. Author manuscript; available in PMC: 2020 Dec 1.

Published in final edited form as: Curr Protoc Hum Genet. 2019 Dec;104(1):e95. doi: 10.1002/cphg.95

Table 3.

Considerations for Generating a Genetic Risk Score

Factor	Considerations
Outcome of Interest	Pleiotropy Definition of complex phenotype (component phenotypes) Clinical covariates
Loci	P-value threshold (polygenic vs. highly significant loci only) Imputation type/quality Linkage disequilibrium Mode of inheritance Agreement of DNA strand between training and test data Reference (risk) allele coding Build of human genome
Sample	Population (ethnic background; admixture) Demographic makeup (age, sex, socioeconomic status, etc.)
Weighting	log (OR) from logistic regression Total number of risk variants LD between risk variants (for PRS)