ArticleMolecular genetics & genomic medicine2020
Development of a new methylation-based fetal fraction estimation assay using multiplex ddPCR.
Article in Molecular genetics & genomic medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- A real-time PCR-based noninvasive prenatal RHD screening assay optimized for population-specific RHD allelic spectra in China.BMC medical genomics · 2026Article
- Digital PCR Assay Utilizing In-Droplet Methylation-Sensitive Digestion for Estimation of Fetal cfDNA From Plasma.Prenatal diagnosis · 2025Article
- Lessons (to be) learned from liquid biopsies: assessment of circulating cells and cell-free DNA in cancer and pregnancy-acquired microchimerism.Seminars in immunopathology · 2025Review
- Cell-free placental DNA: What do we really know?PLoS genetics · 2024Review
- Non-invasive prenatal diagnosis (NIPD): current and emerging technologies.Extracellular vesicles and circulating nucleic acids · 2023Review
- Calculation of Fetal Fraction for Non-Invasive Prenatal Testing.Biotech (Basel (Switzerland)) · 2021Review
- Development of a new methylation-based fetal fraction estimation assay using multiplex ddPCR.Molecular genetics & genomic medicine · 2020Article
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9 authors.
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Abstract
backgroundNon-invasive prenatal testing (NIPT) for fetal aneuploidies has rapidly been incorporated into clinical practice. Current NGS-based methods can reliably detect fetal aneuploidies non-invasively with fetal fraction of at least 4%. Inaccurate fetal fraction assessment can compromise the accuracy of the test as affected samples with low fetal fraction have an increased risk for misdiagnosis. Using a novel set of fetal-specific differentially methylated regions (DMRs) and methylation sensitive restriction digestion (MSRD), we developed a multiplex ddPCR assay for accurate detection of fetal fraction in maternal plasma.
methodsWe initially performed MSRD followed by methylation DNA immunoprecipitation (MeDIP) and NGS on fetal and non-pregnant female tissues to identify fetal-specific DMRs. DMRs with the highest methylation difference between the two tissues were selected for fetal fraction estimation employing MSRD and multiplex ddPCR. Chromosome Y multiplex ddPCR assay (YMM) was used as a reference standard, to develop our fetal fraction estimation model in male pregnancy samples. Additional 123 samples were tested to examine whether the model is sex dependent and/or ploidy dependent.
resultsIn all, 93 DMRs were identified of which seven were selected for fetal fraction estimation. Statistical analysis resulted in the final model which included four DMRs (FFMM). High correlation with YMM-based fetal fractions was observed using 85 male pregnancies (r = 0.86 95% CI: 0.80-0.91). The model was confirmed using an independent set of 53 male pregnancies.
conclusionBy employing a set of well-characterized DMRs, we developed a SNP-, sex- and ploidy-independent methylation-based multiplex ddPCR assay for accurate fetal fraction estimation.
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