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Copy-number variant

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https://www.readbyqxmd.com/read/29028893/canvas-spw-calling-de-novo-copy-number-variants-in-pedigrees
#1
Sergii Ivakhno, Eric Roller, Camilla Colombo, Philip Tedder, Anthony J Cox
Motivation: Whole genome sequencing is becoming a diagnostics of choice for the identification of rare inherited and de novo copy number variants in families with various pediatric and late-onset genetic diseases. However, joint variant calling in pedigrees is hampered by the complexity of consensus breakpoint alignment across samples within an arbitrary pedigree structure. Results: We have developed a new tool, Canvas SPW, for the identification of inherited and de novo copy number variants from pedigree sequencing data...
September 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29027723/the-diagnostic-yield-of-chromosomal-microarray-analysis-in-fetuses-with-increased-nuchal-translucency-a-french-multicentre-retrospective-study
#2
Matthieu Egloff, Bérénice Hervé, Thibaud Quibel, Sylvie Jaillard, Gwenaelle Le Bouar, Kevin Uguen, Anne-Hélène Saliou, Mylène Valduga, Estelle Perdriolle, Charles Coutton, Anne-Laure Coston, Aurélie Coussement, Olivia Anselem, Chantal Missirian, Florence Bretelle, Fabienne Prieur, Cécile Fanget, Christine Muti, Marie-Christine Jacquemot, Claire Beneteau, Claudine Le Vaillant, Michel Vekemans, Laurant J Salomon, François Vialard, Valerie Malan
OBJECTIVE: The aim of our study was to determine the frequency and nature of Copy Number Variants (CNVs) identified by chromosomal microarray analysis (CMA) in a large cohort of fetuses with a strictly isolated, increased nuchal translucency (NT) above or equal to 3.5 mm. METHODS: This is a retrospective, multicentre study including eleven French hospitals over a period between April 2012 and December 2015 in which 720 fetuses were analysed by rapid aneuploidy test and CMA...
October 13, 2017: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/29027068/array-cgh-analysis-in-a-cohort-of-phenotypically-well-characterized-individuals-with-essential-autism-spectrum-disorders
#3
Eleonora Napoli, Serena Russo, Laura Casula, Viola Alesi, Filomena Alessandra Amendola, Adriano Angioni, Antonio Novelli, Giovanni Valeri, Deny Menghini, Stefano Vicari
Copy-number variants (CNVs) are associated with susceptibility to autism spectrum disorder (ASD). To detect the presence of CNVs, we conducted an array-comparative genomic hybridization (array-CGH) analysis in 133 children with "essential" ASD phenotype. Genetic analyses documented that 12 children had causative CNVs (C-CNVs), 29 children had non-causative CNVs (NC-CNVs) and 92 children without CNVs (W-CNVs). Results on clinical evaluation showed no differences in cognitive abilities among the three groups, and a higher number of ASD symptoms and of non-verbal children in the C-CNVs group compared to the W-CNVs and NC-CNVs groups...
October 12, 2017: Journal of Autism and Developmental Disorders
https://www.readbyqxmd.com/read/29025587/addition-of-chromosomal-microarray-and-next-generation-sequencing-to-fish-and-classical-cytogenetics-enhances-genomic-profiling-of-myeloid-malignancies
#4
Sandeep Mukherjee, Malini Sathanoori, Zeq Ma, Matthew Andreatta, Patrick A Lennon, Scott R Wheeler, James L Prescott, Christopher Coldren, Terence Casey, Heather Rietz, Kristina Fasig, Randall Woodford, Taylor Hartley, David Spence, William Donnelan, Jesus Berdeja, Ian Flinn, Natalia Kozyr, Mark Bouzyk, Mick Correll, Hao Ho, Vladimir Kravtsov, Dana Tunnel, Pranil Chandra
Comprehensive genetic profiling is increasingly important for the clinical workup of hematologic tumors, as specific alterations are now linked to diagnostic characterization, prognostic stratification and therapy selection. To characterize relevant genetic and genomic alterations in myeloid malignancies maximally, we utilized a comprehensive strategy spanning fluorescence in situ hybridization (FISH), classical karyotyping, Chromosomal Microarray (CMA) for detection of copy number variants (CNVs) and Next generation Sequencing (NGS) analysis...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29020723/chromosomal-microarray-testing-in-42-korean-patients-with-unexplained-developmental-delay-intellectual-disability-autism-spectrum-disorders-and-multiple-congenital-anomalies
#5
Sun Ho Lee, Wung Joo Song
Chromosomal microarray (CMA) is a high-resolution, high-throughput method of identifying submicroscopic genomic copy number variations (CNVs). CMA has been established as the first-line diagnostic test for individuals with developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), and multiple congenital anomalies (MCAs). CMA analysis was performed in 42 Korean patients who had been diagnosed with unexplained DD, ID, ASDs, and MCAs. Clinically relevant CNVs were discovered in 28 patients...
