Table 1.
The Role of GWAS SNP Arrays in Human Genetic Discoveries
| Analysis | Purpose | Discoveries |
|---|---|---|
| GWAS | detecting trait-SNP associations | ∼10,000 robust associations with diseases and disorders, quantitative traits, and genomic traits |
| Genome-wide CNV analysis | detecting trait-CNV associations | hundreds of associations with diseases and disorders |
| Genome-wide assessment of LD | quantifying genome architecture | large variation in LD in the genome |
| Estimation of SNP heritabilitya | genetic architecture | large proportion of genetic variation captured by common SNPs |
| Estimation of genetic correlationa | detecting and quantifying pleiotropy | pleiotropy is ubiquitous |
| Polygenic risk scoresa | detecting pleiotropy; validating GWAS discoveries | out-of-sample prediction works as expected; detection of novel trait associations |
| Mendelian randomizationa | testing causal relationships | replication of known causal relationships; empirical evidence of observational associations that are not causal |
| Population differences in allele frequencies | reconstructing human population history; detecting selection | genetic structure can mimic geographical structure; evidence of natural selection |
| Trait GWAS with -omics GWASa | fine-mapping; detecting target genes; function | two-thirds of GWAS-associated loci implicate a gene that is not the nearest gene to the most associated SNP |
a
These analyses can be performed with GWAS summary statistics.