Quintanilha, Júlia C.F.

PURPOSE We sought to characterize outcome associations of poly ADP-ribose polymerase inhibitors (PARPi) in patients with ovarian cancer (OVCA) whose cancers contain homozygous loss (deletions) of homologous recombination repair (HRR) pathway genes, an alteration class not uniformly reported on clinical testing and not susceptible to acquired resistance via secondary reversion mutations. METHODS This study used US-based deidentified Flatiron Health-Foundation Medicine OVCA Clinico-Genomic Database. Patients with advanced OVCA and genomic profiling by Foundation Medicine were assembled into cohorts evaluating PARPi monotherapy use, and separately, PARPi maintenance therapy use, with outcomes associated with HRR gene alterations: BRCA1 / 2 , PALB2 , RAD51B/C/D , BARD1 , and BRIP1 . RESULTS 1.5% (82/5,404) had HRR gene homozygous loss, with BRCA1 and BRCA2 loss being most common. Among all OVCAs with BRCA1/2 alterations, 7.5% (63/836) were homozygous losses. Most BRCA1 (34/38, 89%) and BRCA2 (18/25, 72%) homozygous losses were intragenic, with breakpoints not spanning entire gene. Maintenance cohort: 22 patients had HRR gene homozygous loss, with strongly improved progression-free survival (PFS) for PARPi versus no PARPi use (HR, 0.06, 95% CI, 0.01 to 0.37). Monotherapy cohort: patients without HRR alterations (n = 198), HRR mutations or rearrangements (n = 93), and HRR homozygous loss (n = 8) had median PFS of 4.9, 10.6, and 25.4 months, and median overall survival of 18.5, 22.5, and 51.8 months, respectively. CONCLUSION We observe durable PARPi effectiveness for patients with OVCA and HRR gene homozygous loss in routine practice. We demonstrate the importance of detecting and reporting homozygous loss in HRR genes, an aspect not standard to all sequencing assays.

98 Background: Circulating tumor DNA (ctDNA) monitoring provides an additional clinical tool for assessing treatment response and emerging resistance. We evaluated the real-world (RW) use and results of FoundationOne Monitor (F1Monitor), a tissue-free ctDNA monitoring assay, in patients (pts) with prostate cancer (PCa). Methods: The clinical laboratory developed test, F1Monitor, was available to physicians in a limited pilot with full discretion of test eligibility, timing, and frequency. Therapy type was a non-mandatory field on the order form. CtDNA was detected and quantified by ctDNA tumor fraction (TF); variants were tracked with variant allele frequency (VAF), and the origin [tumor somatic (TS), germline, or clonal hematopoiesis (CH)] was predicted algorithmically. Results: F1Monitor was ordered by 28 physicians for 215 pts with PCa. Therapy data were known for 156 pts: ADT+ androgen receptor pathway inhibitor (ARPI, N = 69/156 pts, 44%), ADT alone (N = 32, 21%), ADT + chemotherapy (chemo, N = 20,13%), ADT + radioligand therapy (RLT, N = 17, 11%), and others (N = 18). Median follow-up was 188 days. Longitudinal testing (≥2 tests) occurred in 64 pts, often (N = 37) when the first test was ctDNA TF positive (+). Median cadence for serial testing (≥3 tests, N = 31) was 42 days (IQR: 35, 59). ctDNA TF was + at any timepoint in 50% (107/215) of pts overall and 53% (82/156) of pts known to be on therapy, trending higher in pts on ADT+chemo (80%) and ADT+RLT (65%). Median and maximum ctDNA TF values were 11% (IQR: 0.9,37.8%) and 89% respectively. Lowest ctDNA TF and reportable TS VAF quantified were 0.13% and 0.04%, respectively. ctDNA TF longitudinal changes were observed in 67% (43/64) of pts: 92% of pts on ADT+chemo, 69% on ADT+RLT, 59% on ADT+ARPI, and 38% of pts on ADT alone. Among pts with ≥2 tests, 39% (25/64) had ctDNA TF increase, including 6/27 (22%) pts that were ctDNA TF negative (-) on the first test. Of pts with ≥2 tests and any ctDNA TF+ result, 35% cleared ctDNA TF in later tests. 33% of pts were persistently ctDNA TF -. Each test reported an average of 5 alterations: ~2 TS short variants, copy number variants, or rearrangements, and ~2 predicted CH variants. HRR variants were detected in 37% (80/215) of pts (31 with ≥2 tests) : persistent in 20 pts, cleared in 7, and newly emerging in 14. At least 50% of alterations in CHEK2 and ATM were predicted CH. Alterations in PI3K pathway genes were detected in 20% (43/215) of pts: (16 with ≥2 tests) persistent in 6 pts, cleared in 5, and newly emerging in 5. Conclusions: In this RW pilot of tissue-free ctDNA monitoring in PCa, F1Monitor demonstrated high sensitivity in clinical practice, detecting ctDNA TF as low as 0.13% and TS VAF as low as 0.04% while distinguishing tumor-derived from predicted CH variants. Importantly, ctDNA TF was + in 53% of pts while on therapy with observed longitudinal changes for 67% of pts, supporting potential utility of ctDNA for monitoring treatment response and emerging resistance.

