TestAMLtable

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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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