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Copy number variation

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https://www.readbyqxmd.com/read/28449315/panelcn-mops-copy-number-detection-in-targeted-ngs-panel-data-for-clinical-diagnostics
#1
Gundula Povysil, Antigoni Tzika, Julia Vogt, Verena Haunschmid, Ludwine Messiaen, Johannes Zschocke, Günter Klambauer, Sepp Hochreiter, Katharina Wimmer
Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy number variations (CNVs) in addition to single-nucleotide-variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control, incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn...
April 27, 2017: Human Mutation
https://www.readbyqxmd.com/read/28448765/digital-assays-part-i-partitioning-statistics-and-digital-pcr
#2
Amar S Basu
A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error...
April 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/28448694/the-joint-effect-of-air-pollution-exposure-and-copy-number-variation-on-risk-for-autism
#3
Dokyoon Kim, Heather Volk, Santhosh Girirajan, Sarah Pendergrass, Molly A Hall, Shefali S Verma, Rebecca J Schmidt, Robin L Hansen, Debashis Ghosh, Yunin Ludena-Rodriguez, Kyoungmi Kim, Marylyn D Ritchie, Irva Hertz-Picciotto, Scott B Selleck
Autism spectrum disorder is a complex trait with a high degree of heritability as well as documented susceptibility from environmental factors. In this study the contributions of copy number variation, exposure to air pollutants, and the interaction between the two on autism risk, were evaluated in the population-based case-control Childhood Autism Risks from Genetics and Environment (CHARGE) Study. For the current investigation, we included only those CHARGE children (a) who met criteria for autism or typical development and (b) for whom our team had conducted both genetic evaluation of copy number burden and determination of environmental air pollution exposures based on mapping addresses from the pregnancy and early childhood...
April 27, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28448516/natural-variation-of-pirna-expression-affects-immunity-to-transposable-elements
#4
Sergei Ryazansky, Elizaveta Radion, Anastasia Mironova, Natalia Akulenko, Yuri Abramov, Valeriya Morgunova, Maria Y Kordyukova, Ivan Olovnikov, Alla Kalmykova
In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28448514/a-new-gtf2i-braf-fusion-mediating-mapk-pathway-activation-in-pilocytic-astrocytoma
#5
Tajana Tešan Tomić, Josefin Olausson, Annica Wilzén, Magnus Sabel, Katarina Truvé, Helene Sjögren, Sándor Dósa, Magnus Tisell, Birgitta Lannering, Fredrik Enlund, Tommy Martinsson, Pierre Åman, Frida Abel
Pilocytic astrocytoma (PA) is the most common pediatric brain tumor. A recurrent feature of PA is deregulation of the mitogen activated protein kinase (MAPK) pathway most often through KIAA1549-BRAF fusion, but also by other BRAF- or RAF1-gene fusions and point mutations (e.g. BRAFV600E). These features may serve as diagnostic and prognostic markers, and also facilitate development of targeted therapy. The aims of this study were to characterize the genetic alterations underlying the development of PA in six tumor cases, and evaluate methods for fusion oncogene detection...
2017: PloS One
https://www.readbyqxmd.com/read/28446957/small-copy-number-variations-involving-genes-of-the-fgf-pathway-in-differences-in-sex-development
#6
Andrew Hagan, Ina E Amarillo
Retrospective chromosome microarray analysis of 83 genes within the fibroblast growth factor signaling pathway in 52 patients with heterogeneous differences in sex development (DSD) revealed small copy-number variations (CNVs) in ~31% (n=26) of investigated genes. Roughly half of these genes (39/83) are ⩽50 kb. This study highlights the potential involvement of small CNVs in disrupting normal gene function and dysregulating genes of the FGF pathway associated with DSD.
