Topics Covered
- Why genetic epidemiology?
- Why GWAS and RVAS?
- What we have learned.
- What remains to be done.
- Overview of the course
Practical
- To introduce the Google Colaboratory platform.
- To introduce participants the importance of Quality Control in the analysis pipeline.
- To provide participants with the basic practical skills needed to perform QC of GWAS data using plink.
Recommended Readings/Videos
- Readings on genome-wide association study design and analysis
- Uffelmann, E., Huang, Q. Q., Munung, N. S., de Vries, J., Okada, Y., Martin, A. R., Martin, H. C., & Lappalainen, T. (2021). Genome-wide association studies. Nature Reviews Methods Primers, 1(1), 1–21. https://doi.org/10.1038/s43586-021-00056-9
- Overview of findings from genome-wide association studies
- Penney, K. L., Michailidou, K., Carere, D. A., Zhang, C., Pierce, B., Lindström, S., & Kraft, P. (2017). Genetic Epidemiology of Cancer. https://doi.org/10.1093/oso/9780190238667.003.0005
- Visscher, P. M., Wray, N. R., Zhang, Q., Sklar, P., McCarthy, M. I., Brown, M. A., & Yang, J. (2017). 10 Years of GWAS Discovery: Biology, Function, and Translation. American Journal of Human Genetics, 101(1), 5–22. https://doi.org/10.1016/j.ajhg.2017.06.005
- Readings on Google Colab and Jupyter Notebook
- Google Colaboratory Introduction
- An official guide to Google Colab.
- Jupyter Notebook Documentation
- The official documentation for Jupyter Notebook.
- Google Colaboratory Introduction
- YouTube Videos on Google Colab and Jupyter notebook
- Get started with Google Colaboratory (Coding TensorFlow)
- An introduction to Google Colab by the TensorFlow team.
- Jupyter Notebook Tutorial: Introduction, Setup, and Walkthrough
- A comprehensive introduction to Jupyter Notebook.
- Jupyter Notebook for Beginners: A Tutorial
- Another beginner-friendly guide to understanding and navigating Jupyter Notebook.
- Get started with Google Colaboratory (Coding TensorFlow)
- Readings on GWAS QC
- Turner, S., Armstrong, L. L., Bradford, Y., Carlson, C. S., Crawford, D. C., Crenshaw, A. T., de Andrade, M., Doheny, K. F., Haines, J. L., Hayes, G., Jarvik, G., Jiang, L., Kullo, I. J., Li, R., Ling, H., Manolio, T. A., Matsumoto, M., McCarty, C. A., McDavid, A. N., … Ritchie, M. D. (2011). Quality control procedures for genome-wide association studies. Current Protocols in Human Genetics / Editorial Board, Jonathan L. Haines… [et Al.], Chapter 1, Unit1.19. https://doi.org/10.1002/0471142905.hg0119s68