Identification of candidate intergenic risk loci in autism spectrum disorder

Walker, Susan; Scherer, Stephen W

doi:10.1186/1471-2164-14-499

BMC Genomics

Table 1 ASD specific CNVs in intergenic regions

From: Identification of candidate intergenic risk loci in autism spectrum disorder

Locus	Gene	Sample	CNV	Start	End	Size	Furthest distance from gene	Bin
2p16.3	NRXN1 AK127244 mRNA	1-0045-004	loss	51405882	51524684	118802	1124	ii
		8-3394-003	loss	51439897	51479683	39786
		8-3394-003	loss	51157414	51189362	31948
		8-14144-2420	loss	51157414	51225851	68437
		1-0496-003	gain	52220120	52238172	18052
		1-0449-003	loss	52237072	52253660	16588
3p22.3	ARPP21	2-1213-003	loss	34984049	35102773	118724	563	ii
3p22.3	ARPP21	3-0100-000	gain	35086691	35094736	8045	563	ii
3q24	C3orf58 ZIC1, ZIC4	1-0007-003	loss	146168760	146934953	766193	1383 1955, 1979	i
3q24	C3orf58 ZIC1, ZIC4	8-3093-004	loss	146575437	146631141	55704	1383 1955, 1979	i
4q13.1	EPHA5	8-14208-3350	loss	66505324	66633530	128206	840	i
		8-14186-3050	loss	66515708	66633530	117822
		1-0138-004	loss	66515708	66633530	117822
		2-0082-004	loss	67045815	67134170	88355
		1-0455-003	loss	67058506	67075558	17052
6p21.2	MOCS1	3-0139-000	gain	40021898	40078515	56617	168	i or ii
		2-0139-003	gain	40023327	40062155	38828
		1-0381-003	loss	40174188	40209324	35136
		2-1368-003	loss	40174188	40210694	36506
7q21.11	SEMA3C	8-6258-03	loss	80431202	80512022	80820	96	i
7q21.11	SEMA3C	1-0345-005	loss	80482597	80517630	35033	96	i
8p12	UNC5D NRG1	8-14243-3670	loss	34923482	34956067	32585	256 2183	i
		3-0044-000	loss	34923482	34956067	32585
		3-0300-000	loss	34925149	34957854	32705
		8-14181-2940	loss	34923482	34956067	32585
8q24.13	ZHX2	8-3317-003	gain	123572785	123625681	52896	237	i or ii
8q24.13	ZHX2	3-0186-000	loss	123583028	123639417	56389	237	i or ii
9q33.1	ASTN2	8-3055-004	loss	119254497	119374796	120299	98	i
9q33.1	ASTN2	3-0115-000	loss	119314967	119319559	4592	98	i
9q34.2	OLFM1 RXRA	2-1272-003	gain	136479329	136604233	124904	508 8	i
9q34.2	OLFM1 RXRA	2-1189-003	gain	136480334	136598491	118157	508 8	i
11p14.3	LUZP2	8-14175-2820	loss	24177612	24316053	138441	160	i or ii
		8-14059-1020	loss	24262511	24303132	40621
		8-14208-3350	loss	24262511	24303132	40621
11p12	LRRC4C	8-14208-3350	gain	40304880	40703298	398418	196	iii
		2-0272-003	loss	40379668	40550356	170688
		SK0167-003	loss	40417554	40610400	192846
		3-0208-000	loss	40468058	40492541	24483
11p12	LRRC4C	8-14032-600	loss	41990280	42021250	30970	1738	i or ii
		8-3276-003	loss	42243624	42279094	35470
		2-0286-003	loss	42243624	42279094	35470
11q13.2	MRGPRD	4-0023-003	loss	68486121	68493638	7517	10	i
11q13.2	MRGPRD	2-1075-003	loss	68486121	68500238	14117	10	i
16q21	CDH8	8-14251-3750	loss	61650435	61787984	137549	1030	i or ii
		2-1175-003	loss	61658675	61755232	96557

Location and size of all CNVs discovered are listed with the proposed associated candidate gene. Bin denotes possible mechanism of action by i) altering sequence elements required for regulating expression of neighboring genes ii) affecting undiscovered genes or non-coding RNAs iii) disrupting uncharacterised isoforms of adjacent genes. Genome browser views of all loci are shown in Figure 1 and Additional file 1. All pedigrees are shown in Additional file 2. Additional sample SK0167-003 identified in reference [19].

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ISSN: 1471-2164

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