Impact of IQ on the diagnostic yield of chromosomal microarray in a community sample of adults with schizophrenia

Lowther, Chelsea; Merico, Daniele; Costain, Gregory; Waserman, Jack; Boyd, Kerry; Noor, Abdul; Speevak, Marsha; Stavropoulos, Dimitri J.; Wei, John; Lionel, Anath C.; Marshall, Christian R.; Scherer, Stephen W.; Bassett, Anne S.

doi:10.1186/s13073-017-0488-z

Table 1 Pathogenic CNVs (n = 41) identified in 39 unrelated participants with schizophrenia annotated by IQ group

From: Impact of IQ on the diagnostic yield of chromosomal microarray in a community sample of adults with schizophrenia

No.	ID	IQ group	Sex	Chr	Cytoband	Start (hg 19)	Size (bp)	CN	Segdups^a	Previously published^b	Genes (n)	Selected candidate gene(s)^d
1	2	Average	M	1	1q21.1	145,760,806	2,083,985	Gain	•	•	17	BCL9, GJA5, PRKAB2, GJA8, PDZK1
2	3	Average	F	1	1q21.1	145,932,468	1,898,716	Gain	•	•	15	BCL9, GJA5, PRKAB2, GJA8, PDZK1
3	562^f	Mod ID	F	2	2p16.3	51,066,869	563,162	Loss		•^c	1	NRXN1
4	570	BL	M	2	2p16.3	51,181,653	189,279	Loss		•^c	1	NRXN1
5	7^f	Average	M	2	2q13	111,388,632	1,727,361	Gain	•	•	9	ANAPC1, BCL2L11, MERTK
6	8	Average	M	2	2q13	111,388,632	1,727,361	Loss	•	•	9	ANAPC1, BCL2L11, MERTK
7	9	NVLD	M	2	2q13	111,388,632	1,727,361	Gain	•	•	9	ANAPC1, BCL2L11, MERTK
8	396	NVLD	M	3	3p26.1	4,418,429	277,309	Loss			3	SUMF1, ITPR1
9	13	NVLD	M	3	3q13.31	113,825,760	2,062,410	Loss		•	6	LSAMP, DRD3, ZBTB20, GAP43
10	452	Mild ID	M	3	3q27.1-q27.2	184,400,855	1,580,956	Loss			17	TRA2B
11	565^e,g	BL	F	5	5p15.33-5p15.2	113,577	10,191,390	Loss			83	IRX1, IRX2, IRX4, NDUFS6, SLC6A3, NSUN2, MTRR, CCT5
12	17	Average	F	5	5p15.33-p15.32	1,811,574	3,687,431	Loss		•	7	IRX1, IRX2, IRX4, NDUFS6
13	247	Mild ID	F	6	6p25.3-p25.1	149,661	6,836,705	Loss		•	35	FOXC1, GMDS, NRN1, TUBB2B
14	565^e,g	BL	F	6	6q26-q27	163,617,482	7,302,001	Gain			59	RNASET2, TBP
15	206	BL	F	7	7q22.2-q31.1	105,517,719	10,037,597	Loss		•	34	COG5, DOCK4, FOXP2, GPR85, IMMP2L, LAMB1, NRCAM, PIK3CG, PNPLA8
16	115	BL	F	8	8p23.3-p23.1	158,062	6,830,865	Loss		•	21	ANGPT2, CLN8, CSMD1, DLGAP2, MCPH1
17	40	Average	M	10	10q11.22-q11.23	46,485,761	5,173,684	Gain	•	•	42	CHAT, ERCC6, GDF2, GPRIN2, MAPK8, SLC18A3
18	569	Mild ID	M	13	13q14.13-q14.3	46,589,256	6,220,619	Loss	•		59	HTRA2, SUCLA2, ITMB2, RB1
19	48	BL	M	15	15q11.2-q13.1	20,181,700	6,498,447	Gain	•	•	121	CYFIP1, GABRB3, GABRA5, GABRG3, MAGEL2, NDN, UBE3A
20	556	Mild ID	M	15	15q11.2-q13.1	22,770,422	5,757,338	Gain	•		116
21	427	NVLD	F	15	15q11.2-q13.1	23,290,799	5,353,780	Gain	•		115	GABRB3, GABRA5, GABRG3, MAGEL2, NDN, UBE3A
22	49	NVLD	M	15	15q11.2-q13.1	23,641,514	5,432,624	Gain	•	•	106
23	50	Average	M	15	15q11.2-q13.1	23,641,514	4,892,894	Gain	•	•	101
24	52^j	Mod ID	F	15	15q13.2-q13.3	30,821,637	1,690,584	Loss	•	•	8	CHRNA7, OTUD7A, TRPM1
25	568	BL	M	16	16p11.2	29,432,213	744,308	Loss	•		40	DOC2A, MAPK3, PRRT2, QPRT, SEZ6L2, TBX6
26	55	Mild ID	F	16	16p11.2	29,567,309	624,599	Gain	•	•	26
27	56^f	Mild ID	F	16	16p11.2	29,567,309	659,635	Gain	•	•	33
28	57^e	Mild ID	M	16	16p11.2	29,567,309	624,599	Gain	•	•	26
29	58	Mild ID	M	16	16p11.2	29,567,309	659,635	Gain	•	•	33
30	277	Mild ID	F	19	19p13.3-p13.2	2,754,548	9,685,341	Gain		•	280	Various, including DNMT1, DOCK6
31	577	BL	M	22	22q11.2	18,890,046	2,831,545	Loss	•	•	46	Various, including DGCR8
32	581	Mild ID	F	22	22q11.2	18,890,046	2,831,545	Loss	•	•	46
33	582	Mild ID	M	22	22q11.2	18,890,046	2,831,545	Loss	•	•	46
34	579	BL	M	22	22q11.2	18,895,226	2,466,420	Loss	•	•	46
35	580ⁱ	NVLD	F	22	22q11.2	18,916,840	1,395,833	Loss	•	•	29
36	578^h	Mild ID	F	22	22q11.2	20,717,655	1,087,074	Loss	•		16	SNAP29, CRKL
37	271	Average	F	X	X chr (46, XO)	-	155,065,370	Loss			829	Various, including IL1RAPL1, SYN1
38	173	BL	M	X	X chr (47, XXY)	-	155,065,370	Gain		•	829
39	57^e	Mild ID	M	X	X chr (47, XXY)	-	155,065,370	Gain		•	829
40	194^f	Average	M	X	Xp22.33-p22.2	2,400,835	11,075,950	Loss			40	NLGN4X, VCX, MID1
41	574^f	Mild ID	F	X	Xp11.23-p11.22	48,178,414	4,508,892	Gain	•		97	Various, including SHROOM4, WDR45, SYP, FTSJ1

