Development of Noninvasive Autosomal Recessive Disease Testing in the Saudi Arabian Population

Early diagnosis of prenatal complications, particularly genetic disorders, can enable early intervention and improve outcomes for both mother and infant. However, the current gold-standard testing approaches, including amniocentesis and chorionic villi sampling, are expensive, require a tertiary-care setting, and can induce miscarriage. Advancements in genomic techniques, such as next-generation sequencing (NGS), combined with cell-free noninvasive prenatal testing (NIPT), can enable low-risk prenatal testing that requires only a single maternal blood sample. We expanded the design of an amplicon-based NGS assay that uses oligonucleotide probes designed to target and amplify specific regions of interest within a gene. This method requires only maternal peripheral blood, from which cell-free DNA (cfDNA) can be extracted. We then used NGS technology, a proprietary bioinformatics algorithm, and population-specific data to estimate autosomal recessive disease risk. We recruited pregnant women who were pursuing fetal diagnostic testing because they were known carriers of an autosomal recessive mutation, had a previous child with an autosomal recessive mutation, or had a family history of autosomal recessive mutations. A blood draw was obtained from each participant, and 50 samples passed quality control standards for advancement. We extracted cfDNA and genomic DNA from these samples for amplicon-based NGS. We obtained conclusive results for 38 of 50 samples, and the NGS results for 29 (76.3%) samples were concordant with the invasive testing results. Focusing on samples with heterozygous maternal cfDNA ( n = 20), we were able to predict the genotypes for 10 samples with high confidence and for 6 samples with low confidence, whereas the remaining 4 samples were incompatible with our approach. This novel NIPT method has the potential to improve prenatal care by offering expectant parents a noninvasive and accurate option for screening autosomal recessive conditions with minimal risks.