. 2015 Dec 22;5(1):1. doi: 10.3390/microarrays5010001

Table 1.

Common genetic abnormalities detected by SNP array in hematopoietic malignancies.

Disease	CNVs/CNAs and/or Associated Genes	LOH/UPD and/or Associated Genes	Prognostic Association	Ref.
B-ALL	Deletion of PAX5, EBF1, TCF3, LEF1, IKZF1 (IKAROS), IKZF3 (AIOLOS), ETV6, and CDKN2A/p16INK4A	9p (CDKN2A/B)	-	[26,27,28,29,35]
T-ALL	Deletion of TAL1, RB1, PTEN, CDKN2A, CDKN2B, LEF1, and STIL; Gains of MYB	9p (CDKN2A)	-	[32]
AML	Deletion of 3p14.1–p13 (FOXP1, RYBP, FHIT), 6q27 (RPS6KA2), 8q23.3 (TRPS1), 10q11.21 (HNRPF), 11q25, 12p13.2 (ETV6), 15q21.3 (RFXDC2), 5q31.1 (CTNNA1), 16q22.1 (CBFB), 17p13.1 (TP53), 17q11.2 (NF1)	13q (FLT3), 11p (WT1, PU1) and 11q (MLL), 19q (CEBPA), 6p and 21q (RUNX1)	Worse prognosis: ≥2 genomic lesions detected by SNP array	[42,43,44,45,47,48,49]
AML	Amplifications of 8q23.2 (MYC), 11q23.3 (MLL), and 21q22.2 (ETS2)		P53 mutations, or P53 mutations coupled with 17p-LOH; Genomic lesions including aUPD identified by SNP array	[42,43,44,45,47,48,49]
MDS	Deletion and aUPD of chromosomes 1, 5q, 7, 11, 17, and 21		Worse prognosis: UPDs of 7q; New genetic lesions detected by SNP array; EZH2 mutations	[57,58,60,61,62,63,64]
	Deletion of EZH2 and TET2
	UPD 20p (BMP2 and TRIB3)		Favorable prognosis: TET2 mutations (better response to hypomethylating agents)
CML	Frequent amplifications in chronic phase	1, 8, 9, 17, 19, and 22 in TKI-resistant CML	-	[66,67]
CML	Deletion of IKFZ1 in lymphoid blast phase	1, 8, 9, 17, 19, and 22 in TKI-resistant CML	-	[66,67]
MPN	Rare in ET and PV	9p (JAK2)	Worse prognosis: CNN-LOH on 7q or 9p (JAK2 V617F); Genetic aberrations of chromosome 5, 7, or 17p	[68,69,70,73,74]
MPN	Deletion of 13q14 (RB) or 17q11 (NF1) in PMF	9p (JAK2)		[68,69,70,73,74]
CMML	Frequent microdeletions	7q (EZH2), 11q (CBL), and 4q (TET2)	Worse prognosis: Multiple chromosomal defects detected by SNP array	[75,76]
cHL	Gain of MAP3K14	14q (TRAF3)	-	[79]
DLBCL	Frequent gains and deletions; gains HDAC7A on chromosome 12 predominantly in GCB-DLBCL, losses of BACH2 and CASP8AP2 on chromosome 6 predominantly in ABC-DLBCL; Potential tumor suppressor genes: CASP3, IL5RA ARID1B, ROBO2 and MRS1; Potential oncogenes: KLHL6, IL31 and LRP1	11p11.2 (PTPRJ),	Worse prognosis: Loss of 8p23.1	[81,82,83,84]
FL	CDKN2A, CDKN2B, FHIT, KIT, PEX14, and PTPRD	1p36 (TNFRSF14), 6p, 6q, 9p (CDKN2A), 10q, 12q, 16p, and 17p (TP53)	Worse prognosis: >3 SNP abnormalities; aUPD and deletion of 1p36, aUPD of 16p	[85,86]
CLL	Deletion of 17p13 (TP53), 11q22 (ATM) and 13q14 (DLEU1 and DLEU2), 2p16.1–2p15, 8q24.21, 6q21 (AIM1)	13q, 13 (miR-15a/miR-16-1), 17p, and 11q	Worse prognosis: Genomic complexity; large genomic aberrations; large (type II) 13q14 deletions	[91,92,93,101]
