LoMA-B: a simple and versatile lab-on-a-chip system based on single-channel bisulfite conversion for DNA methylation analysis

Lab on a Chip ◽  
2015 ◽  
Vol 15 (17) ◽  
pp. 3530-3539 ◽  
Author(s):  
Jaeyun Yoon ◽  
Mi Kyoung Park ◽  
Tae Yoon Lee ◽  
Yong-Jin Yoon ◽  
Yong Shin
Keyword(s):  
Dna Methylation ◽  
Single Channel ◽  
Methylation Status ◽  
Lab On A Chip ◽  
Label Free ◽  
Bisulfite Conversion ◽  
Methylation Analysis ◽  
Processing Module ◽  
On Chip ◽  
Dna Methylation Analysis

Here, we present a Lab-on-a-Chip system for DNA Methylation Analysis based on Bisulfite conversion (LoMA-B), which is coupled to a sample pre-processing module for on-chip bisulfite conversion and a label-free, real-time detection module for rapid analysis of DNA methylation status.

scholarly journals Multiplexed DNA Methylation Analysis in Colorectal Cancer Using Liquid Biopsy and Its Diagnostic and Predictive Value

2021 ◽  
Vol 43 (3) ◽  
pp. 1419-1435
Author(s):  
Walter Pulverer ◽  
Kristi Kruusmaa ◽  
Silvia Schönthaler ◽  
Jasmin Huber ◽  
Marko Bitenc ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Dna Methylation ◽  
Therapy Monitoring ◽  
Methylation Status ◽  
Methylation Analysis ◽  
Microarray Experiments ◽  
Specific Pcr ◽  
Colonic Adenomas ◽  
Methylation Sensitive Restriction Enzyme ◽  
Dna Methylation Analysis

Early diagnosis of colorectal cancer (CRC) is of high importance as prognosis depends on tumour stage at the time of diagnosis. Detection of tumour-specific DNA methylation marks in cfDNA has several advantages over other approaches and has great potential for solving diagnostic needs. We report here the identification of DNA methylation biomarkers for CRC and give insights in our methylation-sensitive restriction enzyme coupled qPCR (MSRE-qPCR) system. Targeted microarrays were used to investigate the DNA methylation status of 360 cancer-associated genes. Validation was done by qPCR-based approaches. A focus was on investigating marker performance in cfDNA from 88 patients (44 CRC, 44 controls). Finally, the workflow was scaled-up to perform 180plex analysis on 110 cfDNA samples, to identify a DNA methylation signature for advanced colonic adenomas (AA). A DNA methylation signature (n = 44) was deduced from microarray experiments and confirmed by quantitative methylation-specific PCR (qMSP) and by MSRE-qPCR, providing for six genes’ single areas under the curve (AUC) values of >0.85 (WT1, PENK, SPARC, GDNF, TMEFF2, DCC). A subset of the signatures can be used for patient stratification and therapy monitoring for progressed CRC with liver metastasis using cfDNA. Furthermore, we identified a 35-plex classifier for the identification of AAs with an AUC of 0.80.

Reproducibility-optimized detection of differential DNA methylation

Epigenomics ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 747-755
Author(s):  
Veronika Suni ◽  
Fatemeh Seyednasrollah ◽  
Bishwa Ghimire ◽  
Sini Junttila ◽  
Asta Laiho ◽  
...  
Keyword(s):  
Dna Methylation ◽  
High Throughput Sequencing ◽  
State Of The Art ◽  
Methylation Status ◽  
Real Data ◽  
Epigenetic Mechanism ◽  
Methylation Analysis ◽  
Test Statistic ◽  
Differentially Methylated Regions ◽  
Dna Methylation Analysis

Aim: DNA methylation is a key epigenetic mechanism regulating gene expression. Identifying differentially methylated regions is integral to DNA methylation analysis and there is a need for robust tools reliably detecting regions with significant differences in their methylation status. Materials & methods: We present here a reproducibility-optimized test statistic (ROTS) for detection of differential DNA methylation from high-throughput sequencing or array-based data. Results: Using both simulated and real data, we demonstrate the ability of ROTS to identify differential methylation between sample groups. Conclusion: Compared with state-of-the-art methods, ROTS shows competitive sensitivity and specificity in detecting consistently differentially methylated regions.

scholarly journals On-Chip DNA Methylation Analysis Using Osmium Complexation

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Kaori Sugizaki ◽  
Tadashi Umemoto ◽  
Akimitsu Okamoto
Keyword(s):  
Dna Methylation ◽  
Research Subject ◽  
Methylation Analysis ◽  
Methylated Dna ◽  
Chemical Assay ◽  
Challenging Research ◽  
Detection Probe ◽  
On Chip ◽  
Dna Strand ◽  
Dna Methylation Analysis

The development of a reaction for detecting the presence/absence of one methyl group in a long DNA strand is a chemically and biologically challenging research subject. A newly designed chemical assay on a chip for the typing of DNA methylation has been developed. A methylation-detection probe fixed at the bottom of microwells was crosslinked with methylated DNA mediated by osmium complexation and contributes to selective amplification of methylated DNA.

