GenomeDx Biosciences Research Articles

18F-FluorThanatrace (18F-FTT) positron emission tomography (PET/CT) in prostate cancer measures in vivo PARP-1 expression and is associated with adverse clinicopathologic features.

5030 Background: We performed the first clinical trial to evaluate expression of PARP-1, the target of PARP-inhibitors (PARPi), in prostate cancer (PC) using 18F-FluorThanatrace (18F-FTT), a novel radiopharmaceutical that selectively measures PARP-1 expression with PET/CT. Approvals for PARPi in metastatic castrate resistant prostate cancer (mCRPC) have improved clinical outcomes in men with homologous recombination deficient (HRD) associated PC. Patient selection using genetic biomarkers such as HRD and PARP-1 IHC are insufficient PARPi biomarkers. We report the first trial of assessment of PARP-1 expression in men with prostate cancer. Methods: Men with localized PC with planned prostatectomy were included. Patients were required to have 2+ biopsy cores with > 50% involvement, OR > 1cm dominant prostate lesion on MRI. Men received a single pre-operative [18F]FTT scan. [18F]FTT is. Patients received a single injection of 8-12 mCi [18F]FTT and underwent 60 minutes dynamic scanning and static scan at 90 minutes post-injection. Ex vivo IHC, autoradiography, and germline/somatic genomic testing was performed after surgical removal. The study was approved by the University of Pennsylvania IRB (UPCC #13817, ClinicalTrials.gov, NCT03334500). Results: 30 men consented for participation (29 with presurgical MRI) from 6/2019 to 12/2020. Mean PSA was 9.8 ng/mL (range 2.35 – 60). Gleason Grade (GG) groups included: GG 1 (n = 1), GG 2 (n = 10), GG 3 (n = 5), GG 4 (n = 7), and GG 5 (n = 7). Stages included: pT2 (n = 12), pT3a (n = 10), pT3b (n = 8). Two patients had pN1 disease (cN0 by MRI). Mean injected dose was 10.32 mCi (range 7.52 – 11.62). There were no serious adverse events noted for any patient. Of patients with presurgical MRI, a range of uptake on the PET/CT correlated to the dominant lesion on MRI. The mean and median SUVMax of all lesions was 3.52 and 3.46, respectively (range 1.03 – 6.56). Both patients cN0 on MRI, had those nodes identified on the [18F]FTT scan. SUVMax was significantly associated with increasing Gleason Grade group Rs = 0.37298, p (2-tailed) = 0.04. SUVMax was significantly associated with Decipher scores (GenomeDx Biosciences, San Diego, CA) Rs = 0.63077, p (2-tailed) = 0.02. Ex vivo IHC showed PARP1 localization to the dominant region on the MRI. Ex vivo autoradiography using [I125]KX1, a FTT analogue, and correlation to genomic HRD (DDR aberrations and HRD scores) is underway. Conclusions: [18F]FTT detects in vivo PARP-1 expression in prostate cancer and SUVMax is associated with higher Gleason Grade groups and Decipher scores, This tracer may be used as an imaging biomarker for PARP-1 expression in men with prostate cancer, the target of PARPi. A follow-up study to assess change in [18F]FTT uptake before and after administration of PARPi in men with mCRPC is underway to test [18F]FTT as a biomarker PARPi (UPCC #08821). Clinical trial information: NCT03334500.

290O - Long-term results of phase II trial of reduced modified clinical target volume in low-risk nasopharyngeal carcinoma treated with intensity modulated radiotherapy

