Utilization of multiple genetic methods for prenatal diagnosis of rare thalassemia variants

Background: Thalassemia is the most prevalent monogenic disorder caused by an imbalance between the alpha- and beta-globin chains as a result of pathogenic variants in the alpha- or beta-globin genes. Novel or complex structural changes in globin genes are major hurdles for genetic consulting and prenatal diagnosis. Methods: From 2020 to 2022, genetic analysis was performed on 1,316 families suspected of having children with thalassemia major, including 42 pregnant couples suspected of being thalassemia carriers with rare variants. Multiple techniques including multiplex ligation-dependent probe amplification (MLPA), Sanger sequencing, targeted next-generation sequencing, and single-molecule real-time (SMRT) sequencing were used to diagnose rare thalassemia. Results: The rate of prenatal diagnosis for rare thalassemia variants was 3.19% (42/ 1,316). The most prevalent alleles of alpha- and beta-thalassemia are Chinese (G)gamma((A)gamma delta beta)degrees and -- (THAI) deletion. In addition, ten rare complex genotypes include one Chinese (G)gamma((A)gamma delta beta)degrees deletion combined with HBG1-HBG2 fusion, two rare deletions at HBB gene (hg38, Chr11: 5224211-5232470, hg38, Chr11: 5224303-5227790), one complete 7,412 bp fusion gene for anti-Lepore Hong Kong, two complex rearrangements of the a-globin gene cluster, two novel duplications, and two rare large deletions in the a-globin gene cluster. Conclusion: Accurate gene diagnosis for probands with combined molecular biology techniques is the key to prenatal diagnosis of rare thalassemia.