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DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing

Anneleen Decock (UGent) , Maté Ongenaert (UGent) , Wim Van Criekinge (UGent) , Franki Speleman (UGent) and Jo Vandesompele (UGent)
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Abstract
Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB tumors by methyl-CpG-binding domain (MBD) sequencing, in order to identify prognostic biomarker candidates. In this data descriptor, we give details on how this data set was generated and which bioinformatics analyses were applied during data processing. Through a series of technical validations, we illustrate that the data are of high quality and that the sequenced fragments represent methylated genomic regions. Furthermore, genes previously described to be methylated in NB are confirmed. As such, these MBD sequencing data are a valuable resource to further study the association of NB risk factors with the NB methylome, and offer the opportunity to integrate methylome data with other -omic data sets on the same tumor samples such as gene copy number and gene expression, also publically available.
Keywords
DNA methylation, epigenetics, methyl-CpG-binding domain (MBD) sequencing, neuroblastoma, DIFFERENTIAL EXPRESSION ANALYSIS, BIOCONDUCTOR PACKAGE, GENE-EXPRESSION, READ ALIGNMENT, SEQ, REARRANGEMENTS, INSIGHTS, CLUSTER

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Chicago
Decock, Anneleen, Maté Ongenaert, Wim Van Criekinge, Franki Speleman, and Jo Vandesompele. 2016. “DNA Methylation Profiling of Primary Neuroblastoma Tumors Using methyl-CpG-binding Domain Sequencing.” Scientific Data 3.
APA
Decock, A., Ongenaert, M., Van Criekinge, W., Speleman, F., & Vandesompele, J. (2016). DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing. SCIENTIFIC DATA, 3.
Vancouver
1.
Decock A, Ongenaert M, Van Criekinge W, Speleman F, Vandesompele J. DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing. SCIENTIFIC DATA. 2016;3.
MLA
Decock, Anneleen, Maté Ongenaert, Wim Van Criekinge, et al. “DNA Methylation Profiling of Primary Neuroblastoma Tumors Using methyl-CpG-binding Domain Sequencing.” SCIENTIFIC DATA 3 (2016): n. pag. Print.
@article{7165334,
  abstract     = {Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB tumors by methyl-CpG-binding domain (MBD) sequencing, in order to identify prognostic biomarker candidates. In this data descriptor, we give details on how this data set was generated and which bioinformatics analyses were applied during data processing. Through a series of technical validations, we illustrate that the data are of high quality and that the sequenced fragments represent methylated genomic regions. Furthermore, genes previously described to be methylated in NB are confirmed. As such, these MBD sequencing data are a valuable resource to further study the association of NB risk factors with the NB methylome, and offer the opportunity to integrate methylome data with other -omic data sets on the same tumor samples such as gene copy number and gene expression, also publically available.},
  articleno    = {160004},
  author       = {Decock, Anneleen and Ongenaert, Mat{\'e} and Van Criekinge, Wim and Speleman, Franki and Vandesompele, Jo},
  issn         = {2052-4463},
  journal      = {SCIENTIFIC DATA},
  language     = {eng},
  pages        = {11},
  title        = {DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing},
  url          = {http://dx.doi.org/10.1038/sdata.2016.4},
  volume       = {3},
  year         = {2016},
}

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