Implementation of whole genome massively parallel sequencing for noninvasive prenatal testing in laboratories

Abstract

Noninvasive prenatal testing (NIPT) for fetal aneuploidies using cell-free fetal DNA in maternal plasma has revolutionized the field of prenatal care and methods using massively parallel sequencing are now being implemented almost worldwide. Substantial progress has been made from initially testing for (an)euploidies of chromosomes 13, 18 and 21, to testing for sex chromosome (an)euploidies, additional autosomal aneuploidies as well as partial deletions and duplications genome-wide. Although NIPT is associated with significantly reduced risks for the fetus in comparison to existing invasive prenatal diagnostic methods, it presents several implementation challenges. Here, we review key issues potentially influencing NIPT and illustrate them using both data from literature and in-house data.

Keywords:

• depth of coverage
• NGS
• NIPT
• noninvasive
• prenatal
• whole genome sequencing

Acknowledgements

The authors would like to acknowledge Roy Straver (Delft Bioinformatics Lab, Delft University of Technology, Delft and Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands) and Erik Sistermans (Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands) for providing access to the WISECONDOR algorithm before its actual release. Furthermore, they thank the co-workers of the departments of Gynecology and Obstetrics and Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands, for collecting samples and performing NIPT experiments and they thank dr Lisenka Vissers for carefully reading the manuscript.

Financial & competing interests disclosure

This work was supported partly by the Prenatal Screening Foundation Nijmegen Region, the Netherlands, and the European Commission-European Research Council 281964. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Key issues

• Noninvasive prenatal testing (NIPT) for fetal aneuploidy detection: despite a number of practical issues, it is now offered on an almost worldwide basis with a high sensitivity and specificity, using either whole genome or targeted massively parallel sequencing.

• High throughput and scalability: Due to the rapid turnaround time required for prenatal testing, offering NIPT to large populations of pregnant women requires a high level of automation and sufficient infrastructure (including genetic counseling).

• Detection of fetal fraction: The presence of sufficient fetal DNA in the plasma sample is crucial for reliably performing NIPT. A number of factors influence the amount of fetal DNA present in a sample, yet methods to reliably quantify the fetal fraction are still underdeveloped.

• Discordant findings between NIPT and fetal DNA: Despite the proved accuracy of NIPT, discordant findings due to biological phenomena such as confined placental mosaicisms and maternal aberrations remain unavoidable. Confirmatory testing on additional fetal tissue types is required to determine whether the NIPT identified abnormality indeed reflects the actual fetal genetic status.

• Detection of submicroscopic aberrations genome wide: NIPT will soon be (further) expanded to the detection of partial (micro)deletions and duplications. The development of efficient and robust data analysis methods will play a key role once ethical issues have been resolved.