Epigenetics and Gene Regulation
This module jointly concerns statistical genetic principles around epigenetics and gene regulation. Lectures and practical sessions in the first half of the course will provide an introduction to epigenetics, with particular attention to methylation profiling via epigenome-wide association studies and bisulfite sequencing studies. Additional topics will include methylation QTL analysis, methylation risk scores, preprocessing of DNA methylation data, and future directions in the field.
The second half of the course focuses on methods for predicting genetically regulated gene expression and its association with complex traits and diseases. We will cover Transcriptome-wide Association Study (TWAS) methods, ChIP-Seq analysis, regulatory motif discovery, and machine learning approaches to inference of non-coding DNA function, and integrative analysis with inferred non-coding DNA functional annotations and GWAS summary data. We recommend pairong with Modules IG3 and IG4 cover single-cell gene expression profiling and network and pathway analysis, respectively.
Learning Objectives: After attending this module, participants will be able to:
- Know the major modes of epigenetic profiling, including methylation, chromatin accessibility, histone modification, and chromatin contacts.
- Perform methylation profiling analyses using methylation array and sequencing data.
- Compute mQTLs and methylation risk scores and understand their applications.
- Understand the methods and tools used in TWAS and be able to perform a TWAS analysis.
- Be able to conduct ChIP-Seq analysis and identify Transcription Factor Binding Sites (TFBS).
- Understand the theory behind methods such as Deep-SEA and FAVOR, and know how to use their non-coding DNA functional predictions and annotations to prioritize potential causal variants in GWAS summary data.
Course Dates
- Wed June 3, 1:30 p.m. – 5:00 p.m. EST
- Thu June 4, 8:30 a.m. – 5:00 p.m. EST
- Fri June 5, 8:30 a.m. – 5:00 p.m. EST
Instructors
- Karen Conneely
- Jingjing Yang
Suggested Course Pairings
Integrative Genomics Stream
- Module IG1: Genetics, Genomics and Biobanks
- Module IG3: Gene Expression & Single Cell Genomics
- Module IG4: Gene Networks and Pathways
Course Materials
Course materials will be available shortly before the class.
Please email sisg@biosci.gatech.edu if you have questions or would like more details.
About the Instructors
Karen Conneely is an Associate Professor in the Department of Human Genetics at Emory University in Atlanta. She is particularly interested in the role of DNA methylation as mediator between genetic variation, environment and phenotype. Ongoing work in her lab uses computational approaches to understand the relationship between multiple epigenetic mechanisms, gene expression, and human aging. Access Karen’s publications here. She will be assisted by Emory colleague Alicia Smith, whose lab employs methylation profiling to study the regulation of behavioral and psychological traits.
Jingjing Yang is also an Associate Professor in the Department of Human Genetics at Emory University in Atlanta. The Yang Lab is developing statistical and computational methods and tools for quantitative genomics data analysis and biomedical data analysis. Her TIGAR and OTTERS software supports Transcriptome-wide Association Studies. Learn more about Jingjing’s work here.