CLL	Gain of 12, 2p16 (REL, BCL11A)	13q, 13 (miR-15a/miR-16-1), 17p, and 11q		[91,92,93,101]
MCL	Deletion of INK4A/ARF, ATM, TP53, 1p, 6q, CDKN2C, BCL2L11, CDKN2A, and RB1, FAF1, MAP2, SP100, MOBKL2B, ZNF280A, and PRAME.	9p, 9, 17p (TP53)	-	[104,105]
MCL	Amplification of MYC, 11q13(cyclin D1), 13q (miR17-92, C13 or f25), dup(3q), 18q (BCL2)	9p, 9, 17p (TP53)	-	[104,105]
MZL	Deletion of 6q23 (TNFAIP3, A20), 9p	6q (A20), 3q	-	[106,107,108]
	Gain of 3, 18, 6p and 21q
	Gains of REL, BCL11A, ETS1, PTPN1, PTEN and KRAS in transformation to DLBCL
BL	Losses of 6q14.1–q22.33, 9p21.3 (CDKN2A), and 13q14.2–q14.3	6p12.2-pter, 9p23-pter, and 17p11.2-pter (TP53).	-	[109]
BL	Gains of 1q23.3–q31.3, 7, 13q31.3,	6p12.2-pter, 9p23-pter, and 17p11.2-pter (TP53).	-	[109]
MM	Genomic alterations at 1p, 1q, 6q, 8p, 13, and 16q	1q, 16q (CYLD), and X	Worse prognosis: Amplifications in 1q and deletions in 1p, 12p, 14q, 16q, and 22q	[111,112,115,116,117]
			UPD of 16q (CYLD)
			Favorable prognosis: Amplifications of 5, 9, 11, 15, and 19
PTCL, NOS	Losses of 1p35-36, 3q, 5q33, 6p22, 6q16, 6q21–22, 8p21–23, 9p21, 10p11–12, 10q11-22, 10q25–26, 13q14, 15q24, 16q22, 16q24, 17p11, 17p13 and Xp22	2q32.3	-	[120,121]
PTCL, NOS	Gains of 1q32–43, 2p15–16 (REL), 7, 8q24, 11q14–25, 17q11–21 and 21q11–21, 9p and 19q	2q32.3	-	[120,121]
AILT	Loss of 3q and 9p	2q32.3	Worse prognosis: The presence of CNAs; overexpression of CARMA1 at 7p22 and MYCBP2 at 13q22	[121]
AILT	Gains of 8q, 9p and 19q	2q32.3		[121]
ATLL	Deletion of 10p11.2 ( TCF8)	-	-	[122]
T-PLL	Loss in 6q, 8p, 10p, 11q (microRNA 34b/c, ETS1 and FLI1), and 18p and Gains of 6p, 8q	3q, 17q	-	[124,125]
T-PLL	Aberrations in 5p, 12p, 13q, 17 and 22 (DNAH5, ETV6, miR-15a and miR-16-1, p53, BIRC5, and SOCS3)	3q, 17q	-	[124,125]
SS	Loss at 4q35 (FAT), 4q34 (VEGFC), 12 (NFIB), and 17p11.2 (TRIM16)	9q31q34, 10p11q26, and 13q11q12	-	[126]

CNV, copy number variations; CAN, copy number aberrations; LOH, loss of heterozygosity; UPD, uniparental disomy; Ref, reference; B-ALL, B lymphoblastic leukemia; T-ALL, T lymphoblastic leukemia; AML, acute myeloid leukemia; MDS, myelodysplastic syndrome; CML, chronic myelogenous leukemia; MPN, myeloproliferative neoplasm; PV, polycythemia (Rubra) vera; ET, essential thrombocythemia; PMF, primary myelofibrosis; CMML, chronic myelomonocytic leukemia; cHL, classical Hodgkin lymphoma; DLBCL, diffuse large B-cell lymphoma; FL, follicular lymphoma; CLL, chronic lymphocytic leukemia; MCL, mantle cell lymphoma; MZL, marginal zone lymphoma; BL, Burkitt lymphoma; MM, multiple myeloma; PTCL, NOS, peripheral T-cell lymphoma, NOS; AILT, angioimmunoblastic T-cell lymphoma; ATLL, adult T-cell leukemia/lymphoma; T-PLL, T-cell prolymphocytic leukemia; SS, Sezary syndrome.