Assessment and Clinical Utility of a Non-Next-Generation Sequencing-Based Non-Invasive Prenatal Testing Technology.

Background: Rolling-circle replication (RCR) is a novel technology that has not been applied to cell-free DNA (cfDNA) testing until recently. Given the cost and simplicity advantages of this technology compared to other platforms currently used in cfDNA analysis, an assessment of RCR in clinical laboratories was performed. Here, we present the first validation study from clinical laboratories utilizing RCR technology. Methods: 831 samples from spontaneously pregnant women carrying a singleton fetus, and 25 synthetic samples, were analyzed for the fetal risk of trisomy 21 (T21), trisomy 18 (T18) and trisomy 13 (T13), by three laboratories on three continents. All the screen-positive pregnancies were provided post-test genetic counseling and confirmatory diagnostic invasive testing (e.g., amniocentesis). The screen-negative pregnancies were routinely evaluated at birth for fetal aneuploidies, using newborn examinations, and any suspected aneuploidies would have been offered diagnostic testing or confirmed with karyotyping. Results: The study found rolling-circle replication to be a highly viable technology for the clinical assessment of fetal aneuploidies, with 100% sensitivity for T21 (95% CI: 82.35-100.00%); 100.00% sensitivity for T18 (71.51-100.00%); and 100.00% sensitivity for T13 analyses (66.37-100.00%). The specificities were >99% for each trisomy (99.7% (99.01-99.97%) for T21; 99.5% (98.62-99.85%) for T18; 99.7% (99.03-99.97%) for T13), along with a first-pass no-call rate of 0.93%. Conclusions: The study showed that using a rolling-circle replication-based cfDNA system for the evaluation of the common aneuploidies would provide greater accuracy and clinical utility compared to conventional biochemical screening, and it would provide comparable results to other reported cfDNA methodologies.

Variability of "Reported Fetal Fraction" in Noninvasive Prenatal Screening (NIPS).

BACKGROUND: Fetal fraction is often used to designate no-calls in noninvasive prenatal screening (NIPS). We wished to compare the variability in determining fetal fraction to gold standard methods. METHODS: We identified 6 publications with datasets consisting of methods capable of measuring fetal fraction for all samples that also had comparison data from gold standard methods. Examples of gold standard methods included relative Y-chromosome quantification in cases of male fetus pregnancies or relative quantification of the relevant chromosome for pregnancies affected by one of the 3 major trisomies. RESULTS: The studies showed that the differences of the various fetal fraction measurement assays as compared to a gold standard measurement displayed a standard deviation (SD) in the range of 1.3-3.4% fetal fraction (FF). The 4 studies that measured FF from fragment size and genomic coordinates or single nucleotide polymorphisms had a lower variability, with a median SD of about 1.6%, whereas 2 other studies using different methods displayed significantly higher variability. CONCLUSION: When deciding whether to use the reported FF as a reason to discard samples as no-calls or not, we recommend taking the variability of the FF measurement into consideration.

Evaluation of repeat testing of a non-sequencing based NIPT test on a Finnish general-risk population.

INTRODUCTION: To evaluate the effect of repeating test failures using an automated, non-sequencing based non-invasive prenatal testing test on a general-risk population in Finland. MATERIAL AND METHODS: A total of 545 samples from women who represent the average-risk population in Oulu, Finland were analyzed with Vanadis® non-invasive prenatal testing. Repeat testing of test failures was performed using a second sample. Results before and after repeat testing were compared with the reference outcome, as determined by clinical examination of neonates. RESULTS: There were eight test failures after first-pass analysis, representing 1.5% of samples (95% CI 0.6%-2.9%). Seven out of eight failures could be resolved by analysis of a second sample, thereby reducing the test failure rate from 1.5% to 0.2% (95% CI 0.0%-1.0%). CONCLUSIONS: Repeating test failures with a second plasma sample could significantly reduce the effective failure rate, thereby providing a way to effectively minimize test failures and further improving clinical utility and test performance.