Our blogs and videos choice: dna methylation analysis

PubMed: DNA methylation epigenotypes in breast cancer molecular ...

Using all-subset selection method, we identified the most subtype predictive methylation profiles in multivariable logistic regression analysis. RESULTS: The approach efficiently recognized 15 individual CpG loci differentially methylated in breast cancer tumor subtypes. We further identify novel subtype specific epigenotypes which clearly demonstrate the differences in the methylation profiles of basal-like and human epidermal growth factor 2 (HER2)-overexpressing tumors. CONCLUSIONS: Our results provide evidence that well defined DNA methylation profiles enables breast cancer subtype [more...]

Date: 2010-10-06 10:10:41

Blog posts (25) | Videos (15)

DNA methylation analysis of multiple tissues from newborn twins ...

DNA methylation analysis of multiple tissues from newborn twins reveals both genetic and intrauterine components to variation in the human neonatal epigenome Miina Ollikainen1,2, Katherine R. Smith3, Eric Ji-Hoon Joo1,2, Hong Kiat Ng1,2, Roberta Andronikos1,2, Boris Novakovic1,2, Nur Khairunnisa Abdul Aziz1,2, John B. Carlin2,3, Ruth Morley1,2, Richard Saffery1,2,* and Jeffrey M. Craig1,2,* 1Developmental Epigenetics, Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria 3052, Australia 2Department of Paediatrics, University of Melbourne, Parkville, [more...]

Date: 2010-08-10 12:59:39

Illumina to Announce Third Quarter 2010 Financial Results on ...

We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming healthcare. [more...]

Date: 2010-10-13 04:08:35

GMO Pundit a.k.a. David Tribe: Genome sequence of Peruvian wild ...

We provide innovative sequencing and array-based solutions for genotyping, copy number variation analysis, methylation studies, gene expression profiling, and low-multiplex analysis of DNA, RNA and protein. We also provide tools and services that are fueling advances in consumer genomics and diagnostics. Our technology and products accelerate genetic analysis research and its application, paving the way for molecular medicine and ultimately transforming [more...]

Date: 2010-09-22 23:46:00

Genome-Wide DNA Methylation Maps in Follicular Lymphoma Cells ...

Methodology/Principal Findings We performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19+ B-cells using 454 sequencing technology. The methylated DNA fragments were enriched with methyl-binding proteins, treated with bisulfite, and sequenced using the Roche-454 GS FLX sequencer. The total number of bases covered in the human genome was 18.2 and 49.3 million including 726,003 and 1.3 million CpGs in FL and CD19+ B-cells, respectively. 11,971 and 7,882 methylated regions of interest (MRIs) were identified respectively. The genome-wide distribution of these [more...]

Date: 2010-09-30 21:12:52

DNA Methylation Analysis Determines the High Frequency of Genic ...

Dear Colleagueaaa, Here is an article you may find interesting. Elucidation of a C-Rich Signature Motif in Target mRNAs of RNA-Binding Protein TIAR. http://biowizard.com/abstract.php?pmid=17682065 Kim HS, Kuwano Y, Zhan M, Pullmann R Jr, Mazan-Mamczarz K, Li H, Kedersha N, Anderson P, Wilce MC, Gorospe M, Wilce JA Mol Cell Biol. 2007 Aug 6; PMID: 17682065 BioWizard [more...]

Date: 2010-08-26 23:27:02

Complete Genomics 2010 IPO | InvestorPlace

Complete Genomics Inc. plans to raise up to $86.2 million in an initial public offering to help fund improvements and expansion of its DNA sequencing technology. Complete Genomics will join the Nasdaq exchange after its 2010 IPO, and will trade under the ticker GNOM after the stock offering. The Mountain View, Calif., company said in its SEC registration statement that it has developed and commercialized “an innovative DNA sequencing platform that we believe will become the preferred solution for complete human genome sequencing and analysis.” Price is key for its assembly-line [more...]

Date: 2010-08-06 15:43:34


They performed DNA methylation profiling analysis for more than 800 genes, including tumor suppressors, oncogenes, and genes involved in cancer-related cellular processes. This process contrasts with previous studies that focused on the analysis of a single gene. They found only a few genes that were hypermethylated, but importantly found many more hypomethylated genes, even in the earliest stages of multiple myeloma. "Our data suggest that the overall degree of methylation may have some prognostic value, and further studies are needed to determine the functional and clinical significance [more...]

Date: 2010-10-05 18:12:00

Genomewide DNA methylation analysis reveals novel targets for drug ...

We analyzed genomewide methylation in MCL patients with the HELP (HpaII tiny fragment Enrichment by Ligation–mediated PCR) assay and found significant aberrancy in promoter methylation patterns compared with normal NBCs. [more...]

Date: 2010-08-19 16:02:55

MTHFR A1298C polymorphism and idiopathic male infertility Singh K ...

