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31: Discovery of DNA methylation markers for prenatal aneuploidy testing

      Objective

      Testing circulating cell free fetal RNA in maternal plasma is currently the most promising approach for noninvasive trisomy 21 detection. The method involves measuring the ratios of heterozygous SNPs on fetal RNA. In this study, 10samples were used to assess an alternative technical strategy using epigenetic (methylation) markers to distinguish and enrich fetal DNA for aneuploidy testing.

      Study Design

      A unique approach for genome wide discovery of epigenetic markers was used to fractionate genomic DNA based on the methylation status. Using 10 paired samples, material from placenta and maternal buffy coat were tested for methylation. Highly methylated DNA fractions were then used in comparative genome hybridization studies to identify differentially methylated loci. Validation of our findings was performed using SEQUENOM™EpiTYPER technology. Results were then compared to a previously a published report that used standard bisulfite sequencing for discovery of T21 methylation markers.

      Results

      We have identified 25 differentially methylated regions (DMRs) of DNA that distinguish fetal and maternal genes. 14/25 of these genes had previously been reported using a standard bisulfite procedure. 13/14 of the DMRs were concordant with the previously published results showing that these genes exhibit DMRs. Although 11/13 genes were in concordance with the previously published data, 2/ 13 genes exposed sequencing errors reported in the previous publication. In addition to the 13 genes identified, 9 novel hypermethylated and 5 hypomethylated fetal gene targets were identified. The results from genome wide scanning were confirmed by mass spectrometry analysis.

      Conclusion

      We have developed a new method for the rapid discovery of epigenetic markers presenting a viable approach to NIPD testing for fetal aneuploidy.