel Lessard, Luca Pinello, Yuxuan Wu, Yann Ilboudo, Emily N Stern, Austen J Needleman, Frédéric Galactéros, Carlo Brugnara, Abdullah Kutlar, Colin McKenzie, Marvin Reid, Diane D Chen, Partha Pratim Das, Mitchel A Cole, Jing Zeng, Ryo Kurita, Yukio Nakamura, Guo-Cheng Yuan, Guillaume Lettre, Daniel E Bauer, Stuart H Orkin
Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants identified in genome-wide association studies largely cluster at regulatory loci. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating-mutagenesis libraries with single or multiple nucleases with incorporation of variants...
February 20, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28216108/crispr-enabled-trackable-genome-engineering-for-isopropanol-production-in-escherichia-coli
#5
Liya Liang, Rongming Liu, Andrew D Garst, Thomas Lee, Violeta Sànchez I Nogué, Gregg T Beckham, Ryan T Gill
Isopropanol is an important target molecule for sustainable production of fuels and chemicals. Increases in DNA synthesis and synthetic biology capabilities have resulted in the development of a range of new strategies for the more rapid design, construction, and testing of production strains. Here, we report on the use of such capabilities to construct and test 903 different variants of the isopropanol production pathway in Escherichia coli. We first constructed variants to explore the effect of codon optimization, copy number, and translation initiation rates on isopropanol production...
February 16, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28213546/environmental-surveillance-of-norovirus-genogroups-i-and-ii-for-sensitive-detection-of-epidemic-variants
#6
Shinobu Kazama, Takayuki Miura, Yoshifumi Masago, Yoshimitsu Konta, Kentaro Tohma, Takafumi Manaka, Xiaofang Liu, Daisuke Nakayama, Takashi Tanno, Mayuko Saito, Hitoshi Oshitani, Tatsuo Omura
Sewage samples have been investigated to study the level of noroviruses concentration in sewage or the genotypes of noroviruses circulating in human populations. However, the statistical relationship between the concentration of the virus and the number of infected individuals, and the clinical importance of genotypes or strains detected in sewage are unclear. In this study, we carried out both environmental and clinical surveillance of noroviruses for three years: 2013-2016. We performed cross-correlation analysis between the concentrations of norovirus GI or GII in sewage samples collected weekly and the number of gastroenteritis cases...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213435/genetics-of-synucleinopathies
#7
Robert L Nussbaum
Parkinson's disease (PD), diffuse Lewy body disease (DLBD), and multiple system atrophy (MSA) constitute the three major neurodegenerative disorders referred to as synucleinopathies because both genetic and pathological results implicate the α-synuclein protein in their pathogenesis. PD and DLBD are recognized as closely related diseases with substantial clinical and pathological overlap. MSA, on the other hand, has a distinctive clinical presentation and neuropathological profile. In this review, we will summarize the evidence linking α-synuclein to these three disorders...
February 17, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28210881/comprehensive-genomic-profiling-of-malignant-phyllodes-tumors-of-the-breast
#8
Sahar Nozad, Christine E Sheehan, Laurie M Gay, Julia A Elvin, Jo-Anne Vergilio, James Suh, Shakti Ramkissoon, Alexa B Schrock, Kim M Hirshfield, Nadia Ali, Shridar Ganesan, Siraj M Ali, Vincent A Miller, Philip J Stephens, Jeffrey S Ross, Jon H Chung
PURPOSE: Malignant phyllodes tumors (MPT) are exceptionally rare, and the genomic drivers of these tumors are still being elucidated. We performed comprehensive genomic profiling (CGP) of MPT to identify genomic alterations that will inform approaches to targeted therapy for patients with MPT, including relapsed, refractory, and metastatic disease. METHODS: DNA was extracted from formalin-fixed, paraffin-embedded samples from 24 consecutive patient cases of MPT...
February 17, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28207948/right-sided-aortic-arch-in-the-age-of-microarray
#9
Edward F O'Mahony, Darren P Hutchinson, George McGillivray, Debbie L Nisbet, Ricardo Palma-Dias
OBJECTIVE: For fetuses with a diagnosis of right aortic arch and normal cardiac anatomy we aimed to establish the frequency of chromosomal anomaly diagnosed with SNP microarray analysis, particularly focusing on microduplications or microdeletions which would have gone undetected by conventional karyotyping and 6 probe fish (13,18,21, X,Y, TUPLE). METHOD: Retrospective study of fetal ultrasounds between 2011 and 2016 in an Australian tertiary referral centre. Outcomes of interest were survival and postnatal surgery for vascular ring...