BackgroundIntensity modulated radiation therapy (IMRT) is the standard of care for nasopharyngeal carcinoma (NPC). Part of the IMRT quality assurance process involves accurate target volume delineation, which is crucial for local control and survival. Current practice utilizes a uniform contouring method for clinical target volume (CTV) for all stages of NPC. Here, we conducted a single-arm phase 2 trial investigating the tumor control rates of reduced CTV margins and corresponding doses in low-risk, early-stage NPC. MethodsPatients with biopsy-proven stage I-IIb (6th UICC/AJCC) NPC were enrolled. All patients were treated with IMRT alone. Two CTVs (CTV1 [high risk] and CTV2 [low risk]) were outlined; CTV1 was defined by grossly identified tumour (on MRI or CT) plus 5-mm margin (3-mm posteriorly); CTV2 was CTV1 plus 5-mm margin (3-mm posteriorly). 60 Gy and 50–54 Gy in 30 fractions were prescribed to CTV1 and CTV2, respectively. Primary end-point was locoregional recurrence free survival (LRRFS). ResultsFrom May 2001 to August 2006, 103 patients were recruited; all patients completed IMRT as planned (time duration 39-61 days). At a median follow-up of 12.6 years, five patients developed locoregional failures; of which one was in-field, and four were regional recurrence (two in-field and two marginal). 10-year LRRFS, distant metastasis free survival (DMFS), disease specific survival (DSS) and overall survival (OS) were 95.0% and 94.1%, 94.0% and 91.1%, respectively. The most common grade 1-2 late toxicities included subcutaneous fibrosis (79.6%), hearing loss (53.4%) and skin dystrophy (43.2%); grade 3 included subcutaneous fibrosis (2.9%) and hearing loss (2.9%); and no grade 4 late toxicity. ConclusionsReduced CTV margins and corresponding doses results in optimal longterm tumour control, with minimal late adverse events. Clinical trial identificationNCT03839602. Legal entity responsible for the studyProf. Chong Zhao. FundingHas not received any funding. DisclosureM.L.K. Chua: Honoraria (self), Advisory / Consultancy: Janssen, Astellas, Varian, Ferring Singapore and AstraZeneca; Research grant / Funding (institution): Ferring Singapore, GenomeDx Biosciences, Varian, MedLever. All other authors have declared no conflicts of interest.

1141P - Long-term results of phase II trial of reduced modified clinical target volume in low-risk nasopharyngeal carcinoma treated with intensity modulated radiotherapy

BackgroundIntensity modulated radiation therapy (IMRT) is the standard of care for nasopharyngeal carcinoma (NPC). Part of the IMRT quality assurance process involves accurate target volume delineation, which is crucial for local control and survival. Current practice utilizes a uniform contouring method for clinical target volume (CTV) for all stages of NPC. Here, we conducted a single-arm phase 2 trial investigating the tumor control rates of reduced CTV margins and corresponding doses in low-risk, early-stage NPC. MethodsPatients with biopsy-proven stage I-IIb (6th UICC/AJCC) NPC were enrolled. All patients were treated with IMRT alone. Two CTVs (CTV1 [high risk] and CTV2 [low risk]) were outlined; CTV1 was defined by grossly identified tumour (on MRI or CT) plus 5-mm margin (3-mm posteriorly); CTV2 was CTV1 plus 5-mm margin (3-mm posteriorly). 60Gy and 50–54Gy in 30 fractions were prescribed to CTV1 and CTV2, respectively. Primary end-point was locoregional recurrence free survival (LRRFS). ResultsFrom May 2001 to August 2006, 103 patients were recruited; all patients completed IMRT as planned (time duration 39-61 days). At a median follow-up of 12.6 years, five patients developed locoregional failures; of which one was in-field, and four were regional recurrence (two in-field and two marginal). 10-year LRRFS, distant metastasis free survival (DMFS), disease specific survival (DSS) and overall survival (OS) were 95.0% and 94.1%, 94.0% and 91.1%, respectively. The most common grade 1-2 late toxicities included subcutaneous fibrosis (79.6%), hearing loss (53.4%) and skin dystrophy (43.2%); grade 3 included subcutaneous fibrosis (2.9%) and hearing loss (2.9%); and no grade 4 late toxicity. ConclusionsReduced CTV margins and corresponding doses results in optimal long-term tumour control, with minimal late adverse events. Clinical trial identificationNCT03839602. Legal entity responsible for the studyChong Zhao. FundingNational Natural Science Foundation of China [No. 81872469]; Science and Technology Project of Guangdong Province [No. 2014A020212433]. DisclosureM.L.K. Chua: Honoraria (institution), Advisory / Consultancy: Janssen, Astellas, Varian, Ferring Singapore and AstraZeneca; Research grant / Funding (institution), Structured research agreement/Research funding - Ferring Singapore, GenomeDx Biosciences, Varian, MedLever.: Ferring Singapore, GenomeDx Biosciences, Varian, MedLever. All other authors have declared no conflicts of interest.

