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Title: | A varying-coefficient model for the analysis of methylation sequencing data | Authors: | GORCZAK, Katarzyna BURZYKOWSKI, Tomasz CLAESEN, Jurgen |
Issue Date: | 2024 | Publisher: | ELSEVIER SCI LTD | Source: | COMPUTATIONAL BIOLOGY AND CHEMISTRY, 111 (Art N° 108094) | Abstract: | DNA methylation is an important epigenetic modification involved in gene regulation. Advances in the next generation sequencing technology have enabled the retrieval of DNA methylation information at single -base -resolution. However, due to the sequencing process and the limited amount of isolated DNA, DNAmethylation-data are often noisy and sparse, which complicates the identification of differentially methylated regions (DMRs), especially when few replicates are available. We present a varying -coefficient model for detecting DMRs by using single -base -resolved methylation information. The model simultaneously smooths the methylation profiles and allows detection of DMRs, while accounting for additional covariates. The proposed model takes into account possible overdispersion by using a beta -binomial distribution. The overdispersion itself can be modeled as a function of the genomic region and explanatory variables. We illustrate the properties of the proposed model by applying it to two real -life case studies. | Notes: | Claesen, J (corresponding author), Amsterdam UMC, Dept Epidemiol & Data Sci, VU Amsterdam, Postcode 1089, NL-1081 HV Amsterdam, Netherlands. j.claesen@amsterdamumc.nl |
Keywords: | Methylation sequencing;CpG site;Differentially methylated regions;Beta-binomial model;Varying-coefficient model;Smoothing splines | Document URI: | http://hdl.handle.net/1942/43313 | ISSN: | 1476-9271 | e-ISSN: | 1476-928X | DOI: | 10.1016/j.compbiolchem.2024.108094 | ISI #: | 001244301000001 | Rights: | 2024 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). | Category: | A1 | Type: | Journal Contribution |
Appears in Collections: | Research publications |
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A varying-coefficient model for the analysis of methylation sequencing data.pdf | Published version | 3.3 MB | Adobe PDF | View/Open |
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