Comparative assessment of gene-specific variant distribution in prenatal and postnatal cohorts tested for Noonan syndrome and related conditions.

PURPOSE: To compare the pattern of gene-specific involvement and the spectrum of variants observed in prenatal and postnatal (mean ± SD, 8.9 ± 9.4 years) cohorts tested for Noonan syndrome and related conditions. METHODS: Outcomes of sequencing panel testing were compared between prenatal (n = 845) and postnatal (n = 409) cohorts. RESULTS: PTPN11 and SOS1 harbored the majority of observed variants in both prenatal and postnatal cohorts, and BRAF, HRAS, KRAS, MAP2K1, MAP2K2, RAF1, and SHOC2 had similarities in their pattern of involvement in both cohorts. PTPN11 was the largest contributor of pathogenic variants and had the lowest frequency of variants of uncertain significance (VUS). SOS1 had the highest VUS frequency in both cohorts. The overall VUS frequency was twice as high in prenatal specimens (58.1 vs. 29.3%). PTPN11 and SOS1 had a 1.5-fold higher VUS frequency in the prenatal cohort (10.7 vs. 7.4% and 95 vs. 61.1%, respectively). The diagnostic yield was 3.7% for prenatal samples, with a higher yield of 12.3% in fetuses with cystic hygroma as a sole finding, and 21.3% for postnatal. CONCLUSION: Comparison of prenatal versus postnatal specimens demonstrates that the pattern of specific gene involvement is similar, whereas the classification spectrum of observed variants differs considerably.

Correction: Comparative assessment of gene-specific variant distribution in prenatal and postnatal cohorts tested for Noonan syndrome and related conditions.

The original version of this Article contained an error in the spelling of the author N. T. Leach, which was incorrectly given as N. L. Leach. This has been corrected in both the PDF and HTML versions of the Article.

The application of spectral karyotyping (SKY) and fluorescent in situ hybridization (FISH) technology to determine the chromosomal content(s) of micronuclei.

DNA loss by the process of micronucleation is associated with aging, cancer and environmental exposure. The primary aim of this study was to identify the chromosomal origin of the DNA excluded into micronuclei (MN). This was achieved using a novel application of SKY and FISH technologies. Cytochalasin B (Cyt B)-treated lymphocyte cultures from three females (aged 28, 42 and 72) were analyzed. SKY revealed that the majority of MN (89.8, 82.9, and 97.6% in the 28-, 42- and 72-year-old (y.o.), respectively) had a uniform, single color, suggesting that they were comprised of DNA from a single chromosome. Using a pancentromeric probe, most of the MN (82% in 28 y.o., 69% in 42 y.o. and 80% in 72 y.o.) had one centromere signal present. Overall, the confirmation studies (using FISH with chromosome-specific WCP) were in agreement with the SKY chromosomal assignments for 71.1% of the MN. Although the SKY analysis showed that all of the 23 chromosomes (22 autosomes and the X chromosome) could be present in the MN, overall, the X chromosome was seen most frequently. DNA from the X chromosome was seen in 50.6% of MN in the 42 y.o. individual, whereas in the 28 and 72 y.o. it was seen in 12.2 and 7.1% of MN, respectively. This difference (P<0.0001) in the frequencies of X chromosome exclusion into MN among individuals was independently confirmed using a single whole chromosome painting probe (WCP) for the X chromosome. SKY also showed variation in the frequency of autosomal exclusion into MN between chromosomes and between females. Collectively, this study supports the hypothesis that the majority of MN contain DNA from a single, monocentric chromosome. The use of SKY technology for the identification of the chromosomal content(s) of MN provides an opportunity for expansion of our knowledge of the chromosomal changes that accompany MN formation.