loss of heterozygosity assay for molecular detection of cancer using energytransfer primers and capillary array electrophoresis microsatellite dna loci are useful markers for the detection of loss of heterozygosity loh and microsatellite instability mi associated with primary cancers to carry out largescale studies of loh and mi in cancer progression highthroughput instrumentation and assays with high accuracy and sensitivity need to be validated dna was extracted from 26 renal tumor and paired lymphocyte samples and amplified with twocolor energytransfer et fluorescent primers specific for loci associated with cancerinduced chromosomal changes pcr amplicons were separated on the megabace1000 96 capillary array electrophoresis cae instrument and analyzed with megabace genetic profiler v10 software ninetysix separations were achieved in parallel in 75 minutes loss of heterozygosity was easily detected in tumor samples as was the gainloss of microsatellite core repeats allelic ratios were determined with a precision of 10 or better prior analysis of these samples with slab gel electrophoresis and radioisotope labeling had not detected these changes with as much sensitivity or precision this study establishes the validity of this assay and the megabace instrument for largescale highthroughput studies of the molecular genetic changes associated with cancer