Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models

• Main Authors: Hocking, T.D (Author), Liehrmann, A. (Author), Rigaill, G. (Author)
• Format: Article
• Language: English
• Published: BioMed Central Ltd 2021
• Subjects: algorithm; Algorithms; Change point detection; ChIP-seq; chromatin immunoprecipitation; Chromatin immunoprecipitation; Chromatin Immunoprecipitation; Chromatin Immunoprecipitation Sequencing; DNA sequence; Gene expression; high throughput sequencing; High-Throughput Nucleotide Sequencing; High-throughput sequencing; Histone modification; Histone modifications; Likelihood inference; Multiple changepoint detection; Over-dispersion; Peak calling; Penalty parameters; Poisson distribution; Segmentation models; Sequence Analysis, DNA; Statistical algorithm; Supervised learning; Supervised segmentation
• Online Access: View Fulltext in Publisher

 Background: Histone modification constitutes a basic mechanism for the genetic regulation of gene expression. In early 2000s, a powerful technique has emerged that couples chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq). This technique provides a direct survey of the DNA regions associated to these modifications. In order to realize the full potential of this technique, increasingly sophisticated statistical algorithms have been developed or adapted to analyze the massive amount of data it generates. Many of these algorithms were built around natural assumptions such as the Poisson distribution to model the noise in the count data. In this work we start from these natural assumptions and show that it is possible to improve upon them. Results: Our comparisons on seven reference datasets of histone modifications (H3K36me3 & H3K4me3) suggest that natural assumptions are not always realistic under application conditions. We show that the unconstrained multiple changepoint detection model with alternative noise assumptions and supervised learning of the penalty parameter reduces the over-dispersion exhibited by count data. These models, implemented in the R package CROCS (https://github.com/aLiehrmann/CROCS), detect the peaks more accurately than algorithms which rely on natural assumptions. Conclusion: The segmentation models we propose can benefit researchers in the field of epigenetics by providing new high-quality peak prediction tracks for H3K36me3 and H3K4me3 histone modifications. © 2021, The Author(s).