Clinical validity of single-gene non-invasive prenatal testing for sickle cell disease and beta thalassemia

Background: Sickle cell disease (SCD) and beta thalassemia ({beta}-thalassemia) are among the most common and severe genetically inherited disorders in the world. Although the maternal carrier status of these beta hemoglobinopathies is screened as a part of routine prenatal care in the US, the paternal carrier status is usually unavailable. Under this current screening paradigm, identification of the majority of SCD and beta thalassemia cases could therefore be delayed until newborn screening results are available. An effective reflex, non-invasive prenatal test (NIPT) that uses only maternal blood would permit prenatal detection of sickle cell disease and beta thalassemia by screening for these disorders without the need for paternal DNA. This screening would enable patients and healthcare providers to make informed decisions about diagnostic testing, and it could expand gene therapy treatment options by requesting cord blood banking at delivery. We have previously developed a single-gene NIPT platform (UNITY) for SCD and beta thalassemia with extensive analytic validation and initial clinical validation in our prior studies. Objectives: The objective of this study is to further assess the clinical validity of single-gene NIPT for SCD and beta thalassemia in a larger pregnancy population. Study Design: Pregnant women who screened positive for at least one allele of a beta hemoglobinopathy were enrolled at two academic medical centers for this retrospective cohort study. Single-gene NIPT for SCD and beta thalassemia was performed in blinded fashion on maternal blood samples to determine the fetal genotype and disease status. Single-gene NIPT findings were compared with either newborn screen results or genotyping of umbilical cord blood. Results: Single-gene NIPT detection of fetuses that are affected versus unaffected with SCD and beta thalassemia was 100% concordant with newborn screening follow-up data, even in challenging samples that contained a low fetal fraction (<5%) or at earlier gestational ages. Additionally, we obtained 98.5% concordance with newborn genotypes, including differentiating healthy fetal sickle cell carriers from homozygous healthy fetuses. The sensitivity of detecting fetal carrier status of beta hemoglobinopathies was 100% (90.8% to 100% CI), and the specificity was 96.4% (81.7% to 99.9 % CI). Conclusions: Single-gene NIPT is a highly accurate screen for prenatal detection of SCD and beta thalassemia. The results further suggest that the maternal carrier screen with reflex single-gene NIPT workflow can significantly improve the detection rates of at-risk pregnancies from <50% to >98%.