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Published on: November 5, 2019
Paired Comparison of Whole Genome Sequencing and Comprehensive Targeted Sequencing of Pancreatic Cancer Tissue
Thea Amalie Hvidtfeldt1, Tim Svenstrup Poulsen1, Inna Markovna Chen2
1Department of Pathology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark.
Background/Aim:
As an increasing number of drugs are approved for targeted cancer therapy, comprehensive genomic profiling of cancer patients is frequently conducted to identify potentially relevant genetic variants. Different sequencing technologies are used for this purpose; targeted gene panels cover a selected set of biomarker genes and hotspot regions, while whole genome sequencing (WGS) delivers genome-wide data. This comparison study aimed at evaluating whether one method performs superiorly to the other regarding the detection of targetable variants.
Patients And Methods:
To evaluate the performance of the two sequencing technologies, we compared the results of targeted sequencing using the Ion Torrent Oncomine Comprehensive Assay Plus (OCA-Plus) panel to Illumina WGS reports in 11 patients diagnosed with pancreatic cancer (PC). All pathogenic and likely pathogenic variants, including those relevant for targeted therapy, reported by WGS and OCA-Plus, were included in the final comparison.
Results:
Both techniques identified common driver mutations implicated in PC with high concordance (81%) across all variants. For variants relevant to targeted therapy, a 100% concordance between the technologies was observed.
Conclusion:
A comparable number of variants were reported by WGS and OCA-Plus, and all genetic variants relevant for targeted therapy were identified by both technologies. Thus, WGS does not provide substantial additional information in this patient group.
Insights
Whole genome sequencing (WGS) and targeted gene panels (OCA-Plus) show high concordance for detecting cancer-driving mutations. Both methods equally identify variants crucial for targeted cancer therapy in pancreatic cancer patients.
Area of Science:
- Genomics
- Oncology
- Molecular Diagnostics
Background:
- Comprehensive genomic profiling is essential for targeted cancer therapy.
- Targeted gene panels and whole genome sequencing (WGS) are key methods for variant identification.
- Evaluating the comparative performance of these sequencing technologies is crucial.
Purpose of the Study:
- To compare the diagnostic performance of targeted gene panels versus WGS.
- To assess the detection of targetable variants using Ion Torrent OCA-Plus and Illumina WGS.
- To determine if WGS offers superior information for targeted therapy selection in pancreatic cancer.
Main Methods:
- Comparative analysis of targeted sequencing (Ion Torrent OCA-Plus) and WGS data.
- Study included 11 patients with pancreatic cancer.
- Focused on pathogenic and likely pathogenic variants relevant for targeted therapy.
Main Results:
- High concordance (81%) observed between WGS and OCA-Plus for common driver mutations in pancreatic cancer.
- 100% concordance was achieved for variants relevant to targeted therapy.
- Both technologies reported a comparable number of variants.
Conclusions:
- Targeted gene panels (OCA-Plus) and WGS identify critical variants for targeted therapy with equal efficacy.
- WGS does not offer substantial additional clinically relevant information beyond targeted panels for this patient group.
- Targeted sequencing panels are a viable option for identifying actionable mutations in pancreatic cancer.
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