Term	Definition/Comment
Admixed Population	A population of individuals with ancestors from two or more populations. Admixed can also be used to refer to individuals.
Fine-mapping	Analytical procedures designed to refine GWAS loci to a smaller set of likely causal variant candidates to facilitate interpretation and follow-up studies.
Genetic Correlation	The correlation of genome-wide genetic effects between two phenotypes, which is often estimated for a subset of genomic variants (e.g. SNPs in a GWAS).
Genotype Imputation	Estimation of genotypes at genetic sites that have not been directly measured, using data from a reference panel to infer genotypes based on LD and haplotype structures. Accuracy depends on availability of suitable reference panels.
GWAS	Genome-wide association study. Analysis of common genetic variants across the whole genome for association with a phenotype.
GxE	Gene by environment interaction refers to genetic effects on a phenotype that vary based on environment, or vice-versa.
Haplotype	A group of alleles that are correlated with one another because they are inherited together on a chromosome.
HWE	Hardy-Weinberg equilibrium, the expected balance of genotypes within a population assuming random mating, infinite population size, and no mutation, migration, or selection. Tests of deviations from HWE are used in quality control to detect technical issues with genotyping. Note that there are also non-technical reasons for deviation from HWE (e.g., selection, population structure, admixture, nonrandom mating).
LD	Linkage disequilibrium. Alleles in LD are physically linked on a chromosome, which leads to non-random coinheritance such that their frequencies in a population are correlated.
Major Population	A group of individuals with shared genetic ancestry. A heuristic simplification of the complexity of human demography, but useful for describing groups that are likely to have relatively similar allele frequencies and LD patterns due to shared ancestry. Common examples used in practice include continental ancestry groups or “super populations” as defined by the 1000 Genomes Project (e.g., African, Admixed American, East Asian).
PCA	Principal component analysis. PCA of genotype data is commonly used to examine population structure in a cohort by determining the average genome-wide genetic similarities of individual samples. Derived PCs can be used to group individuals with shared genetic ancestry, identify outliers, and as covariates to reduce false positives due to population stratification.
Population Stratification	Underlying population structure within a sample that is correlated with a phenotype, which can confound genetic association tests.
PRS	Polygenic risk score. A value computed from an individual’s genotype data that quantifies genetic influences on a particular phenotype; also known as polygenic score (PGS), genetic risk score (GRS), or risk profile score (RPS).
Reference Panel	A set of genetic variants from a population. Reference panels are used to design arrays, impute genotypes, catalogue genetic variants, and identify regions that are similar and different between populations.
SNP Heritability	Proportion of phenotypic variance that is explained by additive genetic effects of a set of SNPs.