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Genome-wide association data Where are the standards? (chapter 2)

In this chapter we assess the predictive strength of a number of classical statistical methods by applying them to a publically available set of amyotrophic lateral sclerosis (ALS) data reported in a paper by Schymick and colleagues (2007).1 We used these methods in the context of a single locus genome wide association study (GWAS) experiment. The methods are compared and the degree of similarity/dissimilarity between them is empirically measured to determine if a combination of methods is more predictive of phenotype genotype associations than a single method. All of the methods in our assessment are single nucleotide polymorphism (SNP) based.


Cooley, P. (2016). Genome-wide association data: Where are the standards? (chapter 2). In P. Cooley (Ed.), Methods in statistical genomics: In the context of genome-wide association studies (pp. 17-30). (RTI Press Publication No. BK-0016-1608). Research Triangle Park, NC: RTI Press. https://doi.org/10.3768/rtipress.2016.bk.0016.1608