Non-invasive prenatal aneuploidy testing: Critical diagnostic performance parameters predict sample z-score values

Abstract

Objectives: Non-invasive prenatal aneuploidy testing (NIPT) by next-generation sequencing of circulating cell-free DNA in maternal plasma relies on chromosomal ratio (chr_ratio) measurements to detect aneuploid values that depart from euploid ratios. Diagnostic performances are known to depend on the fraction of fetal DNA (FF) present in maternal plasma, although how this translates into specific quantitative changes in specificity/positive predictive values and which other variables might also be important is not well understood.

Design & methods: To explore this issue, theoretical relationships between FF and various measures of diagnostic performances were assessed for a range of parameter values. Empirical data from three NIPT assays were then used to validate theoretical calculations.

Results: For a given positivity threshold, dramatic changes in specificity and positive predictive values (PPV) as a function of both FF and the coefficient of variation (CV) of the chr_ratio measurement were observed. Theoretically predicted and observed chr_ratio z-scores agreed closely, confirming the determinant impact of small changes in both FF and chr_ratio CV.

Conclusions: Evaluation of NIPT assay performances therefore requires knowledge of the FF distribution in the population in which the test is intended to be used and, in particular, of the precise value of the assay chr_ratio CV for each chromosome or genomic region of interest. Laboratories offering NIPT testing should carefully measure these parameters to ensure test reliability and clinical usefulness in interpreting individual patients' results.

Keywords: Down syndrome; Fetal DNA; NIPT; Next-generation sequencing; Non-invasive prenatal testing; cffDNA.