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Tumors release genomic DNA into the circulation of cancer patients after cellular necrosis and apoptosis. Isolation of the apoptotic fraction of plasma-circulating DNA can enhance detection of low-level mutations that can serve as tumor biomarkers (1). Because the amount of DNA circulating in the plasma of cancer patients is low, on the order of a few nanograms per milliliter of blood, the number of genes that can be examined for tumor-specific alterations is limited, a situation that reduces biomarker sensitivity. We recently applied whole-genome amplification of plasma-circulating DNA to increase the number of targets that can be analyzed from each sample, thus potentially increasing biomarker sensitivity(2). This approach yields highly-expanded DNA amounts for performing genetic screening; however, there is no preferential enrichment of smaller sized DNA fragments. We report a new method for whole-genome amplification of plasma-circulating DNA, based on ligation-mediated PCR of blunted DNA fragments (BLM-PCR)1 , which results in preferential amplification of smaller size, apoptotic DNA fragments.Plasma-circulating DNA was extracted from blood obtained from radiation therapy patients after the patients gave informed consent and the study received institutional review board approval. Within 2–3 h of collection, whole blood was centrifuged at 2000 g for 15–30 min, plasma was separated, and plasma-circulating DNA was purified by use of a QIAamp™ MinElute Virus Spin Kit (Qiagen) and quantified via Taqman real-time-PCR. To test for v-Ki-ras2 Kirsten …

Preferential Amplification of Apoptotic DNA from Plasma: Potential for Enhancing Detection of Minor DNA Alterations in Circulating DNA