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Single-nucleotide polymorphism array (SNP-A) improves the identification of chromosomal abnormalities by metaphase cytogenetics in myelodysplastic syndrome
  1. Fernanda Borges da Silva1,
  2. João Agostinho Machado-Neto1,
  3. Virginia Helena Leira Lipoli Bertini1,
  4. Elvira Deolinda Rodrigues Pereira Velloso2,3,
  5. Cristina Alonso Ratis2,
  6. Rodrigo T Calado1,
  7. Belinda Pinto Simões1,
  8. Eduardo Magalhães Rego1,
  9. Fabiola Traina1
  1. 1Department of Internal Medicine, University of São Paulo at Ribeirão Preto Medical School, Ribeirão Preto, São Paulo, Brazil
  2. 2Cytogenetics Laboratory, Hospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil
  3. 3Department of Hematology, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, São Paulo, Brazil
  1. Correspondence to Dr Fabiola Traina, Department of Internal Medicine, University of São Paulo at Ribeirão Preto Medical School, Av. Bandeirante 3900, Ribeirão Preto, SP 14048-900, Brazil; ftraina{at}


Aims The myelodysplastic syndromes (MDS) are a heterogeneous group of clonal haematopoietic stem cell disorders characterised by inefficient haematopoiesis and risk of progression to acute myeloid leukaemia. Metaphase cytogenetics is an extremely valuable clinical tool in the management of haematological malignancies. However, metaphase cytogenetics requires cellular proliferation, its sensitivity and resolution depends on the proportion of clonal cells in the sample and size of the lesion, respectively. Single-nucleotide polymorphism array (SNP-A) does not depend on the presence of dividing cells, is able to detect copy number variations with a high resolution and to detect copy number neutral loss of heterozygosity or uniparental disomy (UPD). The aim of this study was to illustrate that the use of SNP-A can cover cryptic chromosomal lesions not identified by metaphase cytogenetics in patients with MDS.

Methods Metaphase cytogenetics was performed on bone marrow aspirate using standard methods. Genomic DNA from total bone marrow cells were submitted to SNP-A using Affymetrix Genome-Wide Human SNP CytoScan HD.

Results In our cohort of 15 patients with a diagnosis of MDS and related diseases, chromosomal abnormalities were found in 47% of the cases by SNP-A and in 33% by metaphase cytogenetics. SNP-A detected all lesions identified by metaphase cytogenetics, except a balanced translocation and a marker chromosome. Notably, SNP-A detected a total of 30 new lesions: 1 (3%) gain, 17 (57%) losses and 12 (40%) UPDs in 5 patients with MDS.

Conclusions SNP-A may complement metaphase cytogenetics to improve the detection of chromosomal abnormalities in myeloid neoplasms.


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  • Handling editor Mary Frances McMullin

  • Contributors FBdS performed cytogenetics and SNP-A analysis, patient database, manuscript preparation and completion. JAM-N participated in the analysis of the data and manuscript preparation and completion. VHLLB, EDRPV and CAR participated in metaphase cytogenetics analysis and manuscript editing. RTC, BPS and EMR revised the diagnoses, were responsible for clinical follow-up of patients and participated in the manuscript editing. FT participated in the overall design of the study and experiments, patient follow-up, manuscript preparation, editing and completion. All authors read and approved the final manuscript.

  • Funding Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP).

  • Competing interests None declared.

  • Patient consent Obtained.

  • Ethics approval The ethics committee from the institution approved the study.

  • Provenance and peer review Not commissioned; externally peer reviewed.