Fluorescence in situ hybrACGHCNVsMicroarray-based comparativeWhole-genomeChromosomalMicroarraysAlterationsMutationsChromosomeDeletionsDetectionProbesArraysFluorescentPhenotypic variationGenome-wideGenomicsCopyTumoursGeneticsGenomesGenesSingle nucleotide pMolecularAnalysisPolymorphismsClinicalIntensitiesGenetic variationArray-basedAutismDistinctOligonucleotidesNucleotideResultsClonesRegionsResearch
Fluorescence in situ hybr6
- A short introduction how cytogenetics and molecular cytogenetics were established is followed by technical aspects of fluorescence in situ hybridization (FISH). (frontiersin.org)
- This review is about "molecular cytogenetics" including 1) the historical perspective of its development from cytogenetics, 2) technical aspects, 3) available probe sets, and 4) variants and applications of the basic fluorescence in situ hybridization (FISH) approach. (frontiersin.org)
- Genome wide association studies, fluorescence in situ hybridization, comparative genomic hybridization, and candidate gene studies have enumerated genetic contributors to cancers in women. (hindawi.com)
- To further validate the gain of chromosome 11p region that was identified by array CGH, fluorescence in situ hybridization (FISH) was performed. (korea.ac.kr)
- Reproducible DA was observed at ~10% of 450 distinct genomic regions mapped by single copy fluorescence in situ hybridization (scFISH). (cytognomix.com)
- The complex marker chromosome, der(14)t(14;16)(q11.2;p13.13), was initially identified by routine chromosomal analysis and subsequently characterized by array-comparative genomic hybridization (array CGH) and confirmed by fluorescence in situ hybridization (FISH). (biomedcentral.com)
ACGH10
- The gold standard for CNV detection is array comparative genomic hybridization (aCGH) using long oligonucleotide microarray platforms. (mlo-online.com)
- For generating a comparable rhesus macaque CNV dataset, we designed a rhesus macaque-specific array comparative genomic hybridization (aCGH) platform containing 950,843 unique 60-mer oligonucleotide probes. (biomedcentral.com)
- Comparative genomic hybridization (aCGH) is a powerful diagnostic tool for detecting DNA copy number gains and losses associated with chromosome abnormalities. (enzolifesciences.com)
- aCGH provides an understanding of genetic disorders, cancers and other genomic aberrations. (enzolifesciences.com)
- Array comparative genomic hybridization (aCGH) provides a method to quantitatively measure the changes of DNA copy number with an extremely high resolution and to map them directly onto the complete linear genome sequences. (korea.ac.kr)
- In this study, we used aCGH to compare genomic alterations in fresh-frozen lung cancer tissues of 21 adenocarcinomas (AdCCs) (11 early relapse and 10 nonrelapse) and identified genomic alterations that showed significant by different frequency between early relapse and nonrelapse AdCCs. (korea.ac.kr)
- Genomic alterations of chromosome 11p region in AdCC patients were observed with aCGH, and a relapsable marker was identified in the nonrelapse group. (korea.ac.kr)
- Detection of small copy number variations (CNVs) in autism spectrum disorder (ASD) by custom array comparative genomic hybridization (aCGH). (bvsalud.org)
- By use of aCGH, DNA derived from tumor tissue can be compared with reference DNA, e.g., normal whole blood DNA, and genomic imbalances can effectively be investigated. (biomedcentral.com)
- Array comparative genomic hybridization (aCGH) is a type of microarray now routinely used to identify deleted or duplicated regions of DNA sequence in specific chromosomes on a genome-wide basis. (msdmanuals.com)
CNVs19
- Copy number variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. (biomedcentral.com)
- As with all types of genetic variation, CNVs may influence phenotypic variation and gene expression. (biomedcentral.com)
- CNVs are thus considered major sources of genetic variation. (biomedcentral.com)
- To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 718,256 oligonucleotide probes with a median probe spacing of 500 bp. (biomedcentral.com)
- We detected CNVs in rice by array-based comparative genomic hybridization. (biomedcentral.com)
- Further discussion of CNVs is important, as they are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics. (biomedcentral.com)
- Copy number variations (CNVs), or copy number polymorphisms (CNPs), are forms of structural variation (SV) that are alterations in DNA resulting in the cell having an abnormal number of copies of one or more segments of DNA. (biomedcentral.com)
- CNVs can be detected using cytogenetic techniques such as fluorescent in situ hybridization, array-based comparative genomic hybridization, and SNP genotyping arrays. (biomedcentral.com)
