Chromosomal phase improves aneuploidy detection in non-invasive prenatal testing at low fetal DNA fractions.

Non-invasive prenatal testing (NIPT) to detect fetal aneuploidy by sequencing the cell-free DNA (cfDNA) in maternal plasma is being broadly adopted. To detect fetal aneuploidies from maternal plasma, where fetal DNA is mixed with far-larger amounts of maternal DNA, NIPT requires a minimum fraction of the circulating cfDNA to be of placental origin, a level which is usually attained beginning at 10 weeks gestational age. We present an approach that leverages the arrangement of alleles along homologous chromosomes-also known as chromosomal phase-to make NIPT analyses more conclusive. We validate our approach with in silico simulations, then re-analyze data from a pregnant mother who, due to a fetal DNA fraction of 3.4%, received an inconclusive aneuploidy determination through NIPT. We find that the presence of a trisomy 18 fetus can be conclusively inferred from the patient's same molecular data when chromosomal phase is incorporated into the analysis. Key to the effectiveness of our approach is the ability of homologous chromosomes to act as natural controls for each other and the ability of chromosomal phase to integrate subtle quantitative signals across very many sequence variants. These results show that chromosomal phase increases the sensitivity of a common laboratory test, an idea that could also advance cfDNA analyses for cancer detection.

The effect of processing and cryopreservation on nucleated umbilical cord blood cells.

Recovery of nucleated cord blood cells after storage in liquid nitrogen was evaluated. Red cells were depleted using Ficoll-Paque or Puregene red cell lyses. Freeze Medium contained 10% dimethylsulfoxide and 20% serum for cryoprotection. Recovery of the original cell population remaining serviceable for fluorescence activated cell sorting (FACS) was 12 +/- 10% (average +/- standard deviation), with a range of 1% to 55%. Viability measured by FACS analysis after freezing was significantly lower than that of the same specimens prior to freezing, 62 +/- 20% compared to 91+/-11% (p<0.001). Percentage CD45+34+ cells were the same for fresh and frozen cells. Gestational age at which specimens were collected had no effect on the percent cells carrying the CD45+34+ markers. We conclude that better cryoprotective supplements are needed to insure consistent high recovery of viable nucleated umbilical cord blood cells after preservation in liquid nitrogen.