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Licensed Unlicensed Requires Authentication Published by De Gruyter November 11, 2021

Effect of preexamination conditions in a centralized-testing model of non-invasive prenatal screening

Chad Fibke ORCID logo , Sylvie Giroux , André Caron , Elizabeth Starks , Jeremy D.K. Parker , Lucas Swanson , Loubna Jouan , Sylvie Langlois , Guy Rouleau , François Rousseau and Aly Karsan ORCID logo EMAIL logo

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.


Corresponding author: Aly Karsan, Michael Smith Genome Sciences Centre, BC Cancer Research Institute, 675 West 10th Ave, Vancouver, BC V5Z 1L3, Canada; and Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada, E-mail:
Chad Fibke and Sylvie Giroux contributed equally to this work.

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.

  1. 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.

  2. Author contributions: All authors have accepted responsibility for the entire content of this manuscript and approved its submission.

  3. Competing interests: Authors state no conflict of interest.

  4. Informed consent: Informed consent was obtained from all individuals included in this study.

  5. 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).


Received: 2021-06-07
Accepted: 2021-10-29
Published Online: 2021-11-11
Published in Print: 2022-01-27

© 2021 Walter de Gruyter GmbH, Berlin/Boston

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