80 CHAPTER 3 Baseline WGS-based molecular information Patient Germline BRCA variant (tVAF) Somatic BRCA variant 1 (tVAF) Somatic BRCA variant 2 (tVAF) HRD-signature score Bi-allelic BRCA inactivation Other oncogenic drivers discovered by WGS Sample TCP 1 none BRCA2 copy loss (0 copies) n/a 0.99 Yes FGFR2-TBC1D4 fusion DDR2 amplification 26% 2 none BRCA2 copy loss (0 copies) BRCA1 c.1961dupA; p.Tyr655fs (49%) 1.00 Yes KMT2C c.1837_1843delACTGAAT; p.Thr613fs (100%), TP53 c.742C>T; p.Arg248Trp (91%), CCDC171-NTRK2 fusion 73% 3 TCP < 30% 4 No baseline biopsy: high risk procedure 5 No baseline biopsy: leptomeningeal disease localization only 6 none none n/a 0.00 No PTEN copy loss (0 copies) ACVR2A copy loss (0 copies) KMT2C c.14331dupG; p.Ser4778fs (40%) 22% 7 none BRCA2 c.1310_1313del; p.Lys437fs n/a 0.88 Unknown (due to low purity) KDM6A hozozygous disruption KEAP1 c.1075C>T; p.Gln359* (50%) 18% 8 TCP < 30% 9 none BRCA2 c.9230T>C; p.Phe3077Ser (100%) BRCA2 c.9254C>T; p.Thr3085Ile (100%) 0.98 Yes JAK1 homozygous disruption TMPRSS2-ERG fusion 45% 10 TCP < 30% 11 TCP < 30% 12 TCP < 30% 13 TCP < 30%
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