Assign tiers of clinical significance (AMP/ASCO/CAP framework) to RNA fusions

Function that assigns tiers of clinical significance (AMP/ASCO/CAP framework) to RNA fusions based on biomarker evidence items. The function considers the strength of evidence (evidence levels) and the match between biomarker site and primary site of query tumor. The function also considers oncogene properties of fusion partners to assign tier 3 status to variants with uncertain clinical significance.

Usage

assign_variant_tiers_fusion(
  primary_site = "Any",
  biomarker_mapping_confidence = "medium",
  var_df = NULL,
  etype_for_tiering = c("predictive"),
  biomarker_items = NULL
)

Arguments

primary_site

primary tumor site of query tumor (e.g. 'Lung', 'Breast', 'Any')

biomarker_mapping_confidence

confidence level of variant-biomarker mapping resolution (e.g. 'high' or 'medium')

var_df

data frame with somatic RNA fusions

etype_for_tiering

evidence type(s) to consider for tier classification (e.g. 'predictive', 'prognostic', 'diagnostic')

biomarker_items

data frame with biomarker evidence items

Value

data frame with tier classifications for somatic RNA fusions based on biomarker evidence items and variant properties