LBA77 - Simultaneous multi-cancer detection and tissue of origin (TOO) localization using targeted bisulfite sequencing of plasma cell-free DNA (cfDNA)

BackgroundOur previous discovery work identified whole-genome bisulfite sequencing as outperforming whole-genome and targeted sequencing approaches for multi-cancer detection. We developed a targeted methylation assay for multi-cancer detection and tissue of origin (TOO) localization. MethodsParticipants were from Circulating Cell-free Genome Atlas (CCGA; NCT02889978) and STRIVE (NCT03085888), both prospective, multi-center, observational studies with longitudinal follow-up. cfDNA from 3,583 evaluable samples (1,530 cancer, 2,053 non-cancer) spanned >20 tumor types of all stages; a prespecified subset of these comprised the “multi-cancer” group: anorectal, hormone-receptor (HR)-negative breast, colorectal, esophageal, gallbladder, gastric, head and neck, hepatobiliary, lung, lymphoid leukemia, lymphoma, multiple myeloma, ovarian, and pancreatic (937 cancer [all stages]). A cross-validated targeted methylation test evaluated cfDNA for predictability of cancer presence and TOO; precision defined as the fraction of correct calls. Breast and lung cancer subtypes were also assessed. All analyses targeted 99.4% specificity (0.6% false-positive rate). ResultsParticipants with and without cancer were similar in age. Specificity was set to 99.4%. For the prespecified multi-cancer group, overall sensitivity was 76% (73-78): stage I 32% (25-40), stage II 76% (69-82), stage III 85% (80-89), and stage IV 93% (89-95). Among all samples, overall sensitivity was 55% (52-57%): stage I 19% (15-23%), stage II 43% (38-48%), stage III 78% (73-82%), and stage IV 90% (86-93%). Overall TOO precision for the multi-cancer group and all samples was 89%, and was similar across stages. Squamous-cell and small-cell lung cancer had higher sensitivity than adenocarcinoma: 84% (75-91) vs 83% (69-92) vs 58% (49-67); HR-negative had higher sensitivity than HR-positive breast cancer: 66% (53-77) vs 20% (15-27). ConclusionsThis targeted methylation assay detected cancer signal across >20 cancer types with a single, fixed, low false positive rate and highly accurate TOO localization. These data support the feasibility of a single test that can screen for multiple cancers. Clinical trial identificationNCT02889978, NCT03085888. Editorial acknowledgementSarah Prins, PhD (GRAIL, Inc.), and Megan P. Hall, PhD (GRAIL, Inc.). Legal entity responsible for the studyGRAIL, Inc. FundingGRAIL, Inc. DisclosureG.R. Oxnard: Advisory / Consultancy, Officer / Board of Directors: Inivata; Honoraria (self): Guardant Health; Honoraria (self): Sysmex; Honoraria (self): Bio-Rad; Advisory / Consultancy: DropWorks; Advisory / Consultancy: AstraZeneca; Advisory / Consultancy: GRAIL, Inc.. E.A. Klein: Advisory / Consultancy: GRAIL, Inc.; Advisory / Consultancy: Genomic Health; Advisory / Consultancy: GenomeDx Biosciences. M.V. Seiden: Shareholder / Stockholder / Stock options, Full / Part-time employment: McKesson. E. Hubbell: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. O. Venn: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. A. Jamshidi: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc.; Shareholder / Stockholder / Stock options: Illumina. N. Zhang: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. J.F. Beausang: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. S. Gross: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. K.N. Kurtzman: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc.; Shareholder / Stockholder / Stock options: Illumina. E.T. Fung: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. B. Allen: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. A.P. Fields: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. H. Liu: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. A.M. Aravanis: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. A. Hartman: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. M.C. Liu: Honoraria (institution): GRAIL, Inc. All other authors have declared no conflicts of interest.

916P - Health-related quality of life (HRQoL) and updated follow-up from KEYNOTE-057: Phase II study of pembrolizumab (pembro) for patients (pts) with high-risk (HR) non-muscle invasive bladder cancer (NMIBC) unresponsive to bacillus calmette-guérin (BCG)

916P - Health-related quality of life (HRQoL) and updated follow-up from KEYNOTE-057: Phase II study of pembrolizumab (pembro) for patients (pts) with high-risk (HR) non-muscle invasive bladder cancer (NMIBC) unresponsive to bacillus calmette-guérin (BCG)

PD11-03 RESPONSE TO APALUTAMIDE (APA) AMONG PATIENTS (PTS) WITH NONMETASTATIC CASTRATION-RESISTANT PROSTATE CANCER (NMCRPC) FROM SPARTAN BY DECIPHER GENOMIC CLASSIFIER (GC) SCORE

INTRODUCTION AND OBJECTIVES:The DECIPHER prostate test (GenomeDx Biosciences, Inc., San Diego, CA) is a clinical-grade mRNA-based test with a genomic classifier (GC) score that has been independent...

Identifying molecular determinants of response to apalutamide (APA) in patients (pts) with nonmetastatic castration-resistant prostate cancer (nmCRPC) in the SPARTAN trial.

