Table 3 Exonic copy-number mutations (CNMs) in DMD, SGs, CFTR, CDKL5, DCX, LIS1, KAL and F8 genes used to validate the custom CGH array

From: Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes

Gene	N°	Mutation type	Conventional name	Name	Conventional methods	Status	Size of the CNM determined by CGH array
DMD	1^a	Duplication	DMDdup2	c.32-?_93+?dup	QF-PCR, Q-PCR	He	250 kb
	2^a	Duplication	DMDdup2_34	c.32-?_4845+?dup	QF-PCR	He	772 kb
	3^a	Duplication	DMDdup3_9	c.94-?_960+?dup	QF-PCR	He	310.8 kb
	4^a	Duplication	DMDdup17	c.1993-?2168+?dup	QF-PCR	He	11.1 kb
	5^a	Duplication	DMDdup5_7	c.265-?_649+?del	QF-PCR	He	130 kb
	6^a	Deletion	DMDdele45	c.6439-?_6614+?del	QF-PCR	He	151 kb
	7^a	Deletion	DMDdele45	c.6439-?_6614+?del	QF-PCR	He	17.4 kb
	8^a	Duplication	DMDdup48_49	c.6913-?_7200+?dup	QF-PCR	He	57 kb
	9^a	Deletion	DMDdele51	c.7310-?_7542+?del	QF-PCR	He	49.8 kb
	10^a	Deletion (mosaic)	DMDdele49_52	c.7099?_7660+?del	QF-PCR, RT-PCR	He	106 kb
	11^a	Duplication	DMDdup55	c.8028-?_8217+?dup	QF-PCR	Ht	56 kb
	12^a	Deletion	DMDdele46_47	c.6615-?_6912+?del	QF-PCR	He	23.9 kb
	13	Deletion	DMDdele53	c.7661-?_c.7872+?del	QF-PCR	He	18 kb
	14	Duplication	DMDdup7	c.531-?_649+?dup	QF-PCR	He	2.2 kb
	15^a	Deletion	DMDdele45_47	c.6439-?_6912+?del	QF-PCR	Ht	149.4 kb
	16	Duplication (mosaic)	DMDdup61-62	c.9085-?_9224+?dup	QF-PCR, Q-PCR	Ht	2.3 kb
SGCG	17^a	Deletion	SGdele5_6	c.386-?_578+? del/c.386-?_578+?del	QF-PCR	Ho	37.2 kb
	18^a	Deletion	SGdele3	c.196-?_297+?del/c.196-?_297+?del	QF-PCR	Ho	16.2 kb
	19^a	Deletion	SGdele7	c.579-?_702+?del/c.579-?_702+?del	QF-PCR	Ho	4.2 kb
	20^a	Deletion	SGdele7	c.579-?_702+?del	QF-PCR	Ht	4.2 kb
SGCA	21^a	Deletion	ASGdele7_8	c.748-?_983+?del	QF-PCR	Ht	1.2 kb
CFTR	22^a	Deletion	CFTRdele3_10,14b_16	c.165-?_1584+?del;c.2620-?_2988+?del	MLPA	Ht	84 kb
	23^a	Deletion	CFTRdele17a_17b	c.2989-977_3367+248del2515	MLPA	Ht	2.5 kb
	24^a	Deletion	CFTRdele17a_18	c.2989-449_3468+644del5288	MLPA	Ht	5.2 kb
	25^a	Deletion	CFTRdele2_3	c.54-?_273+?del	MLPA	Ht	21 kb
	26^a	Deletion	CFTRdele22_23	c.3964-78_4242+577del1532	MLPA	Ht	1.5 kb
CDKL5	27	Deletion	CDKL5dele1	c.1-?_345+?del	MLPA	Ht	294. 4 kb
DCX	28	Deletion (mosaic 40:60, mutant:WT)	DCXdele4	c.706_5550_808+39del	QF-PCR, Q-PCR	He	6.2 kb
	29	Duplication	DCXdup4_7	c.705+18032_backbone	QF-PCR	He	81.6 kb
	30	Duplication	DCXdele2 Turner mosaique 20%	c.backbone_364+1054del	QF-PCR	Ht	7.9 kb
LIS1 (Pafah1b1)	31	Deletion Mieller Diecker	LIS1entire gene deletion	c.1-?_1233+?del	QF-PCR	Ht	740 kb
	32	Deletion	LIS1entire gene deletion AFH1B1dele4_11	c.1-?_1233+?del	QF-PCR	Ht	65.2 kb
	33	Deletion	LIS1entire gene deletion	c.1-?_1233+?del	QF-PCR	Ht	8.7 kb
	34	Deletion	LIS1entire gene deletion	c.1-?_1233+?del	QF-PCR	Ht	51.8 kb
KAL1	35	Deletion	KAL1 entire deletion	c.1-?_2043+?del	Southern blot	He	2297 kb
	36		KAL1 entire deletion	c.1-?_2043+?del	Southern blot	He	1600 kb
	37		Kal 1 dele3_13	c.256-?_1984+?del	Southern blot	He	91 kb
F8	38	Deletion	F8dele2_6	c.143-?_670+?del (new) c.86-?_613+?del (old)	PCR	He	38.6 kb

Abbreviations: N°, number; He, hemizygous patients, Ht, heterozygous individuals; Ho, homozygous patients.
A total of 38 control DNAs were studied in a blind trial. Nomenclature corresponds to the approved nomenclature. For hemophilia there are two nomenclatures: one that takes into account the peptide signal (the new nomenclature), one that does not take into consideration the peptide signal (the old nomenclature). Both are still used, to date, for diagnostic reports, and are indicated in the table.
^aControl samples tested with the previous CGH array design.¹³

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Table 3 Exonic copy-number mutations (CNMs) in DMD, SGs, CFTR, CDKL5, DCX, LIS1, KAL and F8 genes used to validate the custom CGH array

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