Kevin Kelly

Pattern of Prostate-Specific Antigen (PSA) Failure Dictates the Probability of a Positive Bone Scan in Patients With an Increasing PSA After Radical Prostatectomy

PURPOSE Physicians often order periodic bone scans (BS) to check for metastases in patients with an increasing prostate-specific antigen (PSA; biochemical recurrence [BCR]) after radical prostatectomy (RP), but most scans are negative. We studied patient characteristics to build a predictive model for a positive scan. PATIENTS AND METHODS From our prostate cancer database we identified all patients with detectable PSA after RP. We analyzed the following features at the time of each bone scan for association with a positive BS: preoperative PSA, time to BCR, pathologic findings of the RP, PSA before the BS (trigger PSA), PSA kinetics (PSA doubling time, PSA slope, and PSA velocity), and time from BCR to BS. The results were incorporated into a predictive model. RESULTS There were 414 BS performed in 239 patients with BCR and no history of androgen deprivation therapy. Only 60 (14.5%) were positive for metastases. In univariate analysis, preoperative PSA (P = .04), seminal vesicle invasion (P = .02), PSA velocity (P < .001), and trigger PSA (P < .001) predicted a positive BS. In multivariate analysis, only PSA slope (odds ratio [OR], 2.71; P = .03), PSA velocity (OR, 0.93; P = .003), and trigger PSA (OR, 1.022; P < .001) predicted a positive BS. A nomogram for predicting the bone scan result was constructed with an overfit-corrected concordance index of 0.93. CONCLUSION Trigger PSA, PSA velocity, and slope were associated with a positive BS. A highly discriminating nomogram can be used to select patients according to their risk for a positive scan. Omitting scans in low-risk patients could reduce substantially the number of scans ordered.

Assessment of hormone refractory prostate cancer

OBJECTIVES To define guidelines for the assessment of treatment in patients with hormone-refractory prostate cancer (HRPC). METHODS In the light of modern research, and taking new treatment options into account, the Committee essays to specify different categories of patients entering clinical trials, and to define response criteria and those endpoints that are relevant in phase III studies and in short-term follow-up. RESULTS HRPC comprises a range of disease states with varying responsiveness to therapy and length of survival. Patients with progression as evaluated by increasing prostate-specific antigen (PSA) values alone have a more favorable prognosis than those presenting with increasing tumor spread. In the assessment of these patients, the modes of previous therapy and the kind of tumor progression must be taken into account. The benefit of treatment of HRPC is often modest. While duration of survival remains the main and ultimate endpoint, the means of measuring short-term responsiveness to therapy are limited. A minority of patients have measurable tumor lesions. Decrease of PSA or other biochemical tumor markers may indicate depression of the tumor activity, but is not always associated with prolongation of survival. A variety of new treatments in HRPC are being investigated. They affect measurable tumor parameters in different ways. CONCLUSIONS When a new agent is to be tested, it is important to measure all possible parameters before deciding which particular ones are appropriate for future investigations of this agent. In symptomatic patients, evaluation of subjective parameters, for example, relief of pain or improvement of performance status, is often the most reliable measure of treatment effect. However, these parameters should be clearly defined.

Fatal respiratory failure associated with treatment of prostate cancer using docetaxel and estramustine

Chemotherapy that targets microtubular trafficking induces responses in most patients with prostate cancer. One regimen under investigation is the combination of docetaxel and estramustine. We report on 2 patients with androgen-independent disease who received continuous weekly docetaxel and estramustine and who died of irreversible respiratory failure. The clinical, pathologic, and radiographic data support drug toxicity as the likely etiology. Inclusive of these patients, only 17 cases (10 fatal) of acute pulmonary toxicity using docetaxel have been reported, despite its wide use. We recommend that patients receiving weekly docetaxel, with or without estramustine, have frequent treatment breaks and be evaluated with computed tomography of the chest every 8 weeks.

Genomic Profiling of Two Histologically Distinct Rare Urothelial Cancers in a Clinical Setting to Identify Potential Therapeutic Options for Treatment and Management of Disease

Molecular profiling of urothelial cancers for therapeutic and prognostic potential has been very limited due to the absence of cancer-specific targeted therapies. We describe here 2 clinical cases with a histological diagnosis of an invasive sarcomatoid and a poorly differentiated carcinoma favoring urothelial with some neuroendocrine differentiation, two of the rarer types of urothelial cancers, which were evaluated for mutations in 212 genes for single-nucleotide variants and copy-number variants and 53 genes for fusions associated with solid tumors. In both cases, we identified variants in 2 genes, ARID1A and CDKN2A, indicative of the role of dysregulation of chromatin remodeling and cell cycle control as being common features of bladder cancer, consistent with the proposed model of tumorigenesis in these rare, highly aggressive pathological subtypes. The presence of a KRAS mutation in the poorly differentiated cancer and a TP53 mutation in the sarcomatoid tumor is indicative of a distinctive profile and adds a potential layer of molecular stratification to these rarer histological subtypes. We present a comparative analysis of the histological, clinical, and molecular profile of both cases and discuss the potential to delineate these tumors at the molecular level keeping in mind the possible therapeutic implications.

