Analysis of Genome-Wide DNA Methylation Profiles by BeadChip Technology
This chapter covers the genome-wide DNA methylation analysis using microarray platforms, such as Illumina Infinium HumanMethylation27 BeadChips or HumanMethylation450 BeadChips. Using our previously published ovarian cancer dataset (Bauerschlag et al., Oncology 80:12–20, 2011), we introduce the underlying design principles of these methylation array platforms and describe common yet effective bioinformatic strategies for data analysis, including data preprocessing, clustering methods, and differential methylation tests. We also describe the downstream analytic techniques for the results derived from the methylation array, i.e., gene set enrichment analysis and sequence-based motif analysis, which can be utilized for generating biological hypotheses.
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Panhandle PCR Approaches to Cloning MLL Genomic Breakpoint Junctions and Fusion Transcript Sequences
Translocations and other rearrangements of the MLL gene at c...
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DNA Methylation in Pancreatic Cancer: Protocols for the Isolation of DNA and Bisulfite Modification
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tum...