title: Different characteristics identified by single nucleotide polymorphism array analysis in leukemia suggest the need for different application strategies depending on disease category.
abstract: The purpose of this study was to evaluate the detection rate of chromosomal rearrangements in leukemia using single nucleotide polymorphism array (SNP-A) in combination with metaphase cytogenetics (MC), with the aim of proposing a practical approach for clinical karyotyping applications of SNP-A. The Genome-Wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA) was applied in 469 patients with a variety of hematologic malignancies. Combined use of SNP-A with MC improved the detection rate in comparison with MC alone: acute myeloid leukemia (AML) with normal karyotype (NK), 32% versus 0%; core binding factor (CBF)-AML 40% versus 29%; myelodysplastic syndrome (MDS), 54% versus 39%; chronic myeloid leukemia (CML), 24% versus 3%; and acute lymphoblastic leukemia (ALL), 88% versus 63%. Different patterns of abnormalities (especially the type, size, and location) were noted in the leukemia subtypes. Copy neutral loss of heterozygosity lesions was detected in 23% of AML-NK, 3% of CBF-AML, 25% of MDS, 2% of CML, and 20% of ALL. SNP-A also provided information on cryptic deletions and a variety of aneuploidies in ALL, while the benefit was minimal in CML. In conclusion, different patterns of abnormal lesions were presented according to the disease category, thus requiring a different approach of adopting SNP-A-based karyotyping among different leukemia subtypes.
authors.affiliation: Department of Laboratory Medicine, Ewha Womans University School of Medicine, Seoul, Korea.
authors.forename: Jungwon
authors.initials: J
authors.lastname: Huh
authors.forename: Chul Won
authors.initials: CW
authors.lastname: Jung
authors.forename: Hyeoung-Joon
authors.initials: HJ
authors.lastname: Kim
authors.forename: Yeo-Kyeoung
authors.initials: YK
authors.lastname: Kim
authors.forename: Joon Ho
authors.initials: JH
authors.lastname: Moon
authors.forename: Sang Kyun
authors.initials: SK
authors.lastname: Sohn
authors.forename: Hee-Je
authors.initials: HJ
authors.lastname: Kim
authors.forename: Woo Sung
authors.initials: WS
authors.lastname: Min
authors.forename: Dong Hwan Dennis
authors.initials: DH
authors.lastname: Kim
mesh_terms: D002869:Chromosome Aberrations; D002898:Chromosomes, Human, Pair 8 / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics; D023281:Genomics; D006801:Humans; D007621:Karyotyping; D007938:Leukemia / Q000145:classification / Q000235:genetics*; D009190:Myelodysplastic Syndromes / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D014314:Trisomy / Q000235:genetics