42 Background: The SPARTAN trial recently demonstrated that addition of APA to androgen deprivation therapy (ADT) improved metastasis-free survival (MFS) and second progression-free survival (PFS2) in nmCRPC pts. We performed transcriptome-wide profiling of available primary tumor samples from pts in SPARTAN to evaluate potential biomarkers of response or resistance to APA+ADT. Methods: Pts included in SPARTAN were at high risk of developing metastasis.We used a commercially available genomic assay (DECIPHER prostate test, GenomeDx Biosciences, Inc., San Diego, CA) to assess gene expression in 233 archived primary tumors from SPARTAN pts. Using a Cox proportional hazard model, we assessed the association between scores and subtypes from previously derived prognostic and predictive gene signatures, such as DECIPHER and basal (BA) vs luminal (LU) subtyping. Results: Pts with high DECIPHER scores had greater treatment effect with APA+ADT than those with low scores. Pts with LU, a subtype known to be sensitive to ADT, greatly benefited from APA+ADT. Pts with BA, typically resistant to ADT, also benefited from APA+ADT. Conclusions: DECIPHER score and BA or LU subtype may be biomarkers of response to APA+ADT. DECIPHER may be useful for identifying pts for early treatment intensification with APA or other agents, and molecular subtyping may be an effective approach for pt selection in trials combining novel therapies with APA. Clinical trial information: NCT01946204. [Table: see text]

Evaluating the Impact of Lead-Time Bias on the Observed Efficacy of Early Salvage Radiation Therapy in Prostate Cancer: A Post-Hoc Analysis of the RTOG 9601 Trial

Background: To evaluate the potential impact of lead-time bias on the reported beneficial role of early salvage radiotherapy (sRT), defined as delivering radiation at a relatively low pre-sRT prostate-specific antigen (PSA) value, in treating prostate cancer patients with biochemical recurrence after radical prostatectomy (RP). Methods: All available demographic, tumor-specific, and overall survival data from 760 men who participated in the RTOG 9601 trial were extracted using the Project Data Sphere platform. Patients were stratified based on pre-sRT PSA ( 1.5-4.0 ng/mL [n=118]) as reported in the original trial. Cox regression analysis assessed the impact of pre-sRT PSA on overall mortality, after controlling for covariates. To ascertain the role of lead-time bias, survival time zero was set to the time of (1) initiation of sRT, and (2) RP. Findings: There were no statistically significant differences amongst men within the three groups, except for a greater proportions of African-American patients and men with post-RP PSA nadirs ≥0.5 ng/mL within the higher pre-sRT PSA groups. For men with pre-sRT PSA 1.5-4 ng/mL, estimated 15-year overall mortality was 39%, 45%, and 50%, respectively (p=0.005) when calculated from time since sRT, and 23%, 29%, and 36% respectively (p=0.08) when assessed from time since RP. On multivariable regression analyses, pre-sRT PSA >1.5-4.0 ng/mL was significantly associated with overall mortality only when measured from time of initiation of sRT (HR 1.61, 95% confidence interval [CI] 1.13-2.28; p=0.008), but not from time since RP (HR 1.24, 95% CI 0.87-1.76; p=0.2). Interpretation: Our findings suggest that the putative survival benefit with early sRT instituted at lower PSA thresholds is mitigated when measured from time since surgery, highlighting the role of lead-time bias. These findings need further validation given their significant clinical implications. Funding Statement: There was no funding for this study. The corresponding author had full access to all data in the study and had final responsibility for the decision to submit for publication. Declaration of Interests: Firas Abdollah is a consultant for GenomeDx Biosciences. Ethics Approval Statement: An institutional review board waiver was obtained before the study was conducted, in accordance with institutional regulation when dealing with de-identified previously collected data.

(OA20) Association of Circulating Tumor Cells (CTCS) and Genomic Signatures in Prostate Cancer Patients

