The Detection of Clonal Evolution in Acute Myeloid Leukemia (AML) Using SNP/CGH Microarray Analysis
Luise Hartmann, Christine F Stephenson, Krystal R Johnson, Douglas B Chapman, Richard K Bennington, Wayne K Fritschle, Lisa Eidenschink, Denise A Wells, Michael R Loken, Monica E de Baca, Barbara K Zehentner. HematoLogics, Inc., Seattle, WA
Background: Single nucleotide polymorphism (SNP) arrays were originally used for genome wide association studies. Of recent interest is SNP array analysis in the context of hematopoietic malignancies. SNP arrays have several advantages over more routine tests (metaphase analysis and fluorescence in situ hybridization [FISH]) as the genome can be evaluated at the submicroscopic level in its entirety with a single assay. SNP arrays detect copy number gains and losses, provide genotype information and allow identification of allelic imbalances such as copy number neutral loss of heterozygosity (cnLOH). SNP arrays are of limited use, however, in the identification of low-level mosaicism. In the 8 AML case studies presented here, we demonstrate how manual re-analysis of initial microarray data can achieve improved resolution of the clonal composition, confirming the presence of clonal sub-populations as well as clonal evolution.
Design: DNA from 8 bone marrow aspirates with acute myeloid leukemia were investigated for the presence of genomic aberrations using the Agilent SurePrint G3 180K Cancer CGH+SNP microarray. Data was analyzed with the Agilent CytoGenomics software. After initial characterization of the major clone abnormalities, manual 'peak re-assignment' analysis was performed to reveal aberrations harbored by a minor clone. Findings were compared with results from interphase/ metaphase FISH studies and conventional cytogenetic analysis.
Results: Several indicators for clonal heterogeneity were detected in the SNP/CGH microarray data set for 8 AML bone marrow specimens. A difference in log2 ratios of separate chromosomal abnormalities was detected in all cases. The log2 ratios were used for manual peak assignment to determine new analysis parameters for the major and the minor cell populations. In addition, several specimens revealed a discordance of SNP calls to CGH analysis and/or complex copy number peak assignment plots as further indication for clonal heterogeneity. Distinct abnormalities could be separately extracted for minor and major cell populations when re-analyzing the SNP/CGH microarray data for all ten AML cases. FISH and/or conventional cytogenetic analysis was also used to confirm and further characterize clonal evolution in all 8 specimens.
Conclusions: SNP/CGH array analysis allows for additional characterization of clonal sub-populations and, therefore, demonstration of clonal evolution. This is a valuable asset for the clinical work-up of hematopoietic neoplasms since clonal evolution is associated with disease progression and adverse clinical outcome.
Wednesday, March 6, 2013 9:30 AM
Poster Session V # 280, Wednesday Morning