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Pan-cancer pharmacogenetics: targeted sequencing panels or exome sequencing?
Laurentijn Tilleman1, Björn Heindryckx2, Dieter Deforce1
1Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, Ghent 9000, Belgium.
Pharmacogenomics
|October 6, 2020
Summary
Exome sequencing panels offer superior coverage for cancer pharmacogenetics compared to targeted sequencing. This finding aids clinicians and researchers in selecting optimal genomic tools for personalized cancer treatment.
Area of Science:
- Genomic Medicine
- Pharmacogenetics
- Oncology
Background:
- Pharmacogenetics is crucial for personalized cancer therapy.
- Selecting appropriate sequencing panels is vital for clinical decision-making.
Purpose of the Study:
- To compare the coverage of commercially available targeted pan-cancer sequencing panels versus exome sequencing panels.
- To evaluate their utility in pan-cancer pharmacogenetics, driver mutations, and fusion genes.
Main Methods:
- Investigated nine targeted pan-cancer panels and the xGen Exome Research Panel v2.
- Assessed coverage of pharmacogenetic variant-drug interactions across five cancer knowledgebases.
- Analyzed coverage of driver mutations and fusion genes in The Cancer Genome Atlas.
Main Results:
- The xGen Exome Research Panel v2 and TrueSight Oncology 500 showed the highest coverage.
- Exome sequencing covered 71.0% of pharmacogenetic interactions and 93.7% of driver mutations.
- Targeted panels demonstrated lower coverage percentages.
Conclusions:
- Exome sequencing panels provide broader coverage for pharmacogenetic variant-drug interactions in cancer.
- Exome sequencing is more comprehensive than targeted panels for pharmacogenetic variant analysis in oncology.
