Size fractionation of cell-free DNA in maternal plasma and its application in noninvasive detection of fetal single gene point mutations.

Recent studies have shown that cell-free fetal DNA in maternal plasma can be enriched by means of size fractionation. This technique makes use of the smaller size of fetal DNA fragments compared with maternal DNA fragments isolated simultaneously. On this basis, a highly improved detection of fetal single gene point mutations is permitted. Here, we introduce the use of agarose gel electrophoresis for the size fractionation of cell-free DNA from maternal plasma and the detection of fetal beta-thalassemia mutations in the size-fractionated cell-free DNA by using peptide nucleic acid-clamping polymerase chain reaction (PCR) combined with an allele-specific real-time PCR assay. Matrix-assisted laser desorption ionization/time of flight mass spectrometry has been reliably used for detection of fetal single gene point mutations in maternal plasma. We also present its use for genotyping paternally inherited single-nucleotide polymorphism alleles in the size-fractionated cell-free DNA from maternal plasma.