February 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28197171/genome-wide-microrna-binding-site-variation-between-extinct-wild-aurochs-and-modern-cattle-identifies-candidate-microrna-regulated-domestication-genes
#10
Martin Braud, David A Magee, Stephen D E Park, Tad S Sonstegard, Sinead M Waters, David E MacHugh, Charles Spillane
The domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non-coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28195579/11-670-whole-genome-sequences-representative-of-the-han-chinese-population-from-the-converge-project
#11
Na Cai, Tim B Bigdeli, Warren W Kretzschmar, Yihan Li, Jieqin Liang, Jingchu Hu, Roseann E Peterson, Silviu Bacanu, Bradley Todd Webb, Brien Riley, Qibin Li, Jonathan Marchini, Richard Mott, Kenneth S Kendler, Jonathan Flint
The China, Oxford and Virginia Commonwealth University Experimental Research on Genetic Epidemiology (CONVERGE) project on Major Depressive Disorder (MDD) sequenced 11,670 female Han Chinese at low-coverage (1.7X), providing the first large-scale whole genome sequencing resource representative of the largest ethnic group in the world. Samples are collected from 58 hospitals from 23 provinces around China. We are able to call 22 million high quality single nucleotide polymorphisms (SNP) from the nuclear genome, representing the largest SNP call set from an East Asian population to date...
February 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28193894/rules-of-rna-specificity-of-hnrnp-a1-revealed-by-global-and-quantitative-analysis-of-its-affinity-distribution
#12
Niyati Jain, Hsuan-Chun Lin, Christopher E Morgan, Michael E Harris, Blanton S Tolbert
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants (n = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5'-YAG-3' and shows how its copy number, position in the loop, and loop structure modulate affinity...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28192796/analysis-of-the-prpf31-gene-in-spanish-autosomal-dominant-retinitis-pigmentosa-patients-a-novel-genomic-rearrangement
#13
Inmaculada Martin-Merida, Rocio Sanchez-Alcudia, Patricia Fernandez-San Jose, Fiona Blanco-Kelly, Raquel Perez-Carro, Luciana Rodriguez-Jacy da Silva, Berta Almoguera, Blanca Garcia-Sandoval, Maria Isabel Lopez-Molina, Almudena Avila-Fernandez, Miguel Carballo, Marta Corton, Carmen Ayuso
Purpose: The aim was to determine the prevalence of PRPF31 mutations in a cohort of Spanish autosomal dominant retinitis pigmentosa (adRP) families to deepen knowledge of the pathogenic mechanisms underlying the disease and to assess genotype-phenotype correlations. Methods: A cohort of 211 adRP patients was screened for variants in PRPF31 by using a combined strategy comprising next-generation sequencing approaches and copy-number variation (CNV) analysis. Quantitative RT-PCR and CNV analysis of the regulatory MSR1 element were also performed to assess PRPF31 gene expression...
February 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28186096/spitz-nevi-and-spitzoid-melanomas-exome-sequencing-and-comparison-with-conventional-melanocytic-nevi-and-melanomas
#14
Rossitza Lazova, Natapol Pornputtapong, Ruth Halaban, Marcus Bosenberg, Yalai Bai, Hao Chai, Michael Krauthammer
We performed exome sequencing of 77 melanocytic specimens composed of Spitz nevi (n=29), Spitzoid melanomas (n=27), and benign melanocytic nevi (n=21), and compared the results with published melanoma sequencing data. Our study highlights the prominent similarity between Spitzoid and conventional melanomas with similar copy number changes and high and equal numbers of ultraviolet-induced coding mutations affecting similar driver genes. Mutations in MEN1, PRKAR1A, and DNMT3A in Spitzoid melanomas may indicate involvement of the protein kinase A pathway, or a role of DNA methylation in the disease...
