Genomic Changes in Gliomas by Single Nucleotide Polymorphism (SNP) Array in Formalin-Fixed Paraffin-Embedded (FFPE) Tissue.
Shuko Harada, Lindsay B Henderson, James R Eshleman, Christopher D Gocke, Peter Burger, Constance A Griffin, Denise A Batista. Johns Hopkins Medical Institutions, Baltimore, MD; Kennedy Kriger Institute, Baltimore, MD
Background: In oligodendrogliomas (ODG), genomic changes in chromosomes 1p and 19q have diagnostic, prognostic and therapeutic implications. Currently, deletion or loss of heterozygosity (LOH) is identified clinically by fluorescence insitu hybridization or short tandem repeat (STR or microsatellite) analysis. These assays suffer from the limitation that the probes or primers interrogate only small portions of the chromosomes. In this study, we investigated the use of SNP array for identifying genomic changes in gliomas utilizing DNA extracted from FFPE tissues.
Design: Genomic DNA was extracted from FFPE tissues of 14 brain tumor cases [7 ODG and 7 non-ODG]. DNA quality was determined using BioScore Screening and Amplification Kit. DNA from each tumor was run on the Illumina SNP array with 300K markers. The data were analyzed using Illumina KaryoStudio. SNP array results were compared with our standard clinical STR assay of chromosomes 1p and 19q. SNP array abnormalities of other chromosomes were also identified and the results were compared with the pathological diagnoses.
Results: Quality of DNA from FFPE samples correlated well with SNP array data quality; higher quality DNA had a smaller variance. Nevertheless, all data were interpretable. Seven ODG cases had LOH by STR and deletion or LOH by SNP array on both 1p and 19q. Two astrocytoma (AC) cases had no evidence of LOH or deletion and two other cases (1 anaplastic AC and 1 glioblastoma) had 19q LOH alone by both assays. Three cases had segmental deletions or LOH of 1p and/or 19q by array that were not detected by STR analysis. The final diagnosis of these three cases was anaplastic AC. There was no major discordance between SNP array and STR results with the added advantage that SNP array can distinguish between deletion and copy neutral LOH. The number of other chromosome abnormalities was higher in high grade gliomas [3.4±0.8 in Grade II (n=5), 8.0±1.6 in Grade III (n=7) and 12.0±1.0 in Grade IV (n=2)].
Conclusions: Assessment of genomic changes in gliomas using SNP array to analyze FFPE samples is feasible and has great potential for an accurate clinical diagnostic test. Small deletions or LOH that may be missed by the current assays are detectable by SNP array. The clinical significance of these small deletions, copy neutral LOH and abnormalities on other chromosomes has yet to be determined and will require further studies.
Monday, February 28, 2011 9:30 AM
Poster Session I Stowell-Orbison/Surgical Pathology/Autopsy Awards Poster Session # 211, Monday Morning