Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management

Noninvasive prenatal testing by massive parallel sequencing of maternal plasma DNA has rapidly been adopted as a mainstream method for detection of fetal trisomy 21, 18 and 13. Despite the relative high accuracy of current NIPT testing, a substantial number of false-positive and false-negative test...

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Veröffentlicht in:European journal of human genetics : EJHG 2015-10, Vol.23 (10), p.1286-1293
Hauptverfasser: Bayindir, Baran, Dehaspe, Luc, Brison, Nathalie, Brady, Paul, Ardui, Simon, Kammoun, Molka, Van der Veken, Lars, Lichtenbelt, Klaske, Van den Bogaert, Kris, Van Houdt, Jeroen, Peeters, Hilde, Van Esch, Hilde, de Ravel, Thomy, Legius, Eric, Devriendt, Koen, Vermeesch, Joris R
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container_end_page 1293
container_issue 10
container_start_page 1286
container_title European journal of human genetics : EJHG
container_volume 23
creator Bayindir, Baran
Dehaspe, Luc
Brison, Nathalie
Brady, Paul
Ardui, Simon
Kammoun, Molka
Van der Veken, Lars
Lichtenbelt, Klaske
Van den Bogaert, Kris
Van Houdt, Jeroen
Peeters, Hilde
Van Esch, Hilde
de Ravel, Thomy
Legius, Eric
Devriendt, Koen
Vermeesch, Joris R
description Noninvasive prenatal testing by massive parallel sequencing of maternal plasma DNA has rapidly been adopted as a mainstream method for detection of fetal trisomy 21, 18 and 13. Despite the relative high accuracy of current NIPT testing, a substantial number of false-positive and false-negative test results remain. Here, we present an analysis pipeline, which addresses some of the technical as well as the biologically derived causes of error. Most importantly, it differentiates high z-scores due to fetal trisomies from those due to local maternal CNVs causing false positives. This pipeline was retrospectively validated for trisomy 18 and 21 detection on 296 samples demonstrating a sensitivity and specificity of 100%, and applied prospectively to 1350 pregnant women in the clinical diagnostic setting with a result reported in 99.9% of cases. In addition, values indicative for trisomy were observed two times for chromosome 7 and once each for chromosomes 15 and 16, and once for a segmental trisomy 18. Two of the trisomies were confirmed to be mosaic, one of which contained a uniparental disomy cell line. As placental trisomies pose a risk for low-grade fetal mosaicism as well as uniparental disomy, genome-wide noninvasive aneuploidy detection is improving prenatal management.
doi_str_mv 10.1038/ejhg.2014.282
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subjects Aneuploidy
Bioinformatics
Chromosome 7
Chromosome Aberrations
Chromosome Disorders - genetics
Chromosomes
Chromosomes, Human - genetics
Chromosomes, Human, Pair 18 - genetics
Deoxyribonucleic acid
DNA
DNA sequencing
Down Syndrome - genetics
Female
Fetus - pathology
Fetuses
Genetic Testing - methods
Genomes
High-Throughput Nucleotide Sequencing - methods
Humans
Mosaicism
Pipelines
Placenta
Placenta - pathology
Plasma
Pregnancy
Prenatal Diagnosis - methods
Retrospective Studies
Trisomy
Trisomy - genetics
Trisomy 18 Syndrome
Ultrasonic imaging
Uniparental disomy
Women
title Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management
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