2017: Human Genome Variation
https://www.readbyqxmd.com/read/28445152/multiplexed-gene-expression-profiling-identifies-the-fgfr4-pathway-as-a-novel-biomarker-in-intrahepatic-cholangiocarcinoma
#7
Changhoon Yoo, Jihoon Kang, Deokhoon Kim, Kyu-Pyo Kim, Baek-Yeol Ryoo, Seung-Mo Hong, Jung Jin Hwang, Seong-Yun Jeong, Shin Hwang, Ki-Hun Kim, Young-Joo Lee, Klaus P Hoeflich, Oleg Schmidt-Kittler, Stephen Miller, Eun Kyung Choi
BACKGROUND: The fibroblast growth factor receptor 4 (FGFR4) pathway is an essential regulatory component of bile acid synthesis, and its relationship with hepatocellular carcinoma (HCC) has been reported. We investigated the gene expression and clinical significance of FGFR4 and related pathways in intrahepatic cholangiocarcinoma (iCCA). RESULTS: The median age was 56 years (range 30-78) and 34 patients (74%) were male. Six patients (13%) had hepatitis B virus infection, with or without liver cirrhosis...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28444910/characterization-of-porcine-endogenous-retrovirus-expression-in-neonatal-and-adult-pig-pancreatic-islets
#8
Nizar I Mourad, Claire Crossan, Victoria Cruikshank, Linda Scobie, Pierre Gianello
BACKGROUND: Pig islets represent an alternative to the current modes of treatment for patients with diabetes. However, the concerns over pathogen transmission including that of PERV limit their immediate, widespread usage in humans. It has been previously demonstrated that PERV copy number and particularly expression levels can vary considerably between individuals and within different tissues of a single animal. In general, expression levels have been found to be particularly low in the pancreas compared to other porcine tissues suggesting a reduced risk associated with the use of this tissue...
April 26, 2017: Xenotransplantation
https://www.readbyqxmd.com/read/28444229/a-novel-but-frequent-variant-in-lpa-kiv-2-is-associated-with-a-pronounced-lp-a-and-cardiovascular-risk-reduction
#9
Stefan Coassin, Gertraud Erhart, Hansi Weissensteiner, Mariana Eca Guimarães de Araújo, Claudia Lamina, Sebastian Schönherr, Lukas Forer, Margot Haun, Jamie Lee Losso, Anna Köttgen, Konrad Schmidt, Gerd Utermann, Annette Peters, Christian Gieger, Konstantin Strauch, Armin Finkenstedt, Reto Bale, Heinz Zoller, Bernhard Paulweber, Kai-Uwe Eckardt, Alexander Hüttenhofer, Lukas A Huber, Florian Kronenberg
Aims: Lp(a) concentrations represent a major cardiovascular risk factor and are almost entirely controlled by one single locus (LPA). However, many genetic factors in LPA governing the enormous variance of Lp(a) levels are still unknown. Since up to 70% of the LPA coding sequence are located in a difficult to access hypervariable copy number variation named KIV-2, we hypothesized that it may contain novel functional variants with pronounced effects on Lp(a) concentrations. We performed a large scale mutation analysis in the KIV-2 using an extreme phenotype approach...
April 25, 2017: European Heart Journal
https://www.readbyqxmd.com/read/28440577/variable-developmental-delays-and-characteristic-facial-features-a-novel-7p22-3p22-2-microdeletion-syndrome
#10
Andrea C Yu, Regina M Zambrano, Ingrid Cristian, Sue Price, Birgitta Bernhard, Marc Zucker, Sunita Venkateswaran, Jean McGowan-Jordan, Christine M Armour
Isolated 7p22.3p22.2 deletions are rarely described with only two reports in the literature. Most other reported cases either involve a much larger region of the 7p arm or have an additional copy number variation. Here, we report five patients with overlapping microdeletions at 7p22.3p22.2. The patients presented with variable developmental delays, exhibiting relative weaknesses in expressive language skills and relative strengths in gross, and fine motor skills. The most consistent facial features seen in these patients included a broad nasal root, a prominent forehead a prominent glabella and arched eyebrows...
April 25, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28440405/copy-number-variation-analysis-in-familial-nonsyndromic-congenital-anomalies-of-the-kidney-and-urinary-tract-evidence-for-the-causative-role-of-a-transposable-element-associated-genomic-rearrangement
#11
Ekaterini Siomou, Artemis G Mitsioni, Vasileios Giapros, Ioanna Bouba, Dimitrios Noutsopoulos, Ioannis Georgiou
Most congenital anomalies of the kidney and urinary tract (CAKUT) are sporadic, but familial occurrence has been described, suggesting a genetic contribution. Copy‑number variations (CNVs) were detected in patients with CAKUT to identify possible novel genomic regions associated with CAKUT. CNVs were investigated in 7 children with CAKUT from three unrelated families using array comparative genomic hybridization: female monozygotic twins with bilateral duplex collecting system/vesicoureteral reflux (VUR)/unilateral renal hypodyspasia (URHD); two male siblings with VUR/URHD; 3 male second cousins, one with bilateral VUR/URHD, one with bilateral VUR and one with ureterovesical junction obstruction (UVJO)...
