scholarly journals A robust and simple-to-design multiplex DNA methylation assay based on MS-MLPA-CE-SSCP

The Analyst ◽  
2013 ◽  
Vol 138 (22) ◽  
pp. 6969 ◽  
Author(s):  
Jeongkyeong Na ◽  
Gi Won Shin ◽  
Gyu Yong Jung ◽  
Gyoo Yeol Jung
Keyword(s):  
Dna Methylation ◽  
Methylation Assay

scholarly journals MBRS-47. RAPID MOLECULAR SUBGROUPING OF MEDULLOBLASTOMA BASED ON DNA METHYLATION BY NANOPORE SEQUENCING

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii406-iii406
Author(s):  
Julien Masliah-Planchon ◽  
Elodie Girard ◽  
Philipp Euskirchen ◽  
Christine Bourneix ◽  
Delphine Lequin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Molecule ◽  
Nanopore Sequencing ◽  
Molecular Subgroup ◽  
Group Assignment ◽  
Group 4 ◽  
Methylation Assay ◽  
Tumor Group ◽  
Long Read ◽  
Group 3

Abstract Medulloblastoma (MB) can be classified into four molecular subgroups (WNT group, SHH group, group 3, and group 4). The gold standard of assignment of molecular subgroup through DNA methylation profiling uses Illumina EPIC array. However, this tool has some limitation in terms of cost and timing, in order to get the results soon enough for clinical use. We present an alternative DNA methylation assay based on nanopore sequencing efficient for rapid, cheaper, and reliable subgrouping of clinical MB samples. Low-depth whole genome with long-read single-molecule nanopore sequencing was used to simultaneously assess copy number profile and MB subgrouping based on DNA methylation. The DNA methylation data generated by Nanopore sequencing were compared to a publicly available reference cohort comprising over 2,800 brain tumors including the four subgroups of MB (Capper et al. Nature; 2018) to generate a score that estimates a confidence with a tumor group assignment. Among the 24 MB analyzed with nanopore sequencing (six WNT, nine SHH, five group 3, and four group 4), all of them were classified in the appropriate subgroup established by expression-based Nanostring subgrouping. In addition to the subgrouping, we also examine the genomic profile. Furthermore, all previously identified clinically relevant genomic rearrangements (mostly MYC and MYCN amplifications) were also detected with our assay. In conclusion, we are confirming the full reliability of nanopore sequencing as a novel rapid and cheap assay for methylation-based MB subgrouping. We now plan to implement this technology to other embryonal tumors of the central nervous system.

scholarly journals A urine-based DNA methylation assay to facilitate early detection and risk stratification of bladder cancer

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Weimei Ruan ◽  
Xu Chen ◽  
Ming Huang ◽  
Hong Wang ◽  
Jiaxin Chen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bladder Cancer ◽  
Risk Stratification ◽  
Early Stage ◽  
Operative Risk ◽  
Low Grade ◽  
Single Center ◽  
Detection Model ◽  
Methylation Assay ◽  
Muscle Invasive

Abstract Background Current non-invasive tests have limited sensitivities and lack capabilities of pre-operative risk stratification for bladder cancer (BC) diagnosis. We aimed to develop and validate a urine-based DNA methylation assay as a clinically feasible test for improving BC detection and enabling pre-operative risk stratifications. Methods A urine-based DNA methylation assay was developed and validated by retrospective single-center studies in patients of suspected BC in Cohort 1 (n = 192) and Cohort 2 (n = 98), respectively. In addition, a prospective single-center study in hematuria patient group (Cohort 3, n = 174) was used as a second validation of the model. Results The assay with a dual-marker detection model showed 88.1% and 91.2% sensitivities, 89.7% and 85.7% specificities in validation Cohort 2 (patients of suspected BC) and Cohort 3 (patients of hematuria), respectively. Furthermore, this assay showed improved sensitivities over cytology and FISH on detecting low-grade tumor (66.7–77.8% vs. 0.0–22.2%, 0.0–22.2%), Ta tumor (83.3% vs. 22.2–41.2%, 44.4–52.9%) and non-muscle invasive BC (NMIBC) (80.0–89.7% vs. 51.5–52.0%, 59.4–72.0%) in both cohorts. The assay also had higher accuracies (88.9–95.8%) in diagnosing cases with concurrent genitourinary disorders as compared to cytology (55.6–70.8%) and FISH (72.2–77.8%). Meanwhile, the assay with a five-marker stratification model identified high-risk NMIBC and muscle invasive BC with 90.5% sensitivity and 86.8% specificity in Cohort 2. Conclusions The urine-based DNA methylation assay represents a highly sensitive and specific approach for BC early-stage detection and risk stratification. It has a potential to be used as a routine test to improve diagnosis and prognosis of BC in clinic.

