Targeted cell‐free DNA analysis with microarray quantitation for assessment of fetal sex and sex chromosome aneuploidy risk

The accuracy of targeted cell-free DNA (cfDNA) testing with DANSRTM and FORTETM for trisomies 21, 18 and 13 has been well demonstrated and is consistent across next generation sequencing and microarray quantitation methods1. Targeted cfDNA analysis for fetal sex chromosome aneuploidy (SCA) has also been validated and shown to have high specificity in prospective studies2,3. This study expands upon the available published data by investigating the performance of targeted cfDNA analysis of the X and Y chromosomes using microarray quantitation for assessment of SCA probability in singleton pregnancy and fetal sex in twin and singleton pregnancies. Samples of banked maternal plasma from 791 singleton and 51 twin pregnancies were obtained as part of ongoing multicenter clinical studies (NCT02201862 and NCT01451671) and from a sample bank at King’s College London, UK. Single cell-free Roche, Streck BCT-DNA or EDTA collection tubes were available for each sample. Collection and processing differed from commercial protocols only in that all samples were frozen prior to analysis and available specimen volumes were lower than standardly used. Patient consent and fetal karyotype information was obtained for all samples. The cohort included 15 singleton pregnancies with sex chromosome aneuploidy. Targeted cfDNA analysis with microarray quantitation was performed, as previously described, using a blinded protocol4. Y-chromosome specific DANSR assays were used to evaluate fetal sex in twin and singleton pregnancies. Results were reported as male or female, depending