Lecture 6 - mixed effects - LDSC

Learning Objectives

• List methods that control for population structure
• Explain how genomic control is used
• Explain how mixed effects modeling can correct for population structure
• Use LD Score regression to distinguish between population structure and polygenicity driven inflation

Slides

https://docs.google.com/presentation/d/1I0-4u_6PAG5Q9LNi3mfQNnvZsVgf16tO/edit?usp=sharing&ouid=100565019341850449624&rtpof=true&sd=true

References

• B. Devlin and Kathryn Roeder (1999) “Genomic Control for Association Studies”, Biometrics, Vol. 55, No. 4, 997-1004.
• H. M. Kang, J. H. Sul, S. K. Service, N. A. Zaitlen, S.-Y. Kong, N. B. Freimer, C. Sabatti, and E. Eskin, “Variance component model to account for sample structure in genome-wide association studies,” Mar. 2010.
• A. L. Price, N. A. Zaitlen, D. Reich, and N. Patterson, “New approaches to population stratification in genome-wide association studies,” Nat Rev Genet, vol. 11, no. 7, pp. 459–463, Jun. 2010. B. K. Bulik-Sullivan, P.-R. Loh, H. K. Finucane, S. Ripke, J. Yang, N. Patterson, M. J. Daly, A. L. Price, and B. M. Neale, “LD Score regression distinguishes confounding from polygenicity in genome-wide association studies,” Nat Genet, vol. 47, no. 3, pp. 291–295, Feb. 2015.