Intermediate and high-risk prostate cancer patients, who are candidates for radiotherapy (RT), are very heterogeneous. The factors considered in the designation of these risk groups are limited in predicting risk of metastasis and lethality. Circulating tumor cells (CTCs) have been associated with risk of metastasis in different carcinomas, including prostate cancer. Genomic classifiers add to clinical-pathologic risk factors and have the potential to become integral to risk stratification and management. Here we investigate the associations of CTC counts and several genomic classifiers in patients enrolled on a randomized Phase II clinical trial. CTCs were enumerated in blood samples from 31 trial patients. The number of single CTCs, CTC clusters and their sum were recorded. Seven gene signatures: Decipher® (metastatic risk), PORTOS (predictor for RT response) and Pam-50 (predictor for treatment outcome that includes gene expression-based “intrinsic” subtypes: luminal A, luminal B, HER2-enriched, and basal-like) were quantified in tissue obtained by MRI-Ultrasound fused biopsies using a high-density gene expression microarray (ThermoFisher, Carlsbad, CA) processed at GenomeDx Biosciences Laboratory (San Diego, CA). The associations between the seven gene signatures and CTCs were examined. A Poisson regression model with demographical and disease characteristics variables (PSA, Gleason Score, T stage, %tumor in biopsy cores, age, race/ethnicity) were used in the univariable analysis (UVA). Multivariable analysis (MVA) included the statistically significant variables where each biomarker was examined along with chosen covariates for association with CTC counts in a one-at-a-time manner. CTCs were evident in over 70% of patients in the trial. In MVA, several of the signatures were associated with CTC number. When the biopsy core containing the highest Gleason Score and percent of tumor were analyzed, the significant relationships included PORTOS (RR 6.00; p<0.001), PAM50_basal (RR 2.21; p<0.001), and Decipher (RR 1.16; p=0.048). Since multiple biopsies were analyzed for gene expression, in subsequent analysis, the cores with highest PORTOS score were selected. In the MVA, the associations with PORTOS surged (RR=47.10; p<0.0001). These results indicate, especially in the view of the relatively small sample size, that there is a strong signal, related to radiation sensitivity. Of note, NCCN risk categories did not result in significant associations with CTC counts or gene signatures. The determinants of prostate cancer lethality in intermediate to high-risk prostate cancer are poorly understood. The crude assessment of risk by established criteria, such as the AJCC and NCCN risk groups, are inadequate because these risk groupings do not consider (i) tumor gene expression alterations and mutations, and (ii) the strongest determinant of metastatic potential, namely CTC numbers and attributes. The data reveal strong associations between gene expression and CTC counts, especially using PORTOS. PORTOS is a measure of radiation sensitivity, which appears to be counterbalanced to a degree by an increased risk of metastasis.

PD15-01 CHARACTERIZATION OF THE GENOMIC LANDSCAPE OF A PROSPECTIVE MUSCLE-INVASIVE BLADDER CANCER COHORT WITH A FOCUS ON SECONDARY VARIANT HISTOLOGY

You have accessJournal of UrologyBladder Cancer: Invasive II1 Apr 2018PD15-01 CHARACTERIZATION OF THE GENOMIC LANDSCAPE OF A PROSPECTIVE MUSCLE-INVASIVE BLADDER CANCER COHORT WITH A FOCUS ON SECONDARY VARIANT HISTOLOGY Vikram Narayan, Ewan Gibb, Nicholas Erho, Andrea Cronican, Tyler Kolisnik, Elai Davicioni, and Badrinath Konety Vikram NarayanVikram Narayan More articles by this author , Ewan GibbEwan Gibb More articles by this author , Nicholas ErhoNicholas Erho More articles by this author , Andrea CronicanAndrea Cronican More articles by this author , Tyler KolisnikTyler Kolisnik More articles by this author , Elai DavicioniElai Davicioni More articles by this author , and Badrinath KonetyBadrinath Konety More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2018.02.800AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Muscle invasive bladder cancer (MIBC) is a highly aggressive disease, often presenting with heterogeneous clinical and pathological features. Though these tumors are commonly urothelial, secondary variant histology is frequently encountered. Recent transcriptome profiling studies have revealed MIBC can be divided into at least four distinct molecular subtypes, with the benefits of neoadjuvant chemotherapy (NAC) potentially varying between subtypes. The presence of secondary variant histology may alter this molecular profile and the treatment responses of these tumors. In this study, we report the genomic characterization of a large prospective MIBC cohort enriched with secondary variant histology. METHODS The cohort consisted of 173 patients diagnosed with urothelial MIBC who received the Decipher Bladder genomic subtyping classifier test (GenomeDx Biosciences Laboratory, San Diego, CA). Descriptions of secondary variant histology were abstracted from clinical pathology reports of submitted cases. TURBT tissue samples were profiled using a high-density genome-wide expression microarray and de-identified for GRID software analysis in R-studio (v3.3.1). RESULTS The cohort included 136 males and 32 females with a mean age of 72±9 at TURBT. A total of 49 cases (28%) had variant histology including non-urothelial (squamous [24], neuroendocrine [4], glandular [4]) and urothelial (micropapillary [6], sarcomatoid [5], plasmacytoid [2], nested [3], clear cell [1]) variants. Molecular subtyping revealed 77% of variant cases were either pure basal-like (22) or basal claudin-low (16), with fewer cases being luminal (7) or infiltrated luminal (4). Squamous cases had profiles consistent with basal tumors, while neuroendocrine cases had high MKI67 and neuronal marker expression. Micropapillary profiles had high CDH3 and MUC1 expression levels. Sarcomatoid tumors were driven by robust expression of EMT markers, including VIM, ZEB1 and ZEB2, with a corresponding loss of CDH1 expression. One plasmacytoid case expressed high levels of CDH1 RNA, but was negative for IHC, while the other case had low CDH1 RNA and lacked IHC data. CONCLUSIONS Secondary variant histology in MIBC contributes to the molecular heterogeneity of these tumors, with the majority of variant histology cases in this cohort being associated with basal MIBC subtypes. These findings may have implications for tailoring NAC by molecular subtype and may contribute to the varied clinical responses encountered in treating patients with variant histology. © 2018FiguresReferencesRelatedDetails Volume 199Issue 4SApril 2018Page: e310 Advertisement Copyright & Permissions© 2018MetricsAuthor Information Vikram Narayan More articles by this author Ewan Gibb More articles by this author Nicholas Erho More articles by this author Andrea Cronican More articles by this author Tyler Kolisnik More articles by this author Elai Davicioni More articles by this author Badrinath Konety More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