- Thus, CNVs are considered likely major sources of genetic variation, and may influence phenotypic variation and gene expression. (biomedcentral.com)
- A comprehensive dissection of the genetic etiology of UC needs to assess the contribution of rare genetic variants including copy number variations (CNVs) to disease risk. (nih.gov)
- Copy number variations (CNVs) have been linked to dozens of human diseases, but can they also represent the genetic variation that was so essential to our evolution? (nature.com)
- During the past several years, hundreds of new variations in repetitive regions of DNA have been identified, leading researchers to believe that copy number variations (CNVs) are as important a component of genomic diversity as single nucleotide polymorphisms (SNPs). (nature.com)
- Copy number variants (CNVs) are a major source of such genetic variation, and are defined as chromosomal segments at least one thousand bases in length that vary in copy number between individuals. (mlo-online.com)
- The prevalence of CNVs throughout the general population suggests that they represent a significant proportion of total genomic variation, and it has been estimated that CNVs may affect as much as 4% to 5% of the human genome. (mlo-online.com)
- Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation. (biomedcentral.com)
- Genetic inheritance is mainly polygenic, and 10% are copy number variations (CNVs). (bvsalud.org)
- Array comparative genomic hybridization (array-CGH) is used to identify CNVs. (bvsalud.org)
- Although the cell line had developed alongside the accumulation of genomic alterations (28 CNV in primary cells and 37 CNV in CAISMOV24), most of them were related to CNVs already present in primary malignant cells. (biomedcentral.com)
- Our results corroborate with the idea that genomic alterations, depicted by CNVs, can be used for subtyping epithelial ovarian carcinomas. (biomedcentral.com)
Microarray-based comparative6
- Microarray-based comparative genomic hybridization is a method of molecular analysis that identifies chromosomal anomalies (or copy number variants) that correlate with clinical phenotypes. (nih.gov)
- Another goal was to test the association between a positive microarray-based comparative genomic hybridization result and the severity of intellectual disability/developmental delay. (nih.gov)
- Microarray-based comparative genomic hybridization identified structural chromosomal alterations responsible for the intellectual disability/developmental delay phenotype in 16% of our sample. (nih.gov)
- We want to emphasize the need to conduct microarray-based comparative genomic hybridization on all individuals with intellectual disability/developmental delay, regardless of the severity, because the degree of intellectual disability/developmental delay does not predict the diagnostic yield of microarray-based comparative genomic hybridization. (nih.gov)
- Clinical Significance of Rare Copy Number Variations in Epilepsy: A Case-Control Survey Using Microarray-Based Comparative Genomic Hybridization. (unito.it)
- High-resolution microarray-based comparative genomic hybridization (CGH) techniques have successfully been applied to study copy number imbalances in a number of settings such as the analysis of cancer genomes. (biomedcentral.com)
Whole-genome3
- Additional experiments introduce fundamental techniques in yeast genomics, including both performance and interpretation of Synthetic Genetic Array analysis, multiplexed whole genome and barcode sequencing, and comparative genomic hybridization to DNA arrays. (cshlpress.com)
- In mammals, it is important source of variability in genomes and it contains 0.4-25% of whole genome variation. (ac.ir)
- Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. (umn.edu)
Chromosomal4
- Indeed, for as long as cytogeneticists have studied chromosomes under microscopes, they have observed variations in chromosomal structure. (nature.com)
- Because the exact genomic position is known, aberrations can also be mapped directly onto the chromosomal location. (mlo-online.com)
- Hidden Markov Models (HMM) are often used for analyzing Comparative Genomic Hybridization (CGH) data to identify chromosomal aberrations or copy number variations by segmenting observation sequences. (biomedcentral.com)
- Continuous observation sequences from either DNA microarrays or next generation sequencing experiments, note that the proportion of mapped reads in an interval is frequently used as a continuous measure of copy number, to detect chromosomal aberrations or copy number variations lead to the same fundamental computational problem and share characteristics of the data. (biomedcentral.com)
Microarrays4
- High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. (idtdna.com)
- DNA microarrays using comparative genomic hybridization (CGH) are frequently used for CNV screening. (bio-rad.com)
