Genome-scale DNA methylation mapping of human disease samples at single-basepair resolution

Abstract

Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, thus providing a robust platform for molecular diagnostics. Here, we optimize bisulfite sequencing for genome-scale analysis of human disease samples. Specifically, we outline how restriction digestion can target bisulfite sequencing to hotspots of epigenetic (de-)regulation in the genome; we show that as little as 30ng of DNA are sufficient for genome-scale analysis; we demonstrate that our protocol works well on formalin-fixed, paraffin-embedded (FFPE) samples; and we describe a statistical method for assessing the significance of altered DNA methylation patterns.

Data

Each of the links below opens DNA methylation tracks in the UCSC Genome Browser. "CpG methylation" reports DNA methylation data per CpG, summarizing over all observed reads. "RRBS reads" shows DNA methylation data for each read separately. For more information, please refer to the RRBS browser tracks documentation sheet.

Colon_normal CpG methylation RRBS reads
Colon_tumor CpG methylation RRBS reads
Colon_normal_FFPE CpG methylation RRBS reads
Colon_tumor_FFPE CpG methylation RRBS reads
Blood_healthy_individual CpG methylation RRBS reads
Blood_CRC_patient CpG methylation RRBS reads
Meth_Jurkat_BS14h CpG methylation RRBS reads
Meth_Jurkat_BS2x5h CpG methylation RRBS reads
Meth_Jurkat_BS5h CpG methylation RRBS reads
Demeth_Jurkat_BS14h CpG methylation RRBS reads
Demeth_Jurkat_BS2x5h CpG methylation RRBS reads
Demeth_Jurkat_BS5h CpG methylation RRBS reads
Colon_normal_BS14h CpG methylation RRBS reads
Colon_tumor_BS14h CpG methylation RRBS reads
Mouse_ES_1000ng CpG methylation RRBS reads
Mouse_ES_300ng CpG methylation RRBS reads
Mouse_ES_100ng CpG methylation RRBS reads
Mouse_ES_30ng CpG methylation RRBS reads

Analysis

Software

Epigenome data analysis was performed with the Epigenome Pipeline Package, a software toolkit that has been developed specifically for the purpose of identifying significant epigenetic alterations in disease samples. The source code, documentation and test data are available through the following links:

Citation

Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods, doi:10.1038/nmeth.1414 [evaluated at F1000 Medicine]