Identification of thalassemia gene cluster deletion by long‐read whole‐genome sequencing (LR‐WGS)

Abstract

At present, a variety of molecular detection methods are obtained to diagnose thalassemia accurately. Although exome sequencing or specific panels have been widely used in clinical diagnosis of genetic diseases, the positive rate is about 25%-30%. Because the detection range is limited to exons and splice sites, and the read length is usually 100-150bp, there are limitations in the detection of globin gene clusters with pseudogenes. In this study, seven thalassemia patients were selected to perform whole-genome sequencing (WGS) with long read at 400bp to make accurate detection for thalassemia deletions. And we used PCR and Sanger sequencing to confirm the gene deletions in the patients. WGS analysis detected a rare 172kb deletion on the α-globin gene cluster at chr16: 57009-330001, 19kb deletion at chr16: 215396-234699, 11kb deletion at chr16:220861-231981; and 27kb deletion on the β-globin gene deletion at chr11: 5222878-5250288, 21.4kb deletion at chr11: 5236361-5257771, 78.9kb deletion at chr11: 5191121-5270050. All the seven patients carried heterozygous deletions, including three in α-gene cluster, three in β-gene cluster, and one in both globin clusters. Our results indicate that long-read WGS will be beneficial to the diagnosis of genetic diseases with pseudogenes or highly duplicated sequences and will enable clinical geneticists to inform high-risk couples and provide prenatal diagnosis.