Identification of a novel 91.5 kb-deletion (αα)^FJ in the α-globin gene cluster using single-molecule real-time (SMRT) sequencing

Abstract

Objectives

To present a novel 91.5-kb deletion of the α-globin gene cluster (αα)^FJ identified by genetic assay and prenatal diagnosis in a Chinese family.

Subjects and Methods

The proband was a 34-year-old G3P1 (Gravida 3, Para 1) female at the gestational age of 21⁺ weeks with a history of an edematous fetus. A routine genetic assay (reverse dot blot hybridization, RDB) was performed to detect common thalassemia mutations. Multiplex ligation-dependent probe amplification (MLPA) and single-molecule real-time technology (SMRT) were used to detect rare thalassemia mutations.

Results

The hematological phenotypes of the proband, her mother, elder sister, husband, daughter, and nephew were consistent with the phenotype of α-thalassemia trait. No mutations were found in these family members by RDB, except for the proband’s husband who carried an α-globin gene deletion --^SEA/αα. MLPA results showed that the proband and other α-thalassemia-suspected relatives had heterozygous deletions around the POLR3K-3-463nt, HS40-178nt, and HBA-HS40-382nt probes. The 5′-breakpoint was out of probe scope and could not be determined. SMRT was performed and a 91.5-kb deletion (NC_000016.10: g.39268_130758del) in the α-globin gene cluster (αα)^FJ was identified in the proband and other suspected relatives, which could explain their phenotypes. At the proband’s gestational age of 22⁺ weeks, an amniotic fluid sample was collected and analyzed. As only the 91.5-kb deletion (αα)^FJ was identified in the fetus with RDB, MLPA, and SMRT. The proband was suggested to continue the pregnancy.

Conclusion

We first reported a 91.5-kb deletion (NC_000016.10: g.hg38-chr16:39268-_130758del) of the HS-40 region in the α-globin gene cluster (αα)^FJ identified in a Chinese family. Since the HS-40 loss of heterozygosity in combination with the heterozygous deletion --^SEA might result in Hb Bart’s hydrops fetalis, routine genetic assay, and SMRT were recommended to individuals at risk for prenatal diagnosis.

Keywords:

• HS-40
• loss of heterozygosity (LOH)
• α-thalassemia
• SMRT
• prenatal diagnosis

Acknowledgments

The authors also thank all patients for participating in this study. We specially thank Di Cui (Berry Genomics Corporation) and Wanli Meng (Berry Genomics Corporation) for their help in the analysis of SMRT and the revision of the manuscript.

Authors’ contributions

Na Lin, Liangpu Xu, and Hailong Huang designed the study; Liangpu Xu and Meihuan Chen performed experimental studies and drafted the manuscript; Junhao Zheng, Siwen Zhang, Min Zhang, Lingji Chen, and Qianqian He collected the literature; Danhua Guo collected the data and prepared the manuscript. All authors approved the final manuscript.

Availability of data and materials

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Disclosure statement

The authors confirm that they have no competing interests.

Ethical approval

This study was proved by the Ethics Review Committee of Fujian Maternity and Child Health Hospital (2017-031).

Additional information

Funding

This study was supported by National Natural Science Foundation of China, Grant/Award Number: 81970170 and Joint Funds for the innovation of science and Technology, Fujian province, Grant/Award Number: 2021Y9173, 2021Y9174.