Non-invasive Prenatal Testing: A Unique Approach with Single Nucleotide Polymorphism

The purpose of this review is to demonstrate the unique properties of a single nucleotide polymorphism (SNP)-based approach in non-invasive prenatal testing (NIPT). The identification of cell free fetal DNA in the plasma of pregnant women led to the development of NIPT. This can be performed with either a quantitative approach (massively parallel shotgun sequencing, chromosome selective sequencing) or a qualitative approach (SNP-based). NIPT tests have been shown to have superior performance as a screen for common fetal chromosome abnormalities compared with maternal serum screening. At low fetal fractions, NIPT sensitivity falls, particularly when quantitative methods are used. A SNP-based approach allows both accurate assessment of fetal fraction, and a robust test performance at lower fetal fractions. The ability of the SNP-based approach to screen for vanishing twins and maternal copy number variants reduces false positives; and the ability to make high confidence calls at lower fetal fraction, minimizes discordance between the NIPT result and the true fetal status.