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7 recordsLinked to original sources
PubMed2025

Visualization using NIPTviewer support the clinical interpretation of noninvasive prenatal testing results.

BACKGROUND: Noninvasive prenatal testing (NIPT) is increasingly used to screen for fetal chromosomal aneuploidy by analyzing cell-free DNA (cfDNA) in peripheral maternal blood. The method provides an opportunity for early detection of large genetic abnormalities without an increased risk of miscarriage due to invasive procedures. Commercial applications for use at clinical laboratories often take advantage of DNA sequencing technologies and include the bioinformatic workup of the sequence data. The interpretation of the test results and the clinical report writing, however, remains the responsibility of the diagnostic laboratory. In order to facilitate this step, we developed NIPTviewer, a web-based application to visualize and guide the interpretation of NIPT data results. RESULTS: NIPTviewer has a database functionality to store the NIPT results and a web interface for user interaction and visualization. The application has been implemented as part of a novel analysis pipeline for NIPT in a diagnostic laboratory at Uppsala University Hospital. The validation data set included 84 previously analyzed plasma samples with known results regarding chromosomes 13, 18, 21, X and Y. They were sequenced in six different experiments, uploaded to NIPTviewer and assigned to a clinical laboratory geneticist for interpretation. The results of all previously analyzed samples were replicated. CONCLUSION: NIPTviewer facilitates NIPT results interpretation and has been implemented as part of a NIPT analysis routine that was accredited by the national accreditation body for Sweden (Swedac).

Humans↗
PubMed2026

Novel and High-Throughput Method of Isolating Single Fetal Cells Using FACS for NIPT.

OBJECTIVE: To evaluate fluorescence activated cell sorting (FACS) as a method of single-cell isolation of rare circulating fetal cells from maternal blood for use in cell-based non-invasive prenatal testing (cbNIPT). METHOD: Blood samples (30 mL) were collected from 75 'low-risk' pregnant women (gestational age 10-15 weeks). Fetal cells were enriched and stained using magnetic activated cell sorting. Following enrichment, single fetal cells were sorted in individual PCR tubes by FACS. After cell lysis, verification of fetal cell origin was performed using short tandem repeat (STR) analysis with the GlobalFiler PCR Amplification kit. RESULTS: An average of 13.7 cells were sorted using FACS. STR analysis identified 8.2 fetal cells on average, representing 60.2% of the sorted cells. The four-step single-cell isolation procedure facilitated an overall enrichment of approximately 16-million-fold. One sample did not render any fetal cell, corresponding to 1.3% of the samples. CONCLUSION: FACS, which is typically used for segregation of large populations of cells, can be used for single-cell isolation of rare fetal cells in an automated setup. This not only helps in making cell isolation faster and high throughput but also provides fetal cells for a more comprehensive genetic analysis of the fetus.

Humans↗
PubMed2026

A Simplified Workflow for the Prediction of Putative Viral Reads Using NIPT Data.

OBJECTIVE: Non-invasive prenatal testing (NIPT) identifies fetal chromosomal abnormalities by sequencing cell-free fetal DNA (cffDNA). Recent studies suggest the prediction of viral sequences from NIPT data, but current methods lack cost-effectiveness for routine use. This study develops a straightforward workflow to investigate potential viral signatures in pregnant women using NIPT data from 888 Iranian participants. METHOD: Two bioinformatic workflows were compared for predicting viral reads: the traditional method involved mapping reads to the human genome, followed by mapping unmapped reads to viral references, and a direct mapping approach to viral genomes, as proposed in this research. RESULTS: While maintaining reproducibility comparable to the conventional method, the proposed workflow minimizes computational complexity and time usage for data processing. Ultimately, this analysis suggested viral DNA in 24.2% of samples, encompassing 29 distinct species, implying the diversity of the maternal virome. CONCLUSION: This study presents a computationally efficient workflow for the in silico prediction of viral-like sequences from routine NIPT data. Further experimental validation is essential to verify the presence, viability, or clinical relevance of these sequences.

Humans↗
PubMed2026

Non-invasive embryo assessment: Cell-free DNA-based genetic testing and amino acid metabolomics in relation to morphology: A case-control study.

BACKGROUND: Cell-free DNA (cfDNA) in spent culture medium (SCM) offers a non-invasive option for preimplantation genetic testing, but its low concentration and fragmentation reduce clinical reliability. Combining genetic assessment with metabolomic profiling may provide complementary information about embryo competence. OBJECTIVE: This study assessed pre-analytical cfDNA processing workflows and examined whether SCM amino acid metabolic patterns could act as practical markers of embryo quality. MATERIALS AND METHODS: In this case-control study (2021-2023), 90 embryos were evaluated using fluorescence in situ hybridization or array comparative genomic hybridization. SCM samples underwent rapid boiling, silica-based purification, or whole-genome amplification (WGA). Sex determination was performed using quantitative polymerase chain reaction (qPCR). For cfDNA quality control and aneuploidy screening, the multiplex IRFiling kit and quantitative fluorescent polymerase chain reaction (QF-PCR) were used. Amino acid profiles across embryonic developmental stages and quality grades were quantified via liquid chromatography-tandem mass spectrometry. RESULTS: Rapid boiling resulted in complete failure of DNA amplification. Conversely, silica-based purification yielded 70.0% concordance for qPCR-based sexing and 56.7% for QF-PCR. WGA achieved the highest efficacy (73.3% qPCR and 56.7% QF-PCR concordance), although quality control checks flagged occasional misclassifications. LC-MS/MS profiling revealed significantly elevated alanine and arginine levels in tripronuclear embryos. Furthermore, high-quality blastocysts exhibited elevated glutamic acid levels alongside a pronounced overall depletion of extracellular amino acids compared to low-quality counterparts and controls. CONCLUSION: WGA improves cfDNA detectability and qPCR accuracy compared with boiling or purification, but remains inadequate as a standalone screening approach. SCM amino acid profiling provides informative, complementary metabolic signatures of developmental competence, supporting a multimodal strategy for non-invasive embryo assessment.

