Document Detail

Genomic changes in gliomas detected using single nucleotide polymorphism array in formalin-fixed, paraffin-embedded tissue: superior results compared with microsatellite analysis.
MedLine Citation:
PMID:  21726663     Owner:  NLM     Status:  MEDLINE    
Deletion or loss of heterozygosity (LOH) in chromosomes 1p and 19q in oligodendrogliomas (ODGs) have diagnostic, prognostic, and therapeutic implications. Current clinical assays are limited because the probes or primers interrogate only limited genomic segments. We investigated the use of single nucleotide polymorphism (SNP) arrays for identifying genomic changes in gliomas from FFPE tissues. DNA was extracted from FFPE tissues of 30 brain tumor cases (15 ODGs and 15 non-ODGs) and assayed on the Illumina array with 300,000 markers. SNP results were compared with standard short tandem repeat (STR) assays of chromosomes 1p and 19q. Fifteen ODGs had LOH by STR and deletion by array on both 1p and 19q. Ten non-ODGs had no evidence of LOH on 1p and 19q by STR, seven of which had no abnormalities for these chromosomes; three had partial deletions by SNP array. Five non-ODG cases had partial LOH or deletion by both assays. No major discordance was found between SNP array and STR results. Advantages of SNP arrays include no need for an accompanying normal sample, the ability to find small segmental deletions, the potential to distinguish between deletions and copy neutral LOH, and whole-genome screening to allow discovery of new, significant loci. Assessment of genomic changes in routine glioma specimens using SNP arrays is feasible and has great potential as an accurate clinical diagnostic test.
Shuko Harada; Lindsay B Henderson; James R Eshleman; Christopher D Gocke; Peter Burger; Constance A Griffin; Denise A S Batista
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Publication Detail:
Type:  Comparative Study; Journal Article     Date:  2011-07-02
Journal Detail:
Title:  The Journal of molecular diagnostics : JMD     Volume:  13     ISSN:  1943-7811     ISO Abbreviation:  J Mol Diagn     Publication Date:  2011 Sep 
Date Detail:
Created Date:  2011-08-22     Completed Date:  2012-01-05     Revised Date:  2013-06-28    
Medline Journal Info:
Nlm Unique ID:  100893612     Medline TA:  J Mol Diagn     Country:  United States    
Other Details:
Languages:  eng     Pagination:  541-8     Citation Subset:  IM    
Copyright Information:
Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.
Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.
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MeSH Terms
Brain Neoplasms / diagnosis,  genetics*
Chromosomes, Human / genetics
DNA, Neoplasm / genetics
Genome, Human / genetics*
Glioma / diagnosis,  genetics*
Microsatellite Repeats / genetics*
Middle Aged
Paraffin Embedding / methods*
Polymorphism, Single Nucleotide / genetics*
Tissue Fixation / methods*
Reg. No./Substance:
0/DNA, Neoplasm; 50-00-0/Formaldehyde

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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