The enzyme methylenetetrahydrofolate reductase (MTHFR) catalyses the formation of folate intermediates that are vital for DNA synthesis and methylation reactions. C677T and A1298C variants of MTHFR result in reduced plasma folate and increase the susceptibility to various multifactorial disorders. We have already shown that homozygosity for 677 (C ®T) mutation in the MTHFR gene, is a risk factor for idiopathic male infertility in an Indian population. Aim: Recently, we showed that homozygosity for the 677(C;T) mutation in the MTHFR gene is a risk factor for idiopathic male infertility and [more...]

Date: 2010-10-08 20:51:33

IVF News - Sperm linked to ART-related genetic disorders

A process called DNA methylation is critical to imprinting. A team led by Dr Takahiro Arima from Tohoku University examined DNA methylation in 78 six to nine-week-old embryos and fetuses conceived using ART, and 38 conceived without ART. They also examined the father's sperm and DNA. In seven of 17 cases where there was abnormal DNA methylation in the ART sample, identical alterations were present in the father's sperm. The abnormal DNA methylation in the sperm was associated with variations in a gene coding for DNMT3L - a key enzyme in DNA methylation associated with abnormal imprinting and [more...]

Date: 2009-12-07 08:00:00

Urinary isoflavone phytoestrogens in German children and ...

Tһе results frοm tһе urinary biomarker analysis indicate isoflavone exposures аt quite variable levels іח German children: Analyte concentrations іח over 500 urine samples cover tһе range reported previously іח adults οח typical German diet аחԁ wіtһ soy intake. ... Previous studies һаνе demonstrated tһаt tһіѕ diet perturbs DNA methylation bу causing a profound loss οf global cytosine methylation, predominantly аt heavily methylated repetitive sequences. [more...]

Date: 2010-10-13 16:46:26

Blood -- Genomewide DNA methylation analysis reveals novel targets ...

Treatment of MCL cell lines with the DNA methyltransferase inhibitor decitabine resulted in reversal of aberrant hypermethylation and synergized with the histone deacetylase inhibitor suberoylanilide hydroxamic acid in induction of the [more...]

Date: 2010-08-19 16:02:55

Epigenetics Papers: DNA Methylation Analysis by MethyLight Technology

Authors discussed each step for this procedure: (1) determining the site of interest for methylation analysis; (2) methylation-specific primers and fluorogenic probes design; (3) genomic DNA isolation; (4) bisulfite conversion; (5) real- time methylation analysis; and (6) data processing. For primer design, some complications particular to the bisulfite modification should be taken into account: All unmethylated cytosine residues in the genome are converted this reduction in genomic complexity reduces the annealing specificity of PCR primers and fluorogenic probes, which not only [more...]

Date: 2007-08-19 01:26:00

Epigenetics & Chromatin | Full text | Extensive sequence ...

© 2010 Hellman and Chess; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. AbstractBackground Epigenetic polymorphisms are a potential source of human diversity, but their frequency and relationship to genetic polymorphisms are unclear. DNA methylation, an epigenetic mark that is a covalent modification of the DNA itself, plays an important [more...]

Date: 2010-05-24 00:00:00

Increase Height with DNA Methylation

Knee joints of male BALB/c mice aged 8 weeks were dissected and subjected to immunohistochemical analysis using anti-RANKL, Runx2, Dlx5 and Msx2 antibodies. The methylation status of the mouse RANKL gene promoter in both the GP and the AC was analyzed by sodium bisulfite mapping using microdissected mouse tissue. The expression of BMP-2, -3, -4, -6 and type X collagen mRNA was examined by in situ hybridization (ISH). At the boundary between the calcifying cartilage and the hypertrophic chondrocytes of the GP, RANKL-expressing chondrocytes overlapped those expressing Runx2, Dlx5 and Msx2, near [more...]

Date: 2010-09-22 20:44:00

Familial Cancer Associated with a Polymorphism in ARLTS1 — NEJM

George Adrian Calin, M.D., Ph.D., Francesco Trapasso, M.D., Ph.D., Masayoshi Shimizu, B.S., Calin Dan Dumitru, M.D., Ph.D., Sai Yendamuri, M.D., Andrew K. Godwin, Ph.D., Manuela Ferracin, Ph.D., Guido Bernardi, Ph.D., Devjani Chatterjee, Ph.D., Gustavo Baldassarre, M.D., Shashi Rattan, B.S., Hansjuerg Alder, Ph.D., Hideaki Mabuchi, M.D., Takeshi Shiraishi, M.D., Lise Lotte Hansen, Ph.D., Jens Overgaard, M.D., D.M.Sc., Vlad Herlea, M.D., Francesca Romana Mauro, M.D., Guillaume Dighiero, M.D., Benjamin Movsas, M.D., Laura Rassenti, Ph.D., Thomas Kipps, M.D., Ph.D., Raffaele Baffa, M.D., Ph.D., [more...]