A biopsy-based genomic classifier to predict biochemical failure after definitive radiation without hormone therapy in a prospective cohort of intermediate risk prostate cancer.

68 Background: Recently, NCCN adopted the Zumsteg-Spratt subclassification to define NCCN favorable and unfavorable intermediate-risk prostate cancer (IR-PCa). NCCN unfavorable disease is recommended to receive combination androgen deprivation therapy (ADT) and radiotherapy. To determine if genomics could help identify a subset who may safely avoid ADT, we evaluated the Decipher genomic classifier (GC) in IR-PCa treated with dose-escalated image-guided radiotherapy (DE-IGRT) alone. Methods: Our cohort comprised of 121 patients with NCCN favorable (N = 49, 40%) and unfavorable (N = 74, 60%) IR-PCa, who received 78 Gy without ADT. Diagnostic needle biopsies with the highest Gleason score (GS) and %tumor involvement were macrodissected for RNA extraction. GC scores were determined from the Decipher prostate cancer classifier assay (GenomeDx Biosciences, San Diego, CA). Primary clinical endpoint was biochemical relapse ([BCR], PSA nadir + 2ng/ml) post-DE-IGRT. We compared association with BCR against known clinicopathologic prognostic indices and the NCCN risk strata. Results: With a median follow up of 7.5y, 24 (19%) patients experienced BCR. Individual clinical indices did not predict BCR-free survival rate (BFS). NCCN risk strata was however associated with a small but significant difference in BFS (5-y 93%, favorable vs 88%, unfavourable, P = 0.046). GC scores stratified 85 (70%), 19 (16%), and 17 (14%) men into low, intermediate, and high risk of recurrence; 5-y BFS were 95%, 89%, and 59%, respectively (P &lt; 0.001). On multivariable analysis, a hazard ratio of 4.71 (95% CI 1.81-12.28, P = 0.0015) for BCR was observed for the GC high risk group compared to low/intermediate; NCCN risk strata and intraductal variant did not achieve significance. Conclusions: In IR-PCa men treated with DE-IGRT monotherapy, Decipher GC was an independent predictor of BCR. While most men in this our cohort were stratified as NCCN unfavorable IR-PCa, the majority were GC low risk with excellent outcomes from DE-IGRT alone. In contrast, a minority with GC high risk had suboptimal outcomes, and may benefit from ADT intensification.

