Methylation oligonucleotide array sequence analysis. Medical search. Frequent questions

The aim of this study was to identify genes in adenoid cystic carcinoma (ACC) of salivary gland strongly deregulated by epigenetic CpG island methylation, to validate selected genes by conventional techniques, and to correlate the findings with clinicopathologic factors. (nih.gov)
Finally, we identified aberrant methylation in multiple genes also targeted by recurring DNA copy number alterations in ALL, suggesting that these genes are inactivated far more frequently than suggested by structural genomic analyses alone. (lu.se)
Of these genes, 33 have associated CpG islands greater than 300 bp in length but only three have been previously described as targets for aberrant methylation in human cancer. (duke.edu)
Northern blotting for five of these genes (alpha-Catenin, DTR, FYN, GADD45a, and Zyxin) verified the array results. (duke.edu)
Further analysis of one of these genes, GADD45a, showed that 5-AzaC induced expression in five additional breast cancer cell lines with little or no induction in three additional lines derived from normal breast epithelial cells. (duke.edu)
Therefore, this simple method of dynamic transcriptional profiling yielded a series of novel methylation-sensitive genes in breast cancer including the BRCA1 and p53 responsive gene, GADD45a. (duke.edu)
Pathway analyses revealed significant downregulation of 34 pathways, predominantly those of genes associated with mitochondrial function, including PPARGC1A. (regionh.dk)
We found that p300/CBP-associated factor (PCAF)-dependent acetylation of histone 3 lysine 9 (H3K9ac), paralleled by a reduction in methylation of H3K9 (H3K9me2), occurred at the promoters of select genes only after PNS axonal injury. (nature.com)
Genes which have been typically affected by DNA methylation contain each the tumor suppressors RASSF1A as well as APC. (hdacassay.com)
Here, we present a large-scale genetic association study of intelligence (n = 269,867), identifying 205 associated genomic loci (190 new) and 1,016 genes (939 new) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. (scite.ai)
Gene-level association analysis reveals a role for tissue-specific expression of multiple genes in longevity. (scite.ai)
Then they perform supervised analyses to identify differentially methylated or expressed genes. (scientistlive.com)
Frontage teams utilize commercially available amplicon- and hybridization-capture-based multigene sequencing panels from Illumina, Invitae, and other suppliers as well as custom sequencing panels focused on key target genes. (frontagelab.com)
In the past ten years, improvements in massively parallel sequencing techniques have led to the development and widespread clinical use of multigene panels, which allow simultaneous testing of two to more than 150 genes. (nih.gov)
These include genes selected by a clinician for analysis by clinical sequencing. (nih.gov)
Results for each gene on the custom multigene panel are reported to the ordering clinician, whereas the results from the remaining genes sequenced (but not requested by the clinician) are not analyzed or included in the final laboratory report. (nih.gov)
Exome sequencing is a laboratory test designed to identify and analyze the sequence of all protein-coding nuclear genes in the genome. (nih.gov)

Imagine two different genomic regions, A and B. Region A has six CpGs (DNA methylation in mammalian somatic cells generally occurs at CpG dinucleotides), three of which are methylated. (wikipedia.org)
We profiled 27,718 genomic regions in abdominal SAT samples of 38 unrelated individuals using differential methylation hybridization (DMH) together with genotypes at 5,227,243 SNPs and expression of 17,209 mRNA transcripts. (ox.ac.uk)
Recent genome-wide meta-analyses have identified 24 genomic loci linked to variation in intelligence, but much about its genetic underpinnings remains to be discovered. (scite.ai)
After sequencing the human genome, numerous projects have focused on characterizing genomic alterations and associating them with the different diseases or functional elements of the genome. (biomedcentral.com)
Amplicon sequencing is a low-cost and rapid procedure to target up to 200 genomic regions with commonly occurring polymorphisms that inform treatment decisions. (frontagelab.com)
Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing. (cdc.gov)
129 genomic copies/L for CpG methylation capture with MDA. (cdc.gov)

