Search

Supplemental Table 1 and Figures 1 and 2

Purpose: We undertook this study to determine the prevalence of estrogen receptor (ER) α (ESR1) mutations throughout the natural history of hormone-dependent breast cancer and to delineate the functional roles of the most commonly detected alterations.Experimental Design: We studied a total of 249 tumor specimens from 208 patients. The specimens include 134 ER-positive (ER+/HER2−) and, as controls, 115 ER-negative (ER−) tumors. The ER+ samples consist of 58 primary breast cancers and 76 metastatic samples. All tumors were sequenced to high unique coverage using next-generation sequencing targeting the coding sequence of the estrogen receptor and an additional 182 cancer-related genes.Results: Recurring somatic mutations in codons 537 and 538 within the ligand-binding domain of ER were detected in ER+ metastatic disease. Overall, the frequency of these mutations was 12% [9/76; 95% confidence interval (CI), 6%–21%] in metastatic tumors and in a subgroup of patients who received an average of 7 lines of treatment the frequency was 20% (5/25; 95% CI, 7%–41%). These mutations were not detected in primary or treatment-naïve ER+ cancer or in any stage of ER− disease. Functional studies in cell line models demonstrate that these mutations render estrogen receptor constitutive activity and confer partial resistance to currently available endocrine treatments.Conclusions: In this study, we show evidence for the temporal selection of functional ESR1 mutations as potential drivers of endocrine resistance during the progression of ER+ breast cancer. Clin Cancer Res; 20(7); 1757–67. ©2014 AACR.

Purpose: Micropapillary urothelial carcinoma (MPUC) is a rare and aggressive form of bladder cancer. We conducted genomic analyses [next-generation sequencing (NGS)] of MPUC and non-micropapillary urothelial bladder carcinomas (non-MPUC) to characterize the genomic landscape and identify targeted treatment options.Experimental Design: DNA was extracted from 40 μm of formalin-fixed paraffin-embedded sections from 15 MPUC and 64 non-MPUC tumors. Sequencing (NGS) was performed on hybridization-captured, adaptor ligation–based libraries to high coverage for 3,230 exons of 182 cancer-related genes plus 37 introns from 14 genes frequently rearranged in cancer. The results were evaluated for all classes of genomic alteration.Results: Mutations in the extracellular domain of ERBB2 were identified in 6 of 15 (40%) of MPUC: S310F (four cases), S310Y (one case), and R157W (one case). All six cases of MPUC with ERBB2 mutation were negative for ERBB2 amplification and Erbb2 overexpression. In contrast, 6 of 64 (9.4%) non-MPUC harbored an ERBB2 alteration, including base substitution (three cases), amplification (two cases), and gene fusion (one case), which is higher than the 2 of 159 (1.3%) protein-changing ERBB2 mutations reported for urinary tract cancer in COSMIC. The enrichment of ERBB2 alterations in MPUC compared with non-MPUC is significant both between this series (P < 0.0084) and for all types of urinary tract cancer in COSMIC (P < 0.001).Conclusions: NGS of MPUC revealed a high incidence of mutation in the extracellular domain of ERBB2, a gene for which there are five approved targeted therapies. NGS can identify genomic alteration, which inform treatment options for the majority of MPUC patients. Clin Cancer Res; 20(1); 68–75. ©2013 AACR.

PDF file - 65K, Supplementary Figure 1. Tile Plot of Genomic Alterations in 64Cases on Non-micropapillary Urothelial Carcinoma.

Purpose:The incidence rates of colorectal cancers are increasing in young adults. The objective of this study was to investigate genomic differences between tumor samples collected from younger and older patients with colorectal cancer.Experimental Design:DNA was extracted from 18,218 clinical specimens, followed by hybridization capture of 3,769 exons from 403 cancer-related genes and 47 introns of 19 genes commonly rearranged in cancer. Genomic alterations (GA) were determined, and association with patient age and microsatellite stable/microsatellite instability high (MSS/MSI-H) status established.Results:Overall genomic alteration rates in the younger (TP53 (FDR < 0.01) and CTNNB1 (FDR = 0.01) alterations were more common in younger patients with colorectal cancer, and APC (FDR < 0.01), KRAS (FDR < 0.01), BRAF (FDR < 0.01), and FAM123B (FDR < 0.01) were more commonly altered in older patients with colorectal cancer. In the MSI-H cohort, the majority of genes showed similar rate of alterations in all age groups, but with significant differences seen in APC (FDR < 0.01), BRAF (FDR < 0.01), and KRAS (FDR < 0.01).Conclusions:Tumors from younger and older patients with colorectal cancer demonstrated similar overall rates of genomic alteration. However, differences were noted in several genes relevant to biology and response to therapy. Further study will need to be conducted to determine whether the differences in gene alteration rates can be leveraged to provide personalized therapies for young patients with early-onset sporadic colorectal cancer.

PDF file - 207K, Supplementary Table Genomic Alterations in 64 Cases of Relapsed/Metastatic Non-Micropapillary Urothelial Carcinoma of the Bladder.

