Computational protocol: Detection of prognostic methylation markers by methylC-capture sequencing in acute myeloid leukemia

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Protocol publication

[…] The glossaries used in this study are summarized in . Raw sequence reads were filtered to remove adapter contamination and poor-quality reads. Clean sequences were first mapped to the human genome (build GRCh37) by using Bismark (v0.10.1; parameters: –pe, –bowtie2, –directional, –unmapped). Methylation calls were extracted after duplicate sequences had been excluded. DMRs were analyzed in R 3.1.0 by using the methylKit package. The minimum read coverage to call a methylation status for a base was set to 5. All off-target reads were removed. The methylation level at each site was determined by dividing the number of reads supporting methylation for that site by the total number of reads covering that site. CpGs were included in subsequent analyses if the number of sequence reads was 5 or greater. Data visualization and analysis were performed using Integrative Genomics Viewer, custom R, and Perl scripts (Supplementary Materials).To ensure the reliability of the sequencing results without bias, both the technicians and bioinformatics analyst were blinded to the clinical information of the samples. […]

Pipeline specifications

Software tools Bismark, Bowtie2, methylKit, IGV
Application BS-seq analysis
Organisms Homo sapiens
Diseases Neoplasms, Leukemia, Myeloid, Acute