This is because of the low cost, high-throughput nature of arrays. (epigenie.com)
Methylation arrays are still very much is use to compliment or kick-off larger projects or perform large-scale, high throughput experiments. (epigenie.com)
Methylation-specific oligonucleotide microarray: A new potential for high-throughput methylation analysis. (epigenie.com)
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. (springer.com)
With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. (springer.com)
The completion of the first human genome drafts (Yamey 2000 ) was just a start of the modern DNA sequencing era which resulted in further invention, improved development toward new advanced strategies of high-throughput DNA sequencing, so called the " high-throughput next generation sequencing " (HT-NGS). (springer.com)
High-throughput RNA sequencing (RNA-seq) has revolutionized our understanding of gene expression. (cdc.gov)

The variety of instrumentation allows for capabilities ranging from highly focused analysis of candidate SNPs and mRNAs to whole genome, exome, epigenome and transcriptome sequencing. (psu.edu)
Whole genome sequencing is used mainly for the detection of major chromosomal rearrangements, deletions, and hypomethylation. (frontagelab.com)
SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now. (cdc.gov)

Arrayit Pathways™ Focused Human Genome Microarrays enable targeted gene expression analysis of every major cellular pathway in the human body. (arrayit.com)
Pathways™ Microarrays offer the highest sensitivity and specificity of any product on the market, empowered by long-mer oligonucleotides, proprietary attachment and surface chemistry, and a unique one gene-one spot™ design. (arrayit.com)
The use of advanced bioinformatics, ultra-pure oligonucleotides, superior surface chemistry and advanced microarray cleanroom manufacturing facilities guarantees that Pathways™ Microarrays outperform the highest industry standards. (arrayit.com)
These microarrays are designed using the complete, fully annotated human genome sequence using sophisticated one spot-one gene™ informatics, useding highest gene content available. (arrayit.com)
All our microarrays offer quality and performance that cannot be obtained from any other microarray, PCR or next generation sequencing approach. (arrayit.com)

CONCLUSION: The DNA methylation signature of NSCLC affects the outcome of stage I patients, and it can be practically determined by user-friendly polymerase chain reaction assays. (edgehill.ac.uk)

Previous studies of DNA methylation suggest epigenetic alterations may also be important, but an integrated genome-wide analysis of genetic and epigenetic alterations in ALL has not been performed. (lu.se)
We found that the different genetic subtypes of ALL are characterized by distinct DNA methylation signatures that exhibit significant. (lu.se)
The presence of methylation quantitative trait loci indicates a direct genetic influence on the level of DNA methylation in adipose tissue. (ox.ac.uk)
Genetic variants that associate with DNA methylation at CpG sites (methylation quantitative trait loci, meQTLs) offer a potential biological mechanism of action for disease associated SNPs. (ox.ac.uk)
Our results indicate that DNA CpG methylation in abdominal SAT is partly under genetic control. (ox.ac.uk)
We confirm previous strong genetic correlations with multiple health-related outcomes, and Mendelian randomization analysis results suggest protective effects of intelligence for Alzheimer's disease and ADHD and bidirectional causation with pleiotropic effects for schizophrenia. (scite.ai)
For the future direction, we need the in-depth genome sequence information and analysis for most of the mammals, including human to fully understand genome variation of economic traits, genetic susceptibility to diseases, and pharmacogenomics of drug response. (springer.com)
The diagnostic utility of exome sequencing has consistently been 20%-30% (i.e., a diagnosis is identified in 20%-30% of individuals who were previously undiagnosed but had features suggestive of a genetic condition) [ Gahl et al 2012 , Lazaridis et al 2016 ]. (nih.gov)

The authors analyzed 16 matched normal and tumor tissues for aberrant DNA methylation using the methylated CpG island amplification and microarray method and the pyrosequencing technique. (nih.gov)

We examined both DNA methylation and various key histone modifications with regards to gene regulation following axonal injury. (nature.com)
These reversible modifications are deemed to contribute to tumor suppressor gene inactivation by way of DNA methylation, histone modifications or miRNA expression. (hdacassay.com)

Scholars@Duke publication: Analysis of methylation-sensitive transcriptome identifies GADD45a as a frequently methylated gene in breast cancer. (duke.edu)

We find that none of the 149 meQTL top SNPs is a significant expression quantitative trait locus in our expression data, but we observed association between expression levels of two mRNA transcripts and cis-methylation status. (ox.ac.uk)
Real-time PCR monitors SNPs, indels, conserved translocations, and methylation changes for one up to a few hundred specific sites (with qPCR panels). (frontagelab.com)

