Detection of human DNA polymorphisms using high throughput methods often relies on generating a labeled DNA fragment which is generated by PCR using sequence-specific primers with an end labeled tag to detect a variant. The disadvantage of the synthesis of an end-labeled, sequence-specific primer to assay each DNA variant lies in the costs and time consume. In this report, we have demonstrated a methodology that can generate labeled DNA fragments using a labeled universal primer instead of requiring sequence-specific primers for each DNA variant.