Noninvasive Prenatal Screening at Low Fetal Fraction: Comparing Whole-Genome Sequencing and Single-Nucleotide Polymorphism Methods

Abstract

CONFLICT OF INTERESTS:All authors other than YY are employees of Counsyl Inc., a company that performs noninvasive prenatal screening. YY is a clinical expert panel member for Illumina Inc., a company that performs noninvasive prenatal screening, and a consultant for Teva Pharmaceuticals, a local distributor of noninvasive prenatal 30 screening. Abstract 60Objective 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) 65 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 70 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. 75Results The 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. 80 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. 85

High-throughput fetal fraction amplification increases analytical performance of noninvasive prenatal screening

“…The literature is replete with reports and professional society statements expressing concern about low-FF samples. 8,38,39 Many publications have explored and debated the merits of different approaches to handling low-FF samples: optimizing NIPS algorithms to issue confident results at low FF, 9 failing such samples entirely, or pursuing mitigation strategies for failed low-FF samples, such as sequential redraw 40,41 and FF-based risk scores. 42,43 However, consensus has remained elusive.…”

“…Because the molecular and bioinformatic implementations of NIPS have evolved, diversified, and generally improved over time, sensitivity at progressively lower FF levels is platform-and laboratorydependent. 6,8 Indeed, a recently published clinical experience study demonstrated that a customized whole-genome sequencing (WGS)-based NIPS, which does not fail low-FF samples, can have comparable accuracy at high FF and low FF for the common aneuploidies on chromosomes 13, 18, and 21. 9 Though the common aneuploidies have long been the main focus of NIPS because of their frequency and highly penetrant phenotype, clinically actionable chromosomal anomalies span a range of sizes and can occur anywhere in the genome.…”

High-throughput fetal-fraction amplification increases analytical performance of noninvasive prenatal screening

“…The literature is replete with reports and professional-society statements expressing concern about low-FF samples. 8,38,39 Many publications have explored and debated the merits of different approaches to handling low-FF samples: optimizing NIPS algorithms to issue confident results at low FF, 9 failing such samples entirely, 40 or pursuing mitigation strategies for failed low-FF samples, such as sequential redraw 41,42 and fetal-fraction-based risk scores. 43,44 However, consensus has remained elusive.…”

“…Because the molecular and bioinformatic implementations of NIPS have evolved, diversified, and generally improved over time, sensitivity at progressively lower FF levels is platform-and laboratory-dependent. 6,8 Indeed, a recently published clinical-experience study demonstrated that a customized whole-genomesequencing (WGS)-based NIPS, which does not fail low-FF samples, can have comparable accuracy at high-FF and low-FF for the common aneuploidies on chromosomes 13, 18, and 21. 9 Though the common aneuploidies have long been the main focus of NIPS because of their frequency and highly penetrant phenotype, clinically actionable chromosomal anomalies span a range of sizes and can occur anywhere in the genome.…”

Fetal fraction and noninvasive prenatal testing: What clinicians need to know

“…They have been previously thoroughly reviewed by Peng and colleagues . Several attempts to compare different FF algorithms have been published that highlight the significant variation between methods . It is now apparent that individual clinical laboratories should optimize their platform‐specific FF methods according to their lower LOD, and not rely on arbitrary FF cutoff values for quality control.…”