Abstract
Objectives
Non-invasive prenatal testing requires the presence of fetal DNA in maternal plasma. Understanding how preexamination conditions affect the integrity of cell-free DNA (cfDNA) and fetal fraction (FF) are a prerequisite for test implementation. Therefore, we examined the adjusted effect that EDTA and Streck tubes have on the cfDNA quantity and FF.
Methods
A total of 3,568 maternal blood samples across Canada were collected in either EDTA, or Streck tubes, and processing metrics, maternal body mass index (BMI), gestational age and fetal karyotype and sex were recorded. Plasma samples were sequenced using two different sequencing platforms in separate laboratories. Sequencing data were processed with SeqFF to estimate FF. Linear regression and multivariate imputation by chained equations were used to estimate the adjusted effect of tube type on cfDNA and FF.
Results
We found a positive association between cfDNA quantity and blood shipment time in EDTA tubes, which is significantly reduced with the use of Streck tubes. Furthermore, we show the storage of plasma at −80 °C is associated with a 4.4% annual relative decrease in cfDNA levels. FF was not associated with collection tube type when controlling for confounding variables. However, FF was positively associated with gestational age and trisomy 21, while negatively associated with BMI, male fetus, trisomy 18, Turners syndrome and triploidy.
Conclusions
Preexamination, maternal and fetal variables are associated with cfDNA quantity and FF. The consideration of these variables in future studies may help to reduce the number of pregnant women with inconclusive tests as a result of low FF.
Funding source: Ariosa Diagnostics
Funding source: Genome Canada
Award Identifier / Grant number: 13527
Funding source: Canadian Institutes for Health Research
Award Identifier / Grant number: GPH-129342
Funding source: Genome BC
Award Identifier / Grant number: 145PEG
Funding source: Genome Alberta
Funding source: Québec Ministère de l’Enseignement Supérieur, de la Recherche, de la Science et de la Technologie
Funding source: Santé’s Réseau de Médecine Génétique Appliquée
Funding source: The Centre de Recherche du CHU de Québec
Acknowledgments
We would like to acknowledge the help and support given by all patients, caregivers, trial staff and researchers.
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Research funding: Genome Canada (13527), Canadian Institutes for Health Research (GPH-129342), Genome BC (145PEG), Genome Alberta (ROU), Québec Ministère de l’Enseignement Supérieur, de la Recherche, de la Science et de la Technologie, The Fonds de Recherche Québec – Santé’s Réseau de Médecine Génétique Appliquée, The Centre de Recherche du CHU de Québec. Ariosa Diagnostics provided in-kind testing of samples.
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Author contributions: All authors have accepted responsibility for the entire content of this manuscript and approved its submission.
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Competing interests: Authors state no conflict of interest.
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Informed consent: Informed consent was obtained from all individuals included in this study.
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Ethical approval: Local Offices of Research Ethics approved study protocols, which have been registered in clinicaltrial.gov as trial NCT01925742.
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Supplementary Material
The online version of this article offers supplementary material (https://doi.org/10.1515/cclm-2021-0652).
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