TABLE 3.
Regions of homozygosity over-represented in schizophrenia cases.
| Region | Chr | Location (base position) | Chromosome Band | Number of samples | Length (kb) | Total SNPs | p | Significant GWAS gene, phenotype1 | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Start | End | SZ cases | Controls | Total | |||||||
| 1 | 1 | 108,860,573 | 110,323,150 | 1p13.3 | 12 | 1 | 13 | 1462.58 | 111 | < 0.05 | SYPL2, cognitive ability GPR61, chronotype |
| 2 | 14 | 32,438,841 | 32,964,338 | 14q12 | 10 | 0 | 10 | 525.50 | 59 | < 0.05 | AKAP6, SZ, BP, cognition |
| 3 | 1 | 89,045,338 | 89,735,314 | 1p22.2 | 9 | 0 | 9 | 689.98 | 57 | < 0.05 | none |
| 4 | 1 | 161,957,719 | 163,494,784 | 1q23.3 | 9 | 0 | 9 | 1537.07 | 205 | < 0.05 | none |
| 5 | 1 | 165,625,023 | 166,337,053 | 1q24.1 | 9 | 0 | 9 | 712.03 | 83 | < 0.05 | FAM78B, cognition |
| 6 | 14 | 29,895,001 | 31,237,170 | 14q12 | 9 | 0 | 9 | 1342.17 | 129 | < 0.05 | none |
| 7 | 1 | 154,791,128 | 156,378,425 | 1q21.3-q22 | 8 | 0 | 8 | 1587.30 | 103 | < 0.05 | KCNN3-PMVK, SZ, BP ZBTB7B, SZ RIT1, SZ |
| 8 | 1 | 160,513,183 | 161,361,979 | 1q23.3 | 8 | 0 | 8 | 848.80 | 79 | < 0.05 | none |
| 9 | 3 | 190,779,327 | 191,862,817 | 3q28 | 8 | 0 | 8 | 1083.49 | 155 | < 0.05 | AC073365.1, SZ |
| 10 | 6 | 108,323,759 | 109,351,125 | 6q21 | 8 | 0 | 8 | 1027.37 | 87 | < 0.05 | AFG1L, cognition FOXO3, SZ, cognition, neuroticism |
| 11 | 11 | 22,141,171 | 22,647,550 | 11p14.3 | 8 | 0 | 8 | 506.38 | 48 | < 0.05 | none |
Regions of homozygosity were identified that were over-represented in consanguineous schizophrenia cases. SZ=schizophrenia; BP=bipolar disorder; Chr=chromosome; kb=kilobases; p=equivalent to an unadjusted p-value using Fisher’s exact test. Genomic locations based on GRCh37/hg19.
1
Genome-wide association studies (GWAS) with significantly associated SNPs identified in prior studies per ROH region. Detailed information for these GWAS is provided in Supplemental Table 2.