Abstract: A method for detecting a putative mutant DNA in a sample of DNA includes the steps of amplifying the sample of DNA using PCR; hybridizing the amplified sample to form a mixture of homoduplexes and heteroduplexes; separating the mixture into fractions by Denaturing Matched Ion Polynucleotide Chromatography; and blind collecting the eluted fractions at a retention time corresponding to the retention time of the heteroduplex. The DNA in the blind collected fractions can be PCR amplified to obtain an increased amount of heteroduplex relative to homoduplex. The method is useful for determining the remission status of a patient in which the tissue-derived DNA sample contains a large background of wild type or where the putative mutant DNA is below the limit of detection.