PDF file - 187K, Supplementary Table 1: Detailed demographic information of all patients with metastatic breast cancer, including cohorts LM+ and EM+. Supplementary Table 2: ESR1 variant sequence data details. Abbreviations: cvg, coverage, N/A, non-applicable. Supplementary Table 3: List of genes sequenced by captured next generation sequencing. Supplementary figure 1: Genomic profiles of primary and metastatic tumors. Genomic alterations were found in 32 genes in primary and metastatic ER+ breast cancers. Genes are listed from the most frequently altered to least altered gene. Supplementary figure 2: No change in WT and mutant ER activity across a wide range of E2 doses. Luciferase activity in 293T cells after co-transfection of the ERE-TK-Luc reporter vector along with WT-ER, Y537N or D538G and E2 stimulation using doses of E2 ranging from 0.01nM to 100nM or vehicle treatment.

XLSX file - 122K

To examine the overlap of homologous recombination deficiency (HRD) and microsatellite instability high (MSI-H) status, and to dissect driver versus bystander status ofA pan-cancer comprehensive genomic profiling cohort (n = 213,199) was examined for overlap betweenHRD and MSI-H phenotypes were generally mutually exclusive events (MSI-H status and HRD are generally mutually exclusive phenomena across cancer types, but may rarely co-occur, especially in prostate cancer. Although MSI-H samples had a higher

PURPOSE Human epidermal growth factor receptor 2 (HER2) overexpression or amplification (ERBB2amp) are biomarkers for approved anti-HER2 therapies. ERBB2amp may better predict response compared with immunohistochemistry or in situ hybridization, and quantitative copy number (CN) may further stratify patients. We characterized ERBB2amp in advanced gastroesophageal adenocarcinomas (GEA) and hypothesized that increased CN was associated with better outcome to trastuzumab. METHODS Comprehensive genomic profiling, including assessment of ERBB2amp, was performed for 12,905 GEA tissue cases. Clinical outcomes were assessed using a clinicogenomic database linking deidentified electronic health record–derived clinical data to genomic data. Multivariable Cox proportional hazard models were used for real-world progression-free survival (rwPFS) comparisons. RESULTS ERBB2amp (CN ≥ 5) was detected in 15% (1,934 of 12,905) of GEA; median CN 22 (interquartile range 9-73). Median ERBB2 amplicon size was 0.27 megabase (interquartile range 0.13-0.95), and smaller amplicons were associated with higher CN (P < .001). In the clinicogenomic database, of 101 evaluable first-line trastuzumab-treated patients, ERBB2 CN was a significant predictor of rwPFS as a continuous variable (adjusted hazard ratio = 0.73; 95% CI, 0.60 to 0.89; P = .002), whereas ERBB2 CN was not predictive of rwPFS on chemotherapy (adjusted hazard ratio = 0.93; 95% CI, 0.73 to 1.20; P = .59). Among trastuzumab-treated patients, no significant associations with ERBB2 CN were observed for disease site, age, stage at advanced diagnosis, or most selected coalterations. CONCLUSION ERBB2amp was detected in 15% of GEA tissue samples, with significant diversity in ERBB2 CN and amplicon focality. ERBB2 CN was predictive of rwPFS as a continuous variable for patients treated with trastuzumab. Further studies exploring the clinical utility of quantitative ERBB2 CN, particularly in the setting of the evolving anti-HER2 landscape and combination therapies, are warranted., ERBB2 copy number is a quantitative biomarker for outcomes to anti-HER2 therapy in advanced gastroesophageal cancer.

Objective The majority of tumor sequencing currently performed on cancer patients does not include a matched normal control, and in cases where germline testing is performed, it is usually run independently of tumor testing. The rates of concordance between variants identified via germline and tumor testing in this context are poorly understood. We compared tumor and germline sequencing results in patients with breast, ovarian, pancreatic, and prostate cancer who were found to harbor alterations in genes associated with homologous recombination deficiency (HRD) and increased hereditary cancer risk. We then evaluated the potential for a computational somatic-germline-zygosity (SGZ) modeling algorithm to predict germline status based on tumor-only comprehensive genomic profiling (CGP) results. Methods A retrospective chart review was performed using an academic cancer center’s databases of somatic and germline sequencing tests, and concordance between tumor and germline results was assessed. SGZ modeling from tumor-only CGP was compared to germline results to assess this method’s accuracy in determining germline mutation status. Results A total of 115 patients with 146 total alterations were identified. Concordance rates between somatic and germline alterations ranged from 0% to 85.7% depending on the gene and variant classification. After correcting for differences in variant classification and filtering practices, SGZ modeling was found to have 97.2% sensitivity and 90.3% specificity for the prediction of somatic versus germline origin. Conclusions Mutations in HRD genes identified by tumor-only sequencing are frequently germline. Providers should be aware that technical differences related to assay design, variant filtering, and variant classification can contribute to discordance between tumor-only and germline sequencing test results. In addition, SGZ modeling had high predictive power to distinguish between mutations of somatic and germline origin without the need for a matched normal control, and could potentially be considered to inform clinical decision-making.

