Application of third-generation sequencing for genetic testing of thalassemia in Guizhou Province, Southwest China

Wu, Jiangfen; Xie, Dan; Wang, Lei; Kuang, Ying; Luo, Shulin; Ren, Lingyan; Li, Di; Mao, Aiping; Li, Jiaqi; Chen, Libao; An, Bangquan; Huang, Sheng‐Wen

doi:10.1080/16078454.2022.2156720

Cited by 2 publications

(2 citation statements)

References 22 publications

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“…Nevertheless, sequencing of RPGR ORF15 , one of RPGR's two main isoforms, is still challenging with NGS, and it can be associated with a considerable amount of false results [8,10]. TGS has recently been proposed for diagnostic purposes, considering that its accuracy has highly improved in recent years [22,23]. Thus, this study aimed to propose PacBio for diagnostic sequencing, focusing on RPGR ORF15 .…”

Section: Discussionmentioning

confidence: 99%

Towards a Long-Read Sequencing Approach for the Molecular Diagnosis of RPGRORF15 Genetic Variants

Bonetti,

Cozza,

Bernini

et al. 2023

IJMS

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Sequencing of the low-complexity ORF15 exon of RPGR, a gene correlated with retinitis pigmentosa and cone dystrophy, is difficult to achieve with NGS and Sanger sequencing. False results could lead to the inaccurate annotation of genetic variants in dbSNP and ClinVar databases, tools on which HGMD and Ensembl rely, finally resulting in incorrect genetic variants interpretation. This paper aims to propose PacBio sequencing as a feasible method to correctly detect genetic variants in low-complexity regions, such as the ORF15 exon of RPGR, and interpret their pathogenicity by structural studies. Biological samples from 75 patients affected by retinitis pigmentosa or cone dystrophy were analyzed with NGS and repeated with PacBio. The results showed that NGS has a low coverage of the ORF15 region, while PacBio was able to sequence the region of interest and detect eight genetic variants, of which four are likely pathogenic. Furthermore, molecular modeling and dynamics of the RPGR Glu-Gly repeats binding to TTLL5 allowed for the structural evaluation of the variants, providing a way to predict their pathogenicity. Therefore, we propose PacBio sequencing as a standard procedure in diagnostic research for sequencing low-complexity regions such as RPGRORF15, aiding in the correct annotation of genetic variants in online databases.

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Section: Discussionmentioning

confidence: 99%

Towards a Long-Read Sequencing Approach for the Molecular Diagnosis of RPGRORF15 Genetic Variants

Bonetti,

Cozza,

Bernini

et al. 2023

IJMS

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“…Recently, TGS has also been applied to prenatal screening for thalassemia. In Wu et al ( 15 ), 53 couples were examined for homozygous thalassemia mutations using TGS. The result showed that seven of them were identified as positive carriers, with five of them at risk of severe thalassemia during pregnancies, highlighting the potential of TGS for prenatal screening in regions with a high incidence of thalassemia.…”

Section: The Application Of Tgs In Thalassemiamentioning

confidence: 99%

Third generation sequencing transforms the way of the screening and diagnosis of thalassemia: a mini-review

et al. 2023

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Thalassemia is an inherited blood disorder imposing a significant social and economic burden. Comprehensive screening strategies are essential for the prevention and management of this disease. Third-generation sequencing (TGS), a breakthrough technology, has shown great potential for screening and diagnostic applications in various diseases, while its application in thalassemia detection is still in its infancy. This review aims to understand the latest and most widespread uses, advantages of TGS technologies, as well as the challenges and solutions associated with their incorporation into routine screening and diagnosis of thalassemia. Overall, TGS has exhibited higher rates of positive detection and diagnostic accuracy compared to conventional methods and next-generation sequencing technologies, indicating that TGS will be a feasible option for clinical laboratories conducting in-house thalassemia testing. The implementation of TGS technology in thalassemia diagnosis will facilitate the development of effective prevention and management strategies, thereby reducing the burden of this disease on individuals and society.

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Application of third-generation sequencing for genetic testing of thalassemia in Guizhou Province, Southwest China

Cited by 2 publications

References 22 publications

Towards a Long-Read Sequencing Approach for the Molecular Diagnosis of RPGRORF15 Genetic Variants

Towards a Long-Read Sequencing Approach for the Molecular Diagnosis of RPGRORF15 Genetic Variants

Third generation sequencing transforms the way of the screening and diagnosis of thalassemia: a mini-review

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