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.

Validation of two-channel sequencing-by-synthesis for noninvasive prenatal testing of fetal whole and partial chromosome aberrations

“…In our department, NIPT was initially validated on a SOLiD 5500xl sequencing platform (Thermo Fisher Scientific, Waltham, MA). 22 In this study, we describe the validation of whole genome NIPT on the NextSeq 500 platform. We show that data quality of the NextSeq 500, when applying the WISECONDOR algorithm, 28 not only allows for a reliable detection of whole chromosome fetal aneuploidies, but also for the detection of partial aberrations, comparable to the SOLiD 5500xl platform.…”

“…GC correction was performed on deduplicated and quality filtered alignments (see primary data analysis) using 10-kb bins and LOESS regression as previously described. 22…”

“…But also the use of other platforms, such as the single molecule sequencer Helicos (Helicos BioSciences), the SOLiD platforms from ThermoFisher and semiconductor sequencers such as the Ion Torrent Personal Genome Machine (PGM) and Ion Proton, have been reported. Initially, NIPT for fetal trisomies 13, 18 and 21 was validated and implemented in our laboratory using the SOLiD 5500xl . However, the time‐consuming library preparation and running time of this platform urged us to look for another platform.…”

“…Most laboratories use an Illumina platform such as the HiSeq2000 instrument. 8,[15][16][17][18] But also the use of other platforms, such as the single molecule sequencer Helicos (Helicos BioSciences), 19,20 the SOLiD platforms from ThermoFisher 2,21,22 and semiconductor sequencers such as the Ion Torrent Personal Genome Machine (PGM) and Ion Proton, [23][24][25][26] have been reported. Initially, NIPT for fetal trisomies 13, 18 and 21 was validated and implemented in our laboratory using the SOLiD 5500xl.…”

“…Initially, NIPT for fetal trisomies 13, 18 and 21 was validated and implemented in our laboratory using the SOLiD 5500xl. 22 However, the timeconsuming library preparation and running time of this platform urged us to look for another platform. For a critical test like NIPT, a platform with fast turnaround times (TATs) and medium-to-high sequencing throughput, preferably lowcost, is required.…”