Table 1.
Characteristics of hypothesis-driven candidate gene studies and the ISC GWAS.
| Characteristic | Candidate gene studies | ISC |
|---|---|---|
|
| ||
| Studies | 1,375 | - |
|
| ||
| Genes (autosomal) | 732 | - |
|
| ||
| Markers (autosomal) | ||
| Total | 6,934 | 1,948,385 |
| Markers per gene, median (IQR) | 2 (1–5) | 9 (1–34) |
| Genes with 1, 2, or 3 markers | 65.9% | n/a |
| Marker density per gene as kb/SNP, median (IQR) | 15.4 (4.69–46.2) | 1.38 (0.69–2.47) |
|
| ||
| Sample size | Median (range) a | Actual |
| Total subjects | 412 (27–5,623) | 6,909 |
| Number of cases | 191 (5–2,434) | 3,322 |
| Number of controls | 214 (12–4,899) | 3,587 |
|
| ||
| Major annotation clusters from pathway analysis | Enrichment score | |
| Synaptic transmission | 52.2 | n/a |
| Neuronal development and morphogenesis | 32.4 | |
| Regulation of synaptic transmission | 22.6 | |
| Response to chemical stimuli | 22.2 | |
|
| ||
| Statistical power b | 0.48 | 0.89 |
|
| ||
| Proportion of autosomal RefSeq genes studied c | 0.037 | 0.902 |
|
| ||
| Proportion of genes in top 4 DAVID annotation clusters studied | 0.067 | n/a |
a
Biased due to subject overlap across publications.
b
See text for assumptions.
c
For ISC, assuming gene boundaries expanded by ±10 kb and SNP density < 20 kb/SNP.
IQR=inter-quartile range. FDR=false discovery rate. GRR=genotypic relative risk. MAF=minor allele frequency.