Identification of a Novel 16.8Kb Deletion of the α-Globin Gene Cluster by Third-Generation Sequencing

Abstract

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 cannot 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, Chr16:1,65,236–1,82,113) deletion by the third-generation sequencing. A fragment ranging from 1,53,226 to 1,54,538(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.

Keywords:

• Thalassemia
• third-generation sequencing
• recombinant fragment
• deletion
• α-globin gene cluster

Acknowledgements

We would like to acknowledge all patients for their cooperation with our study.

Ethical approval

The study was approved by the Ethics Committee of the Guangzhou Women& Children Medical Center and written informed consent was obtained from all subjects.

Authors’ contributions

DZL contributed the central idea, FJ and SH analyzed most of the data and wrote the initial draft of the paper, TNL and CL revised the manuscript, JYZ and JL were responsible for Capillary electrophoresis and genetic testing. LDZ was responsible for project management, JYW collected clinical data.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

All the data generated and/or analyzed in this work are available from the corresponding author according to request ([email protected]).

Additional information

Funding

This work was supported by Guangdong Natural Science Foundation (grant number 2023A1515010402). Guangdong Basic and Applied Basic Research Foundation (grant number 2022 A 1515220140), Guangzhou Science and Technology Plan Project (grant number 202206010100, 2023A03J0875, 202201020632, 202201020638).