Table 2.
Loci Enriched for CNVs in Autism, Mental Retardation, and Schizophrenia Identified by Disease Meta-Analysis
| Chr | Start | Stop | Length | Note | NAHRa | Total CNVs | Type | Disease CNVs | Control CNVs | Diseases and Studies | CNV p Value | Locus p Value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| chr15 | 27,015,263 | 30,650,000 | 3,634,737 | Prader-Willi/15q13 | yes | 19 | loss | 19 | 0 | schizophrenia23 | 1.08E-05 | |
| chr15 | 18,376,200 | 30,756,771 | 12,380,571 | 58 | gain | 45 | 13 | autism,19,22,45–47 mental retardation,44 schizophrenia,23 controls,23 this study | 2.69E-04 | 1.54E-07 | ||
| chr22 | 17,014,900 | 19,993,127 | 2,978,227 | VCFS | yes | 31 | loss | 31 | 0 | autism,19,45,47 mental retardation,44 schizophrenia23,48 | 7.93E-09 | |
| chr22 | 17,200,000 | 21,546,762 | 4,346,762 | 14 | gain | 9 | 5 | autism,19,45–47 schizophrenia,23 controls,23 this study | 0.330 | 9.53E-07 | ||
| chr1 | 142,540,000 | 146,059,433 | 3,519,433 | 1q21 | yes | 27 | loss | 24 | 3 | autism,19 schizophrenia,23 controls23 | 1.67E-04 | |
| chr1 | 142,800,580 | 146,009,436 | 3,208,856 | 15 | gain | 12 | 3 | autism,19,45 mental retardation,44 schizophrenia,23 controls23 | 0.041 | 2.16E-05 | ||
| chr22 | 45,144,027 | 49,509,153 | 4,365,126 | Terminal 22 del syndrome | no | 4 | loss | 4 | 0 | autism22,45,47 | 0.090 | |
| chr22 | 47,572,875 | 48,323,417 | 750,542 | 6 | gain | 5 | 1 | autism,19,46,47 schizophrenia,23 controls23 | 0.160 | 0.022 | ||
| chr16 | 29,470,951 | 30,252,473 | 781,522 | 16p11.2 | yes | 11 | loss | 8 | 3 | autism,19,22,46,47 controls23 | 0.186 | |
| chr16 | 29,474,810 | 30,235,818 | 761,008 | 7 | gain | 6 | 1 | autism,19,47 schizophrenia,23,24 this study | 0.100 | 0.039 | ||
| chr17 | 14,000,000 | 15,421,835 | 1,421,835 | CMT1A/HNPP | yes | 7 | loss | 6 | 1 | autism,19,46 schizophrenia,23 controls23 | 0.100 | |
| chr17 | 12,650,000 | 15,540,000 | 2,890,000 | 5 | gain | 4 | 1 | autism,45 mental retardation,44 schizophrenia,23 controls23 | 0.252 | 0.041 | ||
| chr16 | 60,141,700 | 61,581,600 | 1,439,900 | 16q21, CDH8 | no | 4 | loss | 4 | 0 | autism45 | 0.090 | |
| chr16 | 60,552,237 | 61,294,685 | 742,448 | 1 | gain | 1 | 0 | schizophrenia23 | 0.547 | 0.049 | ||
| chr11 | 78,120,000 | 85,610,000 | 7,490,000 | 11q14.1 | no | 3 | loss | 3 | 0 | mental retardation,44 schizophrenia23 | 0.164 | |
| chr11 | 84,304,683 | 85,042,205 | 737,522 | 1 | gain | 1 | 0 | schizophrenia23 | 0.547 | 0.090 | ||
| chr2 | 185,118,087 | 185,909,729 | 791,642 | 2q32.1 | no | 1 | loss | 1 | 0 | schizophrenia23 | 0.547 | |
| chr2 | 184,270,000 | 186,892,000 | 2,622,000 | 3 | gain | 3 | 0 | autism45 | 0.164 | 0.090 | ||
| chr15 | 82,573,421 | 83,631,697 | 1,058,276 | 15q25 | yes | 4 | loss | 4 | 0 | autism,46,47 schizophrenia23 | 0.090 | |
| chr15 | na | na | na | 0 | gain | 0 | 0 | none | 1 | 0.090 | ||
| chr9 | 140575 | 1175526 | 1,034,951 | 9p24 | no | 1 | loss | 1 | 0 | schizophrenia,23 | 0.547 | |
| chr9 | 206456 | 1599250 | 1,392,794 | 3 | gain | 3 | 0 | autism,45 schizophrenia,23 | 0.164 | 0.090 | ||
| chr3 | 197,179,156 | 198,842,299 | 1,663,143 | 3q29 | yes | 3 | loss | 3 | 0 | schizophrenia23,24 | 0.164 | |
| chr3 | 198,325,925 | 199,384,429 | 1,058,504 | 2 | gain | 1 | 1 | schizophrenia,23 controls23 | 1 | 0.252 | ||
| chr16 | 21,693,739 | 22,611,363 | 917,624 | 16p12 | yes | 5b | loss | 5b | 0 | autism,47 schizophrenia23 | 0.049 | |
| chr16 | 21,441,805 | 22,688,093 | 1,246,288 | 5 | gain | 2 | 3 | autism,47 schizophrenia,23 controls23 | 1 | 0.261 | ||
| chr16 | 80,722,684 | 82,227,917 | 1,505,233 | 16q23.3, CDH13 | no | 2 | loss | 0 | 2 | controls,23 this study | 1 | |
| chr16 | 80,737,839 | 82,208,451 | 1,470,612 | 4 | gain | 4 | 0 | autism,46 schizophrenia23,24 | 0.090 | 0.436 |
a
Indicates if there are large segmental duplications near breakpoints in hg17.
b
A deletion of ∼480 kb in size in a schizophrenic sample is included in this count.