- Traditional methods for tumor characterization are tumor-type specific and include assays such as immunohistochemistry (IHC), in situ hybridization (ISH), quantitative PCR (qPCR), Sanger sequencing and gene signature microarrays [ 1 - 8 ]. (oncotarget.com)
- The technology also increases the density of genomic DNA probes for higher resolution genetic analysis beyond what is used in FISH, genomic microarrays for array comparative genomic hybridization, and solution capture hybrdization arrays for sequence enrichment in deep sequencing. (cytognomix.com)
Alterations9
- Initiation and propagation of tumors reflect underlying genomic alterations such as mutations, polymorphisms, and copy number variations found in genes of multiple cellular pathways. (hindawi.com)
- Based on the heterogeneity within a specific tumor type, a combination of genomic alterations defines the cancer subtype, biologic behavior, and in some cases, response to therapeutics. (hindawi.com)
- Genomic alterations in the endometrium may be a proximate cause for endometriosis. (endometriosi.it)
- Objective: To test the hypothesis that endometriosis may originate from genomic alterations in the endometrium by genomic analysis of endometrial tissues in patients with endometriosis and compare them with those from normal controls. (endometriosi.it)
- Results: We identified several regions of genomic alterations in all five patients. (endometriosi.it)
- For select markers, the genomic alterations were confirmed by real-time PCR and LOH analyses. (endometriosi.it)
- Conclusions: There is evidence that the endometrium in women with endometriosis has genomic alterations. (endometriosi.it)
- Sung, JS, Park, KH & Kim, YH 2010, ' Genomic alterations of chromosome region 11p as predictive marker by array comparative genomic hybridization in lung adenocarcinoma patients ', Cancer Genetics and Cytogenetics , vol. 198, no. 1, pp. 27-34. (korea.ac.kr)
- Additionally, comparative genomic hybridization was employed to compare genomic alterations between the CAISMOV24 cell line and its primary malignant cells. (biomedcentral.com)
Mutations1
- Inherited mutations in a small number of genes account for about five to ten percent of women's cancers.These inherited variations, identified in breast, ovarian, and endometrial cancer susceptibility, can be characterized in the general population by their frequency and the magnitude of their impact upon a patient (Table 1 ).Some inherited variants occur rarely in the general population, but confer large risks to the individual. (hindawi.com)
Chromosome6
- Here especially highlighted variations of FISH are molecular combing, chromosome orientation-FISH (CO-FISH), telomere-FISH, parental origin determination FISH (POD-FISH), FISH to resolve the nuclear architecture, multicolor-FISH (mFISH) approaches, among other applied in chromoanagenesis studies, Comet-FISH, and CRISPR-mediated FISH-applications. (frontiersin.org)
- Comparative genomic hybridisation (CGH) was used to screen 76 vestibular schwannomas from 76 patients (66 sporadic and 10 NF2 related) to identify other chromosome regions that may harbour genes involved in the tumorigenesis. (bmj.com)
- Indeed, if hybridization intensity was an exact, un-biased measurement of DNA concentration before amplification, the sequence of hybridization intensities of probes along a chromosome would yield a piece-wise constant function in ArrayCGH experiments. (biomedcentral.com)
- Nesthor Perez 2.3 Mechanisms of Structural Variation Cytogenetic Techniques: Chromosome Painting: Nesthor Perez 2.3 Mechanisms of Structural Variation Cytogenetic Techniques: Nesthor Perez 2.3 Mechanisms of Structural Variation Cytogenetic Techniques: Fluorescent in Situ Hybridization (FISH): Nesthor Perez (FISH) Nesthor Perez Outline 1. (studylib.net)
- Array comparative genomic hybridization for the detection of submicroscopic copy number variations of the X chromosome in women with premature ovarian failure. (biologie-journal.org)
- Analysis of X chromosome genomic DNA sequence copy number variation associated with premature ovarian failure (POF). (biologie-journal.org)
Deletions2
- In this concern, methods such as comparative genomic hybridization allow the detection of deletions and duplications of genomic segments, known as copy number variation (CNV). (biomedcentral.com)
- Micro-Array measurement found similar SV's for: Duplications Deletions Inversions Then, common SV's are now linked to: Autism Schizophrenia Nesthor Perez 2.1 Germline Structural Variation Human Genetics Study purpose: Identify a unique DNA sequencing. (studylib.net)
Detection2
- Accurate and reliable high-throughput detection of copy number variation in the human genome. (analytica-world.com)
- Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays. (analytica-world.com)
Probes1
