879
Views
3
CrossRef citations to date
0
Altmetric
Brief Report

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

ORCID Icon, , , ORCID Icon, ORCID Icon, , ORCID Icon, , & ORCID Icon show all
Pages 933-939 | Received 04 Jun 2020, Accepted 26 Sep 2020, Published online: 24 Oct 2020

References

  • Chang W, Cheng J, Allaire JJ, et al. shiny: web application framework for R. CRAN R Package. 2018.
  • Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002;16:6–21.
  • Jang HS, Shin WJ, Lee JE, et al. CpG and Non-CpG methylation in epigenetic gene regulation and brain function. Genes (Basel). 2017;8:148.
  • Ramsahoye BH, Biniszkiewicz D, Lyko F, et al. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl. Acad. Sci. 2000;97:5237–5242.
  • Capper D, Jones DTW, Sill M, et al. DNA methylation-based classification of central nervous system tumours. Nature. 2018;555:469–474.
  • Lipka DB, Witte T, Toth R, et al. RAS-pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemia. Nat Commun. 2017;8:2126.
  • Oakes CC, Seifert M, Assenov Y, et al. DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nat Genet. 2016;48:253–264.
  • Sahm F, Schrimpf D, Stichel D, et al. DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis. Lancet Oncol. 2017;18:682–694.
  • Sill M, Plass C, Pfister SM, et al. Molecular tumor classification using DNA methylome analysis. Hum Mol Genet. 2020. DOI:https://doi.org/10.1093/hmg/ddaa147
  • Bock C, Halbritter F, Carmona FJ, et al. Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol. 2016;34:726–737.
  • Arányi T, Váradi A, Simon I, et al. The BiSearch web server. BMC Bioinformatics. 2006;7(1):431.
  • Gruntman E, Qi Y, Slotkin RK, et al. Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics. 2008;9:371.
  • Kovacova V, Janousek B. Bisprimer—A program for the design of primers for bisulfite-based genomic sequencing of both plant and mammalian DNA samples. J Hered. 2012;103:308–312.
  • Li L-C, Dahiya R. MethPrimer: designing primers for methylation PCRs. Bioinformatics. 2002;18:1427–1431.
  • Lu J, Johnston A, Berichon P, et al. PrimerSuite: A high-throughput web-based primer design program for multiplex bisulfite PCR. Sci. Rep. 2017;7:41328.
  • Pattyn F, Hoebeeck J, Robbrecht P, et al. methBLAST and methPrimerDB: web-tools for PCR based methylation analysis. BMC Bioinformatics. 2006;7:496.
  • Lefever S, Hoebeeck J, Pattyn F, et al. methGraph: a genome visualization tool for PCR-based methylation assays. Epigenetics. 2010;5:159–163.
  • Thompson RF, Suzuki M, Lau KW, et al. A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Bioinformatics. 2009;25:2164–2170.
  • Hahne F, Ivanek R. Visualizing Genomic Data Using Gviz and Bioconductor. Methods Mol Biol. 2016;1418:335-51.
  • Untergasser A, Cutcutache I, Koressaar T, et al. Primer3—new capabilities and interfaces. Nucleic Acids Research. 2012;40:e115–e115.
  • Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009;10:R25.
  • Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27:1571–1572.
  • Klobučar T, Kreibich E, Krueger F, et al. IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions. Nucleic Acids Res. 2020;48:e92-e92.
  • Zhang P, Boisson B, Stenson PD, et al. SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data. Nucleic Acids Res. 2019;47:W623–W631.
  • Wickham H. ggplot2. New York, NY: Springer New York; 2009.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.