TestAMLtable

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Recurrent Genomic Alterations in AML Detected by Chromosomal Microarray (Literature Review)

Table 1 - A comprehensive list of CNAs and CN-LOH 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 (Amplification, Loss, CN-LOH) Region Relevant Genes (if known) Clinical Significance Level of Evidence References
1 AML including NK-AML CN-LOH 1p D 3 [1][2][3][4][5][6][7][8][9]
2 AML CN-LOH 2p DNMT3A D 3
3 NK-AML, sAML Loss 3p14.1 FOXP1 D 3
4 sAML, pAML CN-LOH 4q24 TET2 D 3
4 AML, NK-AML, sAML Loss 4q24 TET2 D, P 3
5 pAML, sAML Loss 5q D 1
6 AML including NK-AML CN-LOH 6p D 3
7 AML including NK-AML CN-LOH 7q EZH2 D 3
7 NK-AML, pAML, sAML Loss 7q EZH2, CUX1 D 1
8 AML with complex karyotype Amplification 8q24 MYC D, P 3
9 NK-AML, sAML CN-LOH 9p JAK2 D 3
11* AML with complex karyotype Amplification 11q23 MLL (KMT2A) D, P 3
11* AML CN-LOH 11p WT1 D 3
11 pAML, sAML, NK-AML CN-LOH 11q CBL D 3
12 AML, NK-AML, AML with complex karyotype, sAML Loss 12p13.2 ETV6 D 3
13* pAML, NK-AML, NPM1 mutated AML, FLT3-ITD positive AML, sAML CN-LOH 13q FLT3 D, P 2
16 NK-AML, AML with complex karyotype, pAML, sAML Loss 16q CBFB D 3
17 AML, NK-AML, pAML, sAML CN-LOH 17p TP53 D 3
17 sAML, NK-AML, AML with complex karyotype, de novo AML Loss 17p TP53 D, P 1
17 NK-AML, pAML Loss 17q11.2 NF1, SUZ12 D, P 3
19* AML, NK-AML, sAML CN-LOH 19q CEBPA D 3
20 sAML Loss 20q D 3
21* pAML, AML with complex karyotype Amplification 21q22 ERG, ETS2 D, P, T 3
21* AML, NK-AML, sAML CN-LOH 21q RUNX1 D 3
21* sAML Loss 21q22.12 RUNX1 D 3

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.

Reference

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.

  1. ↑ Gronseth CM, McElhone SE, Storer BE, Kroeger KA, Sandhu V, Fero ML, Appelbaum FR, Estey EH, Fang M. Prognostic significance of acquired copy-neutral loss of heterozygosity in acute myeloid leukemia. Cancer 2015;121:2900–8, PMID 26033747
  2. ↑ Yi JH, Huh J, Kim HJ, Kim SH, Kim HJ, Kim YK, Sohn SK, MoonJH, Kim SH, Kim KH, Won JH, Mun YC, Kim H, Park J, Jung CW, Kim DH. Adverse prognostic impact of abnormal lesions detected by genome-wide single nucleotide polymorphism array-based karyotyping analysis in acute myeloid leukemia with normal karyotype. J Clin Oncol Offic J Am Soc Clin Oncol, 29 (2011), pp. 4702-4708, PMID 2208437
  3. ↑ L Bullinger, J Kronke, C Schon, I Radtke, K Urlbauer, UBotzenhardt, V Gaidzik, A Cario, C Senger, RF Schlenk, JRDowning, K Holzmann, K Dohner, H Dohner. Identification of acquired copy number alterations and uniparental disomies in cytogenetically normal acute myeloid leukemia using high-resolution single-nucleotide polymorphism analysis. Leukemia, 24 (2010), pp. 438-449, PMID 20016533
  4. ↑ AJ Dunbar, LP Gondek, CL O'Keefe, H Makishima, MS Rataul, HSzpurka, MA Sekeres, Wang XF, MA McDevitt, JP Maciejewski 250K single nucleotide polymorphism array karyotyping identifies acquired uniparental disomy and homozygous mutations, including novel missense substitutions of c-Cbl, in myeloid malignancies. Cancer Res, 68 (2008), pp. 10349-10357, PMID 19074904
  5. ↑ Kronke J, Bullinger L, Teleanu V, Tschurtz F, Gaidzik VI, Kuhn MW, Rucker FG, Holzmann K, Paschka P, Kapp-Schworer S, Spath D, Kindler T, Schittenhelm M, Krauter J, Ganser A, Gohring G, Schlegelberger B, Schlenk RF, Dohner H, Dohner K. Clonal evolution in relapsed NPM1-mutated acute myeloid leukemia. Blood 2013;122:100–8, PMID 23704090
  6. ↑ M Koren-Michowitz, A Sato-Otsubo, A Nagler, T Haferlach, S Ogawa, HP Koeffler. Older patients with normal karyotype acute myeloid leukemia have a higher rate of genomic changes compared to young patients as determined by SNP array analysis. Leukem Res, 36 (2012), pp. 467-473, PMID 22071139
  7. ↑ L Bullinger, S Frohling. Array-based cytogenetic approaches in acute myeloid leukemia: clinical impact and biological insights. Sem Oncol, 39 (2012), pp. 37-46, PMID 22289490
  8. ↑ Barresi V, Romano A, Musso N, Capizzi C, Consoli C, Martelli MP, Palumbo G, DiRaimondo F, Condorelli DF. Broad copy neutral loss of heterozygosity regions and rare recurring copy number abnormalities in normal karyotype acute myeloid leukemia genomes. Genes Chromos Cancer 2010;49:1014–23., PMID 20725993
  9. ↑ T Akagi, S Ogawa, M Dugas, N Kawamata, G Yamamoto, YNannya, M Sanada, CW Miller, Yung A, S Schnittger, T Haferlach, C Haferlach, HP Koeffler. Frequent genomic abnormalities in acute myeloid leukemia/myelodysplastic syndrome with normal karyotype. Haematologica, 94 (2009), pp. 213-223, PMID 19144660
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