Causes of Inconclusive 22q11.2 Results on NIPT
Inconclusive 22q11.2 NIPT results occur primarily due to insufficient fetal fraction, technical limitations of the testing methodology used, placental mosaicism, and biological factors including vanishing twin or maternal copy number variations.
Technical and Biological Causes
Primary Technical Factors
Low fetal fraction is the most common technical cause of inconclusive results. The small size of the 22q11.2 microdeletion (typically 3 Mb) makes it technically challenging to detect using standard cell-free DNA screening, requiring adequate fetal fraction for reliable detection 1. Testing platforms that incorporate fetal fraction amplification demonstrate improved performance across a broad range of fetal fractions (5.9%-41.1%) 1.
Methodology-Dependent Performance
Different NIPT technologies are not equivalent and can produce discordant results for the same pregnancy 2. The two main approaches have distinct limitations:
- SNP-based methodology: Higher sensitivity for deletions within the critical 22q11.2 A-D region, with improved positive predictive values (44.2%) when using high-depth resequencing protocols 3
- Genome-wide counting methodology: May have lower sensitivity for deletions within the critical region but can potentially detect deletions outside this area 2
This technological variability explains why the same pregnancy can yield high-risk results on one platform and low-risk on another 2.
Biological Causes of Discordant Results
Placental-Origin Factors
Confined placental mosaicism is a major biological cause of both false-positive and inconclusive results 4, 5. The cell-free DNA analyzed in NIPT originates from the placenta, not directly from the fetus, creating potential for discordance when:
- The placenta harbors the 22q11.2 deletion but the fetus does not
- Mosaic patterns exist within placental tissue
- There is differential representation between cytotrophoblast and mesenchymal core 6
Additional Biological Factors
Other biological causes include 4, 5:
- Vanishing twin: A demised co-twin with the deletion contributing cell-free DNA
- Maternal copy number variations: Maternal 22q11.2 deletions or duplications interfering with fetal signal detection
- True fetal mosaicism: Present in the fetus but at levels difficult to detect
- Maternal malignancy: Rare but documented cause of aberrant results
Clinical Context
The sensitivity of NIPT for 22q11.2 deletion is lower than for common trisomies, with detection rates of 70-83% and positive predictive values of 40-50% for most associated microdeletions 7. The ACMG acknowledges that "sensitivity and specificity of CNV screening in general is below that of the common trisomies and SCAs" 8.
Important Caveats
- No-call or inconclusive results should prompt consideration of repeat testing with a different methodology or at a later gestational age when fetal fraction may be higher
- Body mass index impacts fetal fraction, with higher BMI associated with lower fetal fraction 1
- Gestational age matters: Earlier testing may have insufficient fetal fraction
- 67% of discordant NIPT cases have no obvious biological or technical explanation identified 5, emphasizing the screening nature of this test
Diagnostic Confirmation Requirements
All positive or inconclusive 22q11.2 NIPT results require diagnostic confirmation with chromosomal microarray analysis of chorionic villi or amniocytes 8, 7. When performing CVS for confirmation, separate analysis of cytotrophoblast and mesenchymal core is recommended, as mosaic trisomy in mesenchymal core requiring additional amniocentesis occurs in approximately 13.5% of trisomy 13 cases but is less common for other aneuploidies 6.