Genome-Wide Association Data
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. DOI: 10.3768/rtipress.2016.bk.0016.1608
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.