Lecture 4 - GWAS - QC - Multiple Testing - Power

Haky Im

2021-01-24

Categories: Lecture

Learning Objectives

  • Define Bonferroni correction and false discovery rates
  • Examine quality control measures applied to GWAS (UK Biobank example)
  • Review the definition of power and discuss why it is necessary
  • Calculate power for a quantitative trait

Revisiting multiple testing

  • Multiple testing slides. link
  • Vignette link

UK Biobank GWAS

Power calculation

References

  • Storey & Tibshirani, “Statistical significance for genomewide studies,” Proceedings of the National Academy of Sciences, Jul. 2003.

  • UK Biobank Imputed Genotype Data Release Bycroft, C., Freeman, C., Petkova, D., Band, G., Elliott, L. T., Sharp, K., et al. (2018). The UK Biobank resource with deep phenotyping and genomic data. Nature, 562(7726), 1–25. http://doi.org/10.1038/s41586-018-0579-z

  • S. Turner et al, 2011, “Quality control procedures for genome‐wide association studies”, Current Protocols in Human Genetics

  • Marees AT, de Kluiver H, Stringer S, Vorspan F, Curis E, Marie-Claire C, Derks EM. A tutorial on conducting genome-wide association studies: Quality control and statistical analysis. Int J Methods Psychiatr Res. 2018 Jun;27(2):e1608. doi: 10.1002/mpr.1608. Epub 2018 Feb 27. PMID: 29484742; PMCID: PMC6001694. https://pubmed.ncbi.nlm.nih.gov/29484742/

  • G. Jun et al, “Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees.,” Proceedings of the National Academy of Sciences, vol. 57, no. 2, pp. 201705859–384, Dec. 2017.

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Citation

For attribution, please cite this work as

Haky Im (2021). Lecture 4 - GWAS - QC - Multiple Testing - Power. HGEN 471 Class Notes. /post/2021/01/24/lecture-4-gwas-qc-multiple-testing-power/

BibTeX citation

@misc{
  title = "Lecture 4 - GWAS - QC - Multiple Testing - Power",
  author = "Haky Im",
  year = "2021",
  journal = "HGEN 471 Class Notes",
  note = "/post/2021/01/24/lecture-4-gwas-qc-multiple-testing-power/"
}