Background:
The recent development and enormous application of parallel sequencing technology in
oncology have produced immense cell-specific genetic data. However, publicly available cell-
specific genetic variants are not explained by well-established guidelines. Additionally, cell-
specific variants interpretation and classification has remained a challenging task, and lacks
standardization. The Association for Molecular Pathology (AMP), American Society of Clinical
Oncology (ASCO), and College of American Pathologists (CAP) published the first consensus
guidelines for cell-specific variants cataloging and clinical interpretation.
Results:
We developed a new method that followed the consensus recommendations, and applied our
method on open source tumor-specific databases to produce clinically actionable cancer
somatic variants (CACSV) dataset in integratable formats by most clinical analytical workflows.
We evaluated our method with well-known classification algorithms, and found the new method
to be comparable and more adhering to the recent guidelines.
Conclusion:
CACSV is a step toward cell-specific genetic variants universal interpretation, readily adaptable
by most clinical laboratories pipelines and can escalate somatic variants elucidation and
classification. CACSV is made free available (https://github.com/tsobahytm/CACSV/tree/main/dataset).