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

Abstract

ObjectiveTo standardize the single nucleotide polymorphism array (SNPa) method in acute myeloid leukemia/myelodysplastic syndromes, and to identify the similarities and differences between the results of this method and karyotyping.MethodsTwenty-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® HD) were performed using cells from bone marrow, DNA extracted from mononuclear cells from bone marrow and buccal cells (BC).ResultsThe 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 abnormal (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).ConclusionIt 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.

Mutational Profiling of Acute Myeloid Leukemia with Normal Cytogenetics in Brazilian Patients: The Value of Next-Generation Sequencing for Genomic Classification

“…The combination of SNPa with KT can increase the detection rate of abnormalities in 28%1; however, SNPa is not routinely used in AML practice 8. Although confirming the previous cytogenetics results, SNPa did not add information to the current study.…”

Evaluation of the utility of peripheral blood vs bone marrow in karyotype and fluorescence in situ hybridization for myelodysplastic syndrome diagnosis

“…Chromosomal investigation of bone marrow is essential for MDS diagnosis and also provides information for determining classification, prognosis, and even treatment of disease. The most common method for cytogenetic abnormality assessment in MDS is karyotype; although in about 50% of the cases, karyotype results are uninformative . In addition, fluorescence in situ hybridization (FISH) is a relatively common diagnostic testing and, in comparison with karyotype, it can detect more detailed abnormalities without any cultivation, although there is not enough evidence for the best setting of the useful probe selection …”

“…The cytogenetic examination of bone marrow specimen is an essential step in MDS diagnosis, but bone marrow aspiration is a very painful procedure, especially in hypocellular (10‐16%) or fibrotic cases (17%) and also frequent sampling for disease monitoring is a clinical challenge . The cytogenetic analysis of peripheral blood for diagnosis and disease management provides a less‐invasive method instead of bone marrow aspiration, but the utility of peripheral blood to use in FISH and specially karyotype is not clear and additional studies can provide further information to compare the cytogenetic of BM and PB …”

“…Several studies compared the results of FISH and karyotype methods using BM samples, but in this study, we compared the results of karyotype and FISH in each of the BM and PB specimens . As karyotype is the most popular method for cytogenetic abnormality assessment, the survey in this field can be useful . In this study, we applied optimized karyotype for PB samples.…”

Multiple long runs of homozygosity detected by SNP array: offspring of consanguineous parents and his siblings

“…For genotype analysis, polymorphic probes indicate which SNP is present in a particular chromosome region, the alleles are arbitrarily designated as A for one SNP and B for the other SNP and reveal which of the genotypes (eg, AB, BB or AA) is present along the entire chromosome ( Figure 1B). 5 To demonstrate the use of SNP array in ROHs detection, we present here a case of parental consanguinity that exemplifies this issue. …”