Size fractionation of cell-free DNA in maternal plasma improves the detection of a paternally inherited beta-thalassemia point mutation by MALDI-TOF mass spectrometry

OBJECTIVES: The selective enrichment of cell-free fetal DNA in maternal plasma by size fractionation leads to the improved detection of paternally inherited fetal point mutations when using conventional, real-time PCR, or as has more recently been shown by MALDI-TOF mass spectrometry. We have now examined the use of size fractionation in conjunction with mass spectrometry for the detection of a paternally inherited codon 39 mutation of the beta-globin gene. METHODS: Maternal plasma was obtained from an early second trimester pregnancy at risk for beta-thalassemia, where the father carried the codon 39 mutation and the mother was a carrier for the IVSI-110 mutation of the beta-globin gene. Cell-free DNA was analyzed by mutation-specific PCR and MALDI-TOF mass spectrometry for the presence of the codon 39 mutation. A comparison was made between total cell-free DNA and that which had been enriched for a size of 100-300 bp. RESULTS: The paternally inherited codon 39 mutant allele was detectable in both cell-free DNA preparations, but the signal was much more pronounced and precise in the size-fractionated sample. CONCLUSIONS: Size fractionation of cell-free DNA may lead to the improved non-invasive detection of fetal point mutations for beta-thalassemia by MALDI-TOF mass spectrometry.