GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants | BMC Bioinformatics |...
Origins and functional impact of copy number variation in the human genome. Nature. 2010;464(7289):704-12.View ArticlePubMed ... DNA copy number variantsIntegrative visualizationMicroarrayNGS. Background. DNA copy number variants represent the greatest ... The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However ... Array CGH is recognized as a first-tier test for DNA copy number variants (CNV)  and accordingly, many laboratories have ...https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1430-x
miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability | BMC Genomics |...
Genomic DNA was extracted from peripheral blood using PUREGENE DNA Isolation Kits (Gentra, Minneapolis, MN). A pool of normal ... Micro RNA (miRNA)Copy number variants (CNVs)Copy number variant regions (CNVRs)Intellectual disabilities (ID)Functional ... We declare no conflict of interest in our manuscript titled as "miRNA and miRNA target genes in copy number variations ... It has been recently shown that genomic copy number variations (CNVs) can cause aberrant expression of integral miRNAs and ...https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-544
We investigated DNA copy number variations (CNVs) in a cohort of 55 pediatric cancer patients attending the AC Camargo Hospital ... which is over twice the average length of rare copy number variations identified with the same array-CGH platform in a sample ... Eighteen copy number alterations were detected in 16 patients; these rare CNVs included complex rearrangements and ...http://cancerres.aacrjournals.org/content/71/18_Supplement/PR14
Novel origins of copy number variation in the dog genome | Genome Biology | Full Text
A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet. 2007, 3: e3-10.1371/journal.pgen. ... such as adaptive variation in copy number of the amylase gene in response to diet , and variation in HIV/AIDS susceptibility ... low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European ... and positive log2 ratios indicate gains and negative log2 ratios indicate loss of copy number. Copy number for each called CNV ...https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-8-r73
Abstract A60: Analysis of gene copy number changes in chronic lymphocytic leukemia | Cancer Research
Somatic copy number changes in distinct genes are associated with the development of specific leukemias. Copy number variations ... DNA was isolated from the venous blood samples from 92 patients with CLL and 10 healthy controls. Copy number changes of 20 ... Abstract A60: Analysis of gene copy number changes in chronic lymphocytic leukemia. Nejat Dalay, Mustafa Isin, Guven Cetin and ... Copy number losses in the MYCN, ESR1, EIF3S3, CDKN2A, CDKN2B, ATM, CHFR and TP53 genes were lower with a frequency ranging ...http://cancerres.aacrjournals.org/content/73/13_Supplement/A60
The clinical significance of small copy number variants in neurodevelopmental disorders | Journal of Medical Genetics
A copy number variation morbidity map of developmental delay. Nat Genet 2011;43:838-46. ... WES on genomic DNA of selected patients was performed as described before with minor modifications.13 ,14 All exons and ... 2 copy number reduction in deletions is more easily detectable than the 3:2 copy number gain in duplications, sensitivity and ... Rare copy number variation in cerebral palsy. Eur J Hum Genet 2014;22:40-5. ...http://jmg.bmj.com/content/early/2014/08/08/jmedgenet-2014-102588
"Change-point analysis of paired allele-specific copy number variation " by Yinglei Lai
... us to explore two types of genomic information including chromosomal genotype variations as well as DNA copy number variations ... The recent genome-wide allele-specific copy number variation data enable ... us to explore two types of genomic information including chromosomal genotype variations as well as DNA copy number variations ... Lai, Y. (2012). Change-point analysis of paired allele-specific copy number variation data. Journal of Computational Biology, ...https://hsrc.himmelfarb.gwu.edu/biostatscenter_facpubs/36/
Copy number analysis - Wikipedia
Copy number analysis usually refers to the process of analyzing data produced by a test for DNA copy number variation in ... Positive log-ratios indicate a region of DNA copy number gain and negative log-ratio values mark a region of DNA copy number ... Even a single data point can be declared an indication of a copy number gain or a copy number loss in BAC arrays. Array ... Data analysis for an array-based DNA copy number test can be very challenging though due to very high volume of data that come ...https://en.wikipedia.org/wiki/Copy_number_analysis
Methods and strategies for analyzing copy number variation using DNA microarrays
The association of DNA copy-number variation (CNV) with specific gene function and human disease has been long known, but the ... Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. Genome Res. 2006;16:1575- ... High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 1998; ... Methods and strategies for analyzing copy number variation using DNA microarrays. Nigel P Carter ...http://pubmedcentralcanada.ca/pmcc/articles/PMC2697494/
Study of DNA Copy Numbers Variations and Gene Expression Profile of Bone Marrow Plasma Cells From MGUS and SMM. - Full Text...