February 10, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28181325/recurrent-copy-number-alterations-in-low-grade-and-anaplastic-pleomorphic-xanthoastrocytoma-with-and-without-braf-v600e-mutation
#15
Rachael A Vaubel, Alissa A Caron, Seiji Yamada, Paul A Decker, Jeanette E Eckel Passow, Fausto J Rodriguez, Amulya A Nageswara Rao, Daniel Lachance, Ian Parney, Robert Jenkins, Caterina Giannini
Pleomorphic xanthoastrocytoma (PXA) is a rare localized glioma characterized by frequent BRAF V600E mutation and CDKN2A/B deletion. We explored the association of copy-number variants (CNVs) with BRAF mutations, tumor grade, and patient survival in a cohort of 41 PXA patients using OncoScan chromosomal microarray. Primary resection specimens were available in 38 cases, including 24 PXA and 14 anaplastic PXA (A-PXA), 23 BRAF V600E mutant tumors (61%). CNVs were identified in all cases and most frequently involved chromosome 9 with homozygous CDKN2A/B deletion (n=33, 87%), a higher proportion than previously detected by comparative genomic hybridization (50-60%) (37)...
February 9, 2017: Brain Pathology
https://www.readbyqxmd.com/read/28177878/whole-genome-sequencing-identifies-new-genetic-alterations-in-meningiomas
#16
Mei Tang, Heng Wei, Lu Han, Jiaojiao Deng, Yuelong Wang, Meijia Yang, Yani Tang, Gang Guo, Liangxue Zhou, Aiping Tong
The major known genetic contributor to meningioma formation was NF2, which is disrupted by mutation or loss in about 50% of tumors. Besides NF2, several recurrent driver mutations were recently uncovered through next-generation sequencing. Here, we performed whole-genome sequencing across 7 tumor-normal pairs to identify somatic genetic alterations in meningioma. As a result, Chromatin regulators, including multiple histone members, histone-modifying enzymes and several epigenetic regulators, are the major category among all of the identified copy number variants and single nucleotide variants...
February 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28176757/dosage-sensitivity-is-a-major-determinant-of-human-copy-number-variant-pathogenicity
#17
Alan M Rice, Aoife McLysaght
Human copy number variants (CNVs) account for genome variation an order of magnitude larger than single-nucleotide polymorphisms. Although much of this variation has no phenotypic consequences, some variants have been associated with disease, in particular neurodevelopmental disorders. Pathogenic CNVs are typically very large and contain multiple genes, and understanding the cause of the pathogenicity remains a major challenge. Here we show that pathogenic CNVs are significantly enriched for genes involved in development and genes that have greater evolutionary copy number conservation across mammals, indicative of functional constraints...
February 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28169357/integrative-analysis-of-copy-number-and-transcriptional-expression-profiles-in-esophageal-cancer-to-identify-a-novel-driver-gene-for-therapy
#18
Gaochao Dong, Qixing Mao, Decai Yu, Yi Zhang, Mantang Qiu, Gaoyue Dong, Qiang Chen, Wenjie Xia, Jie Wang, Lin Xu, Feng Jiang
An increasing amount of evidence has highlighted the critical roles that copy number variants play in cancer progression. Here, we systematically analyzed the copy number alterations and differentially transcribed genes. Integrative analysis of the association between copy number variants and differential gene expression suggested that copy number variants will lead to aberrant expression of the corresponding genes. We performed a KEGG pathway and GO analysis, which revealed that cell cycle may have an effective role in the progression of esophageal cancer...
February 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28168542/copy-number-variations-in-tilapia-genomes
#19
Bi Jun Li, Hong Lian Li, Zining Meng, Yong Zhang, Haoran Lin, Gen Hua Yue, Jun Hong Xia
Discovering the nature and pattern of genome variation is fundamental in understanding phenotypic diversity among populations. Although several millions of single nucleotide polymorphisms (SNPs) have been discovered in tilapia, the genome-wide characterization of larger structural variants, such as copy number variation (CNV) regions has not been carried out yet. We conducted a genome-wide scan for CNVs in 47 individuals from three tilapia populations. Based on 254 Gb of high-quality paired-end sequencing reads, we identified 4642 distinct high-confidence CNVs...
February 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28165502/post-polyploidisation-morphotype-diversification-associates-with-gene-copy-number-variation
#20
Sarah Schiessl, Bruno Huettel, Diana Kuehn, Richard Reinhardt, Rod Snowdon
Genetic models for polyploid crop adaptation provide important information relevant for future breeding prospects. A well-suited model is Brassica napus, a recent allopolyploid closely related to Arabidopsis thaliana. Flowering time is a major adaptation trait determining life cycle synchronization with the environment. Here we unravel natural genetic variation in B. napus flowering time regulators and investigate associations with evolutionary diversification into different life cycle morphotypes. Deep sequencing of 35 flowering regulators was performed in 280 diverse B...
February 6, 2017: Scientific Reports
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