September 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28991724/a-sparse-learning-framework-for-joint-effect-analysis-of-copy-number-variants
#6
Zhiyong Wang, Benika Hall, Jinbo Xu, Xinghua Shi
Copy number variants (CNVs), including large deletions and duplications, represent an unbalanced change of DNA segments. Abundant in human genomes, CNVs contribute to a large proportion of human genetic diversity, with impact on many human phenotypes. Although recent advances in genetic studies have shed light on the impact of individual CNVs on different traits, the analysis of joint effect of multiple interactive CNVs lags behind from many perspectives. A primary reason is that the large number of CNV combinations and interactions in the human genome make it computationally challenging to perform such joint analysis...
September 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28991261/esrp1-is-overexpressed-in-ovarian-cancer-and-promotes-switching-from-mesenchymal-to-epithelial-phenotype-in-ovarian-cancer-cells
#7
H M Jeong, J Han, S H Lee, H-J Park, H J Lee, J-S Choi, Y M Lee, Y-L Choi, Y K Shin, M J Kwon
Epithelial splicing regulatory protein 1 (ESRP1) and 2 (ESRP2), epithelial cell-specific regulators of alternative splicing, are downregulated during the epithelial-mesenchymal transition (EMT). These factors have roles in tumor progression and metastasis in some cancers; however, their expression and function in ovarian cancer (OC) remain unclear. We found that ESRP1 and ESRP2 mRNAs were expressed at higher levels in OC cells than in immortalized ovarian surface epithelial (IOSE) cells, and confirmed their overexpression in OC tissues at the protein level...
October 9, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28990704/epithelioid-glioblastomas-stratify-into-established-diagnostic-subsets-upon-integrated-molecular-analysis
#8
Andrey Korshunov, Lukas Chavez, Tanvi Sharma, Marina Ryzhova, Daniel Schrimpf, Damian Stichel, David Capper, Dominik Sturm, Marcel Kool, Antje Habel, Bette K Kleinschmidt-DeMasters, Marc Rosenblum, Oksana Absalyamova, Andrey Golanov, Peter Lichter, Stefan M Pfister, David T W Jones, Arie Perry, Andreas von Deimling
Epithelioid glioblastoma (eGBM) is a newly defined and rare GBM variant in the current WHO 2016 classification. BRAF V600E mutation is overrepresented in these tumors and there is known some morphological overlap with anaplastic epithelioid PXA (ePXA). In order to further elucidate this diagnostic category, we molecularly characterized 64 pediatric and adult examples initially diagnosed as "eGBM". Tumors were analyzed using array based methylation and direct sequencing of the BRAF and TERT genes. Our results demonstrated considerable molecular and clinical heterogeneity among eGBM cohort...
October 9, 2017: Brain Pathology
https://www.readbyqxmd.com/read/28989557/allele-specific-copy-number-estimation-by-whole-exome-sequencing
#9
Hao Chen, Yuchao Jiang, Kara N Maxwell, Katherine L Nathanson, Nancy Zhang
Whole exome sequencing is currently a technology of choice in large-scale cancer genomics studies, where the priority is to identify cancer-associated variants in coding regions. We describe a method for estimating allele-specific copy number using whole exome sequencing data from tumor and matched normal.
June 2017: Annals of Applied Statistics
https://www.readbyqxmd.com/read/28986787/copy-number-variation-analysis-by-droplet-digital-pcr
#10
Suvi K Härmälä, Robert Butcher, Chrissy H Roberts
The health impact of many copy number variants in our genome remains still largely to be discovered. Detecting and genotyping this often complex variation presents a technical challenge. Here we describe a 96-well format droplet digital PCR (ddPCR) protocol for genotyping a common copy variant in the human haptoglobin gene. ddPCR allows for high-throughput and accurate quantitation of gene copy numbers.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28984674/targeted-genomic-profiling-reveals-recurrent-kras-mutations-in-mesonephric-like-adenocarcinomas-of-the-female-genital-tract
#11
Jelena Mirkovic, Marie McFarland, Elizabeth Garcia, Lynette M Sholl, Neal Lindeman, Laura MacConaill, Fei Dong, Michelle Hirsch, Marisa R Nucci, Charles M Quick, Christopher P Crum, W Glenn McCluggage, Brooke E Howitt
Mesonephric adenocarcinoma most commonly arises in the cervix and is presumed to be derived from normal or hyperplastic mesonephric remnants. It is characterized by recurrent KRAS mutations and lack of PIK3CA/PTEN alterations. Adenocarcinomas of the uterine corpus and ovary characterized by morphologic and immunophenotypic similarities to mesonephric adenocarcinoma have been reported. The pathogenesis of these tumors, which have been designated "mesonephric-like adenocarcinomas" is unknown, and it has been debated whether these represent mesonephric adenocarcinomas that arise in the endometrium/ovary or endometrioid adenocarcinomas that closely mimic mesonephric adenocarcinoma...
