Table 2.
Enrichment of rare LoFs among genes involved in immune function and innate immune system
| Gene Groups | Variant class | AD | CEN | OR |
95% CI |
Fisher's exact P-value |
|---|---|---|---|---|---|---|
| Immune genes (n = 4677) | PAVs (n = 2915) | 1965 | 2151 | 1.11 | 1.03–1.19 | 0.0058 |
| LoFs (n = 186) | 137 | 120 | 1.39 | 1.07–1.79 | 0.011 | |
| Stop-gain (n = 62) | 35 | 49 | 0.87 | 0.54–1.37 | 0.58 | |
| Stop-gain_NMD + INIT + splicing (n = 46) | 40 | 26 | 1.87 | 1.11–3.19 | 0.013 | |
| INIT + splicing (n = 41) | 38 | 23 | 2.01 | 1.16–3.53 | 0.0094 | |
| INIT (n = 6) | 7 | 3 | 2.83 | 0.65–16.99 | 0.20 | |
| Splicing (n = 35) | 31 | 20 | 1.88 | 1.04–3.49 | 0.033 | |
| Innate immune genes (n = 1397) | PAVs (n = 815) | 526 | 602 | 1.06 | 0.94–1.20 | 0.36 |
| LoFs (n = 54) | 39 | 33 | 1.43 | 0.88–2.36 | 0.15 | |
| Stop-gain_NMD + INIT+ splicing (n = 16) | 15 | 4 | 4.55 | 1.45–18.85 | 0.0043 |
Enrichment of rare PAVS and LoFs among genes involved in immune function and specifically in innate immune function by comparing allele counts of PAVS and LoFs to allele counts of rare synonymous variants in all genes between AD patients and CEN. In parenthesis are total numbers of variants in each variant class. Rare_syn: rare synonymous variants, Stop-gain_NMD: stop-gain variants that are predicted to affect > 50% of known transcripts. LoFs defined as non-sense, frame shift, initiation codon and splice site variants. PAVs defined as LoFs plus missense, in frame indels, stop-loss variants.