Computational protocol: Aberration in DNA Methylation in B-Cell Lymphomas Has a Complex Origin and Increases with Disease Severity

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Protocol publication

[…] HELP methylation data for CD34+ hematopoietic progenitor cells was obtained from the NCBI Geo database (GSE18700). HELP was performed in the same manner as the normal (NBC and NGC) and lymphoma (FL, GCB and ABC) samples, hybridized on the same methylation microarray and normalized using the same protocol together with the normal and lymphoma samples. Only promoter methylation probes without missing values were considered for further analysis. M-scores were averaged for each group (CD34+, NBC, NGC, FL, GCB and ABC) on each probe. Pairwise distances between groups were then calculated with the Pearson correlation distance on the group-averaged M-scores. This approach was repeated 1000 times, with bootstrapping of promoter methylation probesets and samples. Then, phylogenetic trees were constructed using the FastME method, implemented in the ape R package, on these 1000 distance matrices. A consensus tree was calculated in Dendroscope. The code is available as R package at https://github.com/lima1/maphylogeny. […]

Pipeline specifications

Software tools FastME, Dendroscope
Application Phylogenetics
Organisms Homo sapiens
Diseases Lymphoma, Neoplasms, Lymphoma, B-Cell, Cardiovascular Abnormalities
Chemicals Cytosine