- In both cases, DNA from two samples are differentially labeled with fluorescent dyes and co-hybridized to immobilized genomic capture probes. (biomedcentral.com)
Arrays2
- With optimized, proprietary reagents, the Enzo Life Sciences CGH Labeling Kits for oligo arrays produce high quality data using as little as 0.25 µg of genomic DNA, without a need for pre-amplification. (enzolifesciences.com)
- Genomic analysis using high-resolution single-nucleotide polymorphism arrays reveals novel microdeletions associated with premature ovarian failure. (biologie-journal.org)
Fluorescent1
- In essence, relative ratios of copy number between two DNA samples are obtained by comparing the two fluorescent signal intensities for each probe under the assumption that intensities reflect the amount of corresponding genomic DNA in the respective sample. (biomedcentral.com)
Phenotypic variation2
- They lead to variation in gene expression levels and may account for a large amount of phenotypic variation among individuals and ethnic populations, including differential responses to drugs and environmental stimuli. (analytica-world.com)
- An additional kind of variation, copy number variation, is emerging as a significant factor to phenotypic variation in several varieties. (virtualinnbox.com)
Genome-wide3
- Comparative genomic hybridization (CGH) has been developed to elucidate genome-wide sequence copy number variation (CNV) between different genomes, such as the differential amplification or deletion of genetic regions between tumor DNA and normal DNA from neighboring unaffected tissue [ 7-10 ]. (idtdna.com)
- Below we explain a genome-wide CNV research utilizing array comparative genomic hybridization in a wide range of chicken breeds. (virtualinnbox.com)
- To do this, we will perform genome-wide siRNA screens on MITF-high and -low melanoma cells in combination with genomic analysis and suitable functional assays. (lu.se)
Genomics2
- Comparative genomics is introduced using different yeast strains to study natural variation, evolution, and quantitative traits. (cshlpress.com)
- Chapter 6: Structural Variation and Medical Genomics CS-6293 Bioinformatics Instructor: Dr. Jianhua Ruan Presented by: Nesthor Perez Outline 1. (studylib.net)
Copy11
- Clancy, S. (2008) Copy number variation. (nature.com)
- GC was defined as ≥3 copy number variations (CNV). (confex.com)
- Until recently, real-time quantitative PCR (qPCR) assays and microarray hybridization have been the main methods used to determine copy number variation (CNV) in the genome. (bio-rad.com)
- Copy number variation is defined as the presence of variable numbers of copies of a particular DNA segment relative to a reference genome. (bio-rad.com)
- I am looking at the results for survival analysis for leukaemia patients, categorised based on Copy Number Variation (CNV) levels using array comparative genomic hybridisation. (stackexchange.com)
- In addition, we show how the strategy can be applied to conveniently define adaptive sample-specific boundaries between balanced copy number, losses, and gains to facilitate management of variation in tissue heterogeneity when calling copy number changes. (biomedcentral.com)
- Array comparative genomic hybridization profiling analysis reveals deoxyribonucleic acid copy number variations associated with premature ovarian failure. (biologie-journal.org)
- Copy number variation analysis detects novel candidate genes involved in follicular growth and oocyte maturation in a cohort of premature ovarian failure cases. (biologie-journal.org)
- Copy number variation (CNV) is one of these variations in genome including insertion, deletion and duplication of 1 kb to 1 Mb segment with more than 90% similarity. (ac.ir)
- The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. (umn.edu)
- DNA methylation and copy number variation profiling of T-cell lymphoblastic leukemia and lymphoma. (cancercentrum.se)
Tumours2
- Ways to abrogate heterogeneity will be required to optimise the genomic classification of tumours. (springer.com)
- Not only has knowledge of the genomic landscape helped inform the development of new drugs, this understanding also promises to improve risk stratification of tumours and to determine their sensitivity to systemic therapies. (springer.com)
Genetics1
- But another type of variation, largely overlooked by the genetics community, might ultimately make equally important contributions to health. (the-scientist.com)
Genomes1
- Different variants of FISH can be used to retrieve information on genomes from (almost) base pair to whole genomic level, as besides only second and third generation sequencing approaches can do. (frontiersin.org)
Genes2
- Comparative genomic hybridization (CGH) was used to reveal that each serotype contains a core of about 4000 genes in addition to 400-600 genes that are serotype specific. (usda.gov)
