Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

Array-Based Karyotyping for Prognostic Assessment in Chronic Lymphocytic Leukemia: Performance Comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 Arrays

Array-Based Karyotyping for Prognostic Assessment in Chronic Lymphocytic Leukemia: Performance... 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. Related Article The Vanguard Has Arrived in the Clinical Laboratory: Array-Based Karyotyping for Prognostic Markers in Chronic Lymphocytic Leukemia Shelly R. Gunn J. Mol. Diagn. 2010 12: 144-146. Abstract Full Text PDF http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Molecular Diagnostics American Society for Investigative Pathology

Array-Based Karyotyping for Prognostic Assessment in Chronic Lymphocytic Leukemia: Performance Comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 Arrays

Array-Based Karyotyping for Prognostic Assessment in Chronic Lymphocytic Leukemia: Performance Comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 Arrays

Journal of Molecular Diagnostics , Volume 12 (2): 184 – Mar 1, 2010

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. Related Article The Vanguard Has Arrived in the Clinical Laboratory: Array-Based Karyotyping for Prognostic Markers in Chronic Lymphocytic Leukemia Shelly R. Gunn J. Mol. Diagn. 2010 12: 144-146. Abstract Full Text PDF

Loading next page...
 
/lp/american-society-for-investigative-pathology/array-based-karyotyping-for-prognostic-assessment-in-chronic-ZNA7wzMVMh

References (42)

Publisher
American Society for Investigative Pathology
Copyright
Copyright © 2010 by the American Society for Investigative Pathology and the Association for Molecular Pathology.
ISSN
1525-1578
eISSN
1525-1578
DOI
10.2353/jmoldx.2010.090118
pmid
20075210
Publisher site
See Article on Publisher Site

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. Related Article The Vanguard Has Arrived in the Clinical Laboratory: Array-Based Karyotyping for Prognostic Markers in Chronic Lymphocytic Leukemia Shelly R. Gunn J. Mol. Diagn. 2010 12: 144-146. Abstract Full Text PDF

Journal

Journal of Molecular DiagnosticsAmerican Society for Investigative Pathology

Published: Mar 1, 2010

There are no references for this article.