Computationally efficient correlation of genetic effects with function-valued traits

A computationally-efficient method for identifying a correlation between a single-nucleotide polymorphism (SNP) and a function-valued trait in genome-wide association study (GWAS), the method comprising:

• creating a linked matrix having values of the function-valued trait, values of function domain points, and phenotype values for each allele combination of the SNP;
• generating an alternative model having a single Gaussian process of a vector derived from the linked matrix and a covariance term, the covariance term based upon at least one scalar and a non-linear kernel;
• generating a null model by setting a value of the at least one scalar to zero;
• comparing a first maximum likelihood for the alternative model with a second maximum likelihood for the null model;
• and
• determining that the SNP is correlated with the function-valued trait based on the comparison of the first maximum likelihood for the alternative model with the second likelihood for the null model.

A computationally-efficient system for identifying a correlation between a single-nucleotide polymorphism (SNP) and a function-valued trait in genome-wide association study (GWAS), the system including:

• a data storage device that stores instructions for identifying a correlation between a single-nucleotide polymorphism (SNP) and a function-valued trait in genome-wide association study (GWAS);
• and
• a processor configured to execute the instructions to perform a method including:
• creating a linked matrix having values of the function-valued trait, values of function domain points, and phenotype values for each allele combination of the SNP;
• generating an alternative model having a single Gaussian process of a vector derived from the linked matrix and a covariance term, the covariance term based upon at least one scalar and a non-linear kernel;
• generating a null model by setting a value of the at least one scalar to zero;
• comparing a first maximum likelihood for the alternative model with a second maximum likelihood for the null model;
• and
• determining that the SNP is correlated with the function-valued trait based on the comparison of the first maximum likelihood for the alternative model with the second likelihood for the null model.