It can be applied to large datasets generated using either oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq), providing a quantitative estimation of absolute methylation state in a region of interest. (wikipedia.org)
Rapid and comprehensive analysis of putative proteinous allergens ( allergenome ) by applying such a proteomic strategy … With allergenomics, we can not only detect and assign the putative allergens (proteins specifically interacting with IgE antibodies in a patient's blood) in a short time, but also analyze the quantitative and qualitative change of the antigens, depending on the surroundings and environmental conditions of an allergenic causative. (genomicglossaries.com)
We applied two strategies to eliminate or substantially reduce the obstacles of tRNA modification and structure for efficient and quantitative tRNA sequencing ( Fig. 1a ). (cdc.gov)

Microarray analysis showed hypomethylation in 7 and hypermethylation in 32 CpG islands. (nih.gov)
We analyzed 137 B-lineage and 30 T-lineage childhood ALL cases using microarray analysis of DNA copy number alterations and gene expression, and genome-wide cytosine methylation profiling using the HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) assay. (lu.se)
Transcriptomic analysis was done using microarray analysis and validated using real-time PCR. (bvsalud.org)

DNA methylation is a fundamental epigenetic event associated with physiologic and pathologic conditions, including cancer. (nih.gov)
Given the importance of histone methylation status in defining patterns of gene expression under different physiological and pathophysiological conditions, these findings predict a role for the HIF system in epigenetic regulation. (ox.ac.uk)

We quantified DNA methylation in the Understanding Society cohort (n = 1175), a large population based study, using the Illumina EPIC array to assess the statistical properties of DNA methylation association analyses. (nih.gov)
The Illumina 450k infinium methylation beadchip is one of the most common chips used in human methylation research. (epigenie.com)
Sequencing was performed using the Illumina MiSeq v2 500cycle or NovaSeq 6000 SP platform. (cdc.gov)

The analysis of the best DNA methylation biomarkers improved prognostic accuracy beyond standard staging. (edgehill.ac.uk)

Together, these results demonstrate subtype- and disease-specific alterations in cytosine methylation in ALL that influence transcriptional activity, and are likely to exert a key role in leukemogenesis. (lu.se)
Methylation sequencing checks the methylation of cytosine residues in the DNA. (frontagelab.com)

The isolated fragments of DNA are either hybridized to a microarray chip (MeDIP-chip) or sequenced by next-generation sequencing (MeDIP-seq). (wikipedia.org)
Next generation sequencing in epigenetics: insights and challenges. (epigenie.com)
The company is expanding its product offerings into areas related to PCR, gene expression, sample preparation for next generation sequencing, cellular analysis, epigenetics and RNA analysis. (scientistlive.com)
With improvements seen in next-generation sequencing (NGS) tools, successful sequencing of cfDNA analysis is possible. (frontagelab.com)
Prior to the development of massively parallel sequencing (also known as next-generation sequencing ), the only cost-effective way to test more than one gene was serial single-gene testing (i.e., complete testing of one gene that might account for the phenotype before proceeding to testing of the next gene) ‒ an expensive and time-consuming approach with a potentially low yield. (nih.gov)
Through this new partnership we are pleased to offer you comprehensive next generation sequencing solutions. (idtdna.com)
Integrated DNA Technologies acquires Archer™ next generation sequencing research assays to advance actionable scientific discoveries. (idtdna.com)
Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. (cdc.gov)

Furthermore, because MGMT protein loss may be a result of promoter hypermethylation, it was reported that methylation of the MGMT promoter in gliomas is a useful predictor of the responsiveness to alkylating agents ( 7 ). (aacrjournals.org)
Furthermore, EDN3 promoter hypermethylation was detected in 70% of primary breast carcinomas with significant association to loss of EDN3 mRNA expression ( P = 0.005), whilst normal matched breast tissues revealed no EDN3 promoter methylation. (biomedcentral.com)

Widely used RNA-seq methods start with adapter ligation and cDNA synthesis of biological RNA samples followed by PCR amplification to generate sequencing libraries1. (cdc.gov)

