Table 2.

The 20 most frequent recurring copy number aberrations in childhood leukemia, as detected by molecular inversion probes

						Lineage-specific cases, %
Cases, no.	Typea	Chr	Location	Ref.b	Length bp	B-ALL (n = 23)	T-ALL (n = 6)	AML (n = 14)	Genes in regionc
23	Loss	16	16q22.3	–	10352	44	83	50	MLKL
	Gain	16	16q22.3	–	–	4	–	–	MLKL
22	Loss	10	10q25.2	–	2490	57	67	36	ADRA2A
19	Loss	7	7q21.13	–	1363	35	67	43	FZD1
	Gain	7	7q21.13	–	–	4	–	–	FZD1
19	Loss	17	17p13.1	[10]	1978	17	17	36	none known
	Gain	17	17p13.1	–	–	26	17	14	none known
17	Loss	14	14q24.2	[10]	270	30	50	36	none known
	Gain	14	14q24.2	–	–	9	–	–	none known
16	Loss	4	4p16.3	–	79037	9	–	14	TACC3
	Gain	4	4p16.3	–	–	26	33	29	TACC3
15	Loss	21	21q22.11	[11]	7219	4	–	7	OLIG2
	Gain	21	21q22.11	–	–	30	17	36	OLIG2
15	Loss	5	5q35.3	–	18679	17	67	50	CLK4
15	Loss	1	1p36.12	–	203480	44	50	14	EIF4G3, HP1BP3, SH2D5, KIF17, DDOST
14	Loss	6	6p22.1	–	717	9	–	7	none known
	Gain	6	6p22.1	–	–	26	17	29	none known
14	Loss	9	9p21.3	[10,11]	24424	35	100	–	CDKN2A
13	Loss	11	11q13.2	–	3454	22	33	36	none known
	Gain	11	11q13.2	–	–	4	–	–	none known
13	Gain	2	2q31.1	–	12837	30	33	29	HOXD13
12	Loss	2	2q35	–	2774	9	17	36	FEV
	Gain	2	2q35	–	–	4	17	14	FEV
12	Loss	1	1p35.1	–	25184	4	17	7	MARCKSL1
	Gain	1	1p35.1	–	–	22	17	21	MARCKSL1
13	Loss	8	8p12~p11.2	–	938	17	33	7	ADRB3
	Gain	8	8p12~p11.2	–	–	13	–	21	ADRB3
13	Loss	14	14q32.32.32.33	–	1223220	4	–	14	>5 genes
	Gain	14	14q32.32~32.33	–	–	26	17	21	>5 genes
12	Gain	21	21q22.2	[10]	423958	48	17	–	ETS2, FLJ45139, PSMG1d
11	Loss	14	14q11.2	–	280777	17	50	–	none known
	Gain	14	14q11.2	–	–	9	–	14	none known
11	Loss	17	17q12	–	29229	9	17	21	MLLT6
	Gain	17	17q12	–	–	13	–	14	MLLT6

Abbreviations: ALL, acute lymphoblastic leukemia; AML, acute myeloid leukemia; Chr, chromosome; CNA, copy number aberration; Ref., references.

^aLoss is defined as copy number ≤ 1.2. Gain is defined as copy number ≥ 2.8.

^bReferences: Mullighan et al., 2007 [10]; Kuiper et al., 2007 [11].

^cBased on > 1,000 genes involved in cancer development: oncogenes, tumor suppressors, DNA repair genes, cell growth genes, and metabolism genes.

^dThe PSMG1 gene was previously described as DSCR2.