PMID- 20075210
OWN - NLM
STAT- MEDLINE
DCOM- 20100707
LR  - 20211020
IS  - 1943-7811 (Electronic)
IS  - 1525-1578 (Print)
IS  - 1525-1578 (Linking)
VI  - 12
IP  - 2
DP  - 2010 Mar
TI  - Array-based karyotyping for prognostic assessment in chronic lymphocytic 
      leukemia: performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 
      arrays.
PG  - 184-96
LID - 10.2353/jmoldx.2010.090118 [doi]
AB  - 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.
FAU - Hagenkord, Jill M
AU  - Hagenkord JM
AD  - 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
FAU - Monzon, Federico A
AU  - Monzon FA
FAU - Kash, Shera F
AU  - Kash SF
FAU - Lilleberg, Stan
AU  - Lilleberg S
FAU - Xie, Qingmei
AU  - Xie Q
FAU - Kant, Jeffrey A
AU  - Kant JA
LA  - eng
PT  - Evaluation Study
PT  - Journal Article
DEP - 20100114
PL  - United States
TA  - J Mol Diagn
JT  - The Journal of molecular diagnostics : JMD
JID - 100893612
RN  - 0 (Tumor Suppressor Protein p53)
SB  - IM
CIN - J Mol Diagn. 2010 Mar;12(2):144-6. PMID: 20075205
MH  - B-Lymphocytes/physiology
MH  - *Chromosome Aberrations
MH  - Cytogenetics/methods
MH  - Gene Deletion
MH  - Genome, Human
MH  - Humans
MH  - In Situ Hybridization, Fluorescence
MH  - *Karyotyping/instrumentation/methods
MH  - *Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis/genetics
MH  - Loss of Heterozygosity
MH  - *Oligonucleotide Array Sequence Analysis/instrumentation/methods
MH  - Polymorphism, Single Nucleotide
MH  - Prognosis
MH  - Reproducibility of Results
MH  - Sensitivity and Specificity
MH  - Tumor Suppressor Protein p53/genetics
PMC - PMC2871725
EDAT- 2010/01/16 06:00
MHDA- 2010/07/08 06:00
PMCR- 2011/03/01
CRDT- 2010/01/16 06:00
PHST- 2010/01/16 06:00 [entrez]
PHST- 2010/01/16 06:00 [pubmed]
PHST- 2010/07/08 06:00 [medline]
PHST- 2011/03/01 00:00 [pmc-release]
AID - S1525-1578(10)60047-5 [pii]
AID - JMDI60047 [pii]
AID - 10.2353/jmoldx.2010.090118 [doi]
PST - ppublish
SO  - J Mol Diagn. 2010 Mar;12(2):184-96. doi: 10.2353/jmoldx.2010.090118. Epub 2010 
      Jan 14.