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Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform
Published on: August 17, 2022
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Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples
Priit Paluoja1,2,3, Hindrek Teder3,4, Amin Ardeshirdavani5
1Doctoral Programme in Population Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Plos Computational Biology
|December 20, 2021
Summary
This study benchmarks five computational tools for non-invasive prenatal testing (NIPT) aneuploidy screening. Lower sequencing depth significantly impacts accuracy, increasing false negatives, especially with low fetal DNA fractions.
Area of Science:
- Genetics
- Bioinformatics
- Reproductive Health
Background:
- Non-invasive prenatal testing (NIPT) screens for fetal aneuploidies using cell-free DNA.
- Numerous computational NIPT analysis tools exist, but direct accuracy comparisons are lacking.
Purpose of the Study:
- To conduct a comprehensive head-to-head accuracy comparison of five common computational NIPT analysis tools.
- To evaluate tool performance across varying sequencing depths and fetal DNA fractions.
Main Methods:
- Benchmarking of WisecondorX, NIPTeR, NIPTmer, RAPIDR, and GIPseq using clinically validated samples.
- Analysis of samples with trisomy 21, 18, and 13.
- Assessment of accuracy at different sequencing coverages and fetal DNA percentages.
Main Results:
- All tested NIPT tools showed reduced accuracy with lower sequencing depths.
- Decreasing sequencing depth led to a higher proportion of false-negative trisomy detections.
- Performance was particularly affected in samples with low fetal DNA fractions.
Conclusions:
- Trisomy detection is feasible with lower coverage NIPT data (e.g., 2.5M reads).
- Certain NIPT tools exhibit concerningly inaccurate trisomy detection rates at lower coverages, especially with low fetal DNA.
- Understanding tool-specific performance is crucial for reliable NIPT results.
