MOTIVATION: The recently released Infinium HumanMethylation450 array (the '450k' array) provides a high-throughput assay to quantify DNA methylation (DNAm) at ∼450 000 loci across a range of genomic features. Although less comprehensive than high-throughput sequencing-based techniques, this product is more cost-effective and promises to be the most widely used DNAm high-throughput measurement technology over the next several years. RESULTS: Here we describe a suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. The software is structured to easily adapt to future versions of the technology. We include methods for preprocessing, quality assessment and detection of differentially methylated regions from the kilobase to the megabase scale. We show how our software provides a powerful and flexible development platform for future methods. We also illustrate how our methods empower the technology to make discoveries previously thought to be possible only with sequencing-based methods. AVAILABILITY AND IMPLEMENTATION: http://bioconductor.org/packages/release/bioc/html/minfi.html. CONTACT: email@example.com; firstname.lastname@example.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Epigenetic mechanisms involve chemical and physical changes to the structure of DNA without changes in the underlying sequence. Epigenetics allows for fine-tuned control of gene expression and is the basic mechanism whereby a single human genome can give rise to over 200 different cell types in the adult organism. We are interested in the interplay between genetic and epigenetic factors, and their role in determining cell state and disease etiology. Our research involves developing statistical tools for mapping genomic and epigenomic landscapes and using this data to understand causes of human disease. The current area of focus in our group is the development of single-cell analysis methods to better understand the role that intra-tumor heterogeneity plays in cancer.