Table 5.
Specific examination of regions with rare variants that associate with neuropsychiatric illness
| Region | Reason for inclusion | Chr | Implicated regiona | Region examinedb | Size examinedb | # SNPsc | lowest P | Bonferroni corrected significance thresholdd |
|---|---|---|---|---|---|---|---|---|
| 1q21.1 | Deletion associated with schizophrenia, autism, mental retardation, behavioral abnormalities, micro/macrocephaly and other congenital abnormalities (69,77,78,102) | 1 | 144 106 312–146 293 282 | 143 328 536–148 205 522# | 4.88 Mb | 241 | 0.01 | 0.0002 |
| NRXN1 | Deletions including parts of NRXN1 have been associated with schizophrenia (6,62,64) and autism (61,65) | 2 | 49 999 148–51 113 178 | 49 875 535–51 225 851 | 1.35 Mb | 310 | 0.00003 | 0.0002 |
| CNTN4 | Rare deletions and duplications have been implicated in autism (61,103) | 3 | 2 117 247–3 074 645 | 2 026 065–3 095 571 | 1.07 Mb | 432 | 0.004 | 0.0001 |
| 8p22 | Deletion >2 Mb found in schizophrenia patient, no deletion of this size seen in controls (6) | 8 | 15 112 352–18 360 000 | 15 090 765–18 434 971 | 3.34 Mb | 1062 | 0.0009 | 0.00005 |
| 15q11.2 | Large deletions have been associated with schizophrenia (69,102,104) | 15 | 20 306 549–20 777 695 | 18 421 386–21 339 423 | 2.91 Mb | 140 | 0.04 | 0.0004 |
| APBA2 | Deletions have been associated with schizophrenia (6,62) | 15 | 27 001 135–27 197 807 | 26 017 833–27 230 795 | 1.21 Mb | 82 | 0.04 | 0.0007 |
| 15q13.3 | Deletions and duplications have been associated with schizsophrenia, autism, epilepsy and other neural phenotypes (69,72,102,105,106) | 15 | 28 723 577–30 302 218 | 28 079 091–30 760 289 | 2.68 Mb | 317 | 0.008 | 0.0002 |
| 16p11.2 | Deletions and duplications have been associated with autism, mental retardation and learning and language disabilities (70,107) | 16 | 29 500 000–30 100 000 | 29 045 893–30 453 989 | 1.41 Mb | 86 | 0.003 | 0.0007 |
| 16p12.4–p13.11 | Deletions and duplications have been found in schizophrenia, autism, mental retardation, epilepsy and learning disability (6,79,104,108,109) | 16 | 15 387 381–18 072 544 | 14 458 540–18 874 875 | 4.42 Mb | 526 | 0.001 | 0.0001 |
| 22q11 | 22q11 Deletion syndrome is associated with a high incidence of psychiatric disorders, particularly schizophrenia (110–112) | 22 | 17 257 788–19 792 353 | 16 974 931–2 037 5603 | 3.4 Mb | 534 | 0.0002 | 0.0001 |
Bold case indicates P value significant after Bonferroni correction for number of tested SNPs.
aApproximate: not all events are identical and endpoints depend to some extent on how the deletion was identified (e.g. using a genome-wide SNP array versus CNV-specific assay).
bImplicated region plus ∼100 kb either side.
cIncludes only SNPs included in the association testing (see Materials and Methods).
dCorrected for SNPs testing in this region only.
eDue to sparse coverage in region only five SNPs upstream were included.