Background Contemporary evidence on the size of biomarker-defined cancer populations is crucial for clinical and economic healthcare decision makers. Estimates can be derived from real-world data (RWD), but may be affected by biases stemming from differences in observed populations vs. general populations of patients under the purview of decision makers. These differences may be driven by patient or clinical characteristics, as well as differences in assays used to assess biomarker status. This study demonstrates the applicability of an emerging method in survey science (Multilevel Regression and Poststratification (MRP)), which leverages common covariates across source data and larger, more representative set of observations to inform estimates of biomarker prevalence for target populations of interest. Methods In disease-agnostic cohorts of patients with solid-tumor cancers from two, large clinico-genomic cancer databases (AACR GENIE 12.0, and nationwide (US-based) de-identified Flatiron Health - Foundation Medicine Clinico-Genomic Database(CGDB)), we used covariate-adjusted regression (age, sex, race, stage at diagnosis (for CGDB patients), and cancer type) to predict the probability of a patient having an NTRK fusion and/or a BRAF V600E mutation detected in their sequenced cancer tissue. AACR Project GENIE (n = 118,649) is a cancer registry of real-world data assembled through data sharing between 19 international cancer centers. The de-identified data in the CGDB (n = 91,719) originated from approximately 280 US cancer clinics (~800 sites of care).We then implemented post-stratification adjustments (Gelman, 2006; Downes 2018) using the Surveillance, Epidemiology, and End Results (SEER) 17 2022 cancer registry to estimate prevalence of the alterations in the large, population-based registry. Results Prevalence estimates were generally consistent between sources. Adjusted prevalence (%) estimates for NTRK Fusion (AACR: 0.25% (raw), adjusted to 0.21% (0.01%-0.48%) (MRP-adjusted mean % (95% quantile intervals)); CGDB: 0.29, adjusted to 0.26 (0.02-0.63), and for BRAF V600E (AACR: 2.19, adjusted to 1.72 (0.77-2.66); CGDB: 2.44, adjusted to 2.68 (1.50-3.89)) reflected differential patient characteristics (predominantly tumor type) in these sources compared to SEER. MRP also enabled creation, from posterior distributions, of tumor-level estimates, along with credible interval bounds. Conclusion While both clinico-genomic databases offered generally consistent estimates of biomarker prevalence, representativeness methods that are used in the survey literature may be suited for addressing biases in RWD sources to improve biomarker prevalence estimates of target populations of patients with cancer. Citation Format: Jeremy W. Snider, Brennan Beal, Lilia Bouzit, Cheryl Cho-Phan, Leah Comment, Garrett Frampton, Tamara Snow. Using Multilevel Regression and Poststratification (MRP) to inform estimates of biomarker prevalence for target populations of interest using linked clinico-genomic databases. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4257.

People with different ancestries inherit different risks and encounter different environmental exposures resulting in different somatic profiles. A lack of knowledge about ancestry-specific alterations is a major barrier to implementing precision medicine, leading to inequities in genetic testing, targeted treatment and clinical trial design for cancer patients from the underserved populations. However, a limited number of cancer cases from non-European populations have been sequenced in research setting, and paired normal samples are often not collected in routine clinical care. Here, we inferred African (AFR), South Asian (SAS), East Asian (EAS), American (AMR) and European (EUR) ancestry from comprehensive genomic profiling (CGP) of over 200,000 tumors at Foundation Medicine and identified 18717, 8588, 6594 patients with significant proportions of AFR, AMR, EAS ancestry, respectively. Using logistic regressions with age of diagnosis, gender and tumor mutation burden (TMB) as covariates, we identified 165 ancestry-associated genes across 14 common cancer types. We found that in colorectal cancer, KRAS (OR=1.5, FDR corrected p=4x10-44) and APC (OR=1.4, FDR corrected p=1x10-16) mutations were enriched in patients with AFR ancestry, whereas BRAF mutations were depleted in both AFR (OR=0.5, FDR corrected p=5x10-24) and EAS (OR=0.6, FDR corrected p=6x10-5) patients. CDK12 mutations were enriched in both AFR (OR=1.6, FDR corrected p=2x10-4) and EAS (OR=3.1, FDR corrected p=2x10-7) prostate cancer patients. For patients with AMR ancestry, increased mutation frequency was observed in SETD2 in pancreatic cancer (OR=3.4, FDR corrected p=1x10-4), and VHL in renal clear cell carcinoma (OR=1.9, FDR corrected p=2x10-4). For renal cell carcinoma patients with AFR ancestry, mutations in NF2 were enriched (OR=2.5, FDR =8x10-6). In GBM, TERT alterations were associated with EUR ancestry (OR=1.3, FDR corrected p=0.003). Interestingly, TMB-high status was associated with EUR ancestry in melanoma (OR=5.9, p=6x10-36) and anti-correlated with AFR ancestry in endometrial carcinoma (OR=0.7, p=1x10-6). Our large-scale ancestry analysis characterized the somatic landscape of non-European cancer patients. Future directions include quantifying the germline heritability of identified ancestry-associated mutations using a local ancestry risk score (LRS). Citation Format: Jian Carrot-Zhang, Justin New, Amy Xie, Garrett Frampton. Genomic analysis of patients across continental ancestry groups [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C016.