October 3, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28981940/-prenatal-genetic-analysis-of-a-fetus-with-wolf-hirschhorn-syndrome-and-edward-syndrome
#12
Xueping Shen, Pingya He, Rong Fang, Juan Yao, Wenwen Li
OBJECTIVE: To screen for genomic copy number variants (CNVs) in a fetus with cardiac abnormalities and intrauterine growth retardation through single nucleotide polymorphism microarray (SNP array) and karyotyping analysis. METHODS: The fetus and its parents were subjected to conventional G banding and SNP-array analysis. The results were confirmed with fluorescence in situ hybridization (FISH). RESULTS: G-banding analysis showed that the fetus has a karyotype of 47,XX,+mar...
October 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28981698/distinct-trajectories-of-massive-recent-gene-gains-and-losses-in-populations-of-a-microbial-eukaryotic-pathogen
#13
Fanny E Hartmann, Daniel Croll
Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species...
July 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28981421/erds-exome-a-hybrid-approach-for-copy-number-variant-detection-from-whole-exome-sequencing-data
#14
Renjie Tan, Jixuan Wang, Xiaoliang Wu, Liran Juan, Likun Zheng, Rui Ma, Qing Zhan, Tao Wang, Shuilin Jin, Qinghua Jiang, Yadong Wang
Copy number variants (CNVs) play important roles in human disease and evolution. With the rapid development of next-generation sequencing technologies, many tools have been developed for inferring CNVs based on whole-exome sequencing (WES) data. However, as a result of the sparse distribution of exons in the genome, the limitations of the WES technique, and the nature of high-level signal noises in WES data, the efficacy of these variants remains less than desirable. Thus, there is need for the development of an effective tool to achieve a considerable power in WES CNVs discovery...
October 4, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28974674/insights-into-beta-cell-regeneration-for-diabetes-via-integration-of-molecular-landscapes-in-human-insulinomas
#15
Huan Wang, Aaron Bender, Peng Wang, Esra Karakose, William B Inabnet, Steven K Libutti, Andrew Arnold, Luca Lambertini, Micheal Stang, Herbert Chen, Yumi Kasai, Milind Mahajan, Yayoi Kinoshita, Gustavo Fernandez-Ranvier, Thomas C Becker, Karen K Takane, Laura A Walker, Shira Saul, Rong Chen, Donald K Scott, Jorge Ferrer, Yevgeniy Antipin, Michael Donovan, Andrew V Uzilov, Boris Reva, Eric E Schadt, Bojan Losic, Carmen Argmann, Andrew F Stewart
Although diabetes results in part from a deficiency of normal pancreatic beta cells, inducing human beta cells to regenerate is difficult. Reasoning that insulinomas hold the "genomic recipe" for beta cell expansion, we surveyed 38 human insulinomas to obtain insights into therapeutic pathways for beta cell regeneration. An integrative analysis of whole-exome and RNA-sequencing data was employed to extensively characterize the genomic and molecular landscape of insulinomas relative to normal beta cells. Here, we show at the pathway level that the majority of the insulinomas display mutations, copy number variants and/or dysregulation of epigenetic modifying genes, most prominently in the polycomb and trithorax families...
October 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28965761/genomic-patterns-of-de-novo-mutation-in-simplex-autism
#16
Tychele N Turner, Bradley P Coe, Diane E Dickel, Kendra Hoekzema, Bradley J Nelson, Michael C Zody, Zev N Kronenberg, Fereydoun Hormozdiari, Archana Raja, Len A Pennacchio, Robert B Darnell, Evan E Eichler
To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of ∼1.5 × 10(-8) SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends...
September 27, 2017: Cell
https://www.readbyqxmd.com/read/28963714/clinical-interpretation-of-copy-number-variants-in-the-human-genome
#17
REVIEW
Beata Nowakowska
Molecular methods, by which copy number variants (CNVs) detection is available, have been gradually introduced into routine diagnostics over the last 15 years. Despite this, some CNVs continue to be a huge challenge when it comes to clinical interpretation. CNVs are an important source of normal and pathogenic variants, but, in many cases, their impact on human health depends on factors that are not yet known. Therefore, perception of their clinical consequences can change over time, as our knowledge grows...
