Table 3.

Selected cases in which F1CDx offers therapeutic choices

Patient code	Age, sex	Diagnosis	Disease history	Alterations and signatures already known	Alterations and signatures detected by F1CDx	Comments
01	81 y, F	Stomach adenocarcinoma intestinal type with liver and bone metastases	First line with FOLFOX Second line with Paclitaxel +Ramucirumab	ERBB2 not overexpressed (IHC)	MSI-High TMB-High (58 muts/Mb) AKT2 A139V BRCA1 K339fs*2 CDK12 T1463fs*50 PTCH1 N97fs*43 PTEN E157fs*23 RNF43 G659fs*41	After the second line the patient was in good clinical conditions but without any approved therapy. After the report of MSI status and TMB-high an off-label request for Nivolumab was done to our ethic committee based on the results of ATTRACTION-2 study.34 Patient started therapy on October 2018 and after 3 months had a complete response which is maintained nowadays.35
02	29 y, F	Left colon adenocarcinoma with liver, lymph node and peritoneal metastases	First line with FOLFOX +panitumumab Second line with FOLFIRI +ziv-aflibercept Third line with trifluridine/tipiracil	KRAS wt NRAS wt BRAF wt ERBB2 not overexpressed (IHC)	MS-Stable TMB-Intermediate (six muts/Mb) AXL amplification CCND2 amplification	AXL is a novel target in CRC.36 In our department, a clinical trial with cabozantinib (a multikinase inhibitor of MET, RET, AXL, and VEGFR-2) in previously treated metastatic CRC patients is opened (EudraCT2019-000674-28). This patient was enrolled in this trial and treatment is ongoing.
03	66 y, M	Pancreatic adenocarcinoma with liver, bone and brain metastasis	First line with FOLFIRINOX Second line with gemcitabine +abraxane	None	ETV6-NTRK3 fusion	This patient without any other available therapy was found with NTRK3 fusion, allowing him to participate to STARTRK-2 study.37 Treatment is ongoing.
04	76 y, F	Locally advanced intrahepatic cholangiocarcinoma	First line with CDDP +Gemcitabine	None	MS-Stable TMB-Low (five muts/Mb) FGFR2-BICC1 fusion CDK6 amplification	F1CDx revealed FGFR2-BICC1 fusion after the progression to first line therapy. She resulted eligible for the six trials according to the report. She went in another centre to participate to ARQ 087 trial (NCT03230318, ongoing).
05	54 y, M	Locally advanced left colon adenocarcinoma	First line with FOLFOXIRI	KRAS mut G12D BRAF wt	MSI-High TMB-High 25 muts/Mb)	During the first line with FOLFOXIRI the patient had no clinical benefit and the PFS was only 6 months (Best Response: SD). Cardiovascular contraindications to anti-angiogenic therapies. An off-label request for Pembrolizumab was done according to KEYNOTE-164 results.38 Unfortunately, he started therapy too late and after only one cycle, his performance status declined. He died few weeks later.
06	57 y, M	Intrahepatic cholangiocarcinoma with liver, lung and peritoneal metastases	First line with CDDP +Gemcitabine Second line with FOLFIRI Third line with FOLFOX	None	MS-Stable TMB-Low (0 muts/Mb) ERBB2 amplification FGFR2-BICC1 fusion	After the third line the patient was without any other available therapy. F1CDx revealed two druggable alterations with 15 trial proposed by the report. Unfortunately, the patient’s clinical conditions worsened rapidly (PS 3 ECOG) and he has not been able to participate.
07	67 y, M	Intrahepatic cholangiocarcinoma with peritoneal metastases	First line with CDDP +Gemcitabine	None	MS-Stable TMB-Low (4 Muts/Mb) IDH R132C	F1CDx was performed during the first line therapy. A trial with an IDH inhibitor was available but the patient is still in maintenance with gemcitabine. Recently a positive trial was presented at ESMO 2019 with ivosidenib that improved PFS over placebo in IDH mutant cholangiocarcinoma.39
08	53 y, F	Infiltrating ductal carcinoma of the breast	Quadrantectomy+level I/II axillary lymphadenectomy, stage pT2 N0 M0 Adjuvant therapy with EC90→ paclitaxel +RT	Ki67 80% ER neg PgR neg ERBB2 not overexpressed (IHC)	MS-Stable TMB-Intermediate (10 Muts/Mb) BRCA1 W321* CCND2 amplification FGF23 amplification FGF6 amplification KDM5A amplification RAD21 amplification TP53 P92fs*58	This patient is actually in follow-up but F1CDx revealed an important prognostic information and predictive in case of relapse.40 Germline BRCA test is ongoing.

AXL, AXL receptor tyrosine kinase; BICC1, BicC Family RNA Binding Protein 1; BRAF, v-raf murine sarcoma viral oncogene homolog B1; CDDP, cisplatin; CDK6, cyclin-dependent kinase 6; CRC, colorectal cancer; ERBB2, v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2; ESMO, European Society for Medical Oncology; ETV6, Ets-leukemia virus; F, female; F1CDx, FoundationOne CDx; FGFR2, fibroblast growth factor receptor 2; IDH, isocitrate dehydrogenase; IHC, immunohistochemistry; KRAS, Kirsten rat sarcoma viral oncogene homolog; M, male; MET, tyrosine-protein kinase Met; MSI, microsatellite instability; NRAS, neuroblastoma ras viral oncogene homolog; NTRK3, neurotrophic tyrosine kinase receptor type 3; PFS, progression free survival; PTEN, phosphatase and tensin homolog; TMB, tumour mutational burden; y, year.