title: Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays.
abstract: Specific chromosomal alterations are recognized as important prognostic factors in chronic lymphocytic leukemia (CLL). Array-based karyotyping is gaining acceptance as an alternative to the standard fluorescence in situ hybridization (FISH) panel for detecting these aberrations. This study explores the optimum single nucleotide polymorphism (SNP) array probe density for routine clinical use, presents clinical validation results for the 250K Nsp Affymetrix SNP array, and highlights clinically actionable genetic lesions missed by FISH and conventional cytogenetics. CLL samples were processed on low (10K2.0), medium (250K Nsp), and high (SNP6.0) probe density Affymetrix SNP arrays. Break point definition and detection rates for clinically relevant genetic lesions were compared. The 250K Nsp array was subsequently validated for routine clinical use and demonstrated 98.5% concordance with the standard CLL FISH panel. SNP array karyotyping detected genomic complexity and/or acquired uniparental disomy not detected by the FISH panel. In particular, a region of acquired uniparental disomy on 17p was shown to harbor two mutated copies of TP53 that would have gone undetected by FISH, conventional cytogenetics, or array comparative genomic hybridization. SNP array karyotyping allows genome-wide, high resolution detection of copy number and uniparental disomy at genomic regions with established prognostic significance in CLL, detects lesions missed by FISH, and provides insight into gene dosage at these loci.
authors.affiliation: Molecular Pathology and Clinical Genomics, Creighton University Medical Center, Department of Pathology, 601 N. 30 Street, Suite 2400, Omaha, NE 68131-2197, USA. jillhagenkord@creighton.edu
authors.forename: Jill M
authors.initials: JM
authors.lastname: Hagenkord
authors.forename: Federico A
authors.initials: FA
authors.lastname: Monzon
authors.forename: Shera F
authors.initials: SF
authors.lastname: Kash
authors.forename: Stan
authors.initials: S
authors.lastname: Lilleberg
authors.forename: Qingmei
authors.initials: Q
authors.lastname: Xie
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Kant
mesh_terms: D001402:B-Lymphocytes / Q000502:physiology; D002869:Chromosome Aberrations; D003582:Cytogenetics / Q000379:methods; D017353:Gene Deletion; D015894:Genome, Human; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007621:Karyotyping / Q000295:instrumentation / Q000379:methods; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000175:diagnosis / Q000235:genetics; D019656:Loss of Heterozygosity; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D011379:Prognosis; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
chemical_list: D016159:Tumor Suppressor Protein p53