DNA Methylation Analysis by Bisulfite Conversion, Cloning, and Sequencing of Individual Clones

2009 ◽  
pp. 177-187 ◽  
Author(s):  
Yingying Zhang ◽  
Christian Rohde ◽  
Sascha Tierling ◽  
Heinrich Stamerjohanns ◽  
Richard Reinhardt ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Conversion ◽  
Methylation Analysis ◽  
Cloning And Sequencing ◽  
Dna Methylation Analysis

Label-free DNA methylation analysis using opto-fluidic ring resonators

2010 ◽  
Vol 26 (3) ◽  
pp. 1016-1020 ◽  
Author(s):  
Jonathan D. Suter ◽  
Daniel J. Howard ◽  
Huidong Shi ◽  
Charles W. Caldwell ◽  
Xudong Fan
Keyword(s):  
Dna Methylation ◽  
Ring Resonators ◽  
Label Free ◽  
Methylation Analysis ◽  
Free Dna ◽  
Dna Methylation Analysis

scholarly journals Genome-wide DNA methylation analysis pre- and post-lenalidomide treatment in patients with myelodysplastic syndrome with isolated deletion (5q)

2021 ◽  
Author(s):  
Anna Hecht ◽  
Julia A. Meyer ◽  
Johann-Christoph Jann ◽  
Katja Sockel ◽  
Aristoteles Giagounidis ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Myelodysplastic Syndrome ◽  
Target Genes ◽  
Methylation Status ◽  
Response To Treatment ◽  
Methylation Analysis ◽  
Relevant Effect ◽  
Genome Wide ◽  
Methylation Patterns ◽  
Dna Methylation Analysis

AbstractMyelodysplastic syndrome (MDS) with isolated deletion of chromosome 5q (MDS del5q) is a distinct subtype of MDS with quite favorable prognosis and excellent response to treatment with lenalidomide. Still, a relevant percentage of patients do not respond to lenalidomide and even experience progression to acute myeloid leukemia (AML). In this study, we aimed to investigate whether global DNA methylation patterns could predict response to lenalidomide. Genome-wide DNA methylation analysis using Illumina 450k methylation arrays was performed on n=51 patients with MDS del5q who were uniformly treated with lenalidomide in a prospective multicenter trial of the German MDS study group. To study potential direct effects of lenalidomide on DNA methylation, 17 paired samples pre- and post-treatment were analyzed. Our results revealed no relevant effect of lenalidomide on methylation status. Furthermore, methylation patterns prior to therapy could not predict lenalidomide response. However, methylation clustering identified a group of patients with a trend towards inferior overall survival. These patients showed hypermethylation of several interesting target genes, including genes of relevant signaling pathways, potentially indicating the evaluation of novel therapeutic targets.

scholarly journals Quantitative DNA Methylation Analysis and Epigenotype-Phenotype Correlations in Taiwanese Patients with Beckwith-Wiedemann Syndrome

2021 ◽  
Vol 11 (11) ◽  
pp. 1066
Author(s):  
Hsiang-Yu Lin ◽  
Chung-Lin Lee ◽  
Sisca Fran ◽  
Ru-Yi Tu ◽  
Ya-Hui Chang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Methylation Level ◽  
Statistical Significance ◽  
Methylation Status ◽  
Diagnostic Testing ◽  
Uniparental Disomy ◽  
Clinical Manifestations ◽  
Z Score ◽  
Methylation Analysis ◽  
Dna Methylation Analysis

Background: Beckwith-Wiedemann syndrome (BWS; OMIM 130650) is a rare overgrowth syndrome with tumor predisposition resulting from the abnormal expression or function of imprinted genes of the chromosome 11p15.5 imprinting gene cluster. The aim of this study was to identify the epigenotype-phenotype correlations of these patients using quantitative DNA methylation analysis. Methods: One hundred and four subjects with clinically suspected BWS were enrolled in this study. All of the subjects had been referred for diagnostic testing which was conducted using methylation profiling of H19-associated imprinting center (IC) 1 and KCNQ1OT1-associated IC2 in high-resolution melting analysis and methylation quantification with the MassARRAY assay. Correlations between the quantitative DNA methylation status and clinical manifestations of the enrolled subjects were analyzed. Results: Among the 104 subjects, 19 had IC2 hypomethylation, 2 had IC1 hypermethylation, and 10 had paternal uniparental disomy (pUPD). The subjects with IC2 hypomethylation were characterized by significantly more macroglossia but less hemihypertrophy compared to the subjects with pUPD (p < 0.05). For 19 subjects with IC2 hypomethylation, the IC2 methylation level was significantly different (p < 0.05) between the subjects with and without features including macroglossia (IC2 methylation level: 11.1% vs 30.0%) and prenatal or postnatal overgrowth (8.5% vs 16.9%). The IC2 methylation level was negatively correlated with birth weight z score (p < 0.01, n = 19) and birth height z score (p < 0.05, n = 13). For 36 subjects with clinically diagnosed BWS, the IC2 methylation level was negatively correlated with the BWS score (r = −0.592, p < 0.01). The IC1 methylation level showed the tendency of positive correlation with the BWS score without statistical significance (r = 0.137, p > 0.05). Conclusions: Lower IC2 methylation and higher IC1 methylation levels were associated with greater disease severity in the subjects with clinically diagnosed BWS. Quantitative DNA methylation analysis using the MassARRAY assay could improve the detection of epigenotype-phenotype correlations, which could further promote better genetic counseling and medical care for these patients.

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