Other Association Testing

Click on a button corresponding to an association testing process not generally used for GWAS. Refer to the table below and the Comparison of Association Testing Processes for guidance.

Process	Choose this process for...
Multiple SNP-Trait Association	Testing association between various types of traits and numerically coded genotypes from multiple SNPs at a time using logistic, linear, survival regression, and generalized linear mixed models on SNP genotypes themselves or principal components used to represent the SNP genotypes
Rare Variant Tutorial	Guiding you through the process needed to perform a particular method for association testing between a trait and rare variants within a gene or region
Rare Variant Association	Testing association between a trait or disease and rare variants, and optionally common variants, that occur in the same gene or pathway
Pleiotropic Association	Testing association between multiple traits (separately and jointly) and SNP genotypes or alleles from a single SNP at a time
Marker-Trait Association	Testing association between various types of traits and marker genotypes (using ANOVA) or alleles (using regression testing) from a single marker at a time, with many adjustments possible, including for Q and K matrices representing population structure and relatedness, respectively Caution: This process can take an inordinate amount of time and computational resources. Consider choosing SNP-Trait Association when analyzing SNPs or multiallelic markers that can be treated as SNPs based on the most frequent allele.
SNP-SNP Interactions	Testing association between various types of traits and the interaction between pairs of SNPs, adjusting for SNP main effects
SNP Interaction Discovery	Searching for pairs of SNPs predictive of a binary trait beyond the predictive ability of single SNPs, using penalized logistic regression (PLR)
Q-K Model Fitness	Used to fit different combinations of Q and K variables and model fitness information from each model, such as AIC, AICC.
Q-K Mixed Model	Testing association between various types of traits and SNP genotypes or alleles from a single SNP at a time, while adjusting simultaneously for population structure and family relatedness Note: You must already have computed the Q and K matrices.
Genomic Heritability	Estimating the genetic variance explained by markers variables using a mixed model framework.

See GWAS Testing for additional association testing processes.

See Genetics for other subcategories.