Genetic: Genetic study of DNA copies Gene expression profiling, DNA copy number variation ... Study of DNA Copy Numbers Variations and Gene Expression Profile of Bone Marrow Plasma Cells From MGUS and SMM. (GENOMGUS). ... The purpose of this study is to describe DNA copy number variations and gene expression profiles of bone marrow plasma cells of ... Large Scale Study of DNA Copy Numbers Variations and Gene Expression Profile of Bone Marrow Plasma Cells From Monoclonal ...https://clinicaltrials.gov/ct2/show/NCT01079429
DNA Copy Number Variations | Profiles RNS
"DNA Copy Number Variations" by people in UAMS Profiles by year, and whether "DNA Copy Number Variations" was a major or minor ... DNA Copy Number Variations*DNA Copy Number Variations. *DNA Copy Number Variation ... "DNA Copy Number Variations" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH ( ... Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been ...https://uams-triprofiles.uams.edu/profiles/display/117558
A Statistical Change Point Model Approach for the Detection of DNA Copy Number Variations in Array CGH Data - Semantic Scholar
We derive an approximate p-value for the test statistic and also give the estimate of the locus of the DNA copy number change. ... identifying statistically significant DNA copy number changes in aCGH data is challenging. We propose a novel approach that ... These simulation results show that the approach is effective in identifying copy number changes. The approach is also tested on ... provides a high-resolution and high-throughput technique for screening of copy number variations (CNVs) within the entire ...https://www.semanticscholar.org/paper/A-Statistical-Change-Point-Model-Approach-for-the-Chen-Wang/4892aeaa695c032ed4a39c814be109c9d31095cb
Mitochondrial DNA Copy Number and Genetic Variation in Coronary Heart Disease - Dan Arking
Mitochondrial DNA Copy Number and Genetic Variation in Coronary Heart Disease Arking, Dan E. Johns Hopkins University, ... Mitochondrial DNA Copy Number and Genetic Variation in Coronary Heart Disease. Arking, Dan E. / Johns Hopkins University. ... Mitochondrial DNA Copy Number and Genetic Variation in Coronary Heart Disease. Arking, Dan E. / Johns Hopkins University. ... Mitochondrial DNA Copy Number and Genetic Variation in Coronary Heart Disease. Arking, Dan E. / Johns Hopkins University. $ ...http://grantome.com/grant/NIH/R01-HL131573-03
Identification of genes with a correlation between copy number and expression in gastric cancer
0.5, maximum number of aberration regions. =. 10,000. The log2 ratio of 0.5 corresponds to a 1.4-fold variation in the DNA copy ... Table S4. Copy number associated gene expression changes. Pearson correlation coefficients between DNA copy number aberrations ... DNA copy number variations in gastric cancer. The 27 pairs of gastric samples were analyzed by aCGH as shown in Additional file ... 2B). DNA copy number variation profiling of N0 and N1-3 stages also revealed 18 significantly altered genomic regions (1q32.2, ...http://pubmedcentralcanada.ca/pmcc/articles/PMC3441862/
Variations in gut microbiota and fecal metabolic phenotype associated with Fenbendazole and Ivermectin Tablets by 16S rRNA gene...
Dna Copy Number Variations. Stretches of genomic DNA that exist in different multiples between individuals. Many copy number ... DNA sequencing DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA ... A form of interference microscopy in which variations of the refracting index in the object are converted into variations of ... Variations in gut microbiota and fecal metabolic phenotype associated with Fenbendazole and Ivermectin Tablets by 16S rRNA gene ...https://www.bioportfolio.com/resources/pmarticle/2003507/Variations-in-gut-microbiota-and-fecal-metabolic-phenotype-associated-with-Fenbendazole-and.html
The change of mtDNA copy number after PAHs exposure. mt | Open-i
mtDNA copy number was increased after exposure of PAHs with different pattern in THP-1 cell line (a) and in ... The change of mtDNA copy number after PAHs exposure. ... DNA Copy Number Variations/drug effects*. *DNA, Mitochondrial/ ... fig3: The change of mtDNA copy number after PAHs exposure. mtDNA copy number was increased after exposure of PAHs with ... fig3: The change of mtDNA copy number after PAHs exposure. mtDNA copy number was increased after exposure of PAHs with ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC4121044_BMRI2014-605135.003&req=4
Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma.
