Noninvasive prenatal screening at low fetal fraction: comparing whole-genome sequencing and single-nucleotide polymorphism methods

Abstract

Objective Performance of noninvasive prenatal screening (NIPS) methodologies when applied to low fetal fraction samples is not well established. The single-nucleotide polymorphism (SNP) method fails samples below a predetermined fetal fraction threshold, whereas some laboratories employing the whole-genome sequencing (WGS) method report aneuploidy calls for all samples. Here, the performance of the two methods was compared to determine which approach actually detects more fetal aneuploidies.Methods Computational models were parameterized with up-to-date published data and used to compare the performance of the two methods at calling common fetal trisomies (T21, T18, T13) at low fetal fractions. Furthermore, clinical experience data were reviewed to determine aneuploidy detection rates based on compliance with recent invasive screening recommendations. ResultsThe SNP method's performance is dependent on the origin of the trisomy, and is lowest for the most common trisomies (maternal M1 nondisjunction). Consequently, the SNP method cannot maintain acceptable performance at fetal fractions below~3%. In contrast, the WGS method maintains high specificity independent of fetal fraction and has >80% sensitivity for trisomies in low fetal fraction samples. ConclusionThe WGS method will detect more aneuploidies below the fetal fraction threshold at which many labs issue a no-call result, avoiding unnecessary invasive procedures.

Noninvasive prenatal screening for patients with high body mass index: Evaluating the impact of a customized whole genome sequencing workflow on sensitivity and residual risk

“…Previous comparison of the WGS and SNP methodologies modeled the performance of each platform in idealized conditions, but our aim in this study was to describe empirical sensitivity of our customized WGS methodology. By analyzing data from sequential clinical samples processed in our laboratory (see Supporting Information Data S1), we determined the number of reads per sample at which our WGS‐based NIPS behaves in a Poisson manner (Figure S2) and then used this reads‐per‐sample level in our WGS simulations to predict analytical sensitivity for T13, T18, and T21 at low FF (Figure ). As anticipated, these empirically informed sensitivity estimates were comparable with the idealized levels from our previous analysis …”

“…Relative to serum‐ and imaging‐based approaches, NIPS has higher sensitivity, specificity, and PPV (99.7%, 99.96%, and 96.7%, respectively, for T21). The sensitivity of NIPS is not constant for all pregnancies, rather, the ability to detect aneuploidy scales with the proportional share of fetal‐derived cfDNA in the maternal plasma (ie, the “fetal fraction” or “FF”) . Many NIPS laboratories fail samples below a FF threshold because of concerns about reporting false negatives as a result of diminished sensitivity .…”

“…Many NIPS laboratories fail samples below a FF threshold because of concerns about reporting false negatives as a result of diminished sensitivity . However, low‐FF performance is both platform and laboratory dependent: Modeled versions of the two common NIPS platforms—the whole‐genome sequencing (WGS) and single‐nucleotide polymorphism (SNP) methods—show that WGS has higher sensitivity for low‐FF samples at a fixed specificity level . The many laboratories offering NIPS via WGS have implemented the molecular and computational aspects of the methodology differently, meaning that performance may vary.…”

Response to “Noninvasive prenatal screening at low fetal fraction: comparing whole‐genome sequencing and single‐nucleotide polymorphism methods”

“…This correspondence addresses the issues raised by Ryan and Martin in an accompanying letter to the editor regarding our published manuscript entitled “Noninvasive Prenatal Screening [NIPS] at Low Fetal Fraction: Comparing Whole‐Genome Sequencing and Single‐Nucleotide Polymorphism Methods” 1. The aim of our study was to compare the performance and clinical consequences of the two main methods of NIPS on hundreds of thousands of pregnancies at low fetal fraction.…”

Noninvasive prenatal paternity testing by means of SNP‐based targeted sequencing

“…Single nucleotide polymorphism‐based noninvasive prenatal paternity testing is highly dependent on the accurate genotyping of fetal SNPs in maternal cfDNA. Moreover, since the higher the FF in maternal cfDNA, the more accurate the genotyping result, with a threshold set at 2% to 4%, below which the validity of noninvasive prenatal tests would not be supported, it is important that FFs are also accurately estimated in order to support the test results for samples with high FF and to identify and exclude samples with low FF. The low fetal allele counts in the presence of high maternal allele counts translate to difficulty in reliable detection of fetal alleles and constitute a major challenge in maternal cfDNA analysis.…”