Background Numerous variants of uncertain significance (VUSs) have been identified by whole exome sequencing in clinical practice. However, VUSs are not currently considered medically actionable.
Objective To assess the splicing patterns of 49 VUSs in 48 families identified clinically to improve genetic counselling and family planning.
Methods Forty-nine participants with 49 VUSs were recruited from the Reproductive and Genetic Hospital of CITIC-Xiangya. Bioinformatic analysis was performed to preliminarily predict the splicing effects of these VUSs. RT-PCR and minigene analysis were used to assess the splicing patterns of the VUSs. According to the results obtained, couples opted for different methods of reproductive interventions to conceive a child, including prenatal diagnosis and preimplantation genetic testing (PGT).
Results Eleven variants were found to alter pre-mRNA splicing and one variant caused nonsense-mediated mRNA decay, which resulted in the reclassification of these VUSs as likely pathogenic. One couple chose to undergo in vitro fertilisation with PGT treatment; a healthy embryo was transferred and the pregnancy is ongoing. Three couples opted for natural pregnancy with prenatal diagnosis. One couple terminated the pregnancy because the fetus was affected by short-rib thoracic dysplasia and harboured the related variant. The infants of the other two couples were born and were healthy at their last recorded follow-up.
Conclusion RNA splicing analysis is an important method to assess the impact of sequence variants on splicing in clinical practice and can contribute to the reclassification of a significant proportion of VUSs. RNA splicing analysis should be considered for genetic disease diagnostics.
- genetic testing
- sequence analysis
Data availability statement
Data are available upon reasonable request.
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W-BH, W-JX and C-LD contributed equally.
HH and JD contributed equally.
Contributors HH and JD designed the study. W-BH, WX, CD and Y-Q T analysed the data and wrote the paper. Y-RW and SZ performed the bioinformatic analysis. W-BH, WX, CD, CT and LM performed the study. XL, FG, G-XL and GL performed the clinical work. JD is responsible for the overall content of the manuscript acting as guarantor.
Funding This work was supported by grants from the National Key Research and Development Program of China (2018YFC1004901), the National Natural Science Foundation of China (81771645 and 81971447), the Hunan Provincial Natural Science Foundation of China (2019JJ51006, 2019JJ50397), the Hunan Provincial Grant for Innovative Province Construction (2019SK4012), the Key Grant of Prevention and Treatment of Birth Defect from Hunan Province (2019SK1012), and the Research Grant of CITIC-Xiangya (YNXM-201915, YNXM-201913, YNXM-201912, YNXM-202002).
Competing interests None declared.
Provenance and peer review Not commissioned; externally peer reviewed.
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