DNA Copy Number Variations / genetics. Humans. Kaplan-Meier Estimate. Melanoma / genetics*. Microarray Analysis. Mutation / ... 1). An evaluation of DNA copy number in 30 of the uveal melanomas, including seven with SF3B1 mutations, revealed no loss of ... Thus, we re-sequenced these exons in a total of 102 primary uveal melanomas and matching blood DNA samples and identified SF3B1 ... L.A.W. managed the tissue bank and clinical database, and prepared DNA and RNA samples. A.M.B. participated in the conception ...http://www.biomedsearch.com/nih/Recurrent-mutations-at-codon-625/23313955.html
Chromosomal alterations in exfoliated urothelial cells from bladder cancer cases and healthy men: a prospective screening study...
9-11%). About 1% of cells from tumor-free men showed polysomy of chromosomes 3, 7, or 17 or DNA loss at 9p21. Men aged ≥50 ... Tetrasomy of chromosomes 3, 7 and 17, and DNA loss at 9p21 were the most frequently observed forms of CNV. In bladder cancer ... Also, a small fraction of cells with CNVs were exfoliated into urine of tumor-free men, mainly exhibiting tetraploidy or DNA ... Here, we analyzed the accumulation of copy number variations (CNVs) using fluorescence in situ hybridization in cancer cases ...https://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-14-854
Basic Medical Science Publications (UMKC)
A Bayesian Analysis for Identifying DNA Copy Number Variations Using a Compound Poisson Process Chen, Jie; Yiğiter, Ayten; ... technique is often used for detecting DNA copy number variants (CNVs). Various ... ... Abstract Background With DNA microarray data, selecting a compact subset of discriminative genes from thousands of genes is a ...https://mospace.umsystem.edu/xmlui/handle/10355/14253
Academic Programs Faculty - Last Initial T - Wake Forest School of Medicine
Proto-Oncogenes; DNA Copy Number Variations; Genetic Markers; Prostatectomy; Genes, p16 Academic: 336-716-7975. Department: 336 ...http://www.wakehealth.edu/School/FacultySR.htm?st=T&li=T&ft=R
Umbricht C[au] - PubMed - NCBI
DNA copy number variations characterize benign and malignant thyroid tumors.. Liu Y, Cope L, Sun W, Wang Y, Prasad N, ... DNA methylation-related vitamin D receptor insensitivity in breast cancer.. Marik R, Fackler M, Gabrielson E, Zeiger MA, ... Monitoring of Serum DNA Methylation as an Early Independent Marker of Response and Survival in Metastatic Breast Cancer: TBCRC ... Novel methylated biomarkers and a robust assay to detect circulating tumor DNA in metastatic breast cancer. ...https://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=Umbricht+C%5Bau%5D&dispmax=50
Association of SNPs in EGR3 and ARC with Schizophrenia Supports a Biological Pathway for Schizophrenia Risk
Accordingly, variations in the immediate early gene EGR3, and its target ARC, should influence schizophrenia susceptibility. We ... The role of DNA copy number variation in schizophrenia. Biological psychiatry. 2009;66(11):1005-12. pmid:19748074. * View ... Recent high-profile studies of rare copy number variations (CNVs) and de novo variations enriched in schizophrenia patients ... Analysis of copy number variation (CNV) domains revealed that ARC resides within a CNV region (S1C Fig). ...http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135076
Focal high copy number gains and homozygous deletions i | Open-i
Focal high copy number gains and homozygous deletions in glioblastomas.Copy number analysis using DK and Illumina BeadChips ... DNA Copy Number Variations. *Gene Expression. *Gene Expression Profiling. *Gene Expression Regulation, Neoplastic ... Figure 1: Focal high copy number gains and homozygous deletions in glioblastomas.Copy number analysis using DK and Illumina ... A) Glioblastoma copy number karyotype generated utilizing Nexus Copy Number Professional Software (BioDiscovery Inc.). The most ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC2992381_oncotarget-01-265-g001&req=4
Illustrating the recursive multi-level detection method | Open-i
A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control. ... Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic ... Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic ... A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control. ...https://openi.nlm.nih.gov/detailedresult.php?img=PMC3643574_gkt155f3p&req=4
Cited In for PubMed (Select 16327809) - PubMed - NCBI
Large scale variation in DNA copy number in chicken breeds.. Crooijmans RP, Fife MS, Fitzgerald TW, Strickland S, Cheng HH, ... Copy number variation prevalence in known asthma genes and their impact on asthma susceptibility. ... SLC26A4 gene copy number variations in Chinese patients with non-syndromic enlarged vestibular aqueduct. ... Massive screening of copy number population-scale variation in Bos taurus genome. ...https://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=16327809