Validation of an Enhanced Version of a Single-Nucleotide Polymorphism-Based Noninvasive Prenatal Test for Detection of Fetal Aneuploidies

Abstract

Objective: To validate an updated version (Version 2) of a single-nucleotide polymorphism (SNP)-based noninvasive prenatal test (NIPT) and to determine the likelihood of success when testing for fetal aneuploidies following a redraw. Methods: Version 2 was analytically validated using 587 plasma samples with known genotype (184 trisomy 21, 37 trisomy 18, 15 trisomy 13, 9 monosomy X, 4 triploidy and 338 euploid). Sensitivity, specificity and no-call rate were calculated, and a fetal-fraction adjustment was applied to enable projection of these values in a commercial distribution. Likelihood of success of a second blood draw was computed based on fetal fraction and maternal weight from the first draw. Results: Validation of this methodology yielded high sensitivities (≥99.4%) and specificities (100%) for all conditions tested with an observed no-call rate of 2.3%. The no-call threshold for sample calling was reduced to 2.8% fetal fraction. The redraw success rate was driven by higher initial fetal fractions and lower maternal weights, with the fetal fraction being the more significant variable. Conclusions: The enhanced version of this SNP-based NIPT method showed a reduced no-call rate and a reduced fetal-fraction threshold for sample calling in comparison to the earlier version, while maintaining high sensitivity and specificity.

Response to “Noninvasive prenatal screening at low fetal fraction: comparing whole‐genome sequencing and single‐nucleotide polymorphism methods”

“…Therefore, both to evaluate the upper bound of SNP‐method performance and to simplify the model to be maximally transparent, our simulations assumed the absence of crossovers. Supporting our assertion that the SNP method is well represented by our simulations is the striking correspondence between the published SNP method no‐call threshold (2.8% FF6) and the FF level at which our simulations found a precipitous drop in sensitivity, just below 3%.…”

“…In our manuscript, however, our aim was not to evaluate the methods' respective virtues on rare cases, but rather to assess the analytical performance and clinical impact for a very common occurrence: pregnancies with low fetal fraction. The SNP method routinely no‐calls low‐fetal‐fraction samples, and publications about the SNP method (e.g., Ryan et al 6) effectively inflate calculations of sensitivity by omitting the affected fetuses that are known to be enriched in the low‐fetal‐fraction patients who received no test result 10. By contrast, our analysis importantly and robustly suggests that for low‐fetal‐fraction pregnancies—common among patients with high BMI, at early gestational age, and with trisomy 13 or 18—the WGS method maintains high sensitivity, thereby yielding fewer false negatives, fewer no‐calls, and fewer unnecessary invasive procedures than the SNP method.…”

Current status of non‐invasive prenatal testing in Japan

“…In 2015, Natera added improvements to reduce the number of analyzed SNP. Eliminating uninformative SNP improved the sensitivity and specificity and reduced indeterminable results; the indeterminate rate was reported to improve to 2.3% …”

Noninvasive prenatal screening at low fetal fraction: comparing whole-genome sequencing and single-nucleotide polymorphism methods

“…In order to maintain high per‐patient sensitivity, some tests avoid reporting results to patients with fetal fractions below a preset threshold, referred to as a “no‐call” result. Patients who receive a “no‐call” may submit a second blood draw or be offered invasive testing as higher rates of aneuploidy have been reported in such samples …”