MethBLAST and MethPrimerDB: Web-tools for PCR Based Methylation Analysis

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2006 Nov 11

PMID 17094804

Citations 13

Authors

Filip Pattyn

Jasmien Hoebeeck

Piet Robbrecht

Evi Michels

Anne De Paepe

Guy Bottu

David Coornaert

Robert Herzog

Frank Speleman

Jo Vandesompele

Affiliations

Soon will be listed here.

Abstract

Background: DNA methylation plays an important role in development and tumorigenesis by epigenetic modification and silencing of critical genes. The development of PCR-based methylation assays on bisulphite modified DNA heralded a breakthrough in speed and sensitivity for gene methylation analysis. Despite this technological advancement, these approaches require a cumbersome gene by gene primer design and experimental validation. Bisulphite DNA modification results in sequence alterations (all unmethylated cytosines are converted into uracils) and a general sequence complexity reduction as cytosines become underrepresented. Consequently, standard BLAST sequence homology searches cannot be applied to search for specific methylation primers.

Results: To address this problem we developed methBLAST, a sequence similarity search program, based on the original BLAST algorithm but querying in silico bisulphite modified genome sequences to evaluate oligonucleotide sequence similarities. Apart from the primer specificity analysis tool, we have also developed a public database termed methPrimerDB for the storage and retrieval of validated PCR based methylation assays. The web interface allows free public access to perform methBLAST searches or database queries and to submit user based information. Database records can be searched by gene symbol, nucleotide sequence, analytical method used, Entrez Gene or methPrimerDB identifier, and submitter's name. Each record contains a link to Entrez Gene and PubMed to retrieve additional information on the gene, its genomic context and the article in which the methylation assay was described. To assure and maintain data integrity and accuracy, the database is linked to other reference databases. Currently, the database contains primer records for the most popular PCR-based methylation analysis methods to study human, mouse and rat epigenetic modifications. methPrimerDB and methBLAST are available at http://medgen.ugent.be/methprimerdb and http://medgen.ugent.be/methblast.

Conclusion: We have developed two integrated and freely available web-tools for PCR based methylation analysis. methBLAST allows in silico assessment of primer specificity in PCR based methylation assays that can be stored in the methPrimerDB database, which provides a search portal for validated methylation assays.

Citing Articles

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PMID: 37828369 DOI: 10.1007/s15010-023-02100-0.

AmpliconDesign - an interactive web server for the design of high-throughput targeted DNA methylation assays.

Schonung M, Hess J, Bawidamann P, Stable S, Hey J, Langstein J Epigenetics. 2020; 16(9):933-939.

PMID: 33100132 PMC: 8451469. DOI: 10.1080/15592294.2020.1834921.

Loss of mismatch repair signaling impairs the WNT-bone morphogenetic protein crosstalk and the colonic homeostasis.

Norgaard K, Muller C, Christensen N, Chiloeches M, Madsen C, Nielsen S J Mol Cell Biol. 2019; 12(6):410-423.

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Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy.

Cruickshank M, Oshlack A, Theda C, Davis P, Martino D, Sheehan P Genome Med. 2013; 5(10):96.

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Aberrant DNA methylation and prostate cancer.

Majumdar S, Buckles E, Estrada J, Koochekpour S Curr Genomics. 2012; 12(7):486-505.

PMID: 22547956 PMC: 3219844. DOI: 10.2174/138920211797904061.

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