Determining Phenotypic Traits from Single Nucleotide Polymorphism (SNP) Data

This chapter describes how to determine an individual’s phenotypic traits from their single nucleotide polymorphism (SNP) genetic data obtained from their direct-to-consumer (DTC) genetic test results. We will also cover an overview of traits and the contribution of the environment on an individual’s final observed phenotype. We will cover the concept of heritability of phenotypes, Mendelian inheritance, and Punnett Squares. We will also discuss non-Mendelian inheritance patterns indicative of complex traits. Because genetic test results are often used to impute disease risk and phenotypes, we will also cover how to evaluate the accuracy of a genetic test result given self-reported assessment of the trait’s presence or absence in individuals. We will learn how to use the Genome-Wide Association Studies (GWAS) Catalog to link individual SNPs to phenotypes reported in the literature. We will also cover how to link user’s genetic results to GWAS Catalog results in R and identify homozygous traits and heterozygous traits. Importantly, this chapter is focused on traits that the Food and Drug Administration (FDA) distinguishes from clinical genetic results. However, some “traits” have potential health actionability and are important for human health and disease risk. Therefore, we will discuss some traits of potential health importance, including traits for height, sports performance, vitamin absorption, longevity and reduced mortality, and more! After reading this chapter, you should be able to confidently answer the following questions: