ArticleScientific reports2017
PrimerSuite: A High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 60 citations in OpenAlex.
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- guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel.BMC genomics · 2024Article
- Multiplexed electrochemical liposomes applied to the detection of nucleic acids for Influenza A, Influenza B and SARS-CoV-2.Analytical and bioanalytical chemistry · 2024Article
- A Rapid and Inexpensive PCR Test for Mastitis Diagnosis Based on NGS Data.Pathogens (Basel, Switzerland) · 2024Article
- MethMarkerDB: a comprehensive cancer DNA methylation biomarker database.Nucleic acids research · 2024Article
- Amplicon-Based Bisulfite Conversion-NGS DNA Methylation Analysis Protocol.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Development of a Multiplex PCR Assay for Efficient Detection of Two Potential Probiotic Strains Using Whole Genome-Based Primers.Microorganisms · 2023Article
- Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast.Genome biology and evolution · 2023Article
- Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation.Scientific reports · 2023Article
- Modelling clinical DNA fragmentation in the development of universal PCR-based assays for bisulfite-converted, formalin-fixed and cell-free DNA sample analysis.Scientific reports · 2022Article
- MS-HRM protocol: a simple and low-cost approach for technical validation of next-generation methylation sequencing data.Molecular genetics and genomics : MGG · 2022Article
- Novel method utilizing bisulfite conversion with dual amplification-refractory mutation system polymerase chain reaction to detect circulating pancreatic β-cell cfDNA.Journal of diabetes investigation · 2022Article
- Technical considerations in PCR-based assay design for diagnostic DNA methylation cancer biomarkers.Clinical epigenetics · 2022Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The analysis of DNA methylation at CpG dinucleotides has become a major research focus due to its regulatory role in numerous biological processes, but the requisite need for assays which amplify bisulfite-converted DNA represents a major bottleneck due to the unique design constraints imposed on bisulfite-PCR primers. Moreover, a review of the literature indicated no available software solutions which accommodated both high-throughput primer design, support for multiplex amplification assays, and primer-dimer prediction. In response, the tri-modular software package PrimerSuite was developed to support bisulfite multiplex PCR applications. This software was constructed to (i) design bisulfite primers against multiple regions simultaneously (PrimerSuite), (ii) screen for primer-primer dimerizing artefacts (PrimerDimer), and (iii) support multiplex PCR assays (PrimerPlex). Moreover, a major focus in the development of this software package was the emphasis on extensive empirical validation, and over 1300 unique primer pairs have been successfully designed and screened, with over 94% of them producing amplicons of the expected size, and an average mapping efficiency of 93% when screened using bisulfite multiplex resequencing. The potential use of the software in other bisulfite-based applications such as methylation-specific PCR is under consideration for future updates. This resource is freely available for use at PrimerSuite website (www.primer-suite.com).
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