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

Table 1 Summary of autosomal de novo CNVs identified on the three main AGH platforms selected for genotype-phenotype analysis.

Trio ID	Chr	CNV Type	Start*	Size*	Platforms Identified CNV	# of RefSeq Genes	Validation	Comment on Gene Function
1815	3	DEL	196 904 149	54 518	Agilent	1	NT	Mucin 20 - Expression pattern not consistent with causing MR[40]
4821	5	DEL	68 950 015	1 329 642	NimbleGen	7	NT	Mutations in SMN1 associated with spinal muscle atrophy[41]
8960	5	DUP	180 309 941	55 922	NimbleGen	2	MLPA Pos	Expression pattern not consistent with causing MR[42]
1815	6	DEL	111 807 663	9 889 630	All 3 platforms	57	FISH Pos	Likely pathogenic based on size
7531	9	DEL	139 496 489	333 935	All 3 platforms	7	FISH Pos	CNVs in region previously reported as pathogenic[32]
1815	12	DEL	11 371 263	83 667	NimbleGen	1	MLPA Pos	Expression pattern not consistent with causing MR[43]
1056	13	DEL	107 190 506	2 206 948	All 3 platforms	5	FISH Pos	Encompassed within de novo CNV in DECIPHER patient with MR
4821	16	DEL	3 862 993	78 891	All 3 platforms	1	MLPA Pos	CNVs in region previously reported as pathogenic[35]
3921	17	DEL	41 062 469	657 364	All 3 platforms	8	FISH Pos	CNVs in region previously reported as pathogenic[33]
9609	21	DEL	33 902 218	152 885	All 3 platforms	2	MLPA Pos	Important in spinal development[37]
9609	22	DEL	19 062 809	728 798	All 3 platforms	19	FISH Pos	CNVs in region previously reported as pathogenic[34, 44]
8327	22	DUP	19 412 033	378 797	All 3 platforms	13	MLPA Pos	Mutation has been reported in family with normal phenotype[25]

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