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ORIGINAL RESEARCH article
Front. Genet.
Sec. Human and Medical Genomics
Volume 16 - 2025 |
doi: 10.3389/fgene.2025.1527884
Exploration of cfDNA landscape in NIPT and clinical utilities of cfDNA based gene expression inference in prenatal diagnostics
Provisionally accepted- 1 Shenyang Maternity and Child Health Hospital, Shenyang, Liaoning Province, China
- 2 Haidian Maternal and Child Health Hospital of Beijing, Beijing, China
- 3 Changzhou Maternal and Child Health Care Hospital, Changzhou, Jiangsu Province, China
- 4 Annoroad Gene Technology (China), Beijing, Beijing Municipality, China
- 5 Nanjing Medical University, Nanjing, Jiangsu Province, China
Cell-free DNA (cfDNA) is a dynamic biomarker reflecting the physiological state of the body. Its unique physical and biochemical properties, inherited from the tissue of origin, enable a wide range of clinical applications. From methylation patterns and fragmentation profiles to genetic variants, cfDNA holds immense potential for diagnosing and monitoring various diseases, including cancer. In this study, we leverage a large collection of noninvasive prenatal testing (NIPT) dataset to explore the genomic landscape of fetal cfDNA, aiming to identify novel biomarkers associated with fetal development and maternal-fetal complications. Our study identifies novel fetal-specific genomic regions, further demonstrating the potential of cfDNA as a versatile biomarker. The prediction model achieved a 100% (12 of 12) positive predictive value (PPV) for hypothyroidism. Whereas for preeclampsia the PPV is much lower (25%, 3 of 12). By establishing a foundation for early hypothyroidism prediction and preeclampsia, we contribute to the expanding applications of NIPT. This approach can be adapted to explore other complex phenotypes and inform biomarker discovery, ultimately advancing maternal-fetal medicine.
Keywords: cfDNA, Chromatin, Fragmentomics, Gene Expression, Hypothyroidism, NiPt, Preeclampsia, WGS
Received: 14 Nov 2024; Accepted: 05 Feb 2025.
Copyright: © 2025 Jia, Zhu, Zhang, Sun, Zhang, Du and Qi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Ruo Jia, Shenyang Maternity and Child Health Hospital, Shenyang, 110032, Liaoning Province, China
Feng Zhang, Changzhou Maternal and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
Yangbo Sun, Annoroad Gene Technology (China), Beijing, Beijing Municipality, China
Bin Zhang, Nanjing Medical University, Nanjing, 210029, Jiangsu Province, China
Hong Qi, Haidian Maternal and Child Health Hospital of Beijing, Beijing, China
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