Array-Comparative Genomic Hybridization Detection of Previously Undetected Genomic Aberrations in Formalin-Fixed Paraffin-Embedded Myeloid Sarcoma
M Kamran Mirza, Madina Sukhanova, Poluru Reddy, Loren Joseph, Gordana Raca. University of Chicago Medicine, Chicago, IL
Background: Myeloid sarcoma (MS) is an extramedullary manifestation (EM) of acute myeloid leukemia (AML). Usually presenting as a mass lesion, MS is often not associated with a diagnosis of AML. Cytogenetic evaluation is an essential ancillary study for the accurate classification of AML. However, conventional cytogenetics is limited by the requirement for dividing cells and metaphase chromosomes. Formalin-fixed, paraffin-embedded (FFPE) material is often the only available specimen for analysis in EM AML. In recent years high resolution whole-genome array analysis has become a routine methodology in clinical testing for constitutional genetic disorders, and its utility is now being investigated for neoplastic lesions. Whole genome SNP arrays allow high-resolution, genome-wide detection of copy number abnormalities and loss of heterozygosity (LOH) events in tumor samples, using DNA isolated from either fresh or FFPE tissue. We hypothesize that SNP array analysis represents a sensitive, clinically applicable assay for detection of genetic abnormalities of diagnostic and prognostic significance in MS.
Design: Array testing was performed using CytoScan HD array (Affymetrix Inc), following the manufacturers protocol. DNA was isolated using the Qiagen DNeasy extraction protocol (QIAGEN Inc., Valencia, CA) and Flt3 ITD and D835 mutation testing was performed using a kit from InVivoScribe Technologies (San Diego, CA).
Results: We performed array analysis on a case of MS where conventional cytogenetics had revealed a trisomy 8 (karyotype: 47,XY,+8). Array analysis detected the presence of +8, and additionally showed LOH for all of chromosome 13. Knowing that FLT3 maps to chromosome 13, and that LOH may have been a mechanism to increase the dosage of a mutant FLT3 allele in the tumor, we proceeded with testing the sample for the FLT3 ITD and D835 mutations. Molecular testing demonstrated the presence of the D835 mutation.
Conclusions: Array analysis of this case not only detected trisomy 8 seen by conventional cytogenetics, but led to detection of a mutation in the FLT3 gene, which is an abnormality associated with a poor prognosis in AML. This data illustrates that whole genome arrays represent a suitable tool for the detection of prognostic genomic aberrations from FFPE material in EM AML, in a clinical diagnostic setting.
Wednesday, March 6, 2013 9:30 AM
Poster Session V # 286, Wednesday Morning