Laboratories are demanding ever more sensitivity and reliability from their gene expression analysis technologies. (scientistlive.com)
In order to do this, Meléndez and her team are using Qlucore Omics Explorer to perform gene expression and methylation analyses of brain tumour samples and then validating them with data from other databases. (scientistlive.com)
In addition, oligonucleotide probes are used to analyse gene expression. (scientistlive.com)
Expression analyses allowed us to identify that meningiomas can be classified into an aggressive and a non-aggressive group - despite WHO classification criteria establishing three malignancy groups and about 15 histopathological subtypes. (scientistlive.com)
Supervised analyses have allowed us to identify gene expression profiles associated with more aggressive tumours - findings that have been confirmed by analysing the methylation data with Qlucore,' she concludes. (scientistlive.com)
Here, we analyzed methylation and gene expression in Dnmt3b+/+ (WT), Dnmt3b-/- (3bKO) and Dnmt3bCI/CI (3bKI) embryos at E11.5. (nih.gov)
By means of oligonucleotide microarray and RNA interference, we reveal that the sensitizing effect of IFN-β was possibly due to attenuation of MGMT expression via induction of the protein p53. (aacrjournals.org)
Here, we aimed at a first comprehensive analysis on EDN3 expression and its implication in human breast cancer. (biomedcentral.com)
EDN3 expression and methylation data were statistically correlated with clinical patient characteristics and patient outcome. (biomedcentral.com)
These traits can be the consequences of alterations that are directly changing the protein function, or they can emerge after several gene expression regulation steps, caused for example by alternative splicing or methylation. (biomedcentral.com)
Targeted analysis of 274 cytokines and global proteomics of RCC CM revealed decreased DPP4 and EGF, as well as increased AREG, FN1 and MMP1, with consistently altered gene expression in RCC cell lines and tumors. (bvsalud.org)
Independent transcriptomic and proteomic datasets of ccRCC tumors were used for the analysis of gene and protein expression as well as the level of the immune infiltration. (bvsalud.org)

The human exome includes all coding nuclear DNA sequences, approximately 180,000 exons that are transcribed into mature RNA. (nih.gov)
Approximately 95% of the exome can be sequenced with currently available techniques. (nih.gov)

During this period, tremendous success has been achieved in the fields of decoding of human genome, technological advancement of new era of human genome applications, toward personalized genomes and discovery of rare variants, leveraging genome sequencing to impact on cancer researches and mammalian evolution and population structure. (springer.com)

PATIENTS AND METHODS: A DNA methylation microarray that analyzes 450,000 CpG sites was used to study tumoral DNA obtained from 444 patients with NSCLC that included 237 stage I tumors. (edgehill.ac.uk)
One must sequence deep enough and use strong methods to prevent DNA loss during library preparation (point #4). (frontagelab.com)
The methods used in multigene panels may include sequence analysis , deletion/duplication analysis , and/or other non-sequencing-based tests. (nih.gov)
METHODS: Conditioned media (CM) were collected from five RCC-derived cell lines (Caki-1, 786-O, A498, KIJ265T and KIJ308T) and non-tumorous control cell line (RPTEC/TERT1) and analyzed using cytokine arrays targeting 274 cytokines in addition to global CM proteomics. (bvsalud.org)
METHODS: Proteomic and metabolomics analysis of conditioned media isolated from normal kidney cells as well as five ccRCC cell lines was performed using mass spectrometry, with the following ELISA validation. (bvsalud.org)
Despite its biological importance, transfer RNA (tRNA) could not be adequately sequenced by Author Manuscript standard methods due to abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. (cdc.gov)
Author Manuscript class of cellular RNA for which the standard sequencing methods cannot yet be applied efficiently and quantitatively, although attempts have been made (e.g. ref 2). (cdc.gov)

Integrative analysis of sequencing and array genotype data for discovering disease associations with rare mutations. (unc.edu)

Hybridization-based capture sequencing allows high-depth sequencing of up to 100 million nucleotides from the human genome. (frontagelab.com)

Although DNMT1 methylates newly synthe sized DNA for the duration of cell division, DNMT3a and DNMT3b act on methylation of CpG motifs all through cellular differentiation and regulatory pro cesses. (hdacassay.com)

