LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis

Maia H. Malonzo*, Viivi Halla-aho, Mikko Konki, Riikka J. Lund, Harri Lähdesmäki

*Tämän työn vastaava kirjoittaja

Tutkimustuotos: LehtiartikkeliArticleScientificvertaisarvioitu

67 Lataukset (Pure)

Abstrakti

Background: DNA methylation is commonly measured using bisulfite sequencing (BS-seq). The quality of a BS-seq library is measured by its bisulfite conversion efficiency. Libraries with low conversion rates are typically excluded from analysis resulting in reduced coverage and increased costs. Results: We have developed a probabilistic method and software, LuxRep, that implements a general linear model and simultaneously accounts for technical replicates (libraries from the same biological sample) from different bisulfite-converted DNA libraries. Using simulations and actual DNA methylation data, we show that including technical replicates with low bisulfite conversion rates generates more accurate estimates of methylation levels and differentially methylated sites. Moreover, using variational inference speeds up computation time necessary for whole genome analysis. Conclusions: In this work we show that taking into account technical replicates (i.e. libraries) of BS-seq data of varying bisulfite conversion rates, with their corresponding experimental parameters, improves methylation level estimation and differential methylation detection.

AlkuperäiskieliEnglanti
Artikkeli41
Sivut1-19
Sivumäärä19
JulkaisuBMC Bioinformatics
Vuosikerta23
Numero1
DOI - pysyväislinkit
TilaJulkaistu - jouluk. 2022
OKM-julkaisutyyppiA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä

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