BackgroundNon-small cell lung cancer (NSCLC) patients bearing targetable oncogene alterations typically derive limited benefit from immune checkpoint blockade (ICB), which has been attributed to low tumor mutation burden (TMB) and/or PD-L1 levels. We investigated oncogene-specific differences in these markers and clinical outcome.MethodsThree cohorts of NSCLC patients with oncogene alterations (n=4189 total) were analyzed. Two clinical cohorts of advanced NSCLC patients treated with ICB monotherapy [MD Anderson (MDACC; n=172) and Flatiron Health-Foundation Medicine Clinico-Genomic Database (CGDB; n=894 patients)] were analyzed for clinical outcome. The FMI biomarker cohort (n=4017) was used to assess the association of oncogene alterations with TMB and PD-L1 expression.ResultsHigh PD-L1 expression (PD-L1 ≥50%) rate was 19%–20% in classic EGFR, EGFR exon 20 and HER2-mutant tumors, and 34%–55% in tumors with ALK, BRAF V600E, ROS1, RET, or MET alterations. Compared with KRAS-mutant tumors, BRAF non-V600E group had higher TMB (9.6 vs KRAS 7.8 mutations/Mb, p=0.003), while all other oncogene groups had lower TMB (pEGFR, HER2, ALK, ROS1, RET, or MET alterations had short progression-free survival (PFS; 1.8–3.7 months), while BRAF V600E group was associated with greater clinical benefit from ICB (CGDB cohort: PFS 9.8 months vs KRAS 3.7 months, HR 0.66, p=0.099; MDACC cohort: response rate 62% vs KRAS 24%; PFS 7.4 vs KRAS 2.8 months, HR 0.36, p=0.026). KRAS G12C and non-G12C subgroups had similar clinical benefit from ICB in both cohorts. In a multivariable analysis, BRAF V600E mutation (HR 0.58, p=0.041), PD-L1 expression (HR 0.57, p=0.022), and high TMB (HR 0.66, pConclusionsHigh TMB and PD-L1 expression are predictive for benefit from ICB treatment in oncogene-driven NSCLCs. NSCLC harboring BRAF mutations demonstrated superior benefit from ICB that may be attributed to higher TMB and higher PD-L1 expression in these tumors. Meanwhile EGFR and HER2 mutations and ALK, ROS1, RET, and MET fusions define NSCLC subsets with minimal benefit from ICB despite high PD-L1 expression in NSCLC harboring oncogene fusions. These findings indicate a TMB/PD-L1-independent impact on sensitivity to ICB for certain oncogene alterations.

Introduction Several studies have shown clinical outcomes data that support the use of CD274 (PD-L1) copy-number (CN) gains and/or losses as a biomarker for immune checkpoint inhibitor (ICPI). Here, we present the landscape of CD274 CN changes across a large cohort of solid tumor cases and correlate these with PD-L1 protein expression by immunohistochemistry. Methods We analyzed all cases that underwent comprehensive genomic profiling (CGP) testing at Foundation Medicine between August 2014 and June 2020. CD274 CN changes were correlated with PD-L1 expression in tumor types where there were Food and Drug Administration approved companion diagnostic (CDx) claims and the CDx assay was used to assess PD-L1 expression. Results In all, 244 584 samples representing 290 solid tumor types were included in the study. Overall, 17.6% (42 983/244 584) had CD274 CN gains (>specimen ploidy), 44.6% (108 970/244 584) were CD274 CN neutral, and 37.9% (92 631/244 584) had CD274 CN loss. Using different CN cut offs to define CD274 positivity resulted in different prevalence estimates: ploidy +1, 17.4% (42 636/244 584); ploidy +2, 6.2% (15 183/244 584); ploidy +3, 2.2% (5375/244 584); ploidy +4, 1.1% (2712/244 584); and ploidy +8, 0.2% (434/244 584). The prevalence of CN changes and CN positivity varied based on tumor type. CD274 CN gains were significantly associated with PD-L1 positivity in NSCLC, urothelial carcinoma, breast carcinoma, cervical carcinoma, esophagus squamous cell carcinoma (SCC) and head and neck SCC (ORs 3.3, 3.0, 2.0, 4.5. 3.8, 8.4, 1.4, respectively; p

People with different ancestries inherit different risks and encounter different environmental exposures resulting in different somatic profiles. A lack of knowledge about ancestry-specific alterations is a major barrier to implementing precision medicine, leading to inequities in genetic testing, targeted treatment and clinical trial design for cancer patients from the underserved populations. However, a limited number of cancer cases from non-European populations have been sequenced in research setting, and paired normal samples are often not collected in routine clinical care. Here, we inferred African (AFR), South Asian (SAS), East Asian (EAS), American (AMR) and European (EUR) ancestry from comprehensive genomic profiling (CGP) of over 200,000 tumors and identified 18717, 8588, 6594 patients with significant proportions of AFR, AMR, EAS ancestry, respectively. Using logistic regressions with age of diagnosis, gender and tumor mutation burden (TMB) as covariates, we identified 165 ancestry-associated genes across 14 common cancer types. We used reported race/ethnicity data in the AACR project GENIE cohort for validation. We found that endometrial carcinoma patients with AFR ancestry were enriched with TP53 mutations (OR=2.3, FDR corrected p=5x10-31) but lacked PTEN (OR=0.3, FDR corrected p=2x10-41) and KRAS (OR=0.5, FDR corrected p=8x10-13) mutations. In colorectal cancer, KRAS (OR=1.5, FDR corrected p=4x10-44) and APC (OR=1.4, FDR corrected p=1x10-16) mutations were enriched in patients with AFR ancestry, whereas BRAF mutations were depleted in both AFR (OR=0.5, FDR corrected p=5x10-24) and EAS (OR=0.6, FDR corrected p=6x10-5) patients. CDK12 mutations were enriched in both AFR (OR=1.6, FDR corrected p=2x10-4) and EAS (OR=3.1, FDR corrected p=2x10-7) prostate cancer patients. For patients with AMR ancestry, increased mutation frequency was observed in SETD2 in pancreatic cancer (OR=3.4, FDR corrected p=1x10-4), and VHL in renal clear cell carcinoma (OR=1.9, FDR corrected p=2x10-4). In GBM, TERT alterations were associated with EUR ancestry (OR=1.3, FDR corrected p=0.003). Interestingly, TMB-high status was associated with EUR ancestry in melanoma (OR=5.9, p=6x10-36) and anti-correlated with AFR ancestry in endometrial carcinoma (OR=0.7, p=1x10-6). Our large-scale ancestry analysis characterized the somatic landscape of non-European cancer patients. Future directions include quantifying the germline heritability of identified ancestry-associated mutations using a local ancestry risk score (LRS) and investigating ancestral effects on cancer prognosis and outcome using the GENIE cohort. Citation Format: Jian Carrot-Zhang, Justin Newberg, Garrett Frampton, Rameen Beroukhim. Leveraging existing data to identify ancestry-associated features across multiple cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1166.