Second, we establish whether linear regression, the chosen statistical tool for the majority of studies, is appropriate and whether it is biased by the underlying distribution of DNA methylation data. (nih.gov)
Next, we tested whether the assumptions of linear regression are violated by DNA methylation data and found that the majority of sites do not satisfy the assumption of normal residuals. (nih.gov)
Finally, we performed power calculations for EPIC based DNA methylation studies, demonstrating that existing studies with data on ~ 1000 samples are adequately powered to detect small differences at the majority of sites. (nih.gov)
Moreover, our results indicate that linear regression is a valid statistical methodology for DNA methylation studies, despite the fact that the data do not always satisfy the assumptions of this test. (nih.gov)
Taking advantage of Qlucore Omics Explorer's powerful data analysis capabilities, its speed, and its ability to work on any PC, Dr Bárbara Meléndez and her colleagues in the Unidad de Investigación de Patología Molecular (Molecular Pathology Research Unit) at Hospital Virgen de la Salud in Toledo, Spain, are investigating how such generally benign meningiomas can start to exhibit the sort of histology and recurrence usually associated with more aggressive tumours. (scientistlive.com)
CGHbase-1.42.0 CGHbase: Base functions and classes for arrayCGH data analysis. (fredhutch.org)
The GEO accession number for the sequencing data reported in this paper is GSE66550. (cdc.gov)
Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. (cdc.gov)

The CpG island associated with GADD45a was analysed by bisulfite sequencing, sampling over 100 CpG dinucleotides. (duke.edu)

Promoter arrays are also very common, they typically cover all refeq promoters of the species (human, mouse or rat) of interest. (epigenie.com)
Year 2011 is celebrated as the 10th anniversary since the human genome was first sequenced ( www.nature.com/natureconferences/hg10years/index.html ). (springer.com)

The prognostic DNA methylation markers were validated by a single-methylation pyrosequencing assay in an independent cohort of 143 patients with stage I NSCLC. (edgehill.ac.uk)

In this way Batman converts the signals from MeDIP experiments to absolute methylation levels. (wikipedia.org)

There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. (nih.gov)
We investigated whether meQTLs exist in abdominal subcutaneous adipose tissue (SAT) and if CpG methylation associates with metabolic syndrome (MetSyn) phenotypes. (ox.ac.uk)

Significant obstacles for the sequencing of tRNA include the presence of numerous post-transcriptional modifications and its stable and extensive secondary structure, which interfere with cDNA synthesis and adapter ligation. (cdc.gov)

Also important is Qlucore's 3D graphics capability: '3D lets us see individual groups that we don't always see with cluster analysis alone. (scientistlive.com)

The basic assumptions of Batman: Almost all DNA methylation in mammals happens at CpG dinucleotides. (wikipedia.org)

This does not give the full picture of methylation in these two regions (in region A only half the CpGs are methylated, whereas in region B all the CpGs are methylated). (wikipedia.org)
We find that, at 5% false discovery rate, methylation levels of 149 DMH regions associate with at least one SNP in a ±500 kilobase cis-region in our primary study. (ox.ac.uk)

EDN3 promoter methylation was analysed by methylation-specific PCR in breast cell lines (n = 6) before and after demethylating treatment, normal breast tissues (n = 17) and primary breast carcinomas (n = 128). (biomedcentral.com)

Finally, we assess the sample size required for adequately powered DNA methylation association studies. (nih.gov)
By simulating null DNA methylation studies, we generated the distribution of p-values expected by chance and calculated the 5% family-wise error for EPIC array studies to be 9 × 10 - 8 . (nih.gov)
9 × 10 - 8 adequately controls the false positive rate for EPIC array DNA methylation studies. (nih.gov)
These findings have implications for epidemiological-based studies of DNA methylation and provide a framework for the interpretation of findings from current and future studies. (nih.gov)
Here, we perform two meta-analyses of GWA studies of a rigorous longevity phenotype definition including 11,262/3484 cases surviving at or beyond the age corresponding to the 90th/99th survival percentile, respectively, and 25,483 controls whose age at death or at last contact was at or below the age corresponding to the 60th survival percentile. (scite.ai)

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