5064 Background: FoundationOneCDx (F1CDx) supports two FDA-approved biomarkers to guide treatment decisions for ICI for patients with mCRPC: MSI status and TMB. MSI-H and TMB-H (10+ mut/MB) have strongly overlapping prevalence. We sought to better characterize ICI outcome associations of TMB-H / non-MSI-H population and relative effectiveness of taxanes & ICI among patients who received these agents in sequence. Methods: Following a prespecified analysis plan, this study used the nationwide (US-based) de-identified Flatiron Health-Foundation Medicine mCRPC clinico-genomic database (FH-FMI CGDB), with data originating from ~280 US cancer clinics (~800 sites of care). Inclusion criteria included patients with mCRPC treated with single-agent anti-PD(L)1 therapy in the FH network between 1/1/2011 - 3/30/2024. This study used the MSI and TMB algorithms from the tissue based F1CDx. Time to next treatment (TTNT) and OS were assessed with Kaplan-Meier plots and in multivariable Cox models adjusted for ECOG performance score, socioeconomic status, prior treatment history, and baseline PSA. Among patients who received taxanes in a prior line of therapy, the effectiveness (TTNT1 vs. TTNT2) of taxane and ICI were compared. Results: Among 2995 prostate cancer tissue specimens in the database, 95 (3.1%) were MSI-H and 142 (4.7%) were TMB-H. 94 (3.1%) were MSI-H & TMB-H, 1 was MSI-H & TMB-L, and 48 (1.6%) were TMB-H & not MSI-H. Among these, 84 patients with mCRPC were treated with ICI and met inclusion criteria, including MSI-H & TMB-H (n = 30), non-MSI-H & TMB-H (n = 8), and non-MSI-H and TMB-L (n = 46). The respective median TTNT on ICI was 8.0 vs. 9.6 vs. 3 months. The respective median OS from initiation of ICI was 10.9 vs. not reached vs. 4.4 months. In multivariable models evaluating ICI only, compared to non-MSI-H & TMB-L, the MSI-H & TMB-H group had more favorable TTNT (HR: 0.20, 95%CI: 0.10 – 0.41, p < 0.001) and OS (HR: 0.33, 95%CI: 0.16 – 0.70, p = 0.004), and the non-MSI-H & TMB-H group also had more favorable TTNT (HR: 0.13, 95%CI: 0.04 – 0.45, p = 0.002) and OS (HR: 0.20, 95%CI: 0.05 – 0.75, p = 0.017). 50 of the 84 (60%) patients treated with ICI had prior mCRPC taxane treatment. Better TTNT2 on subsequent ICI vs. prior taxane was observed for MSI-H (HR: 0.49, 95%CI: 0.23 – 1.01, p = 0.051) and TMB-H (0.54, 95%CI: 0.30 – 0.98, p = 0.044), but the opposite was true for non-MSI-H and TMB-L subgroups, with significant treatment interactions for each (p = 0.0018, p = 0.00052). Conclusions: TMB-H (4.7%) is more prevalent than MSI-H (3.1%) by F1CDx in mCRPC. Non-MSI-H / TMB-H (1.6%) in the routine practice cohort have similar outcome associations on ICI to MSI-H. Both MSI-H and TMB-H by F1CDx are predictive of differential benefit for ICI vs. taxanes in later mCRPC treatment lines.

PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is largely considered a nonimmunogenic malignancy; however, approximately 1%, of patients may have tumors with deficient mismatch repair, high microsatellite instability, or high tumor mutational burden (TMB ≥10 mutations/Mb), which may be predictive of response to immune checkpoint inhibitor (ICI) therapy. We sought to analyze outcomes of patients with high-TMB and pathogenic genomic alterations observed in this population. METHODS This study included patients with PDAC who underwent comprehensive genomic profiling (CGP) at Foundation Medicine (Cambridge, MA). Clinical data were obtained from a US-wide real-world clinicogenomic pancreatic database. We report genomic alterations in those with high and low TMB, and compare outcomes on the basis of receipt of single-agent ICI or therapy regimens not containing ICI. RESULTS We evaluated 21,932 patients with PDAC who had tissue CGP data available, including 21,639 (98.7%) with low-TMB and 293 (1.3%) with high-TMB. Among patients with high-TMB, a greater number of alterations were observed in BRCA2, BRAF, PALB2, and genes of the mismatch repair pathway, whereas fewer alterations were observed in KRAS. Among patients who received an ICI (n = 51), those with high-TMB had more favorable median overall survival when compared with the low-TMB subset (25.7 v 5.2 months; hazard ratio, 0.32; 95% CI, 0.11 to 0.91; P = .034). CONCLUSION Longer survival was observed in patients with high-TMB receiving ICI compared with those with low-TMB. This supports the role of high-TMB as a predictive biomarker for efficacy of ICI therapy in PDAC. Additionally, we report higher rates of BRAF and BRCA2 mutations and lower rates of KRAS mutation among patients with PDAC and high-TMB, which to our knowledge, is a novel finding.

4146 Background: Currently, ICI therapy is recommended for patients with metastatic PDAC whose tumors exhibit dMMR, MSI-H, or high TMB (≥10 mutations/Mb). However, due to the low prevalence of high TMB in PDAC (~1%), few studies have evaluated the role of ICI therapy in this subpopulation. This study aimed to compare GA between PDAC patients with high TMB and low TMB ( < 10 mutations/Mb) and to evaluate the effectiveness of ICIs in real-world PDAC patients by TMB status. Methods: This study included PDAC patients who underwent genomic testing using Foundation Medicine tissue comprehensive genomic profiling (CGP) assays. GA were compared between tissue specimens with high and low TMB by chi-squared, adjusted for multiple comparisons. Patient clinical data was obtained by the US-wide de-identified Flatiron Health and Foundation Medicine real-world clinicogenomic pancreatic database (CGDB), originated from ~280 US cancer clinics between 01/2011 and 09/2022. Real-world overall survival (OS) and time to treatment discontinuation (TTD) were compared between patients receiving an ICI (high TMB versus low TMB) and between patients with high TMB (ICI versus other therapies) by Cox models. Results: We included 21,932 patients with PDAC with tissue CGP data available; 98.7% with low TMB and 1.3% with high TMB. Among actionable alterations, patients with high TMB had higher prevalence of mutations in BRCA2 (p < 0.0001), BRAF (p < 0.0001), PALB2 (p < 0.0001), and genes of the mismatch repair pathway ( MSH2, MSH6, MLH1, and PMS2, p < 0.0001), but lower prevalence of KRAS mutations (p < 0.0001). The most common KRAS mutation in both groups of patients was G12D. In CGDB, 51 patients received an ICI (10 with high TMB and 41 with low TMB) and 17 patients with high TMB received other therapies. Among patients receiving an ICI, those with high TMB had more favorable median OS compared to those with low TMB (25.7 versus 5.2 months, hazard ratio (HR) 0.27, 95% confidence interval (CI) 0.09 - 0.76, p = 0.01) and median TTD (20.7 versus 3.0 months, HR 0.33, 95% CI 0.13 - 0.82, p = 0.02). Among patients with high TMB, those receiving an ICI had more favorable OS compared to those receiving other therapies (25.7 versus 6.6 months, HR 0.31, 95% CI 0.10-0.96, p = 0.043), nominally favoring ICI use in this small cohort (n = 10 versus 17). Conclusions: There is no randomized clinical trial evaluating ICI versus other therapies in PDAC. To our knowledge, this is the largest cohort to date comparing ICI effectiveness in PDAC. We observed more favorable OS among PDAC patients with high TMB receiving ICI versus those with low TMB who received an ICI and more favorable to those with high TMB receiving other therapies. This study supports the FDA-approved use of ICIs in patients with PDAC and high TMB and demonstrates the importance of TMB assessment for patients with PDAC.

