In:
PLOS Computational Biology, Public Library of Science (PLoS), Vol. 17, No. 12 ( 2021-12-20), p. e1009684-
Abstract:
Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are available, no prior comprehensive, head-to-head accuracy comparison of the various tools has been published. Here, we compared the outcome accuracies obtained for clinically validated samples with five commonly used computational NIPT aneuploidy analysis tools (WisecondorX, NIPTeR, NIPTmer, RAPIDR, and GIPseq) across various sequencing depths (coverage) and fetal DNA fractions. The sample set included cases of fetal trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome). We determined that all of the compared tools were considerably affected by lower sequencing depths, such that increasing proportions of undetected trisomy cases (false negatives) were observed as the sequencing depth decreased. We summarised our benchmarking results and highlighted the advantages and disadvantages of each computational NIPT software. To conclude, trisomy detection for lower coverage NIPT samples (e.g. 2.5M reads per sample) is technically possible but can, with some NIPT tools, produce troubling rates of inaccurate trisomy detection, especially in low-FF samples.
Type of Medium:
Online Resource
ISSN:
1553-7358
DOI:
10.1371/journal.pcbi.1009684
DOI:
10.1371/journal.pcbi.1009684.g001
DOI:
10.1371/journal.pcbi.1009684.g002
DOI:
10.1371/journal.pcbi.1009684.g003
DOI:
10.1371/journal.pcbi.1009684.g004
DOI:
10.1371/journal.pcbi.1009684.t001
DOI:
10.1371/journal.pcbi.1009684.s001
DOI:
10.1371/journal.pcbi.1009684.s002
DOI:
10.1371/journal.pcbi.1009684.s003
DOI:
10.1371/journal.pcbi.1009684.s004
DOI:
10.1371/journal.pcbi.1009684.s005
DOI:
10.1371/journal.pcbi.1009684.s006
DOI:
10.1371/journal.pcbi.1009684.s007
DOI:
10.1371/journal.pcbi.1009684.s008
DOI:
10.1371/journal.pcbi.1009684.s009
DOI:
10.1371/journal.pcbi.1009684.s010
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2021
detail.hit.zdb_id:
2193340-6
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