The implications of non-invasive prenatal testing failures: a review of an under-discussed phenomenon

Abstract

Introduction Non-invasive prenatal testing (NIPT) using cell-free DNA in maternal blood is a relatively new screening

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

“…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 (NIPT): genetic counseling, dominant methods and overall performance

“…These obstacles are more pronounced when the starting material is suboptimal, like the presence of amplification inhibitors or low fetal fraction: it has been shown that patients medicated with low molecular weight heparin have smaller total cfDNA fragments with an unusual high GC content [16]. Also, a fetal fraction below 4% is mainly responsible for test failures of targeted enrichment based NIPT approaches [7]. To overcome these biases, it is necessary to make targeted enrichment approaches very redundant, e.g.…”

“…Especially low fetal fraction is responsible for test failures in 0.5%-6.1% of all cases. Another parameter for the impossibility of obtaining a NIPT result was suggested to be the methodical approach: in a recent study, targeted enrichment based approaches seemed to exhibit higher failure rates than MPS based approaches (~3%-6% versus ~2%) [7]. It is of note, that two MPS based NIPT studies were excluded from failure rate calculation, as unclassified results were excluded from their test statistic calculation [8,38].…”

“…Equally, it should be pointed out that the PPV is dependent on the disease prevalence, therefore, in very young pregnant women with a low aneuploidy risk, a low significance must be assumed. It should also be noted that it is possible that a test may not have a result [7]. In summary, the basic principles of genetic counseling must also be applied to NIPT.…”

“…Another bias was introduced to [7] by ignoring the test specific differences in terms of fetal fraction measurement: not all NIPT providers measure fetal fraction, which renders their failure rates as almost incomparable. However, by examining all "No call" samples reported, a 2.5-6.7 times higher prevalence of fetal aneuploidy was detected among cases analyzed with targeted enrichment based NIPT approaches [29,39], compared to MPS based NIPT (MPS: not significantly different from the overall aneu ploidy rate, [7,[40][41][42] Figure 2: Meta-analysis based performance metrics of NIPT (modified from Gil et al [26]). Weighted pooled sensitivities and specificities for each chromosome were calculated from 37 relevant studies.…”