ArticlePrenatal diagnosis2019
PREFACE: In silico pipeline for accurate cell-free fetal DNA fraction prediction.
Article in Prenatal diagnosis, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Artificial intelligence and machine learning in cell-free-DNA-based diagnostics.Genome research · 2025Review
- Cell-free placental DNA: What do we really know?PLoS genetics · 2024Review
- SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.Briefings in bioinformatics · 2024Article
- Phenome-wide association study in 25,639 pregnant Chinese women reveals loci associated with maternal comorbidities and child health.Cell genomics · 2024Article
- Noninvasive prenatal screening in a pregnant woman with a history of stem cell transplant from a male donor: A case report and literature review.Molecular genetics & genomic medicine · 2024Review
- Shallow whole-genome sequencing: a useful, easy to apply molecular technique for CNA detection on FFPE tumor tissue-a glioma-driven study.Virchows Archiv : an international journal of pathology · 2022Article
- Shallow-depth sequencing of cell-free DNA for Hodgkin and diffuse large B-cell lymphoma (differential) diagnosis: a standardized approach with underappreciated potential.Haematologica · 2022Article
- Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review.Frontiers in pediatrics · 2022Review
- Development and performance evaluation of an artificial intelligence algorithm using cell-free DNA fragment distance for non-invasive prenatal testing (aiD-NIPT).Frontiers in genetics · 2022Article
- Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information.NPJ genomic medicine · 2021Article
- Total number of reads affects the accuracy of fetal fraction estimates in NIPT.Molecular genetics & genomic medicine · 2021Article
- Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes.International journal of molecular sciences · 2020Review
- Fetal fraction and noninvasive prenatal testing: What clinicians need to know.Prenatal diagnosis · 2020Review
- PREFACE: In silico pipeline for accurate cell-free fetal DNA fraction prediction.Prenatal diagnosis · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectiveDuring routine noninvasive prenatal testing (NIPT), cell-free fetal DNA fraction is ideally derived from shallow-depth whole-genome sequencing data, preventing the need for additional experimental assays. The fraction of aligned reads to chromosome Y enables proper quantification for male fetuses, unlike for females, where advanced predictive procedures are required. This study introduces PREdict FetAl ComponEnt (PREFACE), a novel bioinformatics pipeline to establish fetal fraction in a gender-independent manner.
methodsPREFACE combines the strengths of principal component analysis and neural networks to model copy number profiles.
resultsFor sets of roughly 1100 male NIPT samples, a cross-validated Pearson correlation of 0.9 between predictions and fetal fractions according to Y chromosomal read counts was noted. PREFACE enables training with both male and unlabeled female fetuses. Using our complete cohort (n
conclusionsAllowing individual institutions to generate optimized models sidelines between-laboratory bias, as PREFACE enables user-friendly training with a limited amount of retrospective data. In addition, our software provides the fetal fraction based on the copy number state of chromosome X. We show that these measures can predict mixed multiple pregnancies, sex chromosomal aneuploidies, and the source of observed aberrations.
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