Date: 2009-06-01 21:13:36

Predictors of global methylation levels in blood DNA of healthy ...

Background Estimates of global DNA methylation from repetitive DNA elements, such as Alu and LINE-1, have been increasingly used in epidemiological investigations because of their relative low-cost, high-throughput and quantitative results. Nevertheless, determinants of these methylation measures in healthy individuals are still largely unknown. The aim of this study was to examine whether age, gender, smoking habits, alcohol drinking and body mass index (BMI) are associated with Alu or LINE-1 methylation levels in blood leucocyte DNA of healthy individuals. Methods Individual data from five [more...]

Date: 2010-09-16 05:22:51

Genes | Free Full-Text | The Application of Next Generation ...

Recently various high-throughput approaches based on bisulfite conversion combined with next generation sequencing have been developed and applied for the genome wide analysis of DNA methylation. These methods provide single base pair resolution, quantitative DNA methylation data with genome wide coverage. We review these methods here and discuss some technical points of special interest like the sequence depth necessary to reach conclusions, the identification of clonal DNA amplification after bisulfite conversion and the detection of non-CpG methylation. Future application of these methods [more...]

Date: 2010-06-04 07:00:00

DNA methylation analysis of multiple tissues from newborn twins ...

DNA methylation analysis of multiple tissues from newborn twins reveals both genetic and intrauterine components to variation in the human neonatal epigenome Miina Ollikainen1,3, Katherine R. Smith2, Eric Ji-Hoon Joo1,3, Hong Kiat Ng1,3, Roberta Andronikos1,3, Boris Novakovic1,3, Nur Khairunnisa Abdul Aziz1,3, John B. Carlin2,3, Ruth Morley1,3, Richard Saffery1,3,*† and Jeffrey M. Craig1,3,† 1Developmental Epigenetics and 2Clinical Epidemiology and Biostatistics Unit, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia [more...]

Date: 2010-08-24 16:08:26

Epigenetic regulation of CpG promoter methylation in invasive ...

Epigenetic modifications, specifically DNA methylation, are key events regulating the process of normal human development. To determine the specific methylation pattern in these invasive prostate cells, and if any developmental genes were being differentially regulated, we analyzed differences in global CpG promoter methylation. Results: Differentially methylated genes were determined and select genes were chosen for additional analyses. The non-receptor tyrosine kinase BMX and transcription factor SOX1 were found to play a significant role in invasion. Ingenuity pathway analysis revealed the [more...]

Date: 2010-10-07 00:00:00

DNA Methylation Analysis Determines the High Frequency of Genic ...

We conducted a study to assess differential CpG methylation at 1,500 genic loci during MM progression and profiled CD138+ plasma cells from MGUS, SMM, and MM specimens; human myeloma cell lines; and normal plasma cell (NPC) samples. We showed that the number of differentially methylated loci (DML) increased with tumor grade, and the vast majority were due to hypomethylation. Hierarchical clustering analysis revealed samples that coclustered tightly with NPC. These cases, referred to as “normal-like,” contained significantly fewer DML when compared with their non–normal-like counterparts [more...]

Date: 2010-09-01 04:07:46

Epigenetic Transgenerational Actions of Vinclozolin on Promoter ...

A methylated DNA immunoprecipitation with methyl-cytosine antibody followed by a promoter tilling microarray (MeDIP-Chip) procedure was used to identify 52 different regions with statistically significant altered methylation in the sperm promoter epigenome. Mass spectrometry bisulfite analysis was used to map the CpG DNA methylation and 16 differential DNA methylation regions were confirmed, while the remainder could not be analyzed due to bisulfite technical limitations. Analysis of these validated regions identified a consensus DNA sequence (motif) that associated with 75% of the promoters. [more...]

Date: 2010-10-02 03:04:02

see the world from science lens: Nature Biotechnology Contents ...

Genetic testing for rare heart conditions might someday expand to more common cardiac ailments. Already there are signs testing is dramatically changing how some conditions are treated and doctors' definition of who a patient is. .... Methods for profiling DNA methylation differ in the physical principles used to detect modified cytosines. Harris et al. compare the performances of four sequencing-based technologies for genome-wide analysis of DNA methylation and combine [more...]

Date: 2010-10-13 19:53:00

Methylation Test May Aid Colon Cancer Diagnosis (CME/CE) | Discuss ...

To develop a more sensitive test for DNA methylation, investigators employed a form of technology known as BEAMing (beads, emulsion, amplification, and magnetics). They performed PCR amplification of individual DNA fragments covalently linked to magnetic beads suspended in water-based nanoparticles immersed in oil droplets. The beads contained a DNA sequence specific for exon 1 of the vimentin gene, which is hypermethylated in colon cancer. Following PCR amplification, the beads were hybridized by means of fluorescent probes specific to the state of methylation and then sorted and analyzed by [more...]

Date: 2010-10-09 11:00:27

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