PATIENT TUMOR TYPE QRF# Bladder urothelial (transitional cell) carcinoma Interpretive content on this page and subsequent Biomarker Findings pages is provided as a professional service, and is TTumorumor Mutational BurBurdenden -- TMB-High (23 Muts/Mb) not reviewed or approved by the FDA. MicrMicrosatosatellitellite Statuse Status -- MS-Stable PPAATIENTTIENT Genomic Findings DISEASE Bladder urothelial (transitional cell) carcinoma For a complete list of the genes assayed, please refer to the Appendix. NAME CCCND1CND1 amplification DATE OF BIRTH SEX ERBB3ERBB3 amplification MEDICAL RECORD # RAF1RAF1 amplification PHYPHYSICIANSICIAN BCL2L1BCL2L1 amplification ORDERING PHYSICIAN CDKN2ACDKN2A p16INK4a D84N and p14ARF R98Q MEDICAL FACILITY FFGF19GF19 amplification ADDITIONAL RECIPIENT FFGF3GF3 amplification MEDICAL FACILITY ID PATHOLOGIST FFGF4GF4 amplification SPESPECIMENCIMEN LLYNYN amplification TERTERTT prpromotomoter -er -146C>T146C>T SPECIMEN SITE TP53TP53 E285KE285K SPECIMEN ID SPECIMEN TYPE DATE OF COLLECTION 1818TTherherapiesapies with CClinicallinical Benefit 2266CClinical Tlinical Trialsrials SPECIMEN RECEIVED 00TTherherapiesapies with Lack of RResponseesponse THERAPIES WITH CLINICAL BENEFIT THERAPIES WITH CLINICAL BENEFIT BIOMARKER FINDINGS (IN P(IN PAATIENT’TIENT’S TUS TUMORMOR TYPE) (IN O(IN OTHER TUTHER TUMORMOR TYPE) Tumor Mutational Burden - TMB-High (23 Atezolizumab none Muts/Mb) Avelumab Durvalumab Nivolumab 10 T10 Trialsrials see psee p..1717 Pembrolizumab Microsatellite status - MS-Stable No therNo therapiesapies or clinical trials. see Biomarker Findings section THERAPIES WITH CLINICAL BENEFIT THERAPIES WITH CLINICAL BENEFIT GENOMIC FINDINGS (IN P(IN PAATIENT’TIENT’S TUS TUMORMOR TYPE) (IN O(IN OTHER TUTHER TUMORMOR TYPE) CCND1 - amplification none Abemaciclib Palbociclib 6 T6 Trialsrials see psee p..2020 Ribociclib ERBB3 - amplification none Ado-trastuzumab emtansine Afatinib Lapatinib SAMPLEPertuzumab Trastuzumab 3 T3 Trialsrials see psee p..2121 Trastuzumab-dkst The content provided as a professional service by Foundation Medicine, Inc., has not been reviewed or approved by the FDA. Electronically signed by Julia Elvin, M.D., Ph.D. | Jeffrey Ross, M.D., Medical Director | 25 May 2018 | Sample PSample Prrepareparaation:tion:150 Second St., 1st Floor, Cambridge, MA 02141 ··CLIA: 22D2027531 Foundation Medicine, Inc. | 1.888.988.3639 Sample AnalyAnalysis:sis:150 Second St., 1st Floor, Cambridge, MA 02141 ··CLIA: 22D2027531 PROFESSIONAL SERVICES - PAGE 1 of 23 PATIENT TUMOR TYPE QRF# Bladder urothelial (transitional cell) carcinoma THERAPIES WITH CLINICAL BENEFIT THERAPIES WITH CLINICAL BENEFIT GENOMIC FINDINGS (IN P(IN PAATIENT’TIENT’S TUS TUMORMOR TYPE) (IN O(IN OTHER TUTHER TUMORMOR TYPE) RAF1 - amplification none Cobimetinib Regorafenib Sorafenib 9 T9 Trialsrials see psee p..2222 Trametinib GENOMIC FINDINGS WITH NO REPORTABLE THERAPEUTIC OR CLINICAL TRIAL OPTIONS For more information regarding biological and clinical significance, including prognostic, diagnostic, germline, and potential chemosensitivity implications, see the Genomic Alterations section. BCL2L1 amplification p. 5 FGF4 amplification p. 7 CDKN2A p16INK4a D84N and p14ARF R98Q p. 5 LYN amplification p. 7 FGF19 amplification p. 6 TERT promoter -146C>T p. 8 FGF3 amplification p. 6 TP53 E285K p. 8 Note: Genomic alterations detected may be associated with activity of certain FDA approved drugs; however, the agents listed in this report may have varied clinical evidence in the patient’s tumor type. Neither the therapeutic agents nor the trials identified are ranked in order of potential or predicted efficacy for this patient, nor are they ranked in order of level of evidence for this patient’s tumor type. SAMPLE The content provided as a professional service by Foundation Medicine, Inc., has not been reviewed or approved by the FDA. Electronically signed by Julia Elvin, M.D., Ph.D. | Jeffrey Ross, M.D., Medical Director | 25 May 2018 | Sample PSample Prrepareparaation:tion:150 Second St., 1st Floor, Cambridge, MA 02141 ··CLIA: 22D2027531 Foundation Medicine, Inc. | 1.888.988.3639 Sample AnalyAnalysis:sis:150 Second St., 1st Floor, Cambridge, MA 02141 ··CLIA: 22D2027531 PROFESSIONAL SERVICES - PAGE 2 of 23 PATIENT TUMOR TYPE QRF# Bladder urothelial (transitional cell) carcinoma BIOMARKER FINDINGFINDINGSS BIOMARKER with high mutational burden, including 3 and grade of bladder cancers14. For patients Tumor Mutational patients with endometrial adenocarcinoma with metastatic urothelial carcinoma receiving who reported sustained partial responses atezolizumab, however, higher median Burden following treatment with pembrolizumab8 or mutation load has been reported to be 9 CACATEGORTEGORYY nivolumab , a patient with hypermutant significantly associated with improved TMB-High (23 Muts/Mb) glioblastoma who obtained clinical benefit progression-free and overall survival3,15. from pembrolizumab10, and two pediatric patients with biallelic mismatch repair FINDING SUMMARSUMMARYY POPOTENTIALTENTIAL TREATREATMENT STMENT STRATRATEGIESTEGIES deficiency (bMMRD)-associated Tumor mutation burden (TMB, also known as On the basis of emerging clinical evidence, ultrahypermutant glioblastoma who mutation load) is a measure of the number of increased TMB may be associated with greater experienced clinically and radiologically somatic protein-coding base substitution and 11 sensitivity to immunotherapeutic agents, significant responses to nivolumab . In insertion/deletion mutations occurring in a including anti-CTLA-41, anti-PD-L12-4, and patients with melanoma, mutational load was tumor specimen. TMB is affected by a variety anti-PD-1 therapies5-7; FDA-approved agents associated with long-term clinical benefit from of causes, including exposure to mutagens ipilimumab1,12 and anti-PD-1/anti-PD-L1 16-17 include ipilimumab, atezolizumab, avelumab, such as ultraviolet light in melanoma and 4 durvalumab, pembrolizumab, and nivolumab. treatments . For patients with metastatic cigarette smoke in lung cancer5,18, mutations in In multiple solid tumor types, higher urothelial carcinoma, those who responded to the proofreading domains of DNA polymerases mutational burden has corresponded with atezolizumab treatment had a significantly encoded by the POLE and POLD1 genes19-23, response and improved prognosis. increased mutational load [12.4 mutations and microsatellite instability (MSI)19,22-23. The Pembrolizumab improved progression-free (mut) per megabase (Mb)] compared to tumor seen here harbors a high TMB. This 2 survival (14.5 vs. 3.4-3.7 months) in patients nonresponders (6.4 mut/Mb) , and mutational type of mutation load has been shown to be with non-small cell lung cancer (NSCLC) and load of 16 mut/Mb or higher was associated associated with sensitivity to immune 3 higher mutational load (greater than 200 with significantly longer overall survival . checkpoint inhibitors, including anti-CTLA-4 nonsynonymous mutations; hazard ratio = therapy in melanoma1, anti-PD-L1 therapy in 0.19)5. In studies of patients with either FREQUENCFREQUENCYY & PROGNOPROGNOSISSIS urothelial carcinoma2, and anti-PD-1 therapy NSCLC or colorectal cancer (CRC), patients In the Bladder Urothelial Carcinoma TCGA in non-small cell lung cancer and colorectal whose tumors harbor elevated mutational dataset, the median somatic mutation burden cancer5-6, potentially due to expression of burden reported higher overall response rates was 5.5 mutations per megabase (mut/MB)13. immune-reactive neoantigens in these to pembrolizumab5-7. Anti-PD-1 therapies have One study found somatic mutation number to tumors5. achieved clinical benefit for certain patients positively correlate with increased tumor stage BIOMARKER objective response rate (ORR) in MSS Microsatellite instability (MSI) is a condition of Microsatellite status colorectal cancer (CRC) compared with MSI-H genetic hypermutability that generates CRC (0% vs. 40%)6. Similarly, a clinical study excessive amounts of short insertion/deletion CACATEGORTEGORYY of nivolumab, alone or in combination with mutations in the genome; it generally occurs at MS-Stable ipilimumab, in patients with CRC reported a microsatellite DNA sequences and is caused by significantly higher response rate in patients a deficiency in DNA mismatch repair (MMR) with MSI-H tumors than those without27. in the tumor32. Defective MMR and POPOTENTIALTENTIAL TREATREATMENT STMENT STRATRATEGIESTEGIES consequent MSI occur as a result of genetic or On the basis of clinical evidence, MSS tumors FREQUENCFREQUENCYY & PROGNOPROGNOSISSIS epigenetic inactivation of one of the MMR pathway proteins, primarily MLH1, MSH2, are significantly less likely than MSI-H tumors MSI has been detected in 26-49% of urothelial MSH6, or PMS232-34. The tumor seen here is to respond to anti-PD-1 immune checkpoint carcinomas29-30; MSI-high (MSI-H) has also inhibitors24-26, including approved therapies microsatellite-stable (MSS), equivalent to the been reported in multiple case studies of upper 6,27 clinical definition of an MSS tumor: one with nivolumab and pembrolizumab . In a urinary tract urothelial carcinoma31. MSI, as mutations in none of the tested microsatellite retrospective analysis of 361 patients with determined through loss of MSH2 or MSH6 markers35-37. MSS status indicates MMR solid tumors treated with pembrolizumab, 3% protein expression, correlated with non- proficiency and typically correlates with intact were MSI-H and experienced a significantly invasive, well-differentiated tumors and expression of