Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression.

Transcription factor (TF) proteins regulate gene activity by binding to regulatory regions, most importantly at gene promoters. Many genes have alternative promoters (APs) bound by distinct TFs. The role of differential TF activity at APs during tumour development is poorly understood.

Recommendations for the Equitable and Widespread Implementation of Liquid Biopsy for Cancer Care.

Liquid biopsies-tests that detect circulating tumor cellular components in the bloodstream-have the potential to transform cancer by reducing health inequities in screening, diagnostics, and monitoring. Today, liquid biopsies are being used to guide treatment choices for patients and monitor for cancer recurrence, and promising work in multi-cancer early detection is ongoing. However, without awareness of the barriers to adoption of this new technology and a willingness to build mitigation efforts into the implementation of widespread liquid biopsy testing, the communities that could most benefit may be the last to access and use them.

Predictive Biomarkers of Overall Survival in Patients with Metastatic Renal Cell Carcinoma Treated with IFNα ± Bevacizumab: Results from CALGB 90206 (Alliance).

Purpose: CALGB 90206 was a phase III trial of 732 patients with metastatic renal cell carcinoma (mRCC) comparing bevacizumab plus IFNα (BEV + IFN) with IFNα alone (IFN). No difference in overall survival (OS) was observed. Baseline samples were analyzed to identify predictive biomarkers for survival benefit.

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

The highly transmissible B.1.1.

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

As of January of 2021, the highly transmissible B.1.1.

The DNA methylation landscape of advanced prostate cancer.

Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes that were detectable only with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hypermethylation and somatic mutations in TET2, DNMT3B, IDH1 and BRAF.

Balancing Confounding and Generalizability Using Observational, Real-world Data: 17-gene Genomic Prostate Score Assay Effect on Active Surveillance.

Randomized, controlled trials can provide high-quality, unbiased evidence for therapeutic interventions but are not always a practical or viable study design for certain healthcare decisions, such as those involving prognostic or predictive testing. Studies using large, real-world databases may be more appropriate and more generalizable to the intended target population of physicians and patients to answer these questions but carry potential for hidden bias. We illustrate several emerging methods of analyzing observational studies using propensity score matching (PSM) and coarsened exact matching (CEM).

The 17-Gene Genomic Prostate Score Assay Predicts Outcome After Radical Prostatectomy Independent of PTEN Status.

Objective: To compare the ability of loss of phosphatase and tensin homolog (PTEN) and Genomic prostate score assay (GPS) in predicting the biochemical-recurrence (BCR) and clinical-recurrence (CR) after radical prostatectomy (RP) for clinically localized prostate cancer (PCa).

Methods: Three hundred seventy seven patients with and without CR were retrospectively selected by stratified cohort sampling design from RP database. PTEN status (by immunohistochemistry [IHC] and fluorescence in situ hybridization [FISH]) and GPS results were determined for RP specimens.

Validation of the 16-Gene Recurrence Score in Patients with Locoregional, High-Risk Renal Cell Carcinoma from a Phase III Trial of Adjuvant Sunitinib.

Adjuvant sunitinib prolonged disease-free survival (DFS; HR, 0.76) in patients with locoregional high-risk renal cell carcinoma (RCC) in the S-TRAC trial (ClinicalTrials.gov NCT00375674).

A 17-Gene Genomic Prostate Score Assay Provides Independent Information on Adverse Pathology in the Setting of Combined Multiparametric Magnetic Resonance Imaging Fusion Targeted and Systematic Prostate Biopsy.

Purpose: Multiparametric magnetic resonance imaging and biopsy based molecular tests such as the 17-gene Oncotype DX® Genomic Prostate Score™ assay are increasingly performed to improve risk stratification in men with clinically localized prostate cancer. The prostate score assay was previously shown to be a significant independent predictor of adverse pathology findings at radical prostatectomy in men diagnosed by systematic biopsies only. Therefore, we investigated the ability of the prostate score assay to predict adverse pathology findings in the setting of magnetic resonance imaging guided prostate biopsy.

Active Surveillance Use Among a Low-risk Prostate Cancer Population in a Large US Payer System: 17-Gene Genomic Prostate Score Versus Other Risk Stratification Methods.

Many men with low-risk prostate cancer (PCa) receive definitive treatment despite recommendations that have been informed by two large, randomized trials encouraging active surveillance (AS). We conducted a retrospective cohort study using the Optum™ Research Database (Eden Prairie, MN) of electronic health records and administrative claims data to assess AS use for patients tested with a 17-gene Genomic Prostate Score™ (GPS; Genomic Health, Redwood City, CA) assay and/or prostate magnetic resonance imaging (MRI). De-identified records were extracted on health plan members enrolled from June 2013 to June 2016 who had ≥1 record of PCa (n 5 291,876).

Improving risk stratification among veterans diagnosed with prostate cancer: impact of the 17-gene prostate score assay.

Background: Active surveillance (AS) has been widely implemented within Veterans Affairs' medical centers (VAMCs) as a standard of care for low-risk prostate cancer (PCa). Patient characteristics such as age, race, and Agent Orange (AO) exposure may influence advisability of AS in veterans. The 17-gene assay may improve risk stratification and management selection.

Association between a 17-gene genomic prostate score and multi-parametric prostate MRI in men with low and intermediate risk prostate cancer (PCa).

Background: We aimed to directly compare results from multi-parametric prostate MRI (mpMRI) and a biopsy-based 17-gene RT-PCR assay providing a Genomic Prostate Score (GPS) among individuals who were candidates for active surveillance with low and intermediate risk prostate cancer (PCa).

Patients And Methods: We evaluated the association between GPS results (scale 0-100) and endorectal mpMRI findings in men with clinically localized PCa. MR studies were reviewed to a five-tier scale of increasing suspicion of malignancy.

