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Copy number variation

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https://www.readbyqxmd.com/read/28318489/deletion-of-the-mad2l1-spindle-assembly-checkpoint-gene-is-tolerated-in-mouse-models-of-acute-t-cell-lymphoma-and-hepatocellular-carcinoma
#1
Floris Foijer, Lee A Albacker, Bjorn Bakker, Diana C Spierings, Ying Yue, Stephanie Z Xie, Stephanie H Davis, Annegret Lutum-Jehle, Darin Takemoto, Brian Hare, Brinley Furey, Roderick T Bronson, Peter M Lansdorp, Allan Bradley, Peter K Sorger
Chromosome instability (CIN) is deleterious to normal cells because of the burden of aneuploidy. However, most human solid tumors have an abnormal karyotype implying that gain and loss of chromosomes by cancer cells confers a selective advantage. CIN can be induced in the mouse by inactivating the spindle assembly checkpoint. This is lethal in the germline but we show here that adult T cells and hepatocytes can survive conditional inactivation of the Mad2l1 SAC gene and resulting CIN. This causes rapid onset of acute lymphoblastic leukemia (T-ALL) and progressive development of hepatocellular carcinoma (HCC), both lethal diseases...
March 20, 2017: ELife
https://www.readbyqxmd.com/read/28315830/paternal-induction-of-hybrid-dysgenesis-in-drosophila-melanogaster-is-weakly-correlated-with-both-p-element-and-hobo-element-dosage
#2
Satyam P Srivastav, Erin S Kelleher
Transposable elements (TEs) are virtually ubiquitous components of genomes, yet they often impose significant fitness consequences on their hosts. In addition to producing specific deleterious mutations by insertional inactivation, TEs also impose general fitness costs by inducing DNA damage and participating in ectopic recombination. These latter fitness costs are often assumed to be dosage-dependent, with stronger effects occurring in the presence of higher TE copy numbers. We test this assumption in Drosophila melanogaster by considering the relationship between the copy number of two active DNA transposons, P-element and hobo element, and the incidence of hybrid dysgenesis, a sterility syndrome associated with transposon activity in the germline...
March 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28315673/chromosomal-microarray-detection-of-constitutional-copy-number-variation-using-saliva-dna
#3
Jennifer Reiner, Lisa Karger, Ninette Cohen, Lakshmi Mehta, Lisa Edelmann, Stuart A Scott
Chromosomal microarray (CMA) testing to detect copy number aberrations among individuals with multiple congenital anomalies and/or developmental delay is typically performed on peripheral blood DNA. However, the use of saliva DNA may be preferred for some patients, which prompted our validation study using six saliva DNA samples with a range of bacterial content (approximately 3% to 21%) and 20 paired blood and saliva specimens on the Agilent Technologies, Illumina, and Affymetrix CMA platforms. Ten of the 20 paired specimens were previously determined to carry clinically significant copy number aberrations by clinical CMA testing on blood DNA (100 kb to 2...
March 15, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28315434/identifying-the-clonal-relationship-model-of-multifocal-papillary-thyroid-carcinoma-by-whole-genome-sequencing
#4
Mao Xia, Hengyu Li, Qian Ma, Dong Yu, Jing Li, Yi Zhang, Yuan Sheng, Yingjun Guo
PURPOSE: To evaluate the application of whole genome sequencing (WGS) in determining the inter-foci clonal relationship of multifocal papillary thyroid carcinoma (mPTC). METHODS: After reviewing PTC patient profiles, 8 cancer foci and germline control samples from 3 mPTC patients were analyzed by WGS. Single nucleotide variations (SNVs), copy number variation (CNV), structural variation and mutational signature were examined. RESULTS: The multifocality rate of PTC was 35...
March 14, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28314936/distribution-of-divo-in-coffea-genomes-a-poorly-described-family-of-angiosperm-ltr-retrotransposons
#5
Mathilde Dupeyron, Rogerio Fernandes de Souza, Perla Hamon, Alexandre de Kochko, Dominique Crouzillat, Emmanuel Couturon, Douglas Silva Domingues, Romain Guyot
Coffea arabica (the Arabica coffee) is an allotetraploid species originating from a recent hybridization between two diploid species: C. canephora and C. eugenioides. Transposable elements can drive structural and functional variation during the process of hybridization and allopolyploid formation in plants. To learn more about the evolution of the C. arabica genome, we characterized and studied a new Copia LTR-Retrotransposon (LTR-RT) family in diploid and allotetraploid Coffea genomes called Divo. It is a complete and relatively compact LTR-RT element (~5 kb), carrying typical Gag and Pol Copia type domains...
