title: Detection of significantly differentially methylated regions in targeted bisulfite sequencing data.
abstract: BACKGROUND
  Bisulfite sequencing is currently the gold standard to obtain genome-wide DNA methylation profiles in eukaryotes. In contrast to the rapid development of appropriate pre-processing and alignment software, methods for analyzing the resulting methylation profiles are relatively limited so far. For instance, an appropriate pipeline to detect DNA methylation differences between cancer and control samples is still required.
  
  
  RESULTS
  We propose an algorithm that detects significantly differentially methylated regions in data obtained by targeted bisulfite sequencing approaches, such as reduced representation bisulfite sequencing. In a first step, this approach tests all target regions for methylation differences by taking spatial dependence into account. A false discovery rate procedure controls the expected proportion of incorrectly rejected regions. In a second step, the significant target regions are trimmed to the actually differentially methylated regions. This hierarchical procedure detects differentially methylated regions with increased power compared with existing methods.
  
  
  BACKGROUND
  R/Bioconductor package BiSeq.
  
  
  BACKGROUND
  Supplementary Data are available at Bioinformatics online.
authors: Institute of Medical Informatics, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany. katja.hebestreit@uni-muenster.de
authors: Katja
authors: K
authors: Hebestreit
authors: Martin
authors: M
authors: Dugas
authors: Hans-Ulrich
authors: HU
authors: Klein
mesh_terms: D000465:Algorithms; D018899:CpG Islands; D019175:DNA Methylation; D015894:Genome, Human; D006801:Humans; D015473:Leukemia, Promyelocytic, Acute / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D013447:Sulfites
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite