MDS, MDS/MPN and MPN Tables: Recurrent Genomic Alterations Detected by Chromosomal Microarray

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Table 1 - Evidence for the Clinical Utility of Chromosomal Microarray (CMA) Testing in Myeloid Disorders Excluding Acute Myeloid Leukemia (Literature Review). Table derived from Kanagal-Shawanna et al., 2018 [PMID 30377088] with permission from Cancer Genetics.

Disease Overall CMA detection rate Key and unique

CMA aberrations

Altered

gene(s)

Impact References
MDS 28-83%

(Normal karyotype only: 11-39%)

Total genomic alteration Prognostic poor survival [1][2][3][4][5]
1p CN-LOH Prognostic for progression to AML [6][7][8][9][10]
1q gain Recurrent [6][11][12][10]
4q loss TET2 Prognostic for poor survival [6][11][13][14][15]
4q CN-LOH TET2 Prognostic for poor survival [16][6][17][11][12][3][8][18][19][20][21]
5q loss 5q loss “size” prognostic for progression to AML [6][22][11][1][23][24][10][25]
7q loss CUX1, EZH2 Prognostic for poor survival [6][22][26][12][27][28][19][9][20][29][30][10][31][25]
7q CN-LOH Recurrent [16][6][11][7][12][8][5][32][21]
11q CN-LOH CBL Prognostic/ recurrent [16][6][22][7] [3][8][20][10]
12p loss ETV6 Recurrent [6][17][12][27][15]
13q loss ?RB1 Recurrent [6][11][27][3][10]
17p loss TP53 Recurrent [6][12][33][15][30]
17p CN-LOH TP53 Diagnostic for advanced MDS/sAML [11][12][3][8][28]
20q loss Recurrent [6][9][34][35][30][31][25]
21q CN-LOH or deletion RUNX1 Prognostic for progression to AML [6][26][27][15][9][32]
MDS/MPN 73%/NA 4q CN-LOH TET2 Recurrent [16][36][13][20][35]
7q CN-LOH Likely CUX1 Recurrent [16][36][8][9][20]
11q CN-LOH CBL Recurrent [16][36][13][8][37]
MPN >56%/NA 1q gain Recurrent [38][39]
4q loss TET2 Prognostic for progression to AML [14][40]
9p CN-LOH JAK2 Predictive for JAK2 inhibitors; Prognostic for PV progression to MF [41][37][41][39][42]
14q CN-LOH Presence of CNAs/CN-LOH prognostic for progression to AML [41][39][9]
20q loss Recurrent [41][43]
CML 21-24%/NA 17p loss TP53 Recurrent, progression, associated with TKI resistance [44][45]
2q CN-LOH Diagnostic (only seen in BC) [45]
8p CN-LOH Diagnostic (only seen in BC) [45]
BMFS 19% (AA) 6p CN-LOH ?HLA genes Recurrent [46][29][47]

AA, Aplastic anemia; BMFS, Bone Marrow Failure Syndrome; MDS, Myelodysplastic Syndrome; MDS/MPN, Myelodysplastic/ myeloproliferative Neoplasm; MPN, Myeloproliferative Neoplasm; CML, Chronic Myelogeneous Leukemia; sAML, secondary AML; TGA, Total genomic aberration; TKI, tyrosine kinase inhibitors.

∗Recurrent indicates recurrent aberration with no established prognostic significance


Table 2 - A Comprehensive List of Copy Number Aberrations and CN-LOH of Known or Likely Clinical Significance in MDS Detected by CMA Testing (Literature Review). Table derived from Kanagal-Shawanna et al., 2018 [PMID 30377088] with permission from Cancer Genetics.

Chromosome Disease Abnormality Type (Gain, Loss, CN-LOH) Region Relevant Genes (if known) Clinical Significance* Level of Evidence References
1 MDS Gain 1p36.33-p33 MPL Recurrent 3

[22][6][34]

1 MDS CN-LOH 1p MPL Recurrent 2 [6][7][8][9]
1 MDS Gain 1q Recurrent 2 [6][11][12][10]
2 MDS CN-LOH 2pter-2p13.3 DNMT3A Recurrent 2 [6][24][20][48]
3 MDS CN-LOH 3q21.3-qter MECOM, GATA2 Recurrent 3 [6][17][49][3][9]
4 MDS Loss 4q24 TET2 T*** 2 [6][26][11][13][14][27][15]
4 MDS CN-LOH 4q12-qter TET2 Recurrent 2 [16][6][17][11][50][12][8][18][19][20][21]
5 MDS Gain 5p Suggestive of i(5p) with 5q del Recurrent 3 [6]
5 MDS Loss 5q RPS14 D, P (Good when isolated) 1 [6][22][17][26][49][11][1][12][23][33][3][28][51][19][5][34][24][20][35][30][10][25][52]
7 MDS Loss 7q EZH2, CUX1 D, P (Intermediate) 1 [6][22][26][49][1][12][27][33][28][19][5][9][29][30][10][25]
7 MDS CN-LOH 7q21.11-qter EZH2, CUX1 Recurrent 2 [16][6][17][49][11][7][12][8][5][32][21]
7 MDS Loss (Monosomy) 7 Whole Chromosome D, P (Poor) 1 [33][28][19][20][29][30][10][31][25]
8 MDS Gain (Trisomy) 8 Whole Chromosome P (Intermediate)** 1 [6][11][12][33][15][5][9][34][53][29][30][25]
9 MDS Gain 9p JAK2 Recurrent 3 [6][12][15]
9 MDS CN-LOH 9pter-p24.2 JAK2 Recurrent 2 [6][2][3]
11 MDS Loss 11q14.1-q24.3 CBL D, P (Very Good) 1 [6][34]
11 MDS CN-LOH 11q13.3-qter CBL Recurrent 2 [16][6][22][7][3][8][20][10][31]
11 MDS Gain (Trisomy and q-arm) 11 / 11q CBL Recurrent 3 [6][17][1][12][20]
12 MDS Loss 12p ETV6 D, P (Good) 1 [6][17][12][27][15]
12 MDS CN-LOH 12pter-p11.23 ETV6 Recurrent 2 [3][20]
13 MDS Loss 13q RB1 D, P (Intermediate) 2 [6][11][3][10]
13 MDS CN-LOH 13q12.3-qter FLT3, RB1 Recurrent 3 [6][8][20]
13 MDS Gain (Trisomy) 13 Whole Chromosome Recurrent 3 [6]
14 MDS CN-LOH 14q24.2-qter CHGA Recurrent 3 [6][22][7][50][8]
16 MDS Loss (Monosomy and q-arm) 16 / 16q CDH1 Recurrent 3 [6][15][10]
16 MDS CN-LOH 16q22.1-qter CDH1 Recurrent 3 [6][32]
17 MDS Loss 17p TP53 P (Poor) 1 [6][12][33][51][15][5][30]
17 MDS CN-LOH 17pter-p11.2 TP53 Recurrent 2 [17][11][12][23][3][8][28][5]
17 MDS Loss 17q11.2 NF1 Recurrent 3 [27][15]
17 MDS CN-LOH 17q11.2-qter SRSF2, NF1 Recurrent 2 [6][49][7]
19 MDS CN-LOH 19pter-p13.11 DNMT1, PRDX2 Recurrent 3 [9][20]
19 MDS Loss 19p13.13 PRDX2 Recurrent 3 [1]
19 MDS Gain (Trisomy) 19 Whole Chromosome Recurrent 2 [6][9]
20 MDS Gain 20p Suggestive of ider(20p) with 20q del Recurrent 3 [6]
20 MDS Loss 20q ASXL1 P (Good)** 1 [6][11][1][51][5][9][34][35][32][30][31][25][22][12][19][43][54]
20 MDS CN-LOH 20q11.21-qter ASXL1 Recurrent 2 [5][32]
21 MDS Loss 21q22.12 RUNX1 D, P (Poor) 2 [6][17][26][11][27][33][15]
21 MDS CN-LOH 21q21.1-qter RUNX1, U2AF1 Recurrent 2 [6][7][5][21][52]
21 MDS Gain (Trisomy) 21 Whole Chromosome Recurrent 2 [6][12][30]
22 MDS CN-LOH 22q11.23-qter MN1, SF3A1, EP300 Recurrent 3 [6][10]

Legend: d- diagnostic significance; P-prognostic significance; T- therapeutic significance. Recurrent indicates recurrent aberration with no established prognostic significance.

∗ Clinical significance based on WHO classification using IPSS-R[55][56].

** Isolated trisomy 8 or del(20q) are not diagnostic of MDS in the absence of morphologic findings of disease.

∗∗∗ Potential marker for responsiveness to hypomethylating agents or DNA methyltransferase inhibitors[57][58].


Table 3 - A Comprehensive List of Copy Number Aberrations and CN-LOH of Known or Likely Clinical Significance in MDS/MPN Detected by CMA Testing (Literature Review). Table derived from Kanagal-Shawanna et al., 2018 [PMID 30377088] with permission from Cancer Genetics.

Chromosome Disease Abnormality Type (Gain, Loss, CN-LOH) Region Relevant Genes (if known) Clinical Significance* Level of Evidence References
1 MDS/MPN CN-LOH 1p21.3 MPL Recurrent 2 [8]
4 MDS/MPN Loss 4q24 TET2 Recurrent** 2 [13]
4 MDS/MPN CN-LOH 4q12.4-qter TET2 Recurrent 2 [16][36][13][8][20][35]
5 MDS/MPN Loss (Monosomy and q-arm) 5 / 5q RPS14 P (Intermediate) 1 [13][59][23][37][39][24]
7 MDS/MPN Loss 7q EZH2, CUX1 P (Poor) 1 [16][37]
7 MDS/MPN CN-LOH 7q21.11-qter EZH2, CUX1 Recurrent 2 [16][36][8][9][20]
8 MDS/MPN Gain (Trisomy) 8 Whole chromosome P (Poor) 1 [39][20]
9 MDS/MPN CN-LOH 9pter-p13.3 JAK2 Recurrent 2 [8]
11 MDS/MPN CN-LOH 11q13.2-qter CBL Recurrent 2 [16][36][13][8]
12 MDS/MPN Loss 12p ETV6 P (Intermediate) 1 [36][59]
13 MDS/MPN Loss 13q RB1 P (Intermediate) 1 [37][39]
14 MDS/MPN CN-LOH 14q CHGA Recurrent 3 [8]
17 MDS/MPN Loss 17p TP53 P (Poor)*** 1 [39]
20 MDS/MPN Loss 20q ASXL1 P (Intermediate) 2 [37]
21 MDS/MPN Gain 21q22.12 RUNX1 P (Intermediate) 2 [36][13]
21 MDS/MPN CN-LOH 21q22-qter RUNX1 Recurrent 2 [36][8]

Legend: d- diagnostic significance; P-prognostic significance; T- therapeutic significance.

Recurrent indicates recurrent aberration with no established significance.

∗ Clinical significance based on International MDS/MPN Working Group recommendations[60]; No NCCN guidelines available. Low risk (normal, isolated –Y), Intermediate (others), High risk (+8, abnormal 7, complex).

∗∗ Potential marker for responsiveness to hypomethylating agents or DNA methyltransferase inhibitors[57][58].

∗∗∗ Haploinsufficiency of 17p as part of an isolated isochromosome may be a distinct disease entity with further increased risk of AML progression relative to 17p loss in a complex karyotype.


Table 4 - A Comprehensive List of Copy Number Aberrations and CN-LOH of Known or Likely Clinical Significance in MPN Detected by CMA Testing (Literature Review). Table derived from Kanagal-Shawanna et al., 2018 [PMID 30377088] with permission from Cancer Genetics.

Chromosome Disease Abnormality Type (Gain, Loss, CN-LOH) Region Relevant Genes (if known) Clinical Significance* Level of Evidence Reference (PMID)
1 MPN CN-LOH 1p21.3 MPL Recurrent 2 [41]
1 MPN Gain 1q21.2-q32.1 Recurrent 2 [41][38][39]
4 MPN Loss 4q24 TET2 Recurrent 2 [14][40]
5 MPN Loss 5q RPS14 P (Poor) 1 [24]
6 MPN Loss 6p23-22.3 JARID2 Recurrent 3 [39][61]
7 MPN Loss 7q EZH2, CUX1 P (Poor) 1 [41]
7 MPN CN-LOH 7q22.1-qter EZH2, CUX1 Recurrent 2 [45]
8 MPN Gain (Trisomy) 8 Whole chromosome P (Poor) 1 [44]
9 MPN Gain 9p JAK2 Recurrent 2 [41][38][39]
9 MPN CN-LOH 9pter-p13.3 JAK2 Recurrent 2 [41][37][38][39][42]
9 CML Loss 9q34 Recurrent 3 [62][44]
9 CML Gain 9q34 (+Ph) ABL1 Recurrent 1 [44]
11 MPN CN-LOH 11q13.4-q25  CBL Recurrent 2 [41][38]
12 MPN Loss 12p13.3-p12.2 ETV6 P (Poor) 1 [45]
13 MPN Loss 13q RB1 Recurrent 1 [41]
14 MPN CN-LOH 14q CHGA Recurrent 3 [41][38][39][9]
17 MPN Loss 17p TP53 P (Poor) 1 [44][45][41]
20 MPN Loss 20q ASXL1 Recurrent 1 [41][43]
22 CML Loss 22q11.2 Recurrent 3 [62][44]
22 CML Gain 22q11.2 (+Ph) BCR Recurrent 1 [44]

Legend: d- diagnostic significance; P-prognostic significance; T- therapeutic significance.

Recurrent indicates recurrent aberration with no established significance.

∗ Clinical significance based on NCCN guidelines[63]; For myelofibrosis, unfavorable [complex karyotype or sole or two abnormalities that include inv(3), 5/5q-, 7/7q-,+8, 11q23 rearrangement, 12p-, and (17q)].


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