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Published on: December 9, 2016
Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes
Tyler Landrith1, Bing Li1, Ashley A Cass1
11Ambry Genetics, Aliso Viejo, CA USA.
Abstract:
Germline variants in tumor suppressor genes (TSGs) can result in RNA mis-splicing and predisposition to cancer. However, identification of variants that impact splicing remains a challenge, contributing to a substantial proportion of patients with suspected hereditary cancer syndromes remaining without a molecular diagnosis. To address this, we used capture RNA-sequencing (RNA-seq) to generate a splicing profile of 18 TSGs (APC, ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, MUTYH, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53) in 345 whole-blood samples from healthy donors. We subsequently demonstrated that this approach can detect mis-splicing by comparing splicing profiles from the control dataset to profiles generated from whole blood of individuals previously identified with pathogenic germline splicing variants in these genes. To assess the utility of our TSG splicing profile to prospectively identify pathogenic splicing variants, we performed concurrent capture DNA and RNA-seq in a cohort of 1000 patients with suspected hereditary cancer syndromes. This approach improved the diagnostic yield in this cohort, resulting in a 9.1% relative increase in the detection of pathogenic variants, demonstrating the utility of performing simultaneous DNA and RNA genetic testing in a clinical context.
Insights
Identifying RNA mis-splicing in tumor suppressor genes (TSGs) is crucial for diagnosing hereditary cancer. This study developed a capture RNA-sequencing method that improved diagnostic yield by 9.1% in patients with suspected cancer syndromes.
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.
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