Identifying the similarities and differences between single nucleotide
               polymorphism array (SNPa) analysis and karyotyping in acute myeloid leukemia and
               myelodysplastic syndromes

Noronha, Thiago Rodrigo de; Rohr, Sandra Serson; Chauffaille, Maria de Lourdes Lopes Ferrari

doi:10.1016/j.bjhh.2014.09.011

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Original Articles • Rev. Bras. Hematol. Hemoter. 37 (1) • Jan-Feb 2015 • https://doi.org/10.1016/j.bjhh.2014.09.011 copy

Identifying the similarities and differences between single nucleotide polymorphism array (SNPa) analysis and karyotyping in acute myeloid leukemia and myelodysplastic syndromes

Authorship SCIMAGO INSTITUTIONS RANKINGS

Objective:

To standardize the single nucleotide polymorphism array (SNPa) method in acute myeloid leukemia/myelodysplastic syndromes, and to identify the similarities and differ- ences between the results of this method and karyotyping.

Methods:

Twenty-two patients diagnosed with acute myeloid leukemia and three with myelodysplastic syndromes were studied. The G-banding karyotyping and single nucleotide polymorphism array analysis (CytoScan(r) HD) were performed using cells from bone marrow, DNA extracted from mononuclear cells from bone marrow and buccal cells (BC).

Results:

The mean age of the patients studied was 54 years old, and the median age was 55 years (range: 28-93). Twelve (48%) were male and 13 (52%) female. Ten patients showed abnormal karyotypes (40.0%), 11 normal (44.0%) and four had no mitosis (16.0%). Regarding the results of bone marrow single nucleotide polymorphism array analysis: 17 were abnor- mal (68.0%) and eight were normal (32.0%). Comparing the two methods, karyotyping identiﬁed a total of 17 alterations (8 deletions/losses, 7 trissomies/gains, and 2 translocations) and single nucleotide polymorphism array analysis identiﬁed a total of 42 alterations (17 losses, 16 gains and 9 copy-neutral loss of heterozygosity).

Conclusion:

It is possible to standardize single nucleotide polymorphism array analysis in acute myeloid leukemia/myelodysplastic syndromes and compare the results with the abnormalities detected by karyotyping. Single nucleotide polymorphism array analysis increased the detection rate of abnormalities compared to karyotyping and also identiﬁed a new set of abnormalities that deserve further investigation in future studies.

Acute myeloid leukemia; Myelodysplastic syndromes; Loss of heterozygosity; Single nucleotide polymorphism; Karyotype

Case	Diagnosis	Karyotyping	SNPa (BM)	SNPa (BC)
1	AML	46,XY[20]	Normal	Normal
2	AML	46,XY,del(5)(q15q33),del(17)(p11.2)[16]/46,XY[4]	3p21.31p21.2 CN-LOH; 5q21.1q35.3	DGV^a
			loss (CN: 1.00); −7; +8; 12p13.33p12.3 loss (CN: 1.00);
			12p12.1p11.22 loss (CN: 1.00);
			12q22q23.3 loss (CN: 1.00); −16; 17p13.3p11.2 mosaic loss (CN:
3	AML	46,XX[20]	1.50); −Y Normal	Normal
4	AML	46,XX[20]	Normal	Normal
5	AML	47,XY,+4[10]	+4	Normal
6	AML	92,XXYY[20]	1q31.1q44 mosaic gain (CN: 2.41);	Normal
			2q24.2q37.3 mosaic loss (CN: 1.48);
			5q15q31.1 mosaic loss (CN: 1.72);
			5q31.3q32 mosaic loss (CN: 1.76);
			5q33.1q35.1 mosaic loss (CN: 1.73);
			6q22.33q27 mosaic gain (CN: 2.31);
			+8; 16q21q24.3 CN-LOH
7	AML	47,XX,+8[17]/46,XX[3]	8 mosaic gain (CN: 2.65)	DGV^a
8	AML	46,XY,del(9)(q21)[20]	9q21.11q22.33 loss (CN: 1.00)	9q21.11q22.33 loss (CN:
				1.00)
9	AML	No mitoses	+8; 17q21.2q25.3 CN-LOH	Normal
10	AML	No mitoses	9 mosaic gain (CN: 2.69)	9 mosaic gain (CN: 2.48)
11	AML	No mitoses	Normal	Normal
12	AML	46,XY[15]	Normal	Normal
13	AML	48,XX,+8,+21[11]/46,XX[1]	8 mosaic gain (CN: 2.57); 21 mosaic	Normal
			gain (CN: 2.54); 9p24.3p13.3
			CN-LOH
14	AML	46,XX[10]	+8	8 mosaic gain (CN: 2.93)
15	AML	No mitoses	1q21.1q44 gain (CN: 3.00);	Normal
			5q15.33q11.2 mosaic gain (CN:
			2.39)
16	AML	46,XX[14]	Normal	Normal
17	AML	46,XX[20]	19p13.3p13.11 mosaic gain (CN:	Normal
			2.31); 19q13.31q13.33 mosaic gain
			(CN: 2.22)
18	AML	46,XY[20]	Normal	Normal
19 20	AML AML	46,XY,t(8;21)(q22;q22)[20]/47,XY,+8,t(8;21)(q22;q22) [3]/46,X,−Y,+8,t(8;21)(q22;q22)[2] 45,X,t(8;21)(q22;q22)[5]/46,XX[5]	+8; −Y X mosaic loss (CN: 1.25)	Normal Normal
21	AML	46,XX[15]	Normal	Normal
22	AML	48,XY,?del(3)(q26),del(11)(q23),+i(21)(q10)x2[cp20]	6q27 gain (CN: 3.00); 11q23.3q25	Normal
			loss (CN: 1.00); 21q11.2q22.3 gain
			(CN: 4.75)
23	MDS	46,XX[20]	4q31.21q34.3 CN-LOH;	4q31.21q34.3 CN-LOH;
			12q23.1q24.11 CN-LOH	12q23.1q24.11 CN-LOH
24	MDS	46,XY[15]	6q13q14.3 CN-LOH; 21q21.1q22.3	6q13q14.3 CN-LOH
			CN-LOH
25	MDS	46,XXdel(5)(q13q33)[19]/46,XX[1]	5q15q33.2 loss (CN:1.00)	5q15q33.2 loss (CN:1.00)

Associação Brasileira de Hematologia e Hemoterapia e Terapia Celular R. Dr. Diogo de Faria, 775 cj 114, 04037-002 São Paulo/SP/Brasil, Tel. (55 11) 2369-7767/2338-6764 - São Paulo - SP - Brazil
E-mail: secretaria@rbhh.org

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[1] *Corresponding author at: Universidade Federal de São Paulo (UNIFESP), Rua Dr. Diogo de Faria, 824, 5◦ andar, Citogenética, 04037-002 São Paulo, SP, Brazil. E-mail address: thinoronha@yahoo.com.br (T.R. Noronha).