Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes

Area of Science:

• Genetics and Genomics
• Cancer Research
• Molecular Biology

Background:

• Germline variants in tumor suppressor genes (TSGs) can lead to RNA mis-splicing, increasing cancer predisposition.
• A significant number of patients with suspected hereditary cancer syndromes lack molecular diagnoses due to challenges in identifying splicing-impactful variants.
• Accurate identification of splicing variants is critical for hereditary cancer diagnosis and genetic counseling.

Purpose of the Study:

• To develop and validate a capture RNA-sequencing (RNA-seq) approach for profiling splicing in 18 key tumor suppressor genes (TSGs).
• To assess the utility of this TSG splicing profile in prospectively identifying pathogenic splicing variants in patients with suspected hereditary cancer syndromes.
• To evaluate the diagnostic yield improvement offered by simultaneous DNA and RNA genetic testing in a clinical setting.

Main Methods:

• Generated a comprehensive splicing profile of 18 TSGs using capture RNA-sequencing on 345 whole-blood samples from healthy donors.
• Validated the method by comparing control splicing profiles with those from individuals harboring known pathogenic germline splicing variants.
• Performed concurrent capture DNA and RNA-sequencing on 1000 patients with suspected hereditary cancer syndromes to assess prospective diagnostic utility.

Main Results:

• Established a robust RNA-seq based splicing profile for 18 critical tumor suppressor genes.
• Demonstrated the capability of the method to detect RNA mis-splicing events.
• Achieved a 9.1% relative increase in the detection of pathogenic variants in a prospective cohort, enhancing diagnostic yield.

Conclusions:

• Capture RNA-sequencing provides an effective method for profiling splicing in tumor suppressor genes.
• This approach significantly improves the diagnostic yield for patients with suspected hereditary cancer syndromes.
• Simultaneous DNA and RNA genetic testing is a valuable strategy for clinical molecular diagnosis of hereditary cancers.