Open source non-invasive prenatal testing platform and its performance in a public health laboratory

TY - JOUR

T1 - Open source non-invasive prenatal testing platform and its performance in a public health laboratory

AU - Johansen, Peter

AU - Richter, Stine R

AU - Balslev-Harder, Marie

AU - Miltoft, Caroline Borregaard

AU - Tabor, Ann

AU - Duno, Morten

AU - Kjærgaard, Susanne

N1 - © 2016 John Wiley & Sons, Ltd.

PY - 2016/6/1

Y1 - 2016/6/1

N2 - Objective: The objective of this study was to introduce non-invasive prenatal testing (NIPT) for fetal autosomal trisomies and gender in a Danish public health setting, using semi-conductor sequencing and published open source scripts for analysis. Methods: Plasma-derived DNA from a total of 375 pregnant women (divided into three datasets) was whole-genome sequenced on the Ion Proton™ platform and analyzed using a pipeline based on WISECONDOR for fetal autosomal aneuploidy detection and SeqFF for fetal DNA fraction estimation. We furthermore validated a fetal sex determination analysis. Results: The pipeline correctly detected 27/27 trisomy 21, 4/4 trisomy 18, and 3/3 trisomy 13 fetuses. Neither false negatives nor false positives (chromosomes 13, 18, and 21) were observed in our validation dataset. Fetal sex was identified correctly in all but one triploid fetus (172/173). SeqFF showed a strong correlation (R2=0.72) to Y-chromosomal content of the male fetus samples. Discussion: We have implemented NIPT into Danish health care using published open source scripts for autosomal aneuploidy detection and fetal DNA fraction estimation showing excellent false negative and false positive rates. SeqFF provides a good estimation of fetal DNA fraction. This coupled with an analysis of fetal sex that provides a complete NIPT workflow, which may easily be adapted for implementation in other public health laboratories. What's Already Known About This Topic? Non-invasive prenatal testing for fetal trisomy is an established commercial method, yet few laboratories in the public health sector have implemented the technique. What Does This Study Add? We have established optimized analysis and quality parameters required for performing clinical (NIPT) by semi-conductor sequencing. The data form the basis for introducing NIPT in a Danish public health setting using an open source analysis pipeline, including fetal sex determination and fetal DNA fraction estimation.

AB - Objective: The objective of this study was to introduce non-invasive prenatal testing (NIPT) for fetal autosomal trisomies and gender in a Danish public health setting, using semi-conductor sequencing and published open source scripts for analysis. Methods: Plasma-derived DNA from a total of 375 pregnant women (divided into three datasets) was whole-genome sequenced on the Ion Proton™ platform and analyzed using a pipeline based on WISECONDOR for fetal autosomal aneuploidy detection and SeqFF for fetal DNA fraction estimation. We furthermore validated a fetal sex determination analysis. Results: The pipeline correctly detected 27/27 trisomy 21, 4/4 trisomy 18, and 3/3 trisomy 13 fetuses. Neither false negatives nor false positives (chromosomes 13, 18, and 21) were observed in our validation dataset. Fetal sex was identified correctly in all but one triploid fetus (172/173). SeqFF showed a strong correlation (R2=0.72) to Y-chromosomal content of the male fetus samples. Discussion: We have implemented NIPT into Danish health care using published open source scripts for autosomal aneuploidy detection and fetal DNA fraction estimation showing excellent false negative and false positive rates. SeqFF provides a good estimation of fetal DNA fraction. This coupled with an analysis of fetal sex that provides a complete NIPT workflow, which may easily be adapted for implementation in other public health laboratories. What's Already Known About This Topic? Non-invasive prenatal testing for fetal trisomy is an established commercial method, yet few laboratories in the public health sector have implemented the technique. What Does This Study Add? We have established optimized analysis and quality parameters required for performing clinical (NIPT) by semi-conductor sequencing. The data form the basis for introducing NIPT in a Danish public health setting using an open source analysis pipeline, including fetal sex determination and fetal DNA fraction estimation.

KW - Adult

KW - Chromosome Disorders

KW - Chromosomes, Human, Pair 13

KW - Chromosomes, Human, Pair 18

KW - DNA

KW - Denmark

KW - Down Syndrome

KW - Female

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - Male

KW - Maternal Serum Screening Tests

KW - Pregnancy

KW - Prenatal Diagnosis

KW - Public Health

KW - Semiconductors

KW - Sequence Analysis, DNA

KW - Sex Determination Analysis

KW - Trisomy

KW - Journal Article

U2 - 10.1002/pd.4819

DO - 10.1002/pd.4819

M3 - Journal article

C2 - 27027563

SN - 0197-3851

VL - 36

SP - 530

EP - 536

JO - Prenatal Diagnosis

JF - Prenatal Diagnosis

IS - 6

ER -