A Biopsy-based 17-gene Genomic Prostate Score as a Predictor of Metastases and Prostate Cancer Death in Surgically Treated Men with Clinically Localized Disease.

Background: A 17-gene biopsy-based reverse transcription polymerase chain reaction assay, which provides a Genomic Prostate Score (GPS-scale 0-100), has been validated as an independent predictor of adverse pathology and biochemical recurrence after radical prostatectomy (RP) in men with low- and intermediate-risk prostate cancer (PCa).

Objective: To evaluate GPS as a predictor of PCa metastasis and PCa-specific death (PCD) in a large cohort of men with localized PCa and long-term follow-up.

Design, Setting, And Participants: A retrospective study using a stratified cohort sampling design was performed in a cohort of men treated with RP within Kaiser Permanente Northern California.

Identifying Health Information Technology Needs of Oncologists to Facilitate the Adoption of Genomic Medicine: Recommendations From the 2016 American Society of Clinical Oncology Omics and Precision Oncology Workshop.

At the ASCO Data Standards and Interoperability Summit held in May 2016, it was unanimously decided that four areas of current oncology clinical practice have serious, unmet health information technology needs. The following areas of need were identified: 1) omics and precision oncology, 2) advancing interoperability, 3) patient engagement, and 4) value-based oncology. To begin to address these issues, ASCO convened two complementary workshops: the Omics and Precision Oncology Workshop in October 2016 and the Advancing Interoperability Workshop in December 2016.

Use of a 17-Gene Prognostic Assay in Contemporary Urologic Practice: Results of an Interim Analysis in an Observational Cohort.

Objective: To study the impact of genomic testing in shared decision making for men with clinically low-risk prostate cancer (PCa).

Materials And Methods: Patients with clinically low-risk PCa were enrolled in a prospective, multi-institutional study of a validated 17-gene tissue-based reverse transcription polymerase chain reaction assay (Genomic Prostate Score [GPS]). In this paper we report on outcomes in the first 297 patients enrolled in the study with valid 17-gene assay results and decision-change data.

Health Economic Impact and Prospective Clinical Utility of Oncotype DX® Genomic Prostate Score.

Prostate cancer (CaP) will be diagnosed in approximately 181,000 American men in 2016. Despite the high number of deaths from CaP in the United States, the disease has a protracted natural history and many men diagnosed with CaP will not die of the disease regardless of treatment. Unfortunately, identification of men with truly indolent/ nonaggressive CaP is challenging; limitations of conventional diagnostic modalities diminish the ability of physicians to accurately stage every case of CaP based on biopsy results alone.

Pharmacogenetic Discovery in CALGB (Alliance) 90401 and Mechanistic Validation of a VAC14 Polymorphism that Increases Risk of Docetaxel-Induced Neuropathy.

Purpose: Discovery of SNPs that predict a patient's risk of docetaxel-induced neuropathy would enable treatment individualization to maximize efficacy and avoid unnecessary toxicity. The objectives of this analysis were to discover SNPs associated with docetaxel-induced neuropathy and mechanistically validate these associations in preclinical models of drug-induced neuropathy.

Experimental Design: A genome-wide association study was conducted in metastatic castrate-resistant prostate cancer patients treated with docetaxel, prednisone and randomized to bevacizumab or placebo on CALGB 90401.

Patient-specific Meta-analysis of 2 Clinical Validation Studies to Predict Pathologic Outcomes in Prostate Cancer Using the 17-Gene Genomic Prostate Score.

Objective: To perform patient-specific meta-analysis (MA) of two independent clinical validation studies of a 17-gene biopsy-based genomic assay as a predictor of favorable pathology at radical prostatectomy.

Materials And Methods: Patient-specific MA was performed on data from 2 studies (732 patients) using the Genomic Prostate Score (GPS; scale 0-100) together with Cancer of the Prostate Risk Assessment (CAPRA) score or National Comprehensive Cancer Network (NCCN) risk group as predictors of the likelihood of favorable pathology (LFP). Risk profile curves associating GPS with LFP by CAPRA score and NCCN risk group were generated.

Utility of the Oncotype DX Prostate Cancer Assay in Clinical Practice for Treatment Selection in Men Newly Diagnosed with Prostate Cancer: A Retrospective Chart Review Analysis.

Introduction: The 17-gene Oncotype DX® prostate cancer assay (Genomic Health Inc., Redwood City, California) is a validated, biopsy based gene expression assay that reports the Genomic Prostate Score. Combined with clinical risk features, Genomic Prostate Score provides an individualized estimation of disease aggressiveness at diagnosis.

The Impact of a Biopsy Based 17-Gene Genomic Prostate Score on Treatment Recommendations in Men with Newly Diagnosed Clinically Prostate Cancer Who are Candidates for Active Surveillance.

Introduction: The biopsy based 17-gene GPS was clinically validated to predict the likelihood of adverse surgical pathology in men with NCCN very low, low or low-intermediate risk prostate cancer. We performed a prospective study to assess the impact of incorporating GPS into treatment recommendations in 3 high volume urology practices.

Methods: Men with newly diagnosed prostate cancer meeting specific NCCN criteria were prospectively enrolled in the trial.

In the era of genomics, should tumor size be reconsidered as a criterion for neoadjuvant chemotherapy?

Background: The Oncotype DX recurrence score (RS) assay has been validated for prediction of 10-year risk of distant recurrence and likelihood of benefit from chemotherapy in patients with estrogen receptor (ER)-positive, HER2-negative early breast cancer. Patients with high RS tumors have substantial benefit, and patients with low RS tumors have minimal if any benefit from chemotherapy. Tumor size is used as a key parameter when selecting patients for neoadjuvant chemotherapy.