scholarly journals Liquid Biopsy Test Based on a Sensitive DNA Methylation Assay for Diagnosing Hepatocellular Carcinoma：Which Is a Better Marker, Methylated SST Or SEPT9?

2021 ◽  
Vol 70 (3) ◽  
pp. 89-98
Author(s):  
Ayano YAMASAKI ◽  
Yutaka SUEHIRO ◽  
Tomomi HOSHIDA ◽  
Issei SAEKI ◽  
Yurika YAMAUCHI（KOTOH） ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Liquid Biopsy ◽  
Methylation Assay

scholarly journals Label-Free DNA Biosensor Using Modified Reduced Graphene Oxide Platform as a DNA Methylation Assay

Materials ◽  
2020 ◽  
Vol 13 (21) ◽  
pp. 4936 ◽  
Author(s):  
Eliska Sedlackova ◽  
Zuzana Bytesnikova ◽  
Eliska Birgusova ◽  
Pavel Svec ◽  
Amir M. Ashrafi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Graphene Oxide ◽  
Reduced Graphene Oxide ◽  
Limit Of Detection ◽  
Differential Pulse ◽  
Clinical Diagnostics ◽  
Label Free ◽  
Free Dna ◽  
Methylation Assay ◽  
Reduced Graphene

This work reports the use of modified reduced graphene oxide (rGO) as a platform for a label-free DNA-based electrochemical biosensor as a possible diagnostic tool for a DNA methylation assay. The biosensor sensitivity was enhanced by variously modified rGO. The rGO decorated with three nanoparticles (NPs)—gold (AuNPs), silver (AgNPs), and copper (CuNPs)—was implemented to increase the electrode surface area. Subsequently, the thiolated DNA probe (single-stranded DNA, ssDNA−1) was hybridized with the target DNA sequence (ssDNA-2). After the hybridization, the double-stranded DNA (dsDNA) was methylated by M.SssI methyltransferase (MTase) and then digested via a HpaII endonuclease specific site sequence of CpG (5′-CCGG-3′) islands. For monitoring the MTase activity, differential pulse voltammetry (DPV) was used, whereas the best results were obtained by rGO-AuNPs. This assay is rapid, cost-effective, sensitive, selective, highly specific, and displays a low limit of detection (LOD) of 0.06 U·mL−1. Lastly, this study was enriched with the real serum sample, where a 0.19 U·mL−1 LOD was achieved. Moreover, the developed biosensor offers excellent potential in future applications in clinical diagnostics, as this approach can be used in the design of other biosensors.

scholarly journals DNA methylation assay for colorectal carcinoma

2017 ◽  
Vol 14 (1) ◽  
pp. 42-49 ◽  
Author(s):  
Chen Ji-Jun ◽  
Chen Ji-Jun ◽  
Wang Ai-Qin ◽  
Chen Qing-Qi ◽  
Wang Ai-Qin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Colorectal Carcinoma ◽  
Methylation Assay

A DNA methylation assay for detection of ovarian cancer cells using a HpaII/MspI digestion-based PCR assay in an integrated microfluidic system

2013 ◽  
Vol 15 (5) ◽  
pp. 575-585 ◽  
Author(s):  
Chih-Hung Wang ◽  
Hsien-Chih Lai ◽  
Tong-Miin Liou ◽  
Keng-Fu Hsu ◽  
Cheng-Yang Chou ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Dna Methylation ◽  
Cancer Cells ◽  
Microfluidic System ◽  
Ovarian Cancer Cells ◽  
Pcr Assay ◽  
Methylation Assay
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