Decision rules
LGA, tumor
TUMOR
Decision rules are multi-step, depend on sample quality attribution and include selection of the thresholds for LGA call. Two thresholds were utilized to call LGA at CNA breakpoint: stringent (implying simple genome) and soft (implying complex genome), which are applied in conservative manner for good quality cases (LGA-score was based on LGA number with soft/stringent thresholds for nonHRD/HRD clear-cut diagnostics), and are fixed to the stringent/soft ones for noisy/low tumor content samples, respectively. Simplified decision rules for bad quality samples consist in giving the diagnosis only for clear-cut nonHRD cases with small overall number of the breakpoints. Robust decision rules for fair quality samples consist in giving the diagnosis only for clear-cut cases, leaving the borderline cases with not determined (ND) diagnosis.