Table 2.
Top 3% homozygous consensus regions overrepresented in cases when compared to controls and genes present within these regions
| Chr | Start of region (bp) |
End of region (bp) |
Region length (bp) |
Empirical p-value |
Permutation p-value after adjustment for multiple testing |
Candidate genes | Number of cases with homozygous runs |
Number of controls with homozygous runs |
OR |
|---|---|---|---|---|---|---|---|---|---|
| 8 | 37835460 | 38143780 | 308320 | 0.00099998 | 0.0170397 | RAB11FIP1; MGC33309; ADRB3; EIF4EBP1; ASH2L; STAR; LSM1 |
40 | 9 | 3.02 |
| 10 | 116826992 | 117301088 | 474096 | 0.00633987 | 0.0908982 | ATRNL1 | 45 | 14 | 2.18 |
| 9 | 26314013 | 26648658 | 334645 | 0.0102198 | 0.129957 | - | 9 | 0 | n.a. |
| 8 | 34251617 | 34375482 | 123865 | 0.0105198 | 0.151257 | LOC137107 | 109 | 49 | 1.53 |
| 1 | 213279861 | 213715720 | 435859 | 0.0115798 | 0.152477 | ESRRG | 32 | 9 | 2.39 |
| 2 | 214386585 | 214511938 | 125353 | 0.0127397 | 0.155837 | PF20 | 34 | 10 | 2.29 |
| 5 | 15390663 | 15634707 | 244044 | 0.0148597 | 0.161017 | LOC391741; FBXL7 |
27 | 7 | 2.59 |
| 4 | 98911102 | 99056376 | 145274 | 0.0152997 | 0.198896 | MGC46496 | 162 | 81 | 1.39 |
| 10 | 93788860 | 94018536 | 229676 | 0.0157197 | 0.192296 | CPEB3 | 63 | 25 | 1.71 |
| 3 | 137687127 | 137949289 | 262162 | 0.0180396 | 0.213336 | STAG1 | 149 | 74 | 1.39 |
| 1 | 169919601 | 170135865 | 216264 | 0.0189996 | 0.190176 | LOC343153 | 14 | 2 | 4.66 |
| 13 | 56558450 | 56726080 | 167630 | 0.0199796 | 0.241755 | FLJ40296 | 58 | 23 | 1.71 |
| 2 | 201456660 | 201882057 | 425397 | 0.0203196 | 0.211676 | AOX2; BZW1; LOC391472; CLK1; PPIL3; NIF3L1; ORC2L; MGC39518; NDUFB3; CFLAR; CASP10 |
28 | 8 | 2.34 |
| 4 | 62126310 | 62256398 | 130088 | 0.0203596 | 0.196436 | LPHN3 | 11 | 1 | 7.31 |
| 4 | 59420217 | 59599269 | 179052 | 0.0228195 | 0.235695 | - | 21 | 5 | 2.81 |
| 9 | 95407641 | 95524041 | 116400 | 0.0244795 | 0.240655 | PSMA7P | 16 | 3 | 3.55 |
| 12 | 51809479 | 51949002 | 139523 | 0.0244795 | 0.240655 | LOC400039; CSAD; LOC283337; ITGB7; RARG; MGC11308; ESPL1 |
16 | 3 | 3.55 |
| 12 | 63691379 | 64048325 | 356946 | 0.0244795 | 0.240655 | WIF1; MAN1; LOC253827 |
16 | 3 | 3.55 |
| 15 | 65557360 | 66059106 | 501746 | 0.0246195 | 0.251595 | FLJ12476; LOC145853; MAP2K5; LOC390598; LOC388129 |
23 | 6 | 2.56 |
| 18 | 31690766 | 31818000 | 127234 | 0.0246195 | 0.251595 | C18orf21 | 23 | 6 | 2.56 |
| 4 | 119462492 | 119635887 | 173395 | 0.0252395 | 0.278194 | NDST3; PRSS12 | 53 | 21 | 1.70 |
| 2 | 158898786 | 159035950 | 137164 | 0.0283194 | 0.272655 | LOC130940 | 18 | 4 | 3.00 |
| 3 | 35117703 | 35239453 | 121750 | 0.0283794 | 0.257595 | LOC442078 | 13 | 2 | 4.32 |
| 5 | 52730874 | 53125379 | 394505 | 0.0315194 | 0.268275 | FST; NDUFS4 | 10 | 1 | 6.64 |
| 7 | 132838685 | 133208570 | 369885 | 0.0318394 | 0.343753 | SEC8L1 | 63 | 27 | 1.58 |
| 1 | 80639887 | 80811557 | 171670 | 0.0334193 | 0.300274 | LOC441889; COX6A1P |
22 | 6 | 2.45 |
| 3 | 145678190 | 145958179 | 279989 | 0.0334193 | 0.300274 | - | 22 | 6 | 2.45 |
| 1 | 100201372 | 100553949 | 352577 | 0.0390992 | 0.376492 | HIAT1; DKFZp761A078; FLJ10287; MGC14816; DBT; RTCD1; CDC14A |
49 | 20 | 1.65 |
| 3 | 143407729 | 143828507 | 420778 | 0.0453791 | 0.422592 | MGC40579; XRN1; ATR; PLS1 |
35 | 13 | 1.80 |
| 3 | 17477922 | 17773653 | 295731 | 0.0459391 | 0.448171 | TBC1D5 | 84 | 40 | 1.42 |
| 2 | 112487241 | 112641378 | 154137 | 0.0460991 | 0.385732 | MERTK; FLJ14681; FLJ37440 |
27 | 9 | 2.00 |
| 7 | 42294711 | 42463020 | 168309 | 0.0469591 | 0.329253 | - | 6 | 0 | n.a. |
Chr – Chromosome; bp – Base Pairs; OR – Odds Ratio; n.a. – not available.