Difference between revisions of "TestAMLtable"

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{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
−
! Chromosome
+
!Chromosome
−
! AML Subtype
+
!AML Subtype
−
! Abnormality Type (Amplification, Loss, CN-LOH)
+
!Abnormality Type (Amplification, Loss, CN-LOH)
−
! Region
+
!Region
−
! Relevant Genes (if known)
+
!Relevant Genes (if known)
−
! Clinical Significance
+
!Clinical Significance
−
! Level of Evidence
+
!Level of Evidence
 +
!References
 
|-
 
|-
−
| 1
+
|1
−
| AML including NK-AML
+
|AML including NK-AML
−
| CN-LOH
+
|CN-LOH
−
| 1p
+
|1p
−
|  
+
|
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 2
+
|2
−
| AML
+
|AML
−
| CN-LOH
+
|CN-LOH
−
| 2p
+
|2p
−
| ''DNMT3A''
+
|''[[DNMT3A]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 3
+
|3
−
| NK-AML, sAML
+
|NK-AML, sAML
−
| Loss
+
|Loss
−
| 3p14.1
+
|3p14.1
−
| ''FOXP1''
+
|''[[FOXP1]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 4
+
|4
−
| sAML, pAML
+
|sAML, pAML
−
| CN-LOH
+
|CN-LOH
−
| 4q24
+
|4q24
−
| ''TET2''
+
|''[[TET2]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 4
+
|4
−
| AML, NK-AML, sAML
+
|AML, NK-AML, sAML
−
| Loss
+
|Loss
−
| 4q24
+
|4q24
−
| ''TET2''
+
|''[[TET2]]''
−
| D, P
+
|D, P
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 5
+
|5
−
| pAML, sAML
+
|pAML, sAML
−
| Loss
+
|Loss
−
| 5q
+
|5q
−
|  
+
|
−
| D
+
|D
−
| 1
+
|1
 +
|
 
|-
 
|-
−
| 6
+
|6
−
| AML including NK-AML
+
|AML including NK-AML
−
| CN-LOH
+
|CN-LOH
−
| 6p
+
|6p
−
|  
+
|
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 7
+
|7
−
| AML including NK-AML
+
|AML including NK-AML
−
| CN-LOH
+
|CN-LOH
−
| 7q
+
|7q
−
| ''EZH2''
+
|''[[EZH2]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 7
+
|7
−
| NK-AML, pAML, sAML
+
|NK-AML, pAML, sAML
−
| Loss
+
|Loss
−
| 7q
+
|7q
−
| ''EZH2, CUX1''
+
|''[[EZH2]], [[CUX1]]''
−
| D
+
|D
−
| 1
+
|1
 +
|
 
|-
 
|-
−
| 8
+
|8
−
| AML with complex karyotype
+
|AML with complex karyotype
−
| Amplification
+
|Amplification
−
| 8q24
+
|8q24
−
| ''MYC''
+
|''[[MYC]]''
−
| D, P
+
|D, P
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 9
+
|9
−
| NK-AML, sAML
+
|NK-AML, sAML
−
| CN-LOH
+
|CN-LOH
−
| 9p
+
|9p
−
| ''JAK2''
+
|''[[JAK2]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 11*
+
|11*
−
| AML with complex karyotype
+
|AML with complex karyotype
−
| Amplification
+
|Amplification
−
| 11q23
+
|11q23
−
| ''MLL (KMT2A)''
+
|''[[KMT2A|MLL (KMT2A)]]''
−
| D, P
+
|D, P
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 11*
+
|11*
−
| AML
+
|AML
−
| CN-LOH
+
|CN-LOH
−
| 11p
+
|11p
−
| ''WT1''
+
|''[[WT1]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 11
+
|11
−
| pAML, sAML, NK-AML
+
|pAML, sAML, NK-AML
−
| CN-LOH
+
|CN-LOH
−
| 11q
+
|11q
−
| ''CBL''
+
|''[[CBL]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 12
+
|12
−
| AML, NK-AML, AML with complex karyotype, sAML
+
|AML, NK-AML, AML with complex karyotype, sAML
−
| Loss
+
|Loss
−
| 12p13.2
+
|12p13.2
−
| ''ETV6''
+
|''[[ETV6]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 13*
+
|13*
−
| pAML, NK-AML, ''NPM1'' mutated AML, FLT3-ITD positive AML, sAML
+
|pAML, NK-AML, ''NPM1'' mutated AML, FLT3-ITD positive AML, sAML
−
| CN-LOH
+
|CN-LOH
−
| 13q
+
|13q
−
| ''FLT3''
+
|''[[FLT3]]''
−
| D, P
+
|D, P
−
| 2
+
|2
 +
|
 
|-
 
|-
−
| 16
+
|16
−
| NK-AML, AML with complex karyotype, pAML, sAML
+
|NK-AML, AML with complex karyotype, pAML, sAML
−
| Loss
+
|Loss
−
| 16q
+
|16q
−
| ''CBFB''
+
|''[[CBFB]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 17
+
|17
−
| AML, NK-AML, pAML, sAML
+
|AML, NK-AML, pAML, sAML
−
| CN-LOH
+
|CN-LOH
−
| 17p
+
|17p
−
| ''TP53''
+
|''[[TP53]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 17
+
|17
−
| sAML, NK-AML, AML with complex karyotype, ''de novo'' AML
+
|sAML, NK-AML, AML with complex karyotype, ''de novo'' AML
−
| Loss
+
|Loss
−
| 17p
+
|17p
−
| ''TP53''
+
|''[[TP53]]''
−
| D, P
+
|D, P
−
| 1
+
|1
 +
|
 
|-
 
|-
−
| 17
+
|17
−
| NK-AML, pAML
+
|NK-AML, pAML
−
| Loss
+
|Loss
−
| 17q11.2
+
|17q11.2
−
| ''NF1, SUZ12''
+
|''[[NF1]], [[SUZ12]]''
−
| D, P
+
|D, P
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 19*
+
|19*
−
| AML, NK-AML, sAML
+
|AML, NK-AML, sAML
−
| CN-LOH
+
|CN-LOH
−
| 19q
+
|19q
−
| ''CEBPA''
+
|''[[CEBPA]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 20
+
|20
−
| sAML
+
|sAML
−
| Loss
+
|Loss
−
| 20q
+
|20q
−
|  
+
|
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 21*
+
|21*
−
| pAML, AML with complex karyotype
+
|pAML, AML with complex karyotype
−
| Amplification
+
|Amplification
−
| 21q22
+
|21q22
−
| ''ERG, ETS2''
+
|''[[ERG]], [[ETS2]]''
−
| D, P, T
+
|D, P, T
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 21*
+
|21*
−
| AML, NK-AML, sAML
+
|AML, NK-AML, sAML
−
| CN-LOH
+
|CN-LOH
−
| 21q
+
|21q
−
| ''RUNX1''
+
|''[[RUNX1]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
−
| 21*
+
|21*
−
| sAML
+
|sAML
−
| Loss
+
|Loss
−
| 21q22.12
+
|21q22.12
−
| ''RUNX1''
+
|''[[RUNX1]]''
−
| D
+
|D
−
| 3
+
|3
 +
|
 
|-
 
|-
 
|}
 
|}
Line 223: Line 249:
  
 
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. 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.
 +
 +
2. 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

Revision as of 13:32, 13 June 2019

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
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.

2. 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

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