First report of a rare complex rearrangement in the α-globin gene cluster causing a novel 16.8Kb deletion

α-thalassemia major (α-TM) often causes Hb Bart’s (c4) hydrops fetalis and severe obstetric complications in the mother. Step-wise screening for couples at-risk of having offspring(s) affected by α-TM is the efficient prevention method but some rare genotypes of thalassemia can not be detected. A 32-year-old male with Low HbA2 (2.4%) and mild anemia was performed real-time PCR-based multicolor melting curve analysis (MMCA) because his wife was --SEA deletion carrier. The result of Multiplex ligation-dependent probe amplification (MLPA) suggested the existence of --SEA deletion in the proband. A novel deletion of the α-globin gene cluster was found using self-designed MLPA probes combined with longer PCR, which was further accurately described to be 16.8Kb (hg38, Chr16:165236–182113) deletion by the third-generation sequencing. A fragment ranging from 153226 to 154538(GRch38/hg38) was identified which suggested the existence of the homologous recombination event. The third-generation sequencing is accurate and efficient in obtaining accurate information for complex structural variations.