2 Some background reading
Standing on the shoulders of giants, that’s what this book and I do. I want to acknowledge some great work that has helped me tremendously and, really, this book wouldn’t exist without this awesome work. So, I do want to give you some background reading. Is it a prerequisite? No, not really. For starters, the course covers most and you’ll learn as you go. And if you didn’t come here through the course, you’ll be fine just the same. That said, it’s a always good idea to get familiar with these works as you move forward on your path towards your first GWAS - in fact, I had these printed out with markings and writings all over them as I executed my first GWAS, and they’ve been great as a reference many times after.
Large parts of this work are based on four awesome Nature Protocols from the Zondervan group at the Wellcome Center Human Genetics.
- Zondervan KT et al. Designing candidate gene and genome-wide case-control association studies. Nat Protoc 2007.
- Pettersson FH et al. Marker selection for genetic case-control association studies. Nat Protoc 2009.
- Anderson CA et al. Data QC in genetic case-control association studies. Nat Protoc 2010.
- Clarke GM et al. Basic statistical analysis in genetic case-control studies. Nat Protoc 2011.
An update on the community standards of QC for GWAS can be found here:
With respect to imputation and meta-analyses of GWAS you should also get familiar with the following two works:
- Marchini, J. and Howie, B. Genotype imputation for genome-wide association studies. Nat Rev Genet 2010
- de Bakker PIW et al. Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Hum Mol Genet 2008.
- Winkler TW et al. Quality control and conduct of genome-wide association meta-analyses. Nat Protoc 2014.
Are you ready?
Are you ready? Did you bring coffee and a good dose of energy? Let’s start in Chapter 3.