A varying-coefficient model for the analysis of methylation sequencing data.
Comput Biol Chem
; 111: 108094, 2024 Aug.
Article
in En
| MEDLINE
| ID: mdl-38781748
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, DNA-methylation-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.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Sequence Analysis, DNA
/
DNA Methylation
Limits:
Humans
Language:
En
Journal:
Comput Biol Chem
Journal subject:
BIOLOGIA
/
INFORMATICA MEDICA
/
QUIMICA
Year:
2024
Document type:
Article
Affiliation country:
Bélgica
Country of publication:
Reino Unido