ArticleMolecular genetics & genomic medicine2021
Total number of reads affects the accuracy of fetal fraction estimates in NIPT.
Article in Molecular genetics & genomic medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Article
- GenomeMixer and TRUST: Novel bioinformatics tools to improve reliability of Non-Invasive Prenatal Testing (NIPT) for fetal aneuploidies.Computational and structural biotechnology journal · 2022Article
- Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples.PLoS computational biology · 2021Article
- Calculation of Fetal Fraction for Non-Invasive Prenatal Testing.Biotech (Basel (Switzerland)) · 2021Review
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSufficient fetal fraction (FF) is crucial for quality control of NIPT (Non-Invasive Prenatal Test) results. Different factors influencing bioinformatic estimation of FF should be considered when implementing NIPT. To what extent the total number of sequencing reads influences FF estimate has been unexplored. In this study, to test the robustness of SeqFF FF estimation and provide additional recommendations for NIPT analysis quality control, we compared the SeqFF FF estimates with two other methods and investigated how the number of sequencing reads and FF level affects the accuracy and precision of FF estimates.
methodsWGS data of 516 NIPT samples from a prenatal screening program was obtained. Sample data were randomly downsampled by the read count, and FF was calculated by SeqFF software. Then, the outcome was compared with FF estimates from SNP- and chrY-based methods. FF estimated with different read counts and FF levels were compared with FF at 30 M reads as a reference.
resultsSeqFF FF highly correlates with SNP- and chrY-based FF estimates. Raising read count from 2 M to 10 M drastically increased the accuracy of FF estimates. After adding more reads, we saw a further improvement in FF accuracy, reaching a plateau at 20 M reads. Precision of SeqFF FF estimate is independent of FF level in the sample.
conclusionSeqFF is a robust method for FF estimation for both genders and for any FF level in range 2-13%. Accuracy of FF estimates highly depends on the read count. We recommend using no less than 10 M reads to achieve accurate FF estimates for NIPT analysis in clinical settings.
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