Development of a sensitive PCR to detect allele loss in a model hematopoietic neoplasm

Loss or gain of an entire chromosome and interstitial deletions or amplifications are hallmarks of several hematopoietic neoplasms. These chromosomal anomalies can be identified by conventional cytogenetic analysis of bone marrow aspirates. We have developed a PCR-based assay to detect loss of chromosome 5q31 loci, in the model system of myeloid disorders with the 5q- chromosome (interstitial deletion of 5q), by taking advantage of a highly polymorphic dinucleotide repeat within the interleukin-9 (IL9) gene on 5q31. In a given sample, quantitation of amplification of individual alleles in a Phosphorimager allowed the representation of alleles to be expressed as a ratio of the larger to the smaller allele. Comparison of these ratios in paired DNA samples from Ficoll buoyant and pelletted fractions provides evidence for allele loss. Results presented here demonstrate that this technique of comparison of ratios of isotope incorporation could be expanded to investigate any deletion or numerical abnormality in hematopoietic tumors.