April 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28439972/mitochondrial-biogenesis-and-pgc-1%C3%AE-gene-expression-in-male-broilers-from-ascites-susceptible-and-resistant-lines
#12
N Khodambashi Emami, A Golian, M Danesh Mesgaran, N B Anthony, D D Rhoads
Ascites is a cardiovascular metabolic disease characterized by accumulation of fluid around the heart and in the abdominal cavity that eventually leads to death. This syndrome is the end-point result of a series of metabolic incidents that are generally caused by impaired oxygen availability. Mitochondria are the major sites of oxygen consumption, therefore major contributors to oxidative stress. Genetic, metabolic and dietary factors can influence variations in mitochondrial biogenesis (mitochondrial size, number and mass) that might have an effect on oxygen consumption and reactive oxygen species production...
April 25, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28438122/comprehensive-performance-comparison-of-high-resolution-array-platforms-for-genome-wide-copy-number-variation-cnv-analysis-in-humans
#13
Rajini R Haraksingh, Alexej Abyzov, Alexander Eckehart Urban
BACKGROUND: High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software...
April 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28437156/development-of-a-taqman-based-real-time-pcr-assay-for-rapid-and-specific-detection-of-fowl-aviadenovirus-serotype-4
#14
Jianchang Wang, Jinfeng Wang, Ping Chen, Libing Liu, Wanzhe Yuan
Twelve serotypes of fowl aviadenovirus, namely, FAdV-(1-8a and 8b-11), have been identified, among which FAdV-4 is the aetiologic agent of hepatitis hydropericardium syndrome (HHS) in chickens. Outbreaks of HHS have been documented in many countries, causing significant economic losses. Real-time PCR methods described so far in the literature cross-detect different serotypes of FAdVs. In this study, we aimed to develop a TaqMan-based real-time PCR assay for the specific detection of FAdV-4. A pair of primers targeting the hexon gene and a TaqMan probe were designed...
June 2017: Avian Pathology: Journal of the W.V.P.A
https://www.readbyqxmd.com/read/28435450/exome-sequencing-of-oral-squamous-cell-carcinoma-reveals-molecular-subgroups-and-novel-therapeutic-opportunities
#15
Shih-Chi Su, Chiao-Wen Lin, Yu-Fan Liu, Wen-Lang Fan, Mu-Kuan Chen, Chun-Ping Yu, Wei-En Yang, Chun-Wen Su, Chun-Yi Chuang, Wen-Hsiung Li, Wen-Hung Chung, Shun-Fa Yang
Oral squamous cell carcinoma (OSCC), an epithelial malignancy affecting a variety of subsites in the oral cavity, is prevalent in Asia. The survival rate of OSCC patients has not improved over the past decades due to its heterogeneous etiology, genetic aberrations, and treatment outcomes. Improvement in therapeutic strategies and tailored treatment options is an unmet need. To unveil the mutational spectrum, whole-exome sequencing of 120 OSCC from male individuals in Taiwan was conducted. Analyzing the contributions of the five mutational signatures extracted from the dataset of somatic variations identified four groups of tumors that were significantly associated with demographic and clinical features...
2017: Theranostics
https://www.readbyqxmd.com/read/28433079/utilization-of-whole-exome-next-generation-sequencing-variant-read-frequency-for-detection-of-lesion-specific-somatic-loss-of-heterozygosity-in-a-neurofibromatosis-type-1-cohort-with-tibial-pseudarthrosis
#16
Rebecca L Margraf, Chad VanSant-Webb, David Sant, John Carey, Heather Hanson, Jacques D'Astous, Dave Viskochil, David A Stevenson, Rong Mao
A subset of neurofibromatosis type 1 patients develop tibial dysplasia, which can lead to pseudarthrosis. The tissue from the tibial pseudarthrosis region commonly has a somatic second hit in NF1: single-nucleotide variants, small deletions, or loss of heterozygosity (LOH). We used exome next-generation sequencing (NGS) variant frequency data (allelic imbalance analysis) to detect somatic LOH in pseudarthrosis tissue from three individuals with clinically and diagnostically confirmed neurofibromatosis type 1, and verified the results with microarray...