Background: PARP inhibitors (PARPi) are approved for multiple indications with ongoing trials to explore broader utility. However, identifying the right patients for these therapies across multiple disease types remains a challenge. In ovarian cancer, genomic-scar based measures for homologous recombination deficiency (HRD) are approved diagnostics (genome-wide LOH [gLOH] and genomic instability score [GIS]); however, broader utility has not been established. Methods: A pan-cancer genomic profiling dataset (n = 202,472; Foundation Medicine, Cambridge, MA) was split 70:30 for training and validation of an HRD signature using an XGB machine learning model (mlHRD). A broad set of copy number (Macintyre 2018) and indel features (Alexandrov 2020) were used to identify signatures of HRD. gLOH (Coleman 2017) and GIS (Timms 2014) were calculated using copy number profiles. Biallelic alterations were predicted using a computational zygosity algorithm (Sun, 2018). The nationwide, de-identified Flatiron Health-Foundation Medicine ovarian and prostate clinico-genomic databases (FH-FMI CGDB) were utilized for outcomes analysis. The de-identified data originated from approximately 280 US cancer clinics (~800 sites of care). Time to therapy discontinuation (TTD) was estimated with Kaplan-Meier analysis. Hazard ratios were calculated using unadjusted Cox proportional Hazard models. Results: We developed an algorithm to predict HRD status using indel and copy number features (see methods). Across the pan-cancer dataset, the rate of mlHRD was 6.4% with the highest frequency in fallopian tube (30%), ovarian (30%), peritoneal (23%), breast (16%), and prostate cancers (15%). Sensitivity to detect biallelic BRCA1/2 alterations was high across tumors [ovary (93%), prostate (87%), breast (85%), pancreas (80%)]. Beyond BRCA1/2, mlHRD positivity was associated with biallelic alterations in RAD51D (OR = 24, p16% (HR = 0.55 [0.38-0.79], p = 0.001) and GIS >42 (HR = 0.59 [0.41-0.86], p = 0.006). For 62 patients with prostate cancer treated with PARPi (mlHRD positive = 27; negative = 35), mlHRD was associated with prolonged TTD on PARPi (median 6.8 mo v 3.4 mo; HR = 0.56 [0.30-1.03], p = 0.064), trending more predictive than gLOH >8.29% (Sokol 2020) and GIS >42 (HR = 0.64 [0.29-1.40] and 0.80 [0.37-1.73], respectively; p>0.05). Conclusion: These findings suggest that HRD is associated with genomic scarring beyond ovarian cancer. Additional retrospective and prospective analyses in clinical datasets are needed to explore the utility of this signature. Citation Format: Emmanuel Antonarakis, Jay Moore, Dexter Jin, Tim Chen, Justin Newberg, Zoe Fleischmann, Karthikeyan Murugesan, Garrett Frampton, David Fabrizio, Russell Madison, Ethan Sokol. Development of a pan-cancer algorithm to predict homologous recombination deficiency and sensitivity to PARPi therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1249.

Loss of function mutations in homologous recombination (HR) repair genes predispose individuals to cancer due to the genomic instability brought about by the inability to properly repair DNA. These alterations may also identify patients eligible for treatment with poly (ADP-ribose) polymerase (PARP) inhibitors and platinum drugs that exploit synthetic lethality; however, resistance eventually occurs. This resistance is largely the result of reversion mutations, which restore the DNA repair function of mutated HR genes. We employed a computational approach to identify patients with breast, ovarian, pancreas, or prostate cancer who underwent comprehensive genomic profiling (CGP; Foundation Medicine, Inc.) and had reversion mutations in the BRCA1, BRCA2, PALB2, RAD51C, or RAD51D genes. Reversion mutations were identified in six different categories: 1) missense mutations that occur at the same amino acid position as a deleterious alteration, 2) non-frameshift deletion mutations that encompass a deleterious alteration, 3) frameshift mutations that restore the open reading frame of another frameshift mutation, 4) splice-site mutations that occur at the same exon as a deleterious alteration, 5) copy number losses that remove a deleterious alteration, and 6) intragenic deletions that lead to loss of deleterious mutation. Using our computational approach, we identified 483 patients who 1,112 reversion mutation pairs in both solid tissue- and liquid biopsy-derived samples. The most frequently observed category was a non-frameshift deletion of a deleterious mutation. Overall, a greater number of reversion mutations were found in liquid biopsy samples. BRCA2 was the most frequently reverted gene followed by BRCA1, PALB2, RAD51D, and RAD51C. BRCA1-mutated samples had up to six reversion mutations, and for BRCA2, we observed as many as 228 putative reversion pairs in one sample. PALB2, RAD51C, and RAD51D had no more than two reversion mutations. We further examined co-occurring alterations and found correlations with genes in multiple signaling pathways including the MYC signaling pathway, which contained more mutations in reversion-positive samples. Lastly, we explored real-world longitudinal data from reversion-positive samples and found that the presence of a reversion mutation was significantly associated with lower overall survival for breast, ovarian, and prostate cancer patients. In summary, we characterized the landscape of reversion mutations in patients who underwent tissue or liquid biopsy-based CGP during clinical cancer treatment. Our data provide a better perspective for the identification and treatment of cancers involving a reversion mechanism. Citation Format: Shannon T. Bailey, Meijuan Li, James Thornton, Lei Yang, Chenming Cui, Mark Hartman, Garrett Frampton, Brennan Decker, Christine Vietz. Comprehensive genomic profiling of tissue and liquid biopsies reveals the landscape of reversion mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 798.