September 30, 2017: Journal of Applied Genetics
https://www.readbyqxmd.com/read/28963451/cnv-association-meta-analysis-in-191-161-european-adults-reveals-new-loci-associated-with-anthropometric-traits
#18
Aurélien Macé, Marcus A Tuke, Patrick Deelen, Kati Kristiansson, Hannele Mattsson, Margit Nõukas, Yadav Sapkota, Ursula Schick, Eleonora Porcu, Sina Rüeger, Aaron F McDaid, David Porteous, Thomas W Winkler, Erika Salvi, Nick Shrine, Xueping Liu, Wei Q Ang, Weihua Zhang, Mary F Feitosa, Cristina Venturini, Peter J van der Most, Anders Rosengren, Andrew R Wood, Robin N Beaumont, Samuel E Jones, Katherine S Ruth, Hanieh Yaghootkar, Jessica Tyrrell, Aki S Havulinna, Harmen Boers, Reedik Mägi, Jennifer Kriebel, Martina Müller-Nurasyid, Markus Perola, Markku Nieminen, Marja-Liisa Lokki, Mika Kähönen, Jorma S Viikari, Frank Geller, Jari Lahti, Aarno Palotie, Päivikki Koponen, Annamari Lundqvist, Harri Rissanen, Erwin P Bottinger, Saima Afaq, Mary K Wojczynski, Petra Lenzini, Ilja M Nolte, Thomas Sparsø, Nicole Schupf, Kaare Christensen, Thomas T Perls, Anne B Newman, Thomas Werge, Harold Snieder, Timothy D Spector, John C Chambers, Seppo Koskinen, Mads Melbye, Olli T Raitakari, Terho Lehtimäki, Martin D Tobin, Louise V Wain, Juha Sinisalo, Annette Peters, Thomas Meitinger, Nicholas G Martin, Naomi R Wray, Grant W Montgomery, Sarah E Medland, Morris A Swertz, Erkki Vartiainen, Katja Borodulin, Satu Männistö, Anna Murray, Murielle Bochud, Sébastien Jacquemont, Fernando Rivadeneira, Thomas F Hansen, Albertine J Oldehinkel, Massimo Mangino, Michael A Province, Panos Deloukas, Jaspal S Kooner, Rachel M Freathy, Craig Pennell, Bjarke Feenstra, David P Strachan, Guillaume Lettre, Joel Hirschhorn, Daniele Cusi, Iris M Heid, Caroline Hayward, Katrin Männik, Jacques S Beckmann, Ruth J F Loos, Dale R Nyholt, Andres Metspalu, Johan G Eriksson, Michael N Weedon, Veikko Salomaa, Lude Franke, Alexandre Reymond, Timothy M Frayling, Zoltán Kutalik
There are few examples of robust associations between rare copy number variants (CNVs) and complex continuous human traits. Here we present a large-scale CNV association meta-analysis on anthropometric traits in up to 191,161 adult samples from 26 cohorts. The study reveals five CNV associations at 1q21.1, 3q29, 7q11.23, 11p14.2, and 18q21.32 and confirms two known loci at 16p11.2 and 22q11.21, implicating at least one anthropometric trait. The discovered CNVs are recurrent and rare (0.01-0.2%), with large effects on height (>2...
September 29, 2017: Nature Communications
https://www.readbyqxmd.com/read/28961404/detection-of-breed-specific-copy-number-variations-in-domestic-chicken-genome
#19
Saeed S Sohrabi, Mohammadreza Mohammadabadi, Dong-Dong Wu, Ali Esmailizadeh
Copy number variations (CNVs) are important large scale variants that are widespread in the genome and may contribute to phenotypic variation. Detection and characterization of CNVs can provide new insights into the genetic basis of important traits. Here, we performed whole genome short read sequence analysis to identify CNVs in two indigenous and commercial chicken breeds and evaluate the impact of the identified CNVs on breed specific traits. After filtration, a total of 12955 CNVs spanning (on average) about 9...
September 29, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28958595/the-mtdna-replication-related-genes-tfam-and-polg-are-associated-with-leprosy-in-han-chinese-from-southwest-china
#20
Dong Wang, Guo-Dong Li, Yu Fan, Deng-Feng Zhang, Rui Bi, Xiu-Feng Yu, Heng Long, Yu-Ye Li, Yong-Gang Yao
BACKGROUND: The pathogen Mycobacterium leprae of leprosy is heavily dependent on the host energy metabolites and nutritional products for survival. Previously we and others have identified associations of several mitochondrion-related genes and mitochondrial DNA (mtDNA) copy number alterations with leprosy and/or its subtype. We hypothesized that genetic variants of mtDNA replication-related genes would affect leprosy. OBJECTIVE: We aimed to identify genetic associations between the mtDNA replication-related genes TFAM, POLG and leprosy...
September 14, 2017: Journal of Dermatological Science
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