TU‐CD‐BRB‐12: Radiogenomics of MRI‐Guided Prostate Cancer Biopsy Habitats

Purpose:Diagnostic prostate biopsies are subject to sampling bias. We hypothesize that quantitative imaging with multiparametric (MP)‐MRI can more accurately direct targeted biopsies to index lesions associated with highest risk clinical and genomic features.Methods:Regionally distinct prostate habitats were delineated on MP‐MRI (T2‐weighted, perfusion and diffusion imaging). Directed biopsies were performed on 17 habitats from 6 patients using MRI‐ultrasound fusion. Biopsy location was characterized with 52 radiographic features. Transcriptome‐wide analysis of 1.4 million RNA probes was performed on RNA from each habitat. Genomics features with insignificant expression values (&lt;0.25) and interquartile range &lt;0.5 were filtered, leaving total of 212 genes. Correlation between imaging features, genes and a 22 feature genomic classifier (GC), developed as a prognostic assay for metastasis after radical prostatectomy was investigated.Results:High quality genomic data was derived from 17 (100%) biopsies. Using the 212 ‘unbiased’ genes, the samples clustered by patient origin in unsupervised analysis. When only prostate cancer related genomic features were used, hierarchical clustering revealed samples clustered by needle‐biopsy Gleason score (GS). Similarly, principal component analysis of the imaging features, found the primary source of variance segregated the samples into high (≥7) and low (6) GS. Pearson's correlation analysis of genes with significant expression showed two main patterns of gene expression clustering prostate peripheral and transitional zone MRI features. Two‐way hierarchical clustering of GC with radiomics features resulted in the expected groupings of high and low expressed genes in this metastasis signature.Conclusions:MP‐MRI‐targeted diagnostic biopsies can potentially improve risk stratification by directing pathological and genomic analysis to clinically significant index lesions. As determinant lesions are more reliably identified, targeting with radiotherapy should improve outcome. This is the first demonstration of a link between quantitative imaging features (radiomics) with genomic features in MRI‐directed prostate biopsies.The research was supported by NIH‐ NCI R01 CA 189295 and R01 CA 189295; E Davicioni is partial owner of GenomeDx Biosciences, Inc. M Takhar, N Erho, L Lam, C Buerki and E Davicioni are current employees at GenomeDx Biosciences, Inc.

Characterization of 1577 Primary Prostate Cancers Reveals Novel Biological and Clinicopathologic Insights into Molecular Subtypes

BackgroundProstate cancer (PCa) molecular subtypes have been defined by essentially mutually exclusive events, including ETS gene fusions (most commonly involving ERG) and SPINK1 overexpression. Clinical assessment may aid in disease stratification, complementing available prognostic tests. ObjectiveTo determine the analytical validity and clinicopatholgic associations of microarray-based molecular subtyping. Design, setting, and participantsWe analyzed Affymetrix GeneChip expression profiles for 1577 patients from eight radical prostatectomy cohorts, including 1351 cases assessed using the Decipher prognostic assay (GenomeDx Biosciences, San Diego, CA, USA) performed in a laboratory with Clinical Laboratory Improvements Amendment certification. A microarray-based (m-) random forest ERG classification model was trained and validated. Outlier expression analysis was used to predict other mutually exclusive non-ERG ETS gene rearrangements (ETS+) or SPINK1 overexpression (SPINK1+). Outcome measurementsAssociations with clinical features and outcomes by multivariate logistic regression analysis and receiver operating curves. Results and limitationsThe m-ERG classifier showed 95% accuracy in an independent validation subset (155 samples). Across cohorts, 45% of PCas were classified as m-ERG+, 9% as m-ETS+, 8% as m-SPINK1+, and 38% as triple negative (m-ERG−/m-ETS−/m-SPINK1−). Gene expression profiling supports three underlying molecularly defined groups: m-ERG+, m-ETS+, and m-SPINK1+/triple negative. On multivariate analysis, m-ERG+ tumors were associated with lower preoperative serum prostate-specific antigen and Gleason scores, but greater extraprostatic extension (p<0.001). m-ETS+ tumors were associated with seminal vesicle invasion (p=0.01), while m-SPINK1+/triple negative tumors had higher Gleason scores and were more frequent in Black/African American patients (p<0.001). Clinical outcomes were not significantly different among subtypes. ConclusionsA clinically available prognostic test (Decipher) can also assess PCa molecular subtypes, obviating the need for additional testing. Clinicopathologic differences were found among subtypes based on global expression patterns. Patient summaryMolecular subtyping of prostate cancer can be achieved using extra data generated from a clinical-grade, genome-wide expression-profiling prognostic assay (Decipher). Transcriptomic and clinical analysis support three distinct molecular subtypes: (1) m-ERG+, (2) m-ETS+, and (3) m-SPINK1+/triple negative (m-ERG−/m-ETS−/m-SPINK1−). Incorporation of subtyping into a clinically available assay may facilitate additional applications beyond routine prognosis.

A 22 Gene-expression Assay, Decipher® (GenomeDx Biosciences) to Predict Five-year Risk of Metastatic Prostate Cancer in Men Treated with Radical Prostatectomy.

