. 2013 Feb 7;92(2):221–237. doi: 10.1016/j.ajhg.2012.12.016

Table 2.

Atypical Exon-Disrupting Events of Disease-Associated Hotspot Regions in Children with Autism

Region	Genomic Coordinates (hg18)	Sample	Size (bp)	Genes	Event	Inheritance	Case Probes	Control Probes	Control Events^a	p Value
1q21.1	chr1: 145,182,393–145,442,505	12719.p1	260,112	CHD1L, LINC00624	del	maternal	323	118	0	n/a
1q21.1	chr1: 145,302,783–145,354,227	12345.p1	51,444	LINC00624	del	maternal	59	4	n/a	n/a
1q21.1	chr1: 145,302,783–145,354,227	11712.p1	51,444	LINC00624	del	maternal/paternal	59	4	n/a	n/a
3q29	chr3: 197,762,959–197,767,300	14045.p1	4,341	WDR53	del	paternal	7	3	n/a	n/a
3q29	chr3: 198,022,697–198,054,675	13144.p1	31,978	PAK2	dup	paternal	47	44	0	n/a
3q29	chr3: 198,682,714–198,836,982	AU1087301	154,268	BDH1	dup	paternal	221	75	0	0.242
3q29	chr3: 198,682,714–198,836,982	13746.p1	154,268	BDH1	dup	maternal	221	75	0	0.242
10q23	chr10: 81,575,201–81,959,837	13214.p1	384,636	MBL1P1, SFTPD, LOC219347, C10orf57, PLAC9, ANXA11	del	maternal	534	247	1	0.301
10q23	chr10: 81,809,415–81,833,598	13582.p1	24,183	LOC219347, C10orf57	del	paternal	35	6	n/a	n/a
10q23	chr10: 81,824,603–81,834,112	12969.p1	9,509	LOC219347, C10orf57	del	paternal	16	3	n/a	n/a
10q23	chr10: 82,084,686–82,106,599	12378.p1	21,913	DYDC1	dup	maternal	34	9	n/a	n/a
10q23	chr10: 82,084,686–82,106,599	13634.p1	21,913	DYDC1	dup	paternal	34	9	n/a	n/a
10q23	chr10: 82,084,686–82,106,599	14055.p1	21,913	DYDC1	dup	maternal	34	9	n/a	n/a
10q23	chr10: 82,084,686–82,106,599	14343.p1	21,913	DYDC1	dup	maternal	34	9	n/a	n/a
10q23	chr10: 82,084,686–82,106,599	11545.p1	21,913	DYDC1	dup	maternal	34	9	n/a	n/a
10q23	chr10: 82,084,686–82,106,599	13611.p1	21,913	DYDC1	dup	maternal	34	9	n/a	n/a
10q23	chr10: 82,084,686–82,106,599	AU1763301	21,913	DYDC1	dup	maternal	34	9	n/a	n/a
10q23	chr10: 82,359,933–82,366,203	14348.p1	6,270	SH2D48	del	paternal	10	5	n/a	n/a
10q23	chr10: 84,593,836–84,680,305	13889.p1	86,469	NRG3	dup	maternal	132	40	0	n/a
15q13.3	chr15: 29,142,646–29,178,949	13686.p1	36,303	TRPM1	del	maternal	54	18	0	0.029
15q13.3	chr15: 29,142,646–29,178,949	AU0316301	36,303	TRPM1	del	paternal	54	18	0	0.029
15q13.3	chr15: 29,142,646–29,178,949	AU2275301	36,303	TRPM1	del	paternal	54	18	0	0.029
15q13.3	chr15: 29,142,646–29,178,949	AU079904	36,303	TRPM1	del	maternal/paternal	54	18	0	0.029
15q13.3	chr15: 29,176,938–29,188,508	AU1006301	11,570	TRPM1	del	maternal	17	6	n/a	n/a
15q24.1	chr15: 70,788,521–70,793,560	12132.p1	5,039	BBS4	del	maternal	5	1	n/a	0.242
15q24.1	chr15: 70,788,521–70,793,560	AU084503	5,039	BBS4	del	paternal	5	1	n/a	0.242
15q24.2	chr15: 74,294,283–74,297,672	AU1228303	3,389	ETFA	del	paternal	15	2	n/a	n/a
16p13.11	chr16: 15,476,243–15,515,874	13215.p1	39,631	C16orf45	del	paternal	61	19	0	n/a
16p11.2	chr16: 29,961,147-29974677	14004.p1	13,530	ALDOA	del	maternal	16	6	n/a	n/a
17q12	chr17: 32560142-32732763	11234.p1	172,621	ACACA	del	maternal	304	92	0	n/a
17q12	chr17: 33,179,017–33,351,760	11002.p1	172,743	HNF1B (TCF2), LOC284100	dup	maternal	282	68	0	n/a
22q11.21	chr22: 17,413,909–17,429,856	12686.p1	15,947	DGCR2	del	paternal	26	6	n/a	n/a
22q11.21	chr22: 17,703,043–17,719,750	11599.p1	16,707	HIRA	del	maternal	17	6	n/a	n/a
22q11.21	chr22: 19,455,582–19,462,562	12878.p1	6,980	SERPIND1	del	paternal	11	7	n/a	n/a
22q13.31	chr22: 46,964,885–47,079,942	13698.p1	115,058	MIR3201	dup	paternal	163	95	0	0.242
22q13.32	chr22: 47,131,579–47,224,607	AU1678301	93,028	MIR3201	dup	maternal	134	75	0	0.242
22q13.32	chr22: 48,026,222–48,302,803	13722.p1	276,581	C22orf34	del	maternal	406	284	1	n/a

None of the above events were observed in controls assayed with our custom microarray (n = 580).

Control events, defined here as atypical CNVs that overlap with the reported event, were identified from population controls ran on Illumina 1M SNP array platform (n = 2,090). Control CNVs were assessed only if coverage exceeded ten probes on the SNP array.