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Published on: April 11, 2016
Target-Enhanced Whole-Genome Sequencing Shows Clinical Validity Equivalent to Commercially Available Targeted
Sangmoon Lee1, Jin Roh2, Jun Sung Park3
1Inocras Inc., San Diego, CA, USA.
Purpose:
Cancer poses a significant global health challenge, demanding precise genomic testing for individualized treatment strategies. Targeted-panel sequencing (TPS) has improved personalized oncology but often lacks comprehensive coverage of crucial cancer alterations. Whole-genome sequencing (WGS) addresses this gap, offering extensive genomic testing. This study demonstrates the medical potential of WGS.
Materials And Methods:
This study evaluates target-enhanced WGS (TE-WGS), a clinical-grade WGS method sequencing both cancer and matched normal tissues. Forty-nine patients with various solid cancer types underwent both TE-WGS and TruSight Oncology 500 (TSO500), one of the mainstream TPS approaches.
Results:
TE-WGS detected all variants reported by TSO500 (100%, 498/498). A high correlation in variant allele fractions was observed between TE-WGS and TSO500 (r=0.978). Notably, 223 variants (44.8%) within the common set were discerned exclusively by TE-WGS in peripheral blood, suggesting their germline origin. Conversely, the remaining subset of 275 variants (55.2%) were not detected in peripheral blood using the TE-WGS, signifying them as bona fide somatic variants. Further, TE-WGS provided accurate copy number profiles, fusion genes, microsatellite instability, and homologous recombination deficiency scores, which were essential for clinical decision-making.
Conclusion:
TE-WGS is a comprehensive approach in personalized oncology, matching TSO500's key biomarker detection capabilities. It uniquely identifies germline variants and genomic instability markers, offering additional clinical actions. Its adaptability and cost-effectiveness underscore its clinical utility, making TE-WGS a valuable tool in personalized cancer treatment.
Insights
Target-enhanced whole-genome sequencing (TE-WGS) matches targeted-panel sequencing (TPS) for cancer biomarkers. TE-WGS uniquely identifies germline variants and genomic instability, enhancing personalized cancer treatment strategies.
Area of Science:
- Genomic Medicine
- Oncology
- Molecular Diagnostics
Background:
- Cancer treatment relies on precise genomic testing for personalized strategies.
- Targeted-panel sequencing (TPS) offers personalized oncology but has coverage limitations.
- Whole-genome sequencing (WGS) provides comprehensive genomic insights.
Purpose of the Study:
- To evaluate the clinical utility of target-enhanced WGS (TE-WGS) in personalized oncology.
- To compare TE-WGS performance against a mainstream TPS method (TruSight Oncology 500).
- To demonstrate the medical potential of WGS for comprehensive cancer analysis.
Main Methods:
- Clinical-grade TE-WGS was performed on 49 solid cancer patients.
- Matched normal tissues and peripheral blood were sequenced.
- TE-WGS results were compared with those from TruSight Oncology 500 (TSO500).
Main Results:
- TE-WGS detected all variants identified by TSO500 with high concordance (r=0.978).
- TE-WGS exclusively identified 44.8% of variants as germline from peripheral blood.
- TE-WGS accurately assessed copy number profiles, fusion genes, MSI, and HRD scores.
Conclusions:
- TE-WGS is a comprehensive tool for personalized oncology, matching TPS biomarker capabilities.
- TE-WGS uniquely identifies germline variants and genomic instability markers, enabling further clinical actions.
- TE-WGS offers adaptability and cost-effectiveness, proving its clinical utility in cancer treatment.
