Table 2 Large-scale CNV studies that reveal common and rare variants associated with ASD
From: Autism genetics: searching for specificity and convergence
References | Participants | All CNVs (de novoand inherited) | De novoCNVs only | Recurrent de novoor inherited CNVs in cases | Single genes, ASD-associated genes and regions in de novoCNVs found in cases |
|---|---|---|---|---|---|
Sebat et al. 2007 [49] | 264 families (AGRE/NIMH), 118 simplex, 47 multiplex, 99 control, 195 cases, 196 controls | Focused on CNVs only | 7.2% of cases; 1% of controls; de novo variants larger than 3 Mb: 2.6% of cases; 0.51% of controls | De novo: 2q37.3 (2 del), 3p14.2 (1 dup, 1 del) (cases only) | SLC4A10, FHIT, FLJ16237, A2BP1 |
Szatmari et al. 2007 [50] | 173 families (AGP), multiplex, 196 cases, 292 unaffected sibs | 624 total; no significant difference in frequency of CNVs overall in cases and controls. 1.3 CNVs/genome in cases; mean size, 3.4 Mb; 1.27 CNVs/genome in controls; mean size, 4.3 Mb | 5.1% of cases, 2.1% of controls | 47 CNVs (18 regions) in cases | 17p12, 22q11.2, NRXN1 |
Marshall et al. 2008 [51] | 427 families, 237 simplex, 189 multiplex, 427 cases, 500 controls (unrelated), 1,152 additional controls | 2,873 total. No significant difference in frequency of CNVs overall in cases and controls. 3.1 CNVs/genome in cases; mean size, 603 kb; 3.1 CNVs/genome in controls (n = 500); mean size, 470 kb | 27 ASD cases with de novo variants not found in 1,152 additional controls | 983/94 (overlapping CNV/loci) in 427 cases; 31/13 case-only (overlapping CNV/loci) not found in 1,152 additional controls. De novo: 5p15.31-p15.2 (2 del) 7q31.1-q32.2 (2 del) 15q11.2-q13.3 (2 dup) 16p11.2 (1 dup, 2 del) | CDH18, DPYD, NLGN4, DPP6, DLGAP2, ANKRD11, SHANK3 |
Pinto et al. 2010 [52] | 876 families (AGP), simplex/multiplex, 996 cases, 1,752 parents, 1,287 additional controls | 5,478 total. 1.19-fold increase in CNVs in cases over controls.1.69 case/control ratio for CNVs ≥ 500 kb. 219 inherited CNVs not in controls and disrupting single genes (DDX53-PTCHD1) | 50 out of 876 of ASD cases harbor de novo CNVs. Seven de novo CNVs not in controls and disrupting single genes | NA | SHANK2, SYNGAP1, DLGAP2 |
Sanders et al. 2011 [21] | 1,124 families* (SSC), simplex, 1,124 cases, 2,248 parents, 872 unaffected sibs | No significant difference in frequency of inherited CNVs in cases and controls | Cases (n = 872), controls (n = 872). All de novo CNVs: 5.9% of cases; 1.7% of sibs OR: 3.5. Multigenic de novo CNVs: 4.9% of cases; 0.92% sibs; OR: 5.6. Mean number of genes/CNV 21.4 in cases; 4.6 in sibs. De novo variants larger than 1 Mb: 2.5% cases; 0.5% controls, OR: 5.6 | De novo: 1q21.1 (2 dup); 7q11.23 (4 dup); 15q13.2-q13.3 (1 dup/1 del); 16p11.2 (4 dup, 7 del); 16p13.2 (2 dup); 16q23.3 (2 del) | CDH13, USP7, C16orf72 |
Levy et al. 2011 [20] | 887 families (SSC), simplex, 858 cases, 863 unaffected sibs | No significant difference in frequency of inherited CNVs in cases and controls | 7.9% in cases (median genes per CNV: 4) 2% in unaffected sibs (median genes per CNV: 0) | De novo: 16p11.2 (4 dup, 6 del); 7q11.23 (2 dup); 16p13.2 (2 dup, 1 del); 12 recurrent loci representing 121 events (data combined with [52]) | DDX53-PTCHD1, USP7 |