Figure 4. AR alterations in liquid biopsy.

A) Oncoprints of 940 AR-altered samples, divided as separate cohorts and the aggregate B) Polyclonality of AR activating mutations: numbers of AR short variants and rearrangements per sample. SV= short variant, RE= rearrangement C) Distribution of oncogenic missense mutations in AR. Letters indicate amino acid change when there is >1 missense mutation at the position D) Rare AR alterations identified near the C-terminus of the ligand binding domain: Compound missense mutations in cis (gold) and in-frame deletions (grey) spanning important androgen-binding residues H875, F877, and T878, all resulting in S885 moving into the 878 position (red). One sample contained an isoleucine insertion (light blue). F877L/T878A double mutants are predicted to have enhanced resistance to enzalutamide (bold). 16 compound mutations were found in 12 patients, and 11 in-frame deletions among as many patients. All patients were confirmed to have progressed on at least one of abiraterone, enzalutamide or apalutamide, except 2 patients with compound mutations for whom treatment information was not available. E) Map of AR rearrangements that describe breakpoints for translocations and deleted, duplicated, or inverted regions (22 translocations, 60 deletions, 53 duplications, and 25 inversions). X-axis is a schematic representations of the 8 exons in the AR gene (not to scale). Among the 160 patients with AR rearrangements, 138 were confirmed to have progressed on at least one of abiraterone, enzalutamide or apalutamide, and 22 had no available treatment information. F) Patient-matched sample pairs collected within 30 days of each other with ≥1 AR short variant detected, in ascending order of ctDNA fraction. Bar represents estimated ctDNA fraction of the liquid biopsy. Tumor fraction of tissue biopsy listed on left. Table to the right lists short variants identified exclusively in tissue (orange), in both tissue and liquid (blue), or exclusively in liquid (green). Ratio of VAF/ctDNA fraction listed in parentheses after each variant detected in liquid biopsy. * = VAF can exceed ctDNA fraction if mutation is an amplified copy of AR. G) Tissue-liquid pairs in which an AR amplification was detected in tissue. Correlation of copy number, ctDNA fraction and detection in the matched liquid biopsy.