Non-invasive prenatal testing (NIPT) has transformed prenatal screening, offering high sensitivity and specificity in the detection of common fetal aneuploidies. However, discordant results—where NIPT findings do not align with those of confirmatory diagnostics—pose challenges for clinical interpretation and patient counseling.

This study aims to analyze the contributing factors and clinical implications of discordant NIPT results using two illustrative case studies.

Two cases with discordant NIPT findings were examined. Case 1 involved unexplained fetal growth restriction with normal NIPT results, while Case 2 presented a false-positive NIPT result indicating trisomy 7. Both cases underwent invasive testing (amniocentesis) and comprehensive ultrasound evaluation. In Case 1, a chromosomal microdeletion (4p16.3) associated with Wolf-Hirschhorn syndrome was identified despite normal NIPT results. In Case 2, the suspected trisomy 7 was not confirmed by invasive testing, suggesting confined placental mosaicism or technical limitations as potential causes of discordance.

Discordant non-invasive prenatal testing (NIPT) results may arise from biological factors, such as confined placental mosaicism or maternal conditions, or from technical constraints. These cases underscore the importance of invasive confirmatory testing and multidisciplinary counseling to ensure an accurate diagnosis and enable informed decision-making in prenatal care.

confined placental mosaicism, discordant results, genetic counselling, non-invasive prenatal testing, prenatal diagnosis, trisomy 7, Wolf-Hirschhorn syndrome

Non-invasive prenatal testing (NIPT) has emerged as a revolutionary approach in prenatal screening, primarily for its ability to detect common fetal aneuploidies such as trisomy 21, trisomy 18, and trisomy 13 with high sensitivity and specificity. However, despite its advantages, NIPT is not without limitations, particularly concerning discordant results, where the findings of the test do not align with the clinical or ultrasound findings. The phenomenon of discordant results can be attributed to several factors, including biological variances, technical limitations, and maternal conditions, which complicate the interpretation of NIPT outcomes.^{[1, 2]}

One of the most significant contributors to discordant results is confined placental mosaicism (CPM). This condition arises when there is a discrepancy between the genetic makeup of the placenta and that of the fetus, leading to potential false-positive or false-negative results in NIPT. CPM occurs in approximately 2% of pregnancies and is particularly relevant because cell-free fetal DNA (cffDNA), which is the basis of NIPT, is predominantly derived from the placenta rather than the fetus itself.^[1] Consequently, the NIPT may reflect placental genetic anomalies that do not necessarily indicate fetal abnormalities, complicating the clinical decision-making process.^[2]

Moreover, maternal factors can also influence NIPT results. For instance, maternal malignancies have been reported to cause discordant NIPT outcomes, although these cases are relatively rare and often involve single chromosomal aberrations rather than multiple aneuploidies.^[3] Additionally, conditions such as maternal mosaicism and copy number variations can further obscure the accuracy of NIPT, leading to misinterpretations of fetal health.^[2] The interplay between maternal health and NIPT results underscores the necessity for comprehensive counseling and follow-up testing to confirm any findings from NIPT, as the test is primarily a screening tool rather than a definitive diagnostic method.^[4]

Technical aspects of NIPT also play a crucial role in discordant results. The accuracy of NIPT depends heavily on the quality and concentration of cell-free fetal DNA (cffDNA) in maternal blood samples. Low fetal fraction (FF) can lead to unreliable results because insufficient cffDNA may not accurately represent the fetal genome.^[5] Furthermore, variations in the bioinformatics tools used to analyze NIPT data can result in discrepancies in result interpretation because different algorithms may yield varying levels of sensitivity and specificity.^[6]

In cases of multiple gestations, the complexity of interpreting NIPT results increases significantly. The presence of a vanishing twin, for example, can lead to discordant findings due to the differential contribution of cffDNA from each fetus.^[7] As such, the gestational dynamics in twin pregnancies necessitate careful consideration when evaluating NIPT results, as the genetic status of one fetus may not accurately reflect that of the other.^[7]

Although NIPT is a significant advancement in prenatal screening, discordant results present challenges that require careful navigation. These discrepancies have multifactorial causes, including biological, maternal, and technical influences. This necessitates a nuanced understanding of NIPT’s limitations. Clinicians must vigilantly interpret NIPT outcomes to ensure patients receive appropriate counseling and follow-up testing to clarify uncertainties arising from discordant results. Ongoing research and technological advancements in the field of prenatal testing will be essential in enhancing the reliability and accuracy of NIPT, ultimately improving outcomes for mothers and their fetuses.^[8–10]

A 30-year-old primigravida with no history of genetic disorders underwent routine prenatal screening, including first-trimester combined screening and a non-invasive DNA test (NIPT), both of which yielded normal results. The NIPT report confirmed that the fetus had a low risk of common chromosomal aneuploidies such as trisomy 21, 18, and 13, and rare microdeletions and duplications with a fetal fraction of 14%. The NIPT specifically excluded Wolf-Hirschhorn syndrome (WHS).

