Table 1.
Single-nucleotide variation (SNV) characteristics in whole-genome sequences from Estonian Biobank participants
| (a) Variants in the Estonian Biobank discovery set | Whole genome | ADMET genes (n = 64) | ||
|---|---|---|---|---|
| n | % | n | % | |
| Genes with variants | 18,468 | 56 | ||
| Unique variants | 29,108,287 | 1314 | ||
| Variant carriers | 2240 | 2240 | ||
| Novel variants | 11,508,281 | 39.5 | 267 | 20.3 |
| Known variants | 17,600,006 | 60.5 | 1047 | 79.7 |
| MAF > 5% | 5,403,215 | 18.6 | 164 | 12.5 |
| 1% ≤ MAF < 5% | 2,444,670 | 8.4 | 95 | 7.2 |
| 0.5% ≤ MAF < 1 % | 1,211,084 | 4.2 | 45 | 3.4 |
| 0.05% ≤ MAF < 0.5% | 6,460,248 | 22.2 | 285 | 21.7 |
| MAF < 0.05 % | 13,589,070 | 46.7 | 725 | 55.2 |
| AC = 1 | 10,617,607 | 36.5 | 560 | 42.6 |
| AC = 2 | 2,971,463 | 10.2 | 165 | 12.6 |
| (b) | Loss-of-function | Missense | Promoter region | |||
|---|---|---|---|---|---|---|
| n | % | n | % | n | % | |
| Unique variants | 41 | 567 | 706 | |||
| MAF > 5% | 1 | 2.4 | 39 | 6.8 | 124 | 17.6 |
| 1% < MAF < 5% | 0 | 0 | 38 | 6.7 | 57 | 8.1 |
| 0.5% < = MAF < 1 % | 1 | 2.4 | 16 | 2.8 | 28 | 3.9 |
| 0.05% < = MAF < 0.5% | 15 | 36.6 | 113 | 19.9 | 157 | 22.2 |
| MAF < 0.05 % | 24 | 58.5 | 361 | 63.6 | 340 | 48.1 |
| AC = 1 | 21 | 51.2 | 279 | 49.2 | 260 | 36.8 |
| AC = 2 | 3 | 7.3 | 82 | 14.5 | 80 | 11.3 |
| Novel variants | 10 | 24.3 | 134 | 23.6 | 123 | 17.4 |
| Novel variants AC = 1 | 6 | 14.6 | 99 | 17.5 | 50 | 7.1 |
| Known variants | 31 | 75.6 | 433 | 76.4 | 583 | 82.5 |
| Known variants AC = 1 | 15 | 36.6 | 180 | 31.7 | 210 | 29.7 |
AC allele count, MAF Minor allele frequency, ADMET absorption, distribution, metabolism, excretion, and toxicity, n number of variants
(a) Numbers and frequencies of detected variants in whole-genome sequences and targeted pharmacogenes
(b) Characterization of targeted pharmacogenetic variations in loss of function (LoF), missense, and regulatory (transcription factor binding sites in liver 5-kb upstream of gene start site) regions