- Identification of a duplication within the GDF9 gene and novel candidate genes for primary ovarian insufficiency (POI) by a customized high-resolution array comparative genomic hybridization platform. (biologie-journal.org)
Single nucleotide p1
- A second contributor of variation is single nucleotide polymorphism (SNP), in which two distinct alleles are possible at a single genome position, with each allele appearing at high frequency within the population. (mlo-online.com)
Molecular2
- Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. (idtdna.com)
- We present a general overview of the more commonly used approaches for molecular profiling at the genomic, transcriptomic and proteomic levels. (biomedcentral.com)
Analysis2
- The product is qualified for a variety of genomic analysis. (identificabio.com)
- Recently, a tool called array comparative genomic hybridization was applied to the analysis of ENBs. (medscape.com)
Polymorphisms1
- The massive efforts to systematically find and catalog single nucleotide polymorphisms (SNPs) bear witness to the conviction that small genomic changes may provide clues to the origins of such things as heart problems, obesity, and pharmacologic responses. (the-scientist.com)
Clinical2
- Some insights into clinical risk factors and their genomic correlates have been made. (springer.com)
- According to comparative genomic hybridization (CGH) data published in the literature, the simple and complex karyotypes show a correlation between the prognosis and clinical outcome. (biomedcentral.com)
Intensities1
- 3D anaglyph videos showed genomic regions with DA having nearly 5-fold larger differences in volumetric integrated probe intensities between homologs. (cytognomix.com)
Genetic variation4
- Little is known, however, about their contribution to genetic variation in rice. (biomedcentral.com)
- The contributions of any single genetic variation or mutation in a population depend on its frequency and penetrance as well as tissue-specific functionality. (hindawi.com)
- Although genetic variation is a major driving force behind evolution, certain variants also underlie many congenital diseases. (mlo-online.com)
- Although information on both types of genetic variation is complementary in many of these investigations, each has traditionally been analyzed using separate approaches. (mlo-online.com)
Array-based1
- Using array-based comparative genomic hybridization (CGH), we determined the normal range of variation in CGH signals using normal controls. (endometriosi.it)
Autism1
- This report aimed to discuss autism spectrum disorder and its diagnosis by array comparative genomic hybridization, highlighting the association with the pathogenic duplication of 17q12q21.2. (bvsalud.org)
Distinct1
- The most common non-clear cell renal cancers have also undergone genomic profiling and are characterised by distinct genomic landscapes. (springer.com)
Oligonucleotides1
- These applications demand that the oligonucleotides have consistent base composition and minimal lot-to-lot variation. (idtdna.com)
Nucleotide2
- These genomic regions appear to have an elevated likelihood of positive selection, based on nucleotide level conservation and transcriptional data. (biomedcentral.com)
- This process helps identify single or multiple nucleotide variations as well as areas of insertion or deletion. (msdmanuals.com)
Results2
- For this reason, we performed a fine-tuned interpretation of our DNA ploidy results and compared these to high-resolution comparative genomic hybridization (HR-CGH) outcome, by using the same samples. (biomedcentral.com)
- He thanked the regional and global specialized laboratories for their efforts to provide timely results of the genomic sequencing of wild polioviruses, and for their help in planning and monitoring polio eradication activities in the Region. (who.int)
Clones1
- The sensitivity of CGH in detecting fine changes in CNV depends on the representation of the genomic sequence of the clones, probe characteristics and signal-to-noise ratios. (bio-rad.com)
Regions4
- These hotspots of primate CNV formation provide a novel perspective on divergence and selective pressures acting on these genomic regions. (biomedcentral.com)
- The goal is to segment an observation sequence into regions in which there is little variation around a common mean. (biomedcentral.com)
- Interestingly, genomic regions without DA are enriched in epigenetic marks (DHS, H3K27Ac, H3K4me1) of accessible interphase chromatin to a greater extent than regions with DA, suggesting these differences may be correlated with epigenetic marks established during the previous interphase. (cytognomix.com)
- Still, further experimentation will be required to determine the role of these genomic regions in ENB. (medscape.com)