Investigation into the molecular characteristics and clinical applications of circulating cell -free DNA

The discovery of circulating nucleic acids in plasma and serum has led to the development of numerous promising noninvasive diagnostic tests. To date, circulating nucleic acid analysis has been applied to many different areas, including cancer detection, prenatal diagnosis, monitoring of organ transplant recipients and acute medicine. However, despite the extensive investigations on their clinical applications, the information on the molecular characteristics of the circulating nucleic acids is lacking.;In the second chapter of this thesis, the molecular nature of circulating Epstein-Barr virus (EBV) DNA is studied. Circulating EBV DNA has previously been shown to be a valuable marker for the detection, monitoring and prognostication of nasopharyngeal carcinoma and several cancers associated with EBV infection. Using DNase digestion and ultracentrifugation analysis, circulating EBV DNA was shown to be free DNA fragments instead of being associated with viral particles. Furthermore, a quantitative system was developed for measuring the size of these EBV DNA molecules and showed that over 80% of the circulating EBV DNA molecules are shorter than 180 bp.;In the subsequent chapters, this DNA size measurement technique has been applied for analyzing the integrity of plasma genomic DNA in cancer patients and pregnant women. Increased plasma DNA integrity was observed in both of these groups of individuals. Moreover, the size of plasma DNA in cancer patients was shown to normalize after successful treatment and the failure of such normalization was shown to be associated with poor prognosis. In pregnant women, in addition to the overall increase in plasma DNA size, the maternal-derived DNA molecules were further shown to be longer than the fetal-derived ones. This observation opens up the possibility for fetal DNA enrichment through size fractionation of maternal plasma DNA.;The latter part of the thesis describes the principle of a non-bisulfite-based method for the detection of aberrant DNA methylation in plasma/serum. Using this technique, a universal fetal DNA marker has been developed based on an epigenetic approach. The placentally derived hypermethylated RASSF1A sequence has been developed as a gender and polymorphism-independent marker for fetal DNA in maternal plasma. In pregnant women undergoing noninvasive prenatal rhesus D genotyping, false negative cases were successfully identified through the analysis of this new fetal DNA marker. The quantitative analysis of circulating methylated RASSF1A sequences has further been shown to be useful for the detection and prognostication of hepatocellular carcinoma.;In conclusion, the studies in this thesis have provided new information on the molecular nature of circulating DNA. Alteration of the size of circulating DNA is demonstrated in different physiological and pathological conditions. The non-bisulfite-based approach described in this thesis has provided a more sensitive and precise way for the detection and quantification of aberrantly methylated DNA sequences in the circulation. This method has tremendous potential for being applied for noninvasive cancer detection and prenatal diagnosis.