May 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28431057/quantitative-analysis-of-pkp2-and-neighbouring-genes-in-a-patient-with-arrhythmogenic-right-ventricular-cardiomyopathy-caused-by-heterozygous-pkp2-deletion
#17
Keiko Sonoda, Seiko Ohno, Sou Otuki, Koichi Kato, Nobue Yagihara, Hiroshi Watanabe, Takeru Makiyama, Tohru Minamino, Minoru Horie
Aims: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a disease mainly caused by desmosome gene mutations. The genetic culprit, however, remains elusive in ∼50% of ARVC patients. One of the reasons for missing genetic abnormalities is the difficulty in detecting large deletions/duplications, which are called as copy number variation (CNV) by the Sanger sequencing method. This study aimed to identify CNVs in PKP2 and a part of other desmosome genes in ARVC patients. Methods and Results: The study cohort consisted of 71 ARVC probands who were diagnosed as definite or borderline cases based on 2010 Task Force Criteria...
April 1, 2017: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/28429786/comprehensive-assessment-showed-no-associations-of-variants-at-the-slc10a1-locus-with-susceptibility-to-persistent-hbv-infection-among-southern-chinese
#18
Ying Zhang, Yuanfeng Li, Miantao Wu, Pengbo Cao, Xiaomin Liu, Qian Ren, Yun Zhai, Bobo Xie, Yanling Hu, Zhibin Hu, Jinxin Bei, Jie Ping, Xinyi Liu, Yinghua Yu, Bingqian Guo, Hui Lu, Guanjun Liu, Haitao Zhang, Ying Cui, Zengnan Mo, Hongbing Shen, Yi-Xin Zeng, Fuchu He, Hongxing Zhang, Gangqiao Zhou
The sodium taurocholate cotransporting polypeptide (NTCP) encoded by SLC10A1 was recently demonstrated to be a functional receptor for hepatitis B virus (HBV). The role of SLC10A1 polymorphisms, particularly the Ser267Phe variant (rs2296651) in exon 4, has been frequently investigated in regard to risk of persistent HBV infection. However, these investigations have generated conflicting results. To examine whether common genetic variation at the SLC10A1 locus is associated with risk of persistent HBV infection, haplotype-tagging and imputed single nucleotide polymorphisms (SNPs) were assessed in two case-control sample sets, totally including 2,550 cases (persistently HBV infected subjects, PIs) and 2,124 controls (spontaneously recovered subjects, SRs) of Southern Chinese ancestry...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429076/-search-for-risk-genes-in-schizophrenia
#19
D Rujescu
BACKGROUND: Schizophrenia is a severe psychiatric disease affecting approximately 0.5-1% of the general population. The relative contribution of genetic factors has been estimated to be 64-81%. OBJECTIVE: This review summarizes recent efforts to identify genetic variants associated with schizophrenia. METHODS: Relevant linkage and candidate genes as well as genome wide association studies, studies on copy number variants and next generation sequencing are presented and discussed...
April 20, 2017: Der Nervenarzt
https://www.readbyqxmd.com/read/28428959/copy-number-variations-in-candidate-genes-and-intergenic-regions-affect-body-mass-index-and-abdominal-obesity-in-mexican-children
#20
Diana Lizzete Antúnez-Ortiz, Eugenia Flores-Alfaro, Ana Isabel Burguete-García, Amélie Bonnefond, Jesús Peralta-Romero, Philippe Froguel, Mónica Espinoza-Rojo, Miguel Cruz
Introduction. Increase in body weight is a gradual process that usually begins in childhood and in adolescence as a result of multiple interactions among environmental and genetic factors. This study aimed to analyze the relationship between copy number variants (CNVs) in five genes and four intergenic regions with obesity in Mexican children. Methods. We studied 1423 children aged 6-12 years. Anthropometric measurements and blood levels of biochemical parameters were obtained. Identification of CNVs was performed by real-time PCR...
2017: BioMed Research International
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