Background: NCCN guidelines for first-line treatment of patients with metastatic pancreatic cancer includes either FOLFIRINOX or gemcitabine plus paclitaxel; however, these two treatment regimens have not been compared in a randomized clinical trial. In this study, we investigated genomic predictors of treatment response to guide this treatment decision. Methods: We selected 1,250 patients with metastatic pancreatic cancer who were treated with first-line FOLFIRINOX (FOLF, n = 588) or gemcitabine plus paclitaxel (G+P, n = 662) within the nationwide de-identified Flatiron Health-Foundation Medicine clinico-genomic database (CGDB). The de-identified data originated from approximately 280 US cancer clinics (~800 sites of care). Comprehensive genomic profiling was performed by Foundation Medicine on tumor samples from each patient as part of the standard of care. Gain/loss status as well as loss of heterozygosity (LOH) status of each chromosome arm was assessed using a custom research-use only algorithm that utilizes copy number model calls for each segment and SNP MAF information from sequencing data. Univariable Cox proportional hazards regression was used to identify chromosome arm-level aneuploidies associated with survival in patients treated with first-line FOLF or G+P. In each treatment cohort, a multivariable Cox model was built using the bidirectional stepwise regression procedure to select aneuploidy features associated with survival. A binary risk score was calculated based on the linear predictor of the multivariable Cox model and categorized as high vs low using a median threshold. Results: Among the FOLF-treated cohort, we identified six aneuploidy features associated with survival (Bonferroni adjusted p < 0.05). FOLF-treated patients with a low FOLF risk score had better survival compared to those with a high FOLF risk score (HR: 0.46, 95%CI: 0.34-0.61, p = Conclusions: In metastatic pancreatic cancer, we found different chromosome arm-level aneuploidies were associated with survival for FOLF and G+P regimens which suggests an aneuploidy-based risk score may have utility in choosing first-line treatment. Citation Format: Kuei-Ting Chen, Radwa Sharaf, Garrett Frampton, Lee Albacker, Ericka Ebot. Identification of aneuploidy biomarkers associated with response to first-line treatment of metastatic pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1243.

BACKGROUND In contrast to lung cancer, few precision treatments are available for colorectal cancer (CRC). One rapidly emerging treatment target in CRC is ERBB2 (human epidermal growth factor receptor 2 [HER2]). Oncogenic alterations in HER2, or its dimerization partner HER3, can underlie sensitivity to HER2-targeted therapies. METHODS In this study, 8887 CRC cases were evaluated by comprehensive genomic profiling for genomic alterations in 315 cancer-related genes, tumor mutational burden, and microsatellite instability. This cohort included both colonic (7599 cases; 85.5%) and rectal (1288 cases; 14.5%) adenocarcinomas. RESULTS A total of 569 mCRCs were positive for ERBB2 (429 cases; 4.8%) and/or ERBB3 (148 cases; 1.7%) and featured ERBB amplification, short variant alterations, or a combination of the 2. High tumor mutational burden (≥20 mutations/Mb) was significantly more common in ERBB-mutated samples, and ERBB3-mutated CRCs were significantly more likely to have high microsatellite instability (P

BACKGROUND: Small cell lung cancer (SCLC) has the strongest association with smoking among lung cancers. The characteristics of never smokers with SCLC is not known. RESEARCH QUESTION: Are the clinical characteristics, prognostic factors, survival, genomic alterations, and tumor mutational burdens of SCLC in patients who have never smoked different from those who have smoked? STUDY DESIGN AND METHODS: A retrospective multicenter cohort study of patients with clinician-confirmed SCLC was performed with the use of a longitudinal and nationally representative electronic medical records database. Smoking history was assessed through technology-enabled abstraction and confirmed for never smokers via chart review. Genomic characteristics of never smoker patients with SCLC were examined with the use of a next-generation sequencing-based gene panel and whole exome sequencing. RESULTS: One hundred of 5,632 patients (1.8%) with SCLC were never smokers. Relative to smokers, never smokers were more likely to be female (66.0% vs 52.4%; P = .009) and present with extensive stage (70.0% vs 62.2%; P = .028). Never smokers had a higher proportion of patients in age groups 35 to 49 years (7.0% vs 3.0%; P = .006) and ≥80 years (17.0% vs 8.2%; P = .006). Known risk factors for lung cancer were found in

Despite a therapeutic paradigm shift into targeted-driven medicinal approaches, resistance to therapy remains a hallmark of lung cancer, driven by biological and molecular diversity. Using genomic and expression data from advanced non-small cell lung cancer (NSCLC) patients enrolled in the BATTLE-2 clinical trial, we identified RICTOR alterations in a subset of lung adenocarcinomas and found RICTOR expression to carry worse overall survival. RICTOR-altered cohort was significantly enriched in KRAS/MAPK axis mutations, suggesting a co-oncogenic driver role in these molecular settings. Using NSCLC cell lines, we showed that, distinctly in KRAS mutant backgrounds, RICTOR blockade impairs malignant properties and generates a compensatory enhanced activation of the MAPK pathway, exposing a unique therapeutic vulnerability. In vitro and in vivo concomitant pharmacologic inhibition of mTORC1/2 and MEK1/2 resulted in synergistic responses of anti-tumor effects. Our study provides evidence of a distinctive therapeutic opportunity in a subset of NSCLC carrying concomitant RICTOR/KRAS alterations.