March 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28314280/embryonal-origin-of-mtscc-of-kidney-may-explain-its-morphological-heterogeneity-diagnostic-impact-of-genetic-analysis
#6
Daniel Banyai, Fanni Vastag, Maria Yusenko, Peter Bugert, Gyula Kovacs
BACKGROUND/AIM: Previous genetic and morphologic characterisation of mucinous tubular and spindle cell carcinoma (MTSCC) have yielded controversial results. The aim of this study was to explain the phenotypic heterogeneity of MTSCC diagnosed by genetic means. MATERIALS AND METHODS: We analyzed 7 MTSCC by array CGH and microsatellite allelotyping and by histology for morphological variation. We worked-up two entire kidneys with MTSCC to find microscopic alterations...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28304131/copy-number-variation-in-19-italian-multiplex-families-with-autism-spectrum-disorder-importance-of-synaptic-and-neurite-elongation-genes
#7
Carla Lintas, Chiara Picinelli, Ignazio Stefano Piras, Roberto Sacco, Claudia Brogna, Antonio M Persico
Autism Spectrum Disorder (ASD) is endowed with impressive heritability estimates and high recurrence rates. Its genetic underpinnings are nonetheless very heterogeneous, with common, and rare contributing variants located in hundreds of different loci, each characterized by variable levels of penetrance. Multiplex families from single ethnic groups represent a useful means to reduce heterogeneity and enhance genetic load. We screened 19 Italian ASD multiplex families (3 triplets and 16 duplets, total N = 41 ASD subjects), using array-CGH (Agilent 180 K)...
March 17, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28303143/copy-number-variation-in-acetolactate-synthase-genes-of-thifensulfuron-methyl-resistant-alopecurus-aequalis-shortawn-foxtail-accessions-in-japan
#8
Satoshi Iwakami, Yoshiko Shimono, Yohei Manabe, Masaki Endo, Hiroyuki Shibaike, Akira Uchino, Tohru Tominaga
Severe infestations of Alopecurus aequalis (shortawn foxtail), a noxious weed in wheat and barley cropping systems in Japan, can occur even after application of thifensulfuron-methyl, a sulfonylurea (SU) herbicide. In the present study, nine accessions of A. aequalis growing in a single wheat field were tested for sensitivity to thifensulfuron-methyl. Seven of the nine accessions survived application of standard field rates of thifensulfuron-methyl, indicating that severe infestations likely result from herbicide resistance...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28301526/novel-copy-number-variation-of-the-tgf%C3%AE-3-gene-is-associated-with-tgf%C3%AE-3-gene-expression-and-duration-of-fertility-traits-in-hens
#9
Lantao Gu, Chenghao Sun, Yangzhang Gong, Mei Yu, Shijun Li
Improvements in the duration of fertility (DF) could increase the interval between successive artificial inseminations, thereby decreasing the cost associated with production of hatching eggs. The molecular mechanisms involved in DF in hens remains under-explored. In this study, expression levels of the transforming growth factor-β genes (TGFβs: TGFβ1, TGFβ2, TGFβ3) were investigated in utero-vaginal junctions (UVJs) of hens with long DF (Group L, n = 10) and short DF (Group S, n = 10). TGFβ1 and 2 tended to exhibit higher expression levels in UVJs from Group L hens...
2017: PloS One
https://www.readbyqxmd.com/read/28300822/human-%C3%AE-defensin-2-in-primary-sclerosing-cholangitis
#10
Cindy Chang, Ana Lleo, Anchasa Kananurak, Fabio Grizzi, Koichi Tsuneyama, Pietro Invernizzi, Charles L Bevins, Christopher L Bowlus
OBJECTIVES: Primary sclerosing cholangitis (PSC) is a chronic inflammatory disease of the bile ducts frequently associated with inflammatory bowel disease (IBD), suggesting an important role for the gut-liver axis. Defensins are small (3.5-4.5 kDa) anti-microbial peptides that contribute to innate immunity at mucosal surfaces and have been implicated in IBD. The aim of this study was to investigate copy number variation of the gene (DEFB4) encoding human β-defensin 2 (HBD2) and protein expression of HBD2 in PSC...