Among the estimated 230,000 men diagnosed with prostate cancer in the US each year there has been a rise in the number of radical prostatectomies (RP). There is some debate over the value of immediate adjuvant therapy following RP in men with high-risk pathological features versus delayed salvage radiation therapy when signs of disease progression are observed. Thus, it would be potentially useful to inform post-RP management strategies by more clearly identifying those patients at higher risk of progression and death from prostate cancer. A 22 gene-expression assay, Decipher® (GenomeDx Biosciences), has been developed in men treated with radical prostatectomy to predict the five-year risk of metastatic prostate cancer. Published and unpublished literature was evaluated to determine the analytic validity, clinical validity and clinical utility of Decipher. Limited information is available on the analytic validity of Decipher. In both discovery and validation studies, Decipher was shown to have good performance in discriminating men with metastasis from men without metastasis five years after surgery (AUC 0.75 to 0.90). In terms of clinical utility, no evidence was found reporting improved outcomes (lower prostate cancer specific mortality and treatment related adverse effects) from using this test to guide post-operative treatment. Four studies provided weak indirect evidence of clinical utility in which 31% to 43% of post-operative treatment recommendations were changed in men with high-risk prostate cancer based on test results, with 27% to 52% of treatment recommendations changing from any treatment to no treatment.

Validation of a Genomic Classifier for Predicting Metastasis Following Postoperative Radiation Therapy in High-Risk Prostate Cancer

Validation of a Genomic Classifier for Predicting Metastasis Following Postoperative Radiation Therapy in High-Risk Prostate Cancer R.B. Den, R. Karnes, F.Y. Feng, T.N. Showalter, M.V. Mishra, E.J. Trabulsi, C.D. Lallas, L.G. Gomella, R. Birbe, P. McCue, K. Yousefi, M. Ghadessi, E. Davicioni, W. Kelly, K.E. Knudsen, and A.P. Dicker; Jefferson Medical College of Thomas Jefferson University, Philadelphia, PA, Mayo Clinic, Rochester, MN, University of Michigan, Ann Arbor, MI, University of Virginia, Charlottesville, PA, University of Maryland, Baltimore, PA, GenomeDx Biosciences, Vancouver, BC, Canada

A Molecular Signature of Radiosensitivity (RSI) is an RT-specific Biomarker in Prostate Cancer

Validation of a Genomic Classifier for Predicting Metastasis Following Postoperative Radiation Therapy in High-Risk Prostate Cancer R.B. Den, R. Karnes, F.Y. Feng, T.N. Showalter, M.V. Mishra, E.J. Trabulsi, C.D. Lallas, L.G. Gomella, R. Birbe, P. McCue, K. Yousefi, M. Ghadessi, E. Davicioni, W. Kelly, K.E. Knudsen, and A.P. Dicker; Jefferson Medical College of Thomas Jefferson University, Philadelphia, PA, Mayo Clinic, Rochester, MN, University of Michigan, Ann Arbor, MI, University of Virginia, Charlottesville, PA, University of Maryland, Baltimore, PA, GenomeDx Biosciences, Vancouver, BC, Canada

Validation of a Genomic Classifier that Predicts Metastasis Following Radical Prostatectomy in an At Risk Patient Population

Patients with locally advanced prostate cancer after radical prostatectomy are candidates for secondary therapy. However, this higher risk population is heterogeneous. Many cases do not metastasize even when conservatively managed. Given the limited specificity of pathological features to predict metastasis, newer risk prediction models are needed. We report a validation study of a genomic classifier that predicts metastasis after radical prostatectomy in a high risk population. A case-cohort design was used to sample 1,010 patients after radical prostatectomy at high risk for recurrence who were treated from 2000 to 2006. Patients had preoperative prostate specific antigen greater than 20 ng/ml, Gleason 8 or greater, pT3b or a Mayo Clinic nomogram score of 10 or greater. Patients with metastasis at diagnosis or any prior treatment for prostate cancer were excluded from analysis. A 20% random sampling created a subcohort that included all patients with metastasis. We generated 22-marker genomic classifier scores for 219 patients with available genomic data. ROC and decision curves, competing risk and weighted regression models were used to assess genomic classifier performance. The genomic classifier AUC was 0.79 for predicting 5-year metastasis after radical prostatectomy. Decision curves showed that the genomic classifier net benefit exceeded that of clinical only models. The genomic classifier was the predominant predictor of metastasis on multivariable analysis. The cumulative incidence of metastasis 5 years after radical prostatectomy was 2.4%, 6.0% and 22.5% in patients with low (60%), intermediate (21%) and high (19%) genomic classifier scores, respectively (p<0.001). Results indicate that genomic information from the primary tumor can identify patients with adverse pathological features who are most at risk for metastasis and potentially lethal prostate cancer.