Novel Algorithms for Improved Sensitivity in Non-Invasive Prenatal Testing

Scientific Reports
L F JohanssonB Sikkema-Raddatz

Abstract

Non-invasive prenatal testing (NIPT) of cell-free DNA in maternal plasma, which is a mixture of maternal DNA and a low percentage of fetal DNA, can detect fetal aneuploidies using massively parallel sequencing. Because of the low percentage of fetal DNA, methods with high sensitivity and precision are required. However, sequencing variation lowers sensitivity and hampers detection of trisomy samples. Therefore, we have developed three algorithms to improve sensitivity and specificity: the chi-squared-based variation reduction (χ2VR), the regression-based Z-score (RBZ) and the Match QC score. The χ2VR reduces variability in sequence read counts per chromosome between samples, the RBZ allows for more precise trisomy prediction, and the Match QC score shows if the control group used is representative for a specific sample. We compared the performance of χ2VR to that of existing variation reduction algorithms (peak and GC correction) and that of RBZ to trisomy prediction algorithms (standard Z-score, normalized chromosome value and median-absolute-deviation-based Z-score). χ2VR and the RBZ both reduce variability more than existing methods, and thereby increase the sensitivity of the NIPT analysis. We found the optimal combination ...Continue Reading

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Citations

Jun 6, 2018·The Journal of Maternal-fetal & Neonatal Medicine : the Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians·Minh-Duy PhanHoai-Nghia Nguyen
Jul 10, 2019·PloS One·Hindrek TederPriit Palta
Dec 19, 2018·BMC Bioinformatics·Lennart F JohanssonMorris A Swertz

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Methods Mentioned

BETA
PCR
biopsy
2500 sequencing

Software Mentioned

NIPT
Picard
NIPTeR
LOESS
fastqc
fastq
Sam
BWA
SOLiD
BWA aln samse

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