^aRare CNVs with one or both breakpoints falling within a segmental duplication are denoted by a bullet point
^bAll CNVs with a bullet point in this column were previously published in Costain et al. (2013) [10] or ^cLowther et al. (2017) [35]
^dThese candidate genes were previously reported in Costain et al. 2013 [10] or were based on a comparable method, i.e. genes associated with a neuropsychiatric or neurodevelopmental phenotype identified from a comprehensive literature search and/or in the Online Mendelian Inheritance in Man (http://www.omim.org/) database. Not every gene was systematically searched for those CNVs that overlapped ≥ 100 genes. Selected candidate genes are only reported once for recurrent CNVs
^eThese individuals carry a second CNV classified as pathogenic
^fThese individuals carry a second CNV classified as a VUS
^gThese two CNVs are part of an unbalanced translocation
^h,iThese are 22q11.2 deletions arising between low copy repeats: ^hB-D (atypical deletion) and ⁱA-B (typical, short nested deletion), respectively
^jCase 52 was identified to also have mosaic (6 of 24 cells) Turner syndrome by karyotype [10]
ID case identification number; Chr chromosome, CN copy number, Segdups flanking segmental duplication; Genes (n) number of RefSeq protein-coding genes overlapped, Average average IQ group, BL borderline IQ group, ID intellectual disability group (mild or moderate), NVLD non-verbal learning disability, M male, F female

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