TestAMLtable

Table 1. A comprehensive list of copy number alterations detectable by CMA testing with strong diagnostic, prognostic and treatment implications in AML. Clinical significance and level of evidence are defined as described in the methods.

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.

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