March 16, 2017: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/28298214/climat-het-detecting-subclonal-copy-number-alterations-and-loss-of-heterozygosity-in-heterogeneous-tumor-samples-from-whole-genome-sequencing-data
#11
Zhenhua Yu, Ao Li, Minghui Wang
BACKGROUND: Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH...
March 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28295514/intragenic-copy-number-variation-in-the-filaggrin-gene-in-ethiopian-patients-with-atopic-dermatitis
#12
Kerstin Fernandez, Samina Asad, Fulya Taylan, Carl-Fredrik Wahlgren, Kassahun D Bilcha, Magnus Nordenskjöld, Mårten C G Winge, Maria Bradley
Genetic variants in filaggrin (FLG) involving truncating mutations or intragenic copy number variation are strongly associated with the risk of developing atopic dermatitis (AD) in European and Asian populations. Few loss-of-function mutations have been identified in Africans, although an association between FLG copy number variation and AD severity in a small African American cohort has been proposed. We studied the association between FLG copy number and AD in 132 Ethiopians and found no association between AD severity and FLG copy number, suggesting that other, still unidentified genetic factors are of more importance in predisposing Ethiopians to AD...
March 10, 2017: Pediatric Dermatology
https://www.readbyqxmd.com/read/28292787/extensive-copy-number-variation-in-fermentation-related-genes-among-saccharomyces-cerevisiae-wine-strains
#13
Jacob Steenwyk, Antonis Rokas
Due to the importance of Saccharomyces cerevisiae in wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences of S...
March 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28291231/targeted-deep-sequencing-of-flowering-regulators-in-brassica-napus-reveals-extensive-copy-number-variation
#14
Sarah Schiessl, Bruno Huettel, Diana Kuehn, Richard Reinhardt, Rod J Snowdon
Gene copy number variation (CNV) is increasingly implicated in control of complex trait networks, particularly in polyploid plants like rapeseed (Brassica napus L.) with an evolutionary history of genome restructuring. Here we performed sequence capture to assay nucleotide variation and CNV in a panel of central flowering time regulatory genes across a species-wide diversity set of 280 B. napus accessions. The genes were chosen based on prior knowledge from Arabidopsis thaliana and related Brassica species...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28285357/alternative-outcomes-of-pathogenic-complex-somatic-structural-variations-in-the-genomes-of-nf1-and-nf2-patients
#15
Meng-Chang Hsiao, Arkadiusz Piotrowski, Andrzej Brunon Poplawski, Tom Callens, Chuanhua Fu, Ludwine Messiaen
Multiplex ligation-dependent probe amplification (MLPA) has been widely used to identify copy-number variations (CNVs), but MLPA's sensitivity and specificity in mosaic CNV detection are largely unknown. Here, we present two mosaic deletions identified by MLPA as NF1 deletion of exons 17-21 and NF2 deletion of exons 9-10. Through cDNA analysis, genomic breakpoint-spanning PCR and Sanger sequencing, we found however both NF1 and NF2 deletions are each composed of two consecutive deletions, which cannot be differentiated by MLPA...
March 11, 2017: Neurogenetics
https://www.readbyqxmd.com/read/28284480/copy-number-variations-found-in-patients-with-a-corpus-callosum-abnormality-and-intellectual-disability
#16
Solveig Heide, Boris Keren, Thierry Billette de Villemeur, Sandra Chantot-Bastaraud, Christel Depienne, Caroline Nava, Cyril Mignot, Aurélia Jacquette, Eric Fonteneau, Elodie Lejeune, Corinne Mach, Isabelle Marey, Sandra Whalen, Didier Lacombe, Sophie Naudion, Caroline Rooryck, Annick Toutain, Cédric Le Caignec, Damien Haye, Laurence Olivier-Faivre, Alice Masurel-Paulet, Christel Thauvin-Robinet, Fabien Lesne, Anne Faudet, Dorothée Ville, Vincent des Portes, Damien Sanlaville, Jean-Pierre Siffroi, Marie-Laure Moutard, Delphine Héron
OBJECTIVE: To evaluate the role that chromosomal micro-rearrangements play in patients with both corpus callosum abnormality and intellectual disability, we analyzed copy number variations (CNVs) in patients with corpus callosum abnormality/intellectual disability STUDY DESIGN: We screened 149 patients with corpus callosum abnormality/intellectual disability using Illumina SNP arrays. RESULTS: In 20 patients (13%), we have identified at least 1 CNV that likely contributes to corpus callosum abnormality/intellectual disability phenotype...