Amino acid metabolism↗
PubMed2025

Identification of maternal Gγ(Aγδβ)0 thalassemia through retrospective reanalysis of prenatal cfDNA sequencing data.

OBJECTIVE: Non-invasive prenatal screening (NIPS) is widely used to detect chromosomal abnormalities such as trisomies 21, 13, and 18 and is also effective in screening for copy number variations (CNVs). However, the routine application of NIPS to detect smaller CNVs within the HBB gene, specifically Gγ(Aγδβ)0 thalassemia, has yet to be well documented. This study aims to evaluate the efficacy of cfDNA-based maternal carrier screening in routine screening for Gγ(Aγδβ)0 thalassemia. METHODS: We performed a retrospective analysis of 107,300 pregnant women who underwent NIPS at Longgang Maternal and Child Healthcare Hospital in Shenzhen from December 2017 to May 2022. Using an improved algorithm, we reanalyzed NIPS data to identify maternal Gγ(Aγδβ)0 thalassemia. Positive cases were confirmed by multiplex ligation-dependent probe amplification (MLPA) using peripheral blood leukocytes. RESULTS: Among the 107,300 NIPS analyses, 38 maternal deletion CNVs within the HBB gene were identified using the improved algorithm, with a prevalence of 0.035% (38/107,300). MLPA confirmed that all detected deletions were consistent with Gγ(Aγδβ)0 thalassemia. The positive predictive value (PPV) for detecting Gγ(Aγδβ)0 thalassemia by cfDNA-based maternal carrier screening was 100%. Among the 38 Gγ(Aγδβ)0 cases, 9 were also associated with α-thalassemia deletions, including 4 cases with -SEA/αα, 4 with -α3.7/αα, and 1 with -α4.2/αα. No cases of homozygosity or compound HBB gene variants were observed. CONCLUSIONS: Gγ(Aγδβ)0 thalassemia is not uncommon in China, and repurposed NIPS methodology for maternal genomic analysis in detecting HBB gene deletions is a reliable method for identifying maternal carriers of this disease.

Humans↗
PubMed2026

Identification of rare maternal copy number variants by genome-wide analysis of noninvasive prenatal screening data in 113,017 pregnant women.

OBJECTIVES: Knowledge of copy number variants (CNVs) is relevant to maternal and fetal health and can be obtained from noninvasive prenatal screening (NIPS) of pregnancy. However, genome-wide analysis of maternal CNVs using NIPS data has not been conducted in large populations. METHODS: For CNV analysis, the human genome was segmented into 10 kilobase pairs (Kb) bins, and the relative sequencing depth of each bin was calculated. The circular binary segmentation algorithm was used to estimate CNVs. Detected CNVs from two pregnancies of the same participant were compared to validate the reproducibility. All CNVs were merged into CNV regions (CNVRs) to evaluate their frequency, distributions, and relationship with disease-related genes and regions. RESULTS: In this study, 113,017 pregnant women were recruited. A total of 363,886 CNVs larger than 50 Kb were detected in 101,779 individuals and merged into 43,005 CNVRs. For evaluating the reproducibility of CNVs, 90.18% of deletions and 88.07% of duplications were consistent. In general, 78.13% of individuals carried CNVRs that overlapped protein-coding genes, while 14.76% overlapped OMIM genes. We detected 246 novel CNVRs, 134 (54.47%) involving protein-coding genes. For the perspective of maternal-fetal health, we identified 4,984 (4.41%) individuals as carriers of 5,243 CNVs containing known pathogenic or likely pathogenic regions, including 22q11.2 region and DMD gene.. CONCLUSIONS: NIPS sequencing data is a reliable source for maternal CNV detection. These CNVs constitute an integrate component in maternal-fetal health management.

Humans↗
PubMed2026

Trophoblast Enrichment by Maternal Immune-Cell Depletion Using CD45 and CD56 Surface Markers in Trophoblast Retrieval and Isolation from the Cervix (TRIC).

Background: Trophoblast retrieval and isolation from the cervix (TRIC) has emerged as a promising alternative to invasive prenatal diagnostic procedures. However, contamination by maternal immune cells remains a major challenge that may compromise trophoblast purity and the reliability of downstream fetal genetic analyses. Methods: Maternal immune cells were selectively depleted by immunomagnetic sorting using antibodies targeting CD45 or CD56. The remaining cells were subsequently enriched for HLA-G-positive trophoblasts and characterized by immunofluorescence and gene-expression analyses using CD45, CD56, HLA-G, cytokeratin 7 (CK7), and β-human chorionic gonadotropin (β-hCG). Results: Compared with CD45-mediated depletion, CD56-mediated depletion demonstrated more efficient removal of maternal immune cells, as indicated by significantly reduced CD56 expression. CK7 expression showed an increasing trend following CD56 depletion, whereas β-hCG expression remained largely unchanged. Immunofluorescence analysis further demonstrated a significant increase in the proportion of CK7+/β-hCG+ trophoblast cells after CD56 depletion. Conclusions: Among the evaluated depletion strategies, CD56-mediated depletion demonstrated a more favorable profile for trophoblast-associated characteristics than CD45-mediated depletion, suggesting its potential contribution to further methodological optimization of trophoblast isolation in TRIC-based noninvasive prenatal genetic testing.

maternal immune cell↗