title: The advantage of using SNP array in clinical testing for hematological malignancies--a comparative study of three genetic testing methods.
abstract: Cytogenetic methods, including G-banded chromosome analysis and fluorescence in situ hybridization (FISH) analysis, serve as a critical part of routine clinical testing for hematological malignancies and provide important diagnostic and prognostic information; however, the limitations of cytogenetic methods, including the requirement for actively dividing cells and lower resolution of G-banded chromosome analysis as well as the inability of both G-banded chromosome analysis and FISH to detect copy number neutral loss of heterozygosity (CN-LOH), can result in a failure to detect genomic abnormalities with diagnostic and prognostic significance. Here, we compared the abnormality detection rate of clinically requested testing (i.e., G-banded chromosome analysis and FISH) with high-resolution oligo (i.e., array comparative genomic hybridization (aCGH)) and single-nucleotide polymorphism (SNP)/oligo hybrid (i.e., SNP-CGH) arrays in a series of patients, in an effort to assess the ability of newer technologies to overcome these limitations. This series found the detection rate for SNP-CGH to be 62.5% for myelodysplastic syndrome (MDS) cases and 72.7% for chronic lymphocytic leukemia (CLL) cases, which are significantly higher than the detection rates of aCGH (31.3% for MDS and 54.5% for CLL) and G-banding and/or FISH (43.8% for MDS and 54.5% for CLL). This demonstrates the advantages of combining SNP-CGH with conventional cytogenetics to provide comprehensive clinical information by detecting clonality, large balanced rearrangements, copy number aberrations, and CN-LOH.
authors.affiliation: University of Wisconsin Cytogenetic Services, Wisconsin State Laboratory of Hygiene, Madison, WI, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI, USA.
authors.forename: Xinjie
authors.initials: X
authors.lastname: Xu
authors.forename: Eric B
authors.initials: EB
authors.lastname: Johnson
authors.forename: Lisa
authors.initials: L
authors.lastname: Leverton
authors.forename: Ashley
authors.initials: A
authors.lastname: Arthur
authors.forename: Quinn
authors.initials: Q
authors.lastname: Watson
authors.forename: Faye L
authors.initials: FL
authors.lastname: Chang
authors.forename: Gordana
authors.initials: G
authors.lastname: Raca
authors.forename: Jennifer J
authors.initials: JJ
authors.lastname: Laffin
mesh_terms: D002869:Chromosome Aberrations; D002871:Chromosome Banding / Q000379:methods; D055028:Comparative Genomic Hybridization / Q000379:methods*; D055088:Early Detection of Cancer / Q000379:methods* / Q000706:statistics & numerical data; D019337:Hematologic Neoplasms / Q000175:diagnosis / Q000235:genetics*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
keywords: SNP array; chronic lymphocytic leukemia; loss of heterozygosity; myelodysplastic syndrome