Table 3.
Replication of SNPs found in the preliminary Whole-exome sequencing analysis in different Finnish sarcoidosis subgroups based on disease prognosis (persistent, resolved) and HLA markers (HLA+ = HLA–DRB1*03:01 and/or HLA–DRB1*04:01-DPB1*04:01; HLA– = without either of the markers) and Finnish control population.
| Chromosome | Position | Chromosomal location | MAF* Persistent | MAF* Resolved | MAF gnomAD Finnish | MAF Control | MAF replication** Persistent | MAF replication** Resolved | MAF combined*** Persistent | MAF combined*** Resolved | SNP | P | P Replication | P Combined | rsID | Gene |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PERSISTENT VS. RESOLVED | ||||||||||||||||
| 1 | 12719616 | 1p36.21 | 0.125 | 0.375 | 0.2196 | 0.2166 | 0.1667 | 0.2885 | 0.1505 | 0.3239 | C/T | 0.000915 | 0.03142 | 0.0001009 | rs3010877 | AADACL3 |
| 1 | 12725527 | 1p36.21 | 0.181 | 0.389 | 0.3072 | 0.2866 | 0.2281 | 0.375 | 0.2097 | 0.3807 | T/G | 0.0165913 | 0.01785 | 0.0003522 | rs7513079 | AADACL3 |
| 1 | 12760937 | 1p36.21 | 0.139 | 0.361 | 0.2346 | 0.2261 | 0.1667 | 0.3173 | 0.1559 | 0.3352 | C/T | 0.0083299 | 0.009143 | 7.031E-05 | rs1132185 | C1orf158 |
| 19 | 54664811 | 19q13.42 | 0.208 | 0.375 | 0.3021 | 0.2834 | 0.3421 | 0.3558 | 0.2903 | 0.3636 | G/A | 0.0164497 | 0.8325 | 0.1369 | rs731170 | LILRB4 |
| 19 | 54818581 | 19q13.42 | 0.264 | 0.153 | 0 | 0.2677 | 0.2544 | 0.2692 | 0.2796 | 0.233 | G/A | 0.046766 | 0.8033 | 0.3103 | rs643861 | KIR3DL1, KIR3DS1 |
| HLA+ | ||||||||||||||||
| 1 | 12719616 | 1p36.21 | 0.083 | 0.361 | 0.2196 | 0.2166 | 0.1071 | 0.22 | 0.09375 | 0.314 | C/T | 0.0010228 | 0.2128 | 5.27E-06 | rs3010877 | AADACL3 |
| 1 | 12725527 | 1p36.21 | 0.111 | 0.333 | 0.3072 | 0.2866 | 0.1071 | 0.32 | 0.1094 | 0.3721 | T/G | 0.008796 | 0.03565 | 2.88E-07 | rs7513079 | AADACL3 |
| 1 | 12760937 | 1p36.21 | 0.111 | 0.306 | 0.2346 | 0.2261 | 0.07143 | 0.26 | 0.09375 | 0.3256 | C/T | 0.0204559 | 0.04265 | 2.10E-06 | rs1132185 | C1orf158 |
| 19 | 54664811 | 19q13.42 | 0.139 | 0.333 | 0.3021 | 0.2834 | 0.3929 | 0.42 | 0.25 | 0.407 | G/A | 0.0218551 | 0.8152 | 0.004529 | rs731170 | LILRB4 |
| 19 | 54818581 | 19q13.42 | 0.278 | 0.111 | 0 | 0.2677 | 0.25 | 0.3 | 0.2812 | 0.2674 | G/A | 0.0429011 | 0.6378 | 0.8511 | rs643861 | KIR3DL1, KIR3DS1 |
| HLA– | ||||||||||||||||
| 1 | 12719616 | 1p36.21 | 0.1667 | 0.3056 | 0.2196 | 0.2166 | 0.186 | 0.3519 | 0.1803 | 0.3333 | C/T | 0.1653 | 0.02743 | 0.01049 | rs3010877 | AADACL3 |
| 1 | 12725527 | 1p36.21 | 0.25 | 0.3333 | 0.3072 | 0.2866 | 0.2674 | 0.4259 | 0.2623 | 0.3889 | T/G | 0.4367 | 0.05197 | 0.05005 | rs7513079 | AADACL3 |
| 1 | 12760937 | 1p36.21 | 0.1667 | 0.3056 | 0.2346 | 0.2261 | 0.1977 | 0.3704 | 0.1885 | 0.3444 | C/T | 0.1653 | 0.02409 | 0.01001 | rs1132185 | C1orf158 |
Resolved patients, n = 36; persistent patients, n = 36; HLA+ resolved, n = 18; HLA+ persistent, n = 18; HLA– resolved, n = 18, HLA– persistent, n = 18.
Resolved patients, n = 52; persistent patients, n = 57; HLA+ resolved, n = 25; HLA+ persistent, n = 14; HLA– resolved, n = 27, HLA– persistent, n = 43.
Resolved patients, n = 88; persistent patients, n = 93; HLA+ resolved, n = 43; HLA+ persistent, n = 32; HLA– resolved, n = 45, HLA– persistent, n = 61.
Predicted function according to PolyPhen and Sift, respectively: B, benign; P, probably damaging; T, tolerated; D, deleterious.
MAF, minor allele frequency; AA, amino acid.