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Target-allele-specific probe single-base extension (TASP-SBE): a novel MALDI–TOF–MS strategy for multi-variants analysis and its application in simultaneous detection of α-/β-thalassemia mutations

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Abstract

Single-nucleotide variants (SNVs) and copy number variations (CNVs) are the most common genomic variations that cause phenotypic diversity and genetic disorders. MALDI–TOF–MS is a rapid and cost-effective technique for multi-variant genotyping, but it is challenging to efficiently detect CNVs and clustered SNVs, especially to simultaneously detect CNVs and SNVs in one reaction. Herein, a novel strategy termed Target-Allele-Specific Probe Single-Base Extension (TASP-SBE) was devised to efficiently detect CNVs and clustered SNVs with MALDI–TOF–MS. By comprehensive use of traditional SBE and TASP-SBE strategies, a MALDI–TOF–MS assay was also developed to simultaneously detect 28 α-/β-thalassemia mutations in a single reaction system, including 4 α-thalassemia deletions, 3 HBA and 21 HBB SNVs. The results showed that all 28 mutations were sensitively identified, and the CNVs of HBA/HBB genes were also accurately analyzed based on the ratio of peak height (RPH) between the target allele and reference gene. The double-blind evaluation results of 989 thalassemia carrier samples showed a 100% concordance of this assay with other methods. In conclusion, a one-tube MALDI–TOF–MS assay was developed to simultaneously genotype 28 thalassemia mutations. This novel TASP-SBE was also verified a practicable strategy for the detection of CNVs and clustered SNVs, providing a feasible approach for multi-variants analysis with MALDI–TOF–MS technique.

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Data availability

Original data of the present study are available from the corresponding author upon reasonable request.

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Funding

This study was supported by the National Natural Science Foundation of China (grant no. 81972008), Basic and Applied Basic Research Foundation of Guangdong Province (grant no. 2021A1515012585), and Guangming Soft Science Research Project of Shenzhen (grant no. 2021R01098).

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Authors and Affiliations

Authors

Contributions

LJ, XY, and WZ supervised the project and revised the article. QC, WH, YL, and FT analyzed the data and wrote the original draft. ZL, ZH, and XZ provided samples and interpreted the data. MX, and XY performed the experiments and acquired the data.

Corresponding authors

Correspondence to Linxiao Jiang or Wanjun Zhou.

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Ethics approval was obtained from the Ethics Committee of Zhujiang Hospital (approval number 2021-SJ-001-01)

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Chen, Q., Yang, X., Huang, W. et al. Target-allele-specific probe single-base extension (TASP-SBE): a novel MALDI–TOF–MS strategy for multi-variants analysis and its application in simultaneous detection of α-/β-thalassemia mutations. Hum Genet 142, 445–456 (2023). https://doi.org/10.1007/s00439-023-02520-w

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  • DOI: https://doi.org/10.1007/s00439-023-02520-w

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