Carrier Screening of 48,761 Patients in the IVF Setting Utilizing Next Generation DNA Sequencing Detects Common, Rare and Otherwise Undetectable Pathogenic Variants in Prevalent, Society-Recommended Diseases

Abstract

Carrier screening for specific genetic disorders is recommended by the American Congress of Obstetricians and Gynecologists (ACOG), the American College of Medical Genetics (ACMG), and several societies representing the Ashkenazi Jewish population. Due to cost considerations and limitations of the technologies employed, traditional carrier screening assays are designed to look for only the most common variants within a gene. While this original approach can yield good detection rates in specific populations (e.g., the Ashkenazi Jewish), it is suboptimal for other ethnicities or for patients of mixed or unknown ethnic background. Next generation DNA sequencing (NGS) is able to detect five- to ten-fold the number of pathogenic variants with higher detection rates in all ethnicities compared to traditional carrier screening tests. Consequently, NGS is expected to provide a more comprehensive determination of carrier status. The objective of this study was to evaluate the clinical effectiveness of NGS in detecting common and rare pathogenic variants across a large number of patients in a clinical setting, among 14 diseases recommended for carrier screening. A high-throughput and proprietary methodology (comprised of multiplex gene capture, NGS and computational analysis) was used to test samples from patients representing a broad spectrum of ethnicities. Clinical reports were issued on the presence or absence of disease-causing variants in genes associated with society-recommended disorders. Among the 48,761 clinical samples evaluated, our NGS-based tests routinely detected common variants among 14 disorders, as well as numerous less common variants that would not be detected by traditional screening assays routinely used in IVF centers. 2,309 (4.7%) patients were found to be carriers of 320 distinct pathogenic variants among the 14 disorders. 226 (63.1%) of those distinct pathogenic variants were either uncommon or never-before reported, i.e., unique to our set of variants. Of the 2,309 carriers detected, 15.9% - 22.3% would have been missed by other major laboratories using traditional carrier tests, putting these reproductive couples at increased risk of having a child with a genetic disorder. Due to the vastly larger number of pathogenic variants detectable for each gene assessed, NGS enables more comprehensive assessment of carrier status, and is, therefore, able to yield higher detection rates, irrespective of patient ethnicity, resulting in fewer missed carriers than if traditional carrier tests were used.