High Confidence Fetal Sex Determination from Non-Invasive Prenatal Testing Low Coverage Semiconductor Sequencing Data

Background. The study evaluates performance and confidence of fetal sex determination from circulating cell free DNA (cfDNA) during pregnancy using semiconductor sequencing massively parallel sequencing (MPS) data obtained for trisomy detection.Methods. MPS data of semiconductor sequencing carried out previously for trisomy detection from fifty circulating cfDNA samples from pregnant women were used for this study. Normalized coverage data of the one mega base regions across Y chromosome was used for analysis. Real time PCR detecting SRY (sex-determining region Y) presence/absence was carried out as validation for fetal sex determination.Results. We propose that region spanning approximately 14.6 mega bases in q arm of the Y chromosome should be used to determine sex of the fetus as it contributes the largest amount of observed difference between female and male fetuses when cfDNA semiconductor MPS data are mapped to human hg19 reference. Using this region for fetal sex determination increases observed z-score of Y chromosome coverage in males by average 11.38 (536%) while decreasing z-score by 0.5 (29%) for pregnancies carrying female fetuses. Overall high confidence sex determination cases increased from ten to 29 in our 30 sample validation group.