Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation

Table 2 Summary of X chromosome CNVs identified on the three main AGH platforms selected for genotype-phenotype analysis.

Trio ID	CNV Type	Start*	Size*	Platforms Identified CNV	Genes Involved	Validation	Comment on Gene Function
6428	DEL	148 264 112	156 992	Affy	IDS	NT	Expression pattern not consistent with causing MR
2894	DEL	101 266 713	250 045	NimbleGen	5 RefSeq genes	NT	Expression pattern not consistent with causing MR[45]
3519	DEL	9 454 329	197 920	Affy	TBL1X	NT	Expression pattern not consistent with causing MR[46]
8960	DUP	67 416 262	7 057 217	All 3 platforms	57 RefSeq genes	FISH Pos	FISH Pos
9313	DEL	9 484 049	165 559	Affy	TBL1X	NT	Expression pattern not consistent with causing MR
3921	DUP	74 811 330	208 698	NimbleGen	TTC3L	NT	Expression pattern not consistent with causing MR[47]
1511	DEL	6 856 649	201 556	Affy	HDHD1A	NT	Expression pattern not consistent with causing MR[48]
2714	DEL	76 534 899	67 182	NimbleGen	FGF16	NT	Expression pattern not consistent with causing MR[49]
5993	DEL	6 932 549	130 699	NimbleGen	HDHD1A	NT	Expression pattern not consistent with causing MR[48]
4821	DEL	6 625 133	419 230	NimbleGen	HDHD1A	NT	Expression pattern not consistent with causing MR[48]
3921	DUP	74 811330	208 698	NimbleGen	MAGEE2	NT	Expression pattern not consistent with causing MR[47]
8960	DEL	29 967 317	203 809	Affy	MEGB2E	NT	Expression pattern not consistent with causing MR[50]
1815	DUP	67 767 923	2 019 581	NimbleGen	15 RefSeq genes including DLG3	NT	Amplification not reported to cause MR[31]
7093	DUP	73 429 587	263 642	NimbleGen	3 RefSeq genes including SLC16A2	NT	Females not affected[28]
3094	DEL	99 293 227	205 443	Affy	PCDH19	NT	Males not affected[30]
7093	DEL	6 687 308	906 505	Agilent & NimbleGen	STS	NT	Females not affected[29]

DEL = Deletion; DUP = Amplification, NT - Not tested; Pos = Positive; Neg = Negative; N/T = Not tested
*Start/end coordinates determined from largest region of overlap between any two platforms; size is the difference between these two coordinates (Build 36).

ISSN: 1755-8794