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Copy-Number Profiling and Methylation-Based Tumor Typing during Prenatal Cell-Free DNA Screening
Stefania Tuveri1, Tatjana Jatsenko1, Dhanya Sudhakaran1
1Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.
Clinical Chemistry
|January 7, 2026
Summary
New prenatal screening using cell-free DNA (cfDNA) can identify fetal chromosomal issues and maternal cancer-derived aneuploidies. This methylation-aware approach improves diagnostic accuracy and cancer management during pregnancy.
Area of Science:
- Genomics
- Molecular Biology
- Oncology
Background:
- Prenatal cell-free DNA (cfDNA) screening typically detects fetal chromosomal abnormalities.
- Incidental findings of aneuploidies from other tissues, like maternal cancer, complicate prenatal diagnosis, causing anxiety and lengthy investigations.
Purpose of the Study:
- To develop an expedited method for identifying the origin of copy-number aberrations detected during prenatal cfDNA screening.
- To guide clinical management for pregnant individuals with profiles suggestive of maternal malignancy.
Main Methods:
- Developed a novel prenatal screening pipeline integrating methylation analysis and aneuploidy detection.
- Utilized enzymatic conversion of plasma cfDNA to identify methylated cytosines during sequencing.
- Employed a methylation-based deconvolution algorithm (MetDecode) with a cell-type-specific methylome atlas to predict tissue of origin.
Main Results:
- Aneuploidy profiling of enzymatically converted cfDNA achieved accuracy comparable to conventional prenatal cfDNA screening for both placental and cancer-derived aneuploidies.
- The MetDecode algorithm correctly identified the tumor origin in 91.67% of pregnant women with a tumor fraction exceeding 3%.
Conclusions:
- Methylome and aneuploidy-aware cfDNA screening significantly enhances diagnostic processes during pregnancy.
- This approach accurately pinpoints the origin of aneuploidies, improving cancer detection and management in expectant mothers.