March 8, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28282870/genetic-variations-associated-with-vitamin-a-status-and-vitamin-a-bioavailability
#17
REVIEW
Patrick Borel, Charles Desmarchelier
Blood concentration of vitamin A (VA), which is present as different molecules, i.e., mainly retinol and provitamin A carotenoids, plus retinyl esters in the postprandial period after a VA-containing meal, is affected by numerous factors: dietary VA intake, VA absorption efficiency, efficiency of provitamin A carotenoid conversion to VA, VA tissue uptake, etc. Most of these factors are in turn modulated by genetic variations in genes encoding proteins involved in VA metabolism. Genome-wide association studies (GWAS) and candidate gene association studies have identified single nucleotide polymorphisms (SNPs) associated with blood concentrations of retinol and β-carotene, as well as with β-carotene bioavailability...
March 8, 2017: Nutrients
https://www.readbyqxmd.com/read/28281572/genome-wide-copy-number-variation-analysis-in-a-chinese-autism-spectrum-disorder-cohort
#18
Hui Guo, Yu Peng, Zhengmao Hu, Ying Li, Guanglei Xun, Jianjun Ou, Liangdan Sun, Zhimin Xiong, Yanling Liu, Tianyun Wang, Jingjing Chen, Lu Xia, Ting Bai, Yidong Shen, Qi Tian, Yiqiao Hu, Lu Shen, Rongjuan Zhao, Xuejun Zhang, Fengyu Zhang, Jingping Zhao, Xiaobing Zou, Kun Xia
Autism spectrum disorder (ASD) describes a group of neurodevelopmental disorders with high heritability, although the underlying genetic determinants of ASDs remain largely unknown. Large-scale whole-genome studies of copy number variation in Han Chinese samples are still lacking. We performed a genome-wide copy number variation analysis of 343 ASD trios, 203 patients with sporadic cases and 988 controls in a Chinese population using Illumina genotyping platforms to identify CNVs and related genes that may contribute to ASD risk...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28279470/novel-targeted-therapies-for-esophagogastric-cancer
#19
REVIEW
Steven B Maron, Daniel V T Catenacci
Gastroesophageal cancer (GEC) remains a major cause of cancer-related mortality worldwide. Although the incidence of distal gastric adenocarcinoma (GC) is declining in the United States, proximal esophagogastric junction adenocarcinoma (EGJ) is increasing in incidence. GEC, including GC and EGJ, is treated uniformly in the metastatic setting. Overall survival in the metastatic setting remains poor. Molecular characterization of GEC has identified mutations and copy number variations, along with other oncogenes, biomarkers, and immuno-oncologic checkpoints that may serve as actionable therapeutic targets...
April 2017: Surgical Oncology Clinics of North America
https://www.readbyqxmd.com/read/28274670/detection-of-copy-number-variations-in-melanocytic-lesions-utilising-array-based-comparative-genomic-hybridisation
#20
Nima Mesbah Ardakani, Carla Thomas, Cleo Robinson, Kym Mina, Nathan Tobias Harvey, Benhur Amanuel, Benjamin Andrew Wood
Distinction between melanocytic naevi and melanoma occasionally poses a diagnostic challenge in ambiguous cases showing overlapping histological features. Melanomas are characterised by the presence of multiple genomic copy number variants (CNVs), while this is not a feature of naevi. We assessed the feasibility and utility of array-based comparative genomic hybridisation (aCGH) to assess CNVs in melanocytic lesions. DNA was extracted from formalin fixed, paraffin embedded (FFPE) sections of unambiguous naevi (n=19) and melanomas (n=19)...
March 5, 2017: Pathology
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