Hypertension is a common bevacizumab‐induced toxicity. No markers are available to predict patients at risk of developing hypertension. We hypothesized that genetic risk of essential hypertension, as measured by a blood pressure polygenic risk score (PRS), would be associated with risk of severe bevacizumab‐induced hypertension. PRSs were calculated for 1,027 bevacizumab‐treated patients of European descent with cancer from four clinical trials (Alliance for Clinical Trials in Oncology (Alliance) / Cancer and Leukemia Group B (CALGB) 80303, 40503, 90401, 40502) using summary systolic blood pressure (SBP) and diastolic blood pressure (DBP) genome‐wide association results obtained from 757,601 individuals of European descent. The association between PRS and grade 3 bevacizumab‐induced hypertension (Common Toxicity Criteria for Adverse Events version 3) in each trial was performed by multivariable logistic regression. Fixed‐effect meta‐analyses odds ratios (ORs) per standard deviation (SD) of the association of PRS (quantitative) and hypertension across trials were estimated by inverse‐variance weighting. PRSs were additionally stratified into quintiles, with the bottom quintile as the referent group. The OR of the association between hypertension and each quintile vs. the referent group was determined by logistic regression. The most significant PRS (quantitative)‐hypertension association included up to 67 single‐nucleotide variants (SNPs) associated with SBP (P = 0.0077, OR per SD = 1.31, 95% confidence interval (CI), 1.07–1.60), and up to 53 SNPs associated with DBP (P = 0.0209, OR per SD = 1.27, 95% CI, 1.04–1.56). Patients in the top quintile had a higher risk of developing bevacizumab‐induced hypertension compared with patients in the bottom quintile using SNPs associated with SBP (P = 4.75 × 10−4, OR = 3.72, 95% CI, 1.84–8.16) and DBP (P = 0.076, OR = 1.83, 95% CI, 0.95–3.64). Genetic variants associated with essential hypertension, mainly SBP, increase the risk of severe bevacizumab‐induced hypertension.

3030 Background: Diarrhea, HFS, and hypertension are common toxicities of sorafenib. No markers are validated to predict patients at risk of these toxicities. This study aimed to identify genetic predictors of sorafenib-induced toxicities. Methods: A two-step, discovery-validation approach was used. The discovery set included 140 renal cell carcinoma patients from the TARGET study treated with sorafenib (400 mg twice daily) and genotyped for 1040 single-nucleotide polymorphisms (SNPs) in 56 genes. The three most statistically significant SNPs associated with grade ≥2 composite toxicity (either hypertension, diarrhea, HFS, or other skin toxicities, CTCAE v.3.0) were tested for association with grade 3 composite toxicity (either hypertension, diarrhea, or HFS, CTCAE v.4.0) in a validation set of 240 hepatocellular carcinoma patients from Alliance/CALGB 80802 treated with sorafenib (400 mg twice daily) alone or with doxorubicin. Associations between SNPs and composite toxicity was performed by logistic regression, with adjusting covariates (age, gender, race, and treatment arm, the latter two covariates for the validation set only). A meta-analysis odds ratio (OR) of each SNP-grade 3 toxicity association between the discovery and validation sets was obtained by inverse variance to point toward effects specific to a type of toxicity. Results: In the discovery set, the top three SNPs associated with grade ≥2 composite toxicity were rs12366035 (C>T, minor allele frequency, MAF 0.34) in VEGFB (p 0.0007), rs4035887 (G>A, MAF 0.49) in EPAS1 (p 0.0021), and rs4864950 (T>A, MAF 0.23) in KDR (p 0.0058). These SNPs were genotyped in the validation set and only rs4864950 in KDR was replicated. No grade 4 toxicities were reported. Similar to the discovery set (OR 2.41, 95% CI 1.29-4.51), the A allele of rs4864950 increased the risk of grade 3 composite toxicity (p 0.032, OR 2.12, 95% CI 1.70-4.27) in the validation set. Grade 3 toxicity prevalence in the discovery and validation sets were 3.6% and 7.4% diarrhea, 8.6% and 12.3% HFS, 3.6% and 8.8% hypertension, respectively. The meta-analysis of the two datasets showed that the A allele of rs4864950 increased the risk of grade 3 diarrhea (p 0.045, OR 3.09, 95% CI 1.03-9.29), grade 3 HFS (p 0.012, OR 2.57, 95% CI 1.24-5.37), but not grade 3 hypertension (p 0.207, OR 0.51, 95% CI 0.18-1.45). Conclusions: We provide the first evidence of clinical validity of a marker of sorafenib-induced diarrhea and HFS. Sorafenib inhibits VEGFR2 (coded by KDR), leading to epithelial hypoxia and causing diarrhea and HFS. Variant rs4864950 might affect the function VEGFR2, which, during VEGFR2 inhibition, increases the risk of diarrhea and HFS. This SNP is common and can be genotyped in patients before receiving sorafenib for a better risk assessment. Support: U10CA180821, U10CA180882, U24CA196171; https://acknowledgments.alliancefound.org ClinicalTrials.gov Id: NCT01015833.