332 The Jackson Laboratory for Genomic Medicine ActionSeq Plus Offering Provides a Comprehensive Analysis of Cancer Diagnoses

technologists tasked with running the assay. The benefits and value of building a custom LIMS is no doubt appealing, but the challenges and risks faced while accomplishing that goal proved to be a difficult endeavor. Our clinical genomics laboratory was granted the opportunity to construct a custom LIMS to be utilized for whole exome sequencing workflows. With careful consideration of the cost and time required to develop a custom software tool that needs to mimic our current procedures, our team quickly set forth to develop a project plan. Unlike many “out of the box” systems, our development would require specific insight and technical configurations. Our team arranged workshops with both laboratory technicians and software developers to gather user requirements. We vigilantly managed time as to not disrupt ongoing clinical work. Ultimately, despite setbacks and pivots, we accomplished our mission. Due to intense project planning, multi-team communication, a clear vision, and, most importantly, user input, we created and implemented a robust automated LIMS without disrupting our clinical workflow. At the conclusion of this project, much was learned. It is critical to avoid “scope-creep” (the tendency for project goals to grow beyond the original vision). For the sake of time, implement a minimal viable product, test it, release it, and then iterate on later versions. Budget for both cost and personnel bandwidth. Understand risks, and be resourceful enough to adapt to changing goals.

Abstract 757: Development and validation of the ActionSeqTMtest system

Introduction In the constantly changing field of oncology precision medicine, it is exceedingly important to keep diagnostic and therapeutic assays clinically relevant. Next generation sequencing (NGS) panels in oncology are greatly impacted by new findings in clinical actionability. In order to ensure that cancer panels continue to provide the most beneficial results to patients, they must be regularly updated. In keeping with this idea, JAX has launched a new 212 oncology gene panel which focuses on genes and variants with documented actionability, referred to as ActionSeq. Methods Development of ActionSeq included the optimization of a new targeted capture assay. This process included running multiple batches of samples through the assay to determine appropriate DNA input, ligation times, PCR cycles, and pooling conditions. The fully optimized assay was then validated using 24 uncharacterized FFPE samples. The validation was executed in 5 phases: (1) confirm that assay optimizations yielded sufficient wet lab results; (2) LOD & sensitivity (3) inter-assay concordance; (4) intra-assay concordance; (5) specificity and accuracy. Results During development, the standard protocol was optimized using a 200ng input, 30 minute ligation period, 5 cycles of pre-PCR, and the pooling of 4 samples per hybridization reaction. Wet lab processing results of the first validation batch can be seen in Table 1. The inter- and intra-assay concordances were found to be ≥ 96% for variants and 100% for CNVs. The sensitivity was calculated to be 98.92% at a LOD of 3% for SNVs, 100% at a LOD of 8% for INDELs, 100% at a LOD of 6 copies for CNV amplifications, and 100% at a LOD of 0 copies for CNV deletions. The specificity and accuracy were found to be 100% for all mutation types. Conclusion Based on the success of this validation ActionSeq has been incorporated into the JAX clinical test menu. This addition accomplished the goal of providing a more clinically relevant (actionable) somatic tumor profiling assay to patients and clinicians. Citation Format: Samantha Helm, Vanessa Spotlow, Aleksandra Ras, Kevin Kelly, Guruprasad Ananda, Sara Patterson, Honey V. Reddi. Development and validation of the ActionSeq TM test system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 757. doi:10.1158/1538-7445.AM2017-757

A Comprehensive Evaluation of Solid Tumor Analysis in the Clinical Space

Solid tumors remain a major health concern with approximately 14 million new cases and 8.2 million cancerrelated deaths per year. Currently multimodality treatment regimens are being explored to make advances against this deadly disease. Tumors are characterized by genomic instability and tailored therapies are being considered based on genetic profiling of cancers, driving precision medicine. This review outlines the various genetic changes present in solid tumors, evaluates the technologies currently used for identification of variants and compares the large panels available for clinical utility and comprehensiveness.

Simultaneous extraction of DNA and total RNA from varying specimen types to enhance tissue utilization for molecular analysis.

e23209Background: The isolation of both genomic DNA (gDNA) and total RNA (RNA) from tissues of various types is critical for comprehensive molecular profiling, especially as submitted specimens bec...

Abstract 3634: Simultaneous isolation of genomic DNA and total RNA using the Qiagen AllPrep® method: Table 1.

Introduction: The purification of genomic DNA (gDNA) and total RNA (RNA) from various specimen types using a single sample is currently in high demand in genomic settings due to the limitation of available biological material. There is an increased need for simultaneous isolation of nucleic acids in cancer genetics for use in downstream applications such as genotyping, microarrays or next generation sequencing. The Qiagen AllPrep® technique provides a comprehensive solution for extraction of gDNA and RNA from a single specimen. In this study, we tested the AllPrep® kits for concurrent isolation of gDNA and RNA from five different sample types. Materials and Methods: Genomic DNA and RNA were extracted simultaneously according to Qiagen AllPrep® manufacturer9s instructions from five specimen types: bone marrow mononuclear cells (BMMC), cryopreserved cultured cell lines, whole blood, fresh frozen and FFPE samples. Quantity and quality of both nucleic acids were assessed by the NanoDrop 2000 and Qubit fluorometer 2.0. Purified gDNA from BMMC, fresh frozen, whole blood and FFPE samples was further evaluated by library preparation, targeted hybridization capture and sequencing on an Illumina NextSeq500. FastQ files were submitted to a Clinical Genome Analytics (CGA) pipeline for quality metrics analysis. Results: The AllPrep® technique resulted in effective isolation of high quality gDNA and RNA (Table1). All set wet lab and sequencing QC metrics were met for each sample type. Conclusion: We have successfully verified the AllPrep® method can be used for simultaneous extraction of both gDNA and RNA using the same input material without compromising the yield or purity of both final products. This simple procedure based on spin column technology not only gave the advantage of generating high quality results using limited specimen resources, but also decreased the hands on time by 3.5 hours and cost when compared to extraction done with two separate kits. Citation