However, during the second-trimester fetal morphology scan at 20-22 weeks of gestation, symmetrical fetal growth restriction was observed (Table 1) .

Despite normal levels of amniotic fluid and reassuring fetal Doppler findings, the growth restriction raised concerns for an underlying genetic abnormality. Given the unexplained intrauterine growth restriction (IUGR) and the lack of other evident causes, invasive diagnostic testing was offered and accepted.

An amniocentesis was performed, and a ChromoSeq test was ordered to provide a detailed chromosomal analysis. The electronic karyotype obtained from this test revealed a fragmentary deletion on chromosome 4p16.3, as shown in the detailed karyotype report (Fig. 1) .

Figure 1.

Karyotype analysis from Case 1 confirming a fragmentary deletion on chromosome 4p16.3, indicative of Wolf-Hirschhorn syndrome.

Specifically, the deletion spanned approximately 3.41 Mb on the short arm of chromosome 4 (4p16.3-p16.6), a region known to be associated with Wolf-Hirschhorn syndrome (WHS), a genetic condition characterized by growth retardation, intellectual disability, distinctive craniofacial features, and seizures.

The clinical interpretation of the genetic findings confirmed the presence of a pathogenic deletion, and the patient was diagnosed with a high risk for Wolf-Hirschhorn syndrome based on the extent of the deletion and clinical correlates from similar cases documented in the DECIPHER and ClinVar databases. The patient was extensively counselled regarding the prognosis, which included a severe risk for neurodevelopmental abnormalities, seizures, and other physical malformations typical of WHS.

Given the poor prognosis and potential for profound developmental disabilities, the pregnancy was terminated for medical reasons in accordance with the patient’s wishes. The decision was made following multidisciplinary consultations involving a maternal-fetal medicine specialist, a clinical geneticist, and a genetic counsellor. This case underscores the importance of invasive testing in pregnancies where unexplained fetal growth restriction is present, even in the context of normal non-invasive prenatal screening results.

A 34-year-old woman, gravida 2 para 1, presented at 13 weeks of gestation following a routine non-invasive prenatal test, which she elected to undergo due to advanced maternal age. The NIPT results indicated a high risk for trisomy 7 (Fig. 2) . The patient reported no significant medical or obstetric history.

Following the abnormal NIPT result, she was referred for genetic counseling and a detailed ultrasound at 14 weeks of gestation. The ultrasound revealed a single live fetus with no visible structural abnormalities, normal amniotic fluid levels, and appropriate growth parameters for gestational age (Fig. 3) .

Figure 2.

Positive NIPT for trisomy 7.

Figure 3.

Ultrasound findings in Case 2 showing a structurally normal fetus, contrasting with the high-risk NIPT result for trisomy 7.

Given the discordance between the reassuring ultrasound findings and the abnormal NIPT result, the patient opted for confirmatory invasive testing. An amniocentesis was performed at 16 weeks of gestation. The karyotype from amniotic fluid analysis showed a normal female complement (46,XX), and subsequent fluorescent in situ hybridization (FISH) confirmed the absence of trisomy 7.

For additional confirmation, ChromoSeq, a next-generation sequencing technique, was performed and also revealed a normal chromosomal profile. These findings were consistent with an aneuploid fetus, and the patient was counseled about the likely explanation for the discordance, including confined placental mosaicism or technical limitations of NIPT for detecting rare trisomies.

The pregnancy progressed uneventfully, and a healthy female infant was delivered at term. Postnatal chromosomal testing confirmed a normal karyotype.

Non-invasive prenatal testing (NIPT) has gained widespread adoption due to its high sensitivity and specificity for detecting common aneuploidies, such as trisomies 21, 18, and 13. However, as illustrated by these cases, its utility for detecting rare chromosomal abnormalities or predicting fetal outcomes remains limited, and discordance between NIPT and invasive testing results is a critical consideration in clinical practice.

While NIPT offers significant advantages in prenatal screening, the occurrence of discordant results necessitates careful consideration of various contributing factors. By understanding these complexities, clinicians can enhance their decision-making processes and provide better support to expectant parents facing the uncertainties of prenatal testing.