1. OverviewΒΆ

VarSeq VSClinical AMP

The VSClinical workflow is used to first pass selected variants through a user-defined filter chain, analyze the filtered variants according to industry standard guidelines in a streamlined fashion to reach an interpretation and then generate a clinical report. The user-defined filter chain can be included to eliminate low quality, common, or known benign variants for example and then the filtered variants can be pulled into VSClincial for the processing of somatic and germline variants according to the AMP and ACMG guidelines, respectively. Users will be guided through all the available evidence for the variant or biomarker in a streamlined fashion that locks in a consistent interpretation process. After reaching the final classification and interpretation, a clinical report can rapidly be generated. Please view the VSClinical ACMG Guidelines tutorial for workflow generation and details specific to the ACMG Guidelines and germline variant analysis.

The VSClinical AMP guidelines differ from the ACMG Guidelines by analyzing the oncogenicity of somatic biomarkers. These biomarkers include single nucleotide variants, insertions or deletions, copy number variants, gene fusions, and considerations for wild type genes. Furthermore, the goal is to not only account for the various biomarkers but to store the final classifications and interpretations and supply treatment options for the patient in a clinical setting. This means the drug sensitivity and resistance information, and prognostic and diagnostic information will be used to determine the biomarker classification and oncogenicity score.

oncogenic scale

Figure 1-1: Oncogenic weighting scale.