Background Genomic fusions of the anaplastic lymphoma kinase gene (ALK) are a well-established therapy target in non-small cell lung cancer (NSCLC). From a survey of 114,200 clinical cases, we determined the prevalence of ALK rearrangements (rALK) in non-NSCLC tumors and report their responsiveness to therapies targeting ALK. Materials and Methods Comprehensive genomic profiling of 114,200 relapsed and metastatic malignancies, including both solid tumors and hematolymphoid cancers, was performed using a hybrid-capture, adaptor ligation-based next-generation sequencing assay. Results Of 114,200 clinical samples, 21,522 (18.8%) were NSCLC and 92,678 (81.2%) were other tumor types. Of the 876 (0.8%) cases with ALK fusions (fALK) or rALK, 675 (77.1%) were NSCLC and 201 (22.9%) were other tumor types. ALK fusions were significantly more frequent in NSCLC (3.1%) than non-NSCLC (0.2%; p Conclusion ALK rearrangements can be identified in a wide variety of epithelial and mesenchymal malignancies beyond NSCLC. Anti-ALK therapies can be effective in non-NSCLC tumors driven by fALK, and further study of therapies targeting ALK in clinical trials involving a wider variety of cancer types appears warranted.

BACKGROUND In contrast to lung cancer, few precision treatments are available for colorectal cancer (CRC). One rapidly emerging treatment target in CRC is ERBB2 (human epidermal growth factor receptor 2 [HER2]). Oncogenic alterations in HER2, or its dimerization partner HER3, can underlie sensitivity to HER2‐targeted therapies. METHODS In this study, 8887 CRC cases were evaluated by comprehensive genomic profiling for genomic alterations in 315 cancer‐related genes, tumor mutational burden, and microsatellite instability. This cohort included both colonic (7599 cases; 85.5%) and rectal (1288 cases; 14.5%) adenocarcinomas. RESULTS A total of 569 mCRCs were positive for ERBB2 (429 cases; 4.8%) and/or ERBB3 (148 cases; 1.7%) and featured ERBB amplification, short variant alterations, or a combination of the 2. High tumor mutational burden (≥20 mutations/Mb) was significantly more common in ERBB‐mutated samples, and ERBB3‐mutated CRCs were significantly more likely to have high microsatellite instability (P, Greater than 6% of colorectal cancer cases harbor activating alterations in ERBB2 or ERBB3, representing a significant population of patients who may benefit from therapies targeting human epidermal growth factor receptor 2 (HER2) and the ERBB pathway. The success of anti‐HER2 therapies in ongoing clinical trials is a promising development for patients with colorectal cancer.

Background. Cancer gene mutations exhibit mutation patterns of prevalence that vary across different ancestry groups. For example, EGFR variants are more frequent in non-small cell lung cancer among people with Asian ancestry, and KRAS variants are observed more frequently in colorectal cancer among patients with African American ancestry. Additionally, many histological subtypes of cancers demonstrate differences in prevalence between people of different ancestry. However, many cancer studies lack the statistical power to identify such nuances. The large cohort of patients who have undergone comprehensive cancer genomic profiling at Foundation Medicine may provide a useful starting point for characterizing these mutation patterns across ancestry groups. Methods. To establish the ancestry on de-identified samples, we superimposed SNPs targeted by each of our comprehensive genomic profiling tests (FoundationOne, FoundationOne CDx, FoundationOne Heme) with Phase 3 1000 Genomes data. Using an established approach, we projected the SNPs down to the top five principal components and used random forest ensemble learning to train a classifier on each bait set. 10-fold cross-validation indicates this approach performs with 98-99% precision and recall for the different genomic profiling tests. Results. Ancestry calls were made on over 170,000 de-identified samples consented for research. Initial analyses indicated that classification of American samples was not as robust as other groups. To address this, we trained classifiers on a per-chromosome basis, and re-assigned samples which exhibited less than 80% consensus across chromosomes to an admixture group. Overall prevalence of patient ancestry in the dataset is 75.9% European, 8.3% African, 4.7% East Asian, 0.8% South Asian, and 0.8% American, and 9.5% admixed. From the resulting data, we summarize cancer types that are well-represented across populations, identifying at least 28 tumor types for which we likely have power to identify ancestry-dependent somatic mutations. Discussion. The dataset described contains a previously unavailable set of cancer types to be mined for ancestry-dependent cancer-driving alterations. Those results will be presented. The ancestry classification approach described in this work can be applied to a range of genomic profiling tests, and refinements on this approach can be integrated into clinical trials and ultimately clinical care to better elucidate varied biologic behavior across advanced cancer. Citation Format: Justin Newberg, Caitlin Connelly, Garrett Frampton. Determining patient ancestry based on targeted tumor comprehensive genomic profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1599.

