Case Reports: Expanding the Diagnostic Spectrum of Non-invasive Prenatal Testing to Structural Chromosomal Abnormalities

Jong Chul Kim¹Hyunjin Kim¹Heeyeon Jang^1,2Minyeon Go^1,2Ji Eun Park¹Chang Soo Ryu²Mi Uk Chin¹Eun Hye Kim¹Young Jin Lee¹Sung Han Shim^1,2*Dong Hyun Cha^1,3*

• ¹CHA Biotech Co., Ltd., Seoul, Republic of Korea
• ²CHA University, Pocheon-si, Republic of Korea
• ³CHA Gangnam Medical Center, Gangnam-gu, Republic of Korea

Non-invasive prenatal testing (NIPT) has recently expanded to include sex chromosomal aneuploidies (SCAs) and copy number variations (CNVs), as well as the commonly screened trisomies (T21, T18, and T13). While the clinical utility of NIPT for detecting common fetal chromosomal aneuploidies is well established, its application in assessing structural chromosomal abnormalities (StrCAs) remains controversial, with limited consensus within the medical community. Furthermore, the accuracy of NIPT for detecting SCAs and CNVs is relatively lower than that for common trisomies. This study reports three cases in which NIPT results suggestive of SCAs were clarified by invasive diagnostic testing to represent underlying structural sex chromosome abnormalities. NIPT results suggestive of SCAs were validated through invasive diagnostic tests, including karyotyping, chromosomal microarray (CMA), quantitative fluorescence PCR (QF-PCR), and multiplex ligation-dependent probe amplification (MLPA). In the first case, the NIPT result suggestive of a monosomy X-like pattern reflected an underlying structural abnormality. Fetal chromosomal microarray (CMA) revealed a 3.6 Mb deletion involving the Xq27.3–q28 region and a 4.8 Mb duplication encompassing Xq28, with subsequent analysis confirming inactivation of the deleted X chromosome. In the second case, the NIPT result suggesting monosomy X with a low Y chromosome fraction (1.46%) resembled a vanishing twin pattern but was ultimately explained by mosaicism involving a ring Y chromosome (46,X,r(Y)/45,X). CMA revealed a 7.4 Mb duplication of Yp11.31–p11.2 and a 15 Mb deletion of Yq11.21–q11.23, confirming mosaic ring Y formation. In the third case, the NIPT finding suggestive of XYY with Xp22.33–p22.2 deletion was clarified by confirmatory testing as a maternal sex chromosome translocation, 46,X,der(X)t(X;Y)(p22.2;q11.222), detected in the mother with short stature but no other clinical features. In conclusion, these three NIPT findings initially interpreted as SCAs were clarified by confirmatory invasive diagnostics, illustrating the complexity of interpreting results associated with StrCAs. These findings support the potential of NIPT to extend beyond numerical aneuploidy screening and contribute to the detection of structural chromosomal abnormalities.