Methyl Bisulfite Analysis
Karen Conneely, PhD
Associate Professor
Emory University
Dr. Conneely received her Ph.D in Biostatistics from University of Michigan. Her research focuses on statistical methods for genetic association studies and large-scale studies of DNA methylation. She is currently involved in GWAS, candidate gene studies, and methylation studies involving psychiatric outcomes, environmental stressors, and aging. Through the development of novel techniques and adaptation of existing ones, her work seeks to identify biomarkers and variants involved in disease, and to explore the role of DNA methylation as a mediator between environment and phenotype.
Course Contents
Single-base resolution coverage offered by Whole Genome Bisulfate Sequencing(WGBS) has made it a gold standard for assaying DNA methylation. An higher resolution version of WGBS, but just enriched for CpG-rich regions, is the Reduced Representative Bisulfate Sequencing (RRBS). Analysis of WGBS and RRBS data involves use of several bioinformatics tools and statistical methods to perform a complete end-to-end pipeline starting from read alignment to the quantification of differentially methylated sites and regions. The first module of this video series will walk you through the different analysis strategies for quantifying differentially methylated sites from already aligned RRBS data. In order to compare and contrast the dense nature of WGBS with RRBS, latter modules were developed to show how a smoothing approach like Bsmooth algorithm can be used to generate high confidence differentially methylated regions.
- Analysis Instructions (pdf)
- Analysis Dataset (zip)
Methylation Analysis using Bisulfite Sequencing Data- Module 1
Published on March, 2018
Methylation Analysis using Bisulfite Sequencing Data – Module 2
Published on March, 2018
Methylation Analysis using Bisulfite Sequencing Data – Module 3
Published on March, 2018
External Funding:
- NIGMS – online video portal & resources
- NHGRI – lecture series resources
- Hudson-Alpha Institute for Biotechnology
UAB Internal Funding:
- Center for Clinical and Translational Science
- Dean for Research, School of Medicine
- Department of Biostatistics, School of Public Health
- Heflin Center for Genomic Science
- Office of the Provost
- Nutrition Obesity Research Center
- School of Medicine
- Vice President for Reseach and Economic Development