Background: Micropapillary urothelial carcinoma of the urinary bladder (MPUC) encompasses approximately 5% of all bladder cancers and comprises approximately 3,000 to 4,000 new cases diagnosed each year in the US. MPUUPC is a highly aggressive form of bladder cancer associated with distant metastases and shortened patient survival. Once MPUC recurs progresses from loco-regional and progresses to metastatic disease, there is no currently no recognized effective treatment. We conducted a genomic analysis of a series of patients with MPUC to characterize the genomic landscape of MUPUC and identify targeted treatment options for patients with this lethal form of urologic malignancy. Methods: DNA was extracted from 40 microns of formalin-fixed paraffin embedded (FFPE) sections from 15 MPUC and 64 non-MPUC. Sequencing to high, uniform coverage was performed on hybridization-captured, adaptor ligated, hybridization capturedion based libraries for for 3,230 exons of 182 cancer-related genes plus 37 introns offrom 14 genes frequently rearranged in cancer to high, uniform coverage and evaluated for all classes of genomic alteration. Results: Extracellular domain mutations of ERBB2 were identified in 6/15 (40%) MPUC including: S310F (4 cases), S310Y (1 case) and R157W (1 case). All 6 cases of MPUC with ERBB2 mutation were negative for ERBB2 amplification which was confirmed by immunohistochemistry (IHC) in the 3 cases where additional tissue was available. In contrast, 6/64 (9.4%) of non-MPUC harbored an ERBB2 alteration: base substitutions (3 cases), amplifications (2 cases) and gene fusion (1 case), which is higher than the 2/159 (1.3%) of protein changing ERBB2 mutations reported in urinary tract cancer in COSMIC. The enrichment of ERBB2 alterations in MPUC compared to non-MPUC is significant inbetween this series (p < 0.0084) and for all types of urinary tract cancer in COSMIC (p < 0.001). All 9 ERBB2 WT MPUC cases harbored at least 1 actionable alteration, including alterations in AKT1, AKT2, CCND1, EGFR, PIK3CA, PIK3R1 and RAF1. Conclusions: Comprehensive genomic profiling of MPUC revealed actionable genomic alterations in all 15 specimens including a high incidence of ERBB2 extracellular domain mutation. We conclude that genomic profiling of MUPUC samples can reveal actionable alterations that can inform potential targeted treatment decisions for the majority of patients. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B122. Citation Format: Kai Wang, Jeff S. Ross, Laurie M. Gay, Rami N. Al-Rohil, Tipu Nazeer, Christine E. Sheehan, Timothy A. Jennings, Geoff A. Otto, Amy Donahue, Jie He, Gary Palmer, Siraj Ali, Michelle Nahas, Geneva Young, Elaine LaBrecque, Garrett Frampton, Rachel Erlich, John A. Curran, Tina Brennan, Sean R. Downing, Roman Yelensky, Doron Lipson, Matthew J. Hawryluk, Vincent A. Miller, Philip J. Stephens. A high frequency of activating extracellular domain ERBB2 (HER2) mutation in micropapillary urothelial carcinoma. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B122.

Background: Recent advances in our understanding of the mutational landscape of prostate cancer (PCa) have occurred through sequencing of primary prostate tumors. Highly aggressive PCa most often does not come to surgery preventing access to frozen sample for high-throughput studies. The purpose of this study is to determine the spectrum of mutations in a subgroup of highly aggressive PCa and to evaluate for targetable molecular alterations using a novel mutation analysis platform from archival formalin-fixed paraffin embedded (FFPE) samples. Methods: 21 PCa (of which 9 were Gleason 5, 8 metastatic), 18 Neuroendocrine PCa (NEPC), and 18 benign FFPE prostate samples from 35 unique cases were evaluated and 77 high-density foci were selected for DNA extraction and sequencing library construction. Hybridization-based capture of 3230 exons and 37 intronic intervals of 189 cancer-related genes was performed, followed by deep, massively-parallel sequencing. Sequence data were analyzed for single nucleotide variants (sub), small insertions and deletions (indels), significant copy number changes, and selected re-arrangements/fusion genes. Results: 5/8 biopsies and 62/65 (overall 93%) of prostate or metastatic foci yielded sufficient DNA (≥50 ng) for analysis from 40μ of FFPE tissue. Average uniquely-mapping sequence coverage was 885x. 133 mutations were identified in 30 genes with 58/67 samples containing at least one mutation. TMPRSS2-ERG fusion was present in 31% of cases. Recurrent high confidence cancer alterations included: gain of MYC (9%), gain or sub/indel of AR (43%), deletion or sub/indel of PTEN (23%), RB1 (20%), BRCA2 (11%), and sub/indel of TP53 (40%), CTNNB1 (11%), PIK3CA (6%), ATM (6%). Several novel mutations were identified, including in BRAF and BRCA2. AR alterations were more common in PCa compared to NEPC, and were present even in clinically localized PCa. There was high concordance between NEPC and PCa foci in mixed tumors, as well as between primary tumor and metastases. Conclusions: This study demonstrates feasibility of in-depth DNA analysis using FFPE tissue, and even biopsy material. The spectrum of driver mutations observed highlights potential value of comprehensive genomic profiling for targeted therapy selection in clinical care. These analyses have laid the foundation for ongoing comparison with indolent PCa, and have identified potential new drug targets (e.g., PARP inhibitors for ATM and BRCA2 mutations), with a goal towards better defining biomarkers that distinguish aggressive and indolent PCa and designing more effective treatment approaches for patients with lethal PCa. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5074. doi:1538-7445.AM2012-5074