TestAMLtable

Table 1 - A comprehensive list of copy number alterations detectable by CMA testing with strong diagnostic, prognostic and treatment implications in AML. Table derived from Xu et al., 2018 [PMID 30344013] with permission from Cancer Genetics.

Chromosome	AML Subtype	Abnormality Type (Gain, Loss, CN-LOH)	Region	Relevant Genes (if known)	Clinical Significance	Level of Evidence	Reference
1	AML including NK-AML	CN-LOH	1p		D	3	[11, 29, 30, 67-69, 102-104]
2	AML	CN-LOH	2p	DNMT3A	D	3	[11, 65, 100]
3	NK-AML, sAML	Loss	3p14.1	FOXP1	D	3	[30, 57, 66]
4	sAML, pAML	CN-LOH	4q24	TET2	D	3	[67, 71, 105]
4	AML, NK-AML, sAML	Loss	4q24	TET2	D, P	3	[42, 45, 66]
5	pAML, sAML	Loss	5q		D	1	[24, 33, 45, 49, 57, 66, 77, 87, 88, 106-108]
6	AML including NK-AML	CN-LOH	6p		D	3	[29, 30, 102, 104]
7	AML including NK-AML	CN-LOH	7q	EZH2	D	3	[67, 102, 109]
7	NK-AML, pAML, sAML	Loss	7q	EZH2, CUX1	D	1	[28, 57, 66, 110]
8	complex karyotype AML	Amplification	8q24	MYC	D, P	3	[24, 49, 61]
9	NK-AML, sAML	CN-LOH	9p	JAK2	D	3	[66, 67, 104]
11*	AML w complex karyotype	Amplification	11q23	MLL (KMT2A)	D, P	3	[49, 111]
11*	AML	CN-LOH	11p	WT1	D	3	[11, 30, 65, 102]
11	pAML, sAML, NK-AML	CN-LOH	11q	CBL	D	3	[11, 65-67, 102]
12	AML, NK-AML, AML w complex karyotype, sAML	Loss	12p13.2	ETV6	D	3	[24, 30, 33, 49, 57, 61, 66, 77, 104, 108, 111-115]
13*	pAML, NK-AML, NPM1 mutated AML, FLT3-ITD pos AML, sAML	CN-LOH	13q	FLT3	D, P	2	[11, 28-31, 65-69, 102, 104, 109, 116-118]
16	NK-AML, AML w complex karyotype, pAML, sAML	Loss	16q	CBFB	D	3	[29, 49, 61, 108]
17	AML, NK-AML, pAML, sAML	CN-LOH	17p	TP53	D	3	[11, 28, 29, 65, 67, 102, 107]
17	sAML, NK-AML, AML w complex karyotype, de novo AML	Loss	17p	TP53	D, P	1	[24, 28, 29, 49, 61, 66, 88, 106-108, 114]
17	NK-AML, pAML	Loss	17q11.2	NF1, SUZ12	D, P	3	[24, 28, 29, 47-49, 61, 66, 104, 111]
19*	AML, NK-AML, sAML	CN-LOH	19q	CEBPA	D	3	[11, 29, 30, 69, 102, 105]
20	sAML	Loss	20q		D	3	[24, 66, 119, 120]
21*	pAML, AML w complex karyotype	Amplification	21q22	ERG, ETS2	D, P, T	3	[49, 57, 61, 62, 121]
21*	AML, NK-AML, sAML	CN-LOH	21q	RUNX1	D	3	[11, 29, 67, 70, 102-105]
21*	sAML	Loss	21q22.12	RUNX1	D	3	[57]

D = diagnostic significance; P = prognostic significance; T = therapeutic significance. Classification of levels of evidence: Level 1 = WHO classification or professional practice guidelines; Level 2 = well-powered studies with consensus from experts in the field; Level 3 = multiple small studies without any contradicting data; Level 4 = individual small studies, case reports, preclinical studies.

Abrreviations: CMA = chromosomal microarray; CNA = copy number aberration; CN-LOH = copy-neutral loss-of-heterozygosity; AML = acute myeloid leukemia; NK-AML = normal karyotype AML; pAML = primary AML; and sAML = secondary AML.

The * indicates CNAs and CN-LOH regions that are predominantly seen in AML.

References

1. Xu X, Bryke C, Sukhanova M, Huxley E, Dash DP, Dixon-Mciver A, Fang M, Griepp PT, Hodge JC, Iqbal A, Jeffries S, Kanagal-Shamanna R, Quintero-Rivera F, Shetty S, Slovak ML, Yenamandra A, Lennon PA, Raca G. (2018). Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group. Cancer Genet [Epub ahead of print], PMID 30344013.