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Non-Invasive Prenatal Testing (NIPT) in pregnancies with trisomy 21, 18 and 13 performed in a public setting - factors of importance for correct interpretation of results

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@article{6d7f191340854274b819d0760bbe1d1a,
title = "Non-Invasive Prenatal Testing (NIPT) in pregnancies with trisomy 21, 18 and 13 performed in a public setting - factors of importance for correct interpretation of results",
abstract = "OBJECTIVES: We have established an open source platform for non-invasive prenatal testing (NIPT) based on massively parallel whole-genome sequencing in a public setting. The objective of this study was to investigate factors of importance for correct interpretation of NIPT results to ensure a high sensitivity and specificity.STUDY DESIGN: This investigation is a retrospective case-control study performed in a public NIPT center. The study included 108 aneuploid cases and 165 euploid controls. MPS was performed on circulating cell-free DNA in maternal blood. The pipeline included automated library preparation and sequencing on a HiSeq1500 (Illumina). The software programmes WISECONDOR and SeqFF were used for data analysis of aneuploidy status and fetal fraction of cell-free DNA, respectively. Lower limit of fetal fraction for aneuploidy testing was 0.02.RESULTS: We identified four false negative aneuploidy cases of which two were explained by a vanishing twin. The number of no-call cases due to low fetal fraction was 8 out of 273 (2.9{\%}). The sensitivity and specificity, when no-calls and vanished twins were excluded, were 100{\%} and 99.5{\%} for T21, 91{\%} and 99.2{\%} for T18, and 100{\%} and 99.6{\%} for T13. By multiple regression analysis we found a significant association between fetal fraction and gestational age, maternal BMI and ART treatment.CONCLUSION: With a non-commercial open source NIPT set-up having the same high test-performance as reported by large private laboratories, we show that fetal fraction, a vanishing twin, BMI, gestational age and ART treatment are important factors in the interpretation of NIPT results.",
author = "Hartwig, {Tanja S} and Louise Ambye and Lene Werge and Weiergang, {Martin Kenneth} and Pernille N{\o}rgaard and Steen S{\o}rensen and J{\o}rgensen, {Finn Stener}",
note = "Copyright {\circledC} 2018 Elsevier B.V. All rights reserved.",
year = "2018",
month = "5",
doi = "10.1016/j.ejogrb.2018.04.042",
language = "English",
volume = "226",
pages = "35--39",
journal = "European Journal of Obstetrics and Gynecology and Reproductive Biology",
issn = "0028-2243",
publisher = "Elsevier Ireland Ltd",

}

RIS

TY - JOUR

T1 - Non-Invasive Prenatal Testing (NIPT) in pregnancies with trisomy 21, 18 and 13 performed in a public setting - factors of importance for correct interpretation of results

AU - Hartwig, Tanja S

AU - Ambye, Louise

AU - Werge, Lene

AU - Weiergang, Martin Kenneth

AU - Nørgaard, Pernille

AU - Sørensen, Steen

AU - Jørgensen, Finn Stener

N1 - Copyright © 2018 Elsevier B.V. All rights reserved.

PY - 2018/5

Y1 - 2018/5

N2 - OBJECTIVES: We have established an open source platform for non-invasive prenatal testing (NIPT) based on massively parallel whole-genome sequencing in a public setting. The objective of this study was to investigate factors of importance for correct interpretation of NIPT results to ensure a high sensitivity and specificity.STUDY DESIGN: This investigation is a retrospective case-control study performed in a public NIPT center. The study included 108 aneuploid cases and 165 euploid controls. MPS was performed on circulating cell-free DNA in maternal blood. The pipeline included automated library preparation and sequencing on a HiSeq1500 (Illumina). The software programmes WISECONDOR and SeqFF were used for data analysis of aneuploidy status and fetal fraction of cell-free DNA, respectively. Lower limit of fetal fraction for aneuploidy testing was 0.02.RESULTS: We identified four false negative aneuploidy cases of which two were explained by a vanishing twin. The number of no-call cases due to low fetal fraction was 8 out of 273 (2.9%). The sensitivity and specificity, when no-calls and vanished twins were excluded, were 100% and 99.5% for T21, 91% and 99.2% for T18, and 100% and 99.6% for T13. By multiple regression analysis we found a significant association between fetal fraction and gestational age, maternal BMI and ART treatment.CONCLUSION: With a non-commercial open source NIPT set-up having the same high test-performance as reported by large private laboratories, we show that fetal fraction, a vanishing twin, BMI, gestational age and ART treatment are important factors in the interpretation of NIPT results.

AB - OBJECTIVES: We have established an open source platform for non-invasive prenatal testing (NIPT) based on massively parallel whole-genome sequencing in a public setting. The objective of this study was to investigate factors of importance for correct interpretation of NIPT results to ensure a high sensitivity and specificity.STUDY DESIGN: This investigation is a retrospective case-control study performed in a public NIPT center. The study included 108 aneuploid cases and 165 euploid controls. MPS was performed on circulating cell-free DNA in maternal blood. The pipeline included automated library preparation and sequencing on a HiSeq1500 (Illumina). The software programmes WISECONDOR and SeqFF were used for data analysis of aneuploidy status and fetal fraction of cell-free DNA, respectively. Lower limit of fetal fraction for aneuploidy testing was 0.02.RESULTS: We identified four false negative aneuploidy cases of which two were explained by a vanishing twin. The number of no-call cases due to low fetal fraction was 8 out of 273 (2.9%). The sensitivity and specificity, when no-calls and vanished twins were excluded, were 100% and 99.5% for T21, 91% and 99.2% for T18, and 100% and 99.6% for T13. By multiple regression analysis we found a significant association between fetal fraction and gestational age, maternal BMI and ART treatment.CONCLUSION: With a non-commercial open source NIPT set-up having the same high test-performance as reported by large private laboratories, we show that fetal fraction, a vanishing twin, BMI, gestational age and ART treatment are important factors in the interpretation of NIPT results.

U2 - 10.1016/j.ejogrb.2018.04.042

DO - 10.1016/j.ejogrb.2018.04.042

M3 - Journal article

VL - 226

SP - 35

EP - 39

JO - European Journal of Obstetrics and Gynecology and Reproductive Biology

JF - European Journal of Obstetrics and Gynecology and Reproductive Biology

SN - 0028-2243

ER -

ID: 54585508