Neoantigen presentation arises as a result of tumor-specifi c mutations and is a critical component of immune surveillance that can be abrogated by somatic LOH of the human leukocyte antigen class I (HLA-I) locus. To understand the role of HLA-I LOH in oncogenesis and treatment, we utilized a pan-cancer genomic dataset of 83,644 patient samples, a small subset of which had treatment outcomes with immune checkpoint inhibitors (ICI). HLA-I LOH was common (17%) and unexpectedly had a nonlinear relationship with tumor mutational burden (TMB). HLA-I LOH was frequent at intermediate TMB, yet prevalence decreased above 30 mutations/megabase, suggesting highly mutated tumors require alternate immune evasion mechanisms. In ICI-treated patients with nonsquamous non-small cell lung cancer, HLA-I LOH was a signifi cant negative predictor of overall survival. Survival prediction improved when combined with TMB, suggesting TMB with HLA-I LOH may better identify patients likely to benefi t from ICIs. SIGnIFICAnCE:This work shows the pan-cancer landscape of HLA-I LOH, revealing an unexpected "Goldilocks" relationship between HLA-I LOH and TMB, and demonstrates HLA-I LOH as a signifi cant negative predictor of outcomes after ICI treatment. These data informed a combined predictor of outcomes after ICI and have implications for tumor vaccine development.

PURPOSE Combined hepatocellular cholangiocarcinoma (cHCC-CCA) is a rare, aggressive primary liver carcinoma, with morphologic features of both hepatocellular carcinomas (HCC) and liver cholangiocarcinomas (CCA). METHODS The genomic profiles of 4,975 CCA, 1,470 HCC, and 73 cHCC-CCA cases arising from comprehensive genomic profiling in the course of clinical care were reviewed for genomic alterations (GA), tumor mutational burden, microsatellite instability status, genomic loss of heterozygosity, chromosomal aneuploidy, genomic ancestry, and hepatitis B virus status. RESULTS In cHCC-CCA, GA were most common in TP53 (65.8%), TERT (49.3%), and PTEN (9.6%), and 24.6% cHCC-CCA harbored potentially targetable GA. Other GA were predominantly associated with either HCC or CCA, including, but not limited to, TERT, FGFR2, IDH1, and presence of hepatitis B virus. On the basis of these features, a machine learning (ML) model was trained to classify a cHCC-CCA case as CCA-like or HCC-like. Of cHCC-CCA cases, 16% (12/73) were ML-classified as CCA-like and 58% (42/73) cHCC-CCA were ML-classified as HCC-like. The ML model classified more than 70% of cHCC-CCA as CCA-like or HCC-like on the basis of genomic profiles, without additional clinico-pathologic input. CONCLUSION These findings demonstrate the use of ML for classification as based on a targeted exome panel used during routine clinical care. Classification of cHCC-CCA by genomic features alone creates insights into the biology of the disease and warrants further investigation for relevance to clinical care.

Background Chemotherapies have limited efficacy in pancreatic cancer (PC) and biliary tract cancer (BTC), underscoring the need for new regimens. Recently, tumor-agnostic approaches have been developed for some targeted therapies in advanced solid tumors, however, the frequency of alterations by clinical and genomic background are unclear in PC and BTC. Methods To assess the frequencies of druggable gene alterations and to investigate new potential therapeutic targetable genomic alterations, advanced PC and BTC patients were tested with comprehensive genomic profiling (CGP) at Foundation Medicine during the course of clinical care. Results 16,913 PC patients and 3,031 BTC patients were available for analyses and frequencies of genomic alterations were stratified by age (≥40/<40), microsatellite instability (MSI) status, tumor mutational burden (TMB) status (high ≥10/low <10 Muts/Mb), and select genomic alterations. Alterations in BRCA2, BRAF, ERBB2, CDK12, PIK3CA, FGFR2, EGFR, and other potential targets were seen across cohorts, with enrichment observed within particular subsets such as in PC patients lacking a KRAS mutation. In BTC patients, rate of ERBB2 amplification was significantly higher in TMB-high population (23.3% vs. 13.7%). Interestingly, CDK12 rearrangement was observed in BTC patients with ERBB2 amplification tumors. In patients with <40-y, FGFR2 rearrangement (4%) was observed in PC: GATA6 amplification (11.1%) and rearrangement of BRAF (2.8%)/FGFR2 (5.6%) were observed in BTC patients. Conclusions We identified an appreciable frequency of immunotherapy biomarkers and targetable genes alterations in both PC and BTC, with notable frequencies in PC samples lacking KRAS mutations and children/adolescent and young adult (AYA) populations, that should encourage CGP testing.

5003 Background: Prostate cancer (PCa) incidence, mortality, and outcomes vary widely across race/ethnicity. The underlying drivers of these differences are multifactorial, including systemic barriers that lead to wide variation in access to care including genomic and precision medicine. Men of African ancestry (AFR) are particularly underrepresented in genomic and precision medicine studies. Therefore, we sought to comprehensively assess patterns of gene alterations, comprehensive genomic profiling (CGP) utilization, and treatment patterns in a large, diverse advanced PCa cohort. Methods: 11,741 PCa patients with CGP, as part of routine clinical care (Foundation Medicine Inc., FMI) were evaluated for their genomic landscape. Predominant ancestry was inferred using a SNP-based approach (Connelly et al, AACR 2018). Independently, the US-based de-identified Flatiron Health (FH)-FMI clinico-genomic database (CGDB) of 897 evaluable PCa patients was also queried. Clinical characteristics and treatment selections were described for patients who received metastatic or castrate-resistant diagnosis between 1/2011 and 6/2020. Results: The FMI cohort included 1,422 (12%) men of AFR and 9,244 (79%) men of European ancestry (EUR). Median age was lower in AFR compared with EUR men (64 vs. 67, p < 0.001). TP53 and PTEN alterations and TMPRSS2-ERG rearrangements occurred less frequently in AFR than EUR men (35% vs. 43%, 21% vs. 33%, 15% vs. 33% respectively, p < 0.05). In contrast, alterations in SPOP (11.9% vs. 7.3%), CDK12 (10.0% vs. 5.2%), CCND1 (6.0% vs. 3.8%), KMT2D (7.7% vs. 5.1%), HGF (4.1% vs. 2.5%), and MYC (13.4% vs. 10.6%) were enriched in the AFR cohort (p < 0.05). Alteration frequency in BRCA1/2, AR, DNA damage response pathway genes, and actionable genes with therapy implications, were similar across ancestry. Of note, BRAF alterations were slightly enriched in AFR (5.0% vs. 3.2%, p < 0.05). In the CGDB cohort (79 AFR, 762 EUR), AFR men received a median of 2 lines of therapy prior to CGP, compared to 1 line for EUR men. Notably, the proportion of patients receiving immunotherapy and PARPi was similar across ancestry, however AFR men were less likely to receive clinical study drug compared with EUR men (11% vs 30%, p < 0.001), even among men with actionable alterations (1% vs 6%, p < 0.001). Conclusions: To our knowledge, this study encompasses the largest cohort, particularly of AFR men in a genomic study, that defines CGP utilization, the genomic landscape and therapeutic implications of CGP in PCa across ancestry. Overall, there were largely similar rates of actionable gene alterations across ancestry. Notably, AFR men were less likely to receive CGP earlier in their treatment course, and less likely to be treated on clinical trials, which could impact the genomic landscape, outcomes, and ultimately disparities.

Small cell lung cancer (SCLC) is a recalcitrant neuroendocrine carcinoma with dismal survival outcomes. A major barrier in the field has been the relative paucity of human tumors studied. Here we provide an integrated analysis of 3,600 real-world SCLC cases. This large cohort allowed us to identify new recurrent alterations and new genetic subtypes, including STK11-mutant tumors (1.7%) and TP53/RB1 wild-type tumors (5.5%), of which 12.7% were human papillomavirus-positive. In our cohort, gene amplifications on 4q12 are associated with increased overall survival while CCNE1 amplification is associated with decreased overall survival. We also identify more frequent alterations in the PTEN pathway in brain metastases. Finally, profiling cases of SCLC containing oncogenic drivers typically associated with NSCLC demonstrates that SCLC transformation may occur across multiple distinct molecular cohorts of NSCLC. These novel and unsuspected genetic features of SCLC may help personalize treatment approaches for this fatal form of cancer.