78 CHAPTER 3 Pre-enrollment molecular information Patient Molecular test Date molecular test result was issued Germline BRCA variant (VAF) Somatic BRCA variant 1 (VAF) Somatic BRCA variant 2 (VAF) HRDsignature score Bi-allelic BRCA inactivation Other oncogenic drivers discovered by WGS Sample TCP 1 WGS 09 Oct 2017 none BRCA2 copy loss (0 copies) n/a 0.97 Yes FGFR2-TBC1D4 fusion DDR2 amplification 30% 2 WGS 22 May 2018 none BRCA2 copy loss (0 copies) BRCA1 c.1961 dupA; p.Ty r655fs (49%) 1.00 Yes KMT2C c.1837_1843 delACTGAAT; p.Thr613fs (89%), TP53 c.742C>T; p.Arg248Trp (91%) 70% 3 WGS 28 May 2018 BRCA1 c.191G>A; p.Cys64Tyr (26%) BRCA1 c.160C>T; p.Gln54* (73%) n/a 1.00 Yes NCOR1 homozygous disruption 70% 4 WGS 03 Apr 2017 BRCA1 p.Asp693fs (50%) BRCA1 c.2338C>T; p.Gln780* (50%) n/a 0.89 Yes KMT2C c.9524C>A p.Ser3175* (44%); RB1 homozygous disruption 90% 5 Germline test 19 Feb 2013 BRCA1 c.5277+1G>A n/a n/a n/a Unknown n/a n/a 6 smMIP 15 Jun 2018 unknown BRCA2 c.1147del; p.Ile383fs (24%) n/a n/a Unknown n/a 60% 7 smMIP 30 Jun 2017 unknown BRCA2 c.1310_1313del; p.Lys437fs n/a n/a Unknown n/a 20-30% 8 Germline test + WGS 16 Feb 2018 BRCA2 p.Asp252fs LOH BRCA1 c.5618 C>A; p.Thr 1873Asn (83%) 0.94 Yes TP53 c.524G>A; p.Arg175His (91%) 49% 9 WGS 14 Dec 2018 none BRCA2 c.9230T>C; p.Phe3077Ser (100%) BRCA2 c.9254 C>T; p.Thr 3085Ile (100%) 0.98 Yes JAK1 homozygous disruption TMPRSS2-ERG fusion 21% 10 WGS 31 Oct 2017 none BRCA2 copy loss (0 copies) n/a 0.99 Yes TP53 c.588_605del; p.Val197_Arg202del (82%), PTEN copy loss (0 copies), RNF43 c.582+2_582+15del (splice site) (88%), TMPRSS2-ERG fusion 80% 11 WGS 26 Mar 2018 BRCA2 c.6816_ 6817delAA; p.Arg2272fs BRCA2 partial loss (0.7 copies) n/a 0.98 Yes PTEN copy loss (0 copies) RB1 homozygous disruption FOXA1 c.797_838del; p.Phe266_Ser280delinsCys (39%) 48% 12 Germline test Unknown BRCA1 c.2019delA; p.Glu673fs n/a n/a n/a Unknown n/a n/a 13 WGS 14 Sep 2017 BRCA1 c.181T>G; p.Cys61Gly (100%) LOH n/a 1.00 Yes TP53 c.407A>C; plGln136Pro (100%), CDKN2A copy loss (0 copies), ARID1A c.3294_3298delGTGTC; p.Gln1098fs (89%) 70%
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