Table 1.
Top regions based on the burden or SKAT test with p ≤ 5e−06 in the discovery family-based dataset using whole-genome scan.
| First SNV in the region (chr:pos:ref:alt) | Last SNV in the region (chr:pos:ref:alt) | Nearest protein-coding gene | Discovery dataset (NIMH + NIA families) | Replication dataset NHW ADSP | Meta-analysis of family-based discovery and NHW ADSP replication datasets | Replication dataset AA ADSP | Replication dataset HISP ADSP | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P value | Number of simulations | P value | Number of SNVs in the region used in the test | Fisher chi-squared test statistic | P value | P value | Number of SNVs in the region used in the test | P value | Number of SNVs in the region used in the test | |||
| Burden test | ||||||||||||
| 2:25703040:G:A | 2:25707419:T:G | DTNB | 7.00E−08 | 1.00E + 08 | 0.032 | 5 | 39.808 | 4.74E−08 | 0.390 | 9 | 0.353 | 8 |
| 2:79854141:T:G | 2:79856252:C:T | CTNNA2 | 8.10E−07 | 1.00E + 08 | 0.799 | 6 | 28.500 | 9.88E−06 | 0.774 | 8 | 0.785 | 7 |
| 3:181942653:A:G | 3:181946475:G:A | SOX2 | 2.40E−06 | 1.00E + 07 | 0.317 | 6 | 28.177 | 1.15E−05 | 0.619 | 9 | 0.163 | 8 |
| 22:35048628:G:C | 22:35053269:C:T | ISX | 4.40E−06 | 1.00E + 07 | 0.766 | 8 | 25.201 | 4.58E−05 | 0.827 | 9 | 0.014 | 10 |
| Variance component test | ||||||||||||
| 11:83498255:A:G | 11:83500398:T:G | DLG2 | 4E−06 | 1.00E + 07 | 0.014 | 5 | 33.352 | 1E−06 | 0.053 | 8 | 0.893 | 9 |
| 2:25703040:G:A | 2:25707419:T:G | DTNB | 1.4E−06 | 1.00E + 08 | 0.054 | 5 | 32.737 | 1.4E−06 | 0.409 | 9 | 0.455 | 8 |
| 7:82268137:T:C | 7:82271095:A:T | CACNA2D1 | 8E−07 | 1.00E + 07 | 0.591 | 5 | 29.131 | 7.4E−06 | 0.278 | 8 | 0.090 | 8 |
| 7:81141368:T:G | 7:81143780:C:T | SEMA3C | 3.6E−06 | 1.00E + 07 | 0.251 | 5 | 27.832 | 1.4E−05 | 0.046 | 9 | 0.694 | 10 |
SNV single nucleotide variant, chr chromosome, pos position according to GRCh38, ref reference allele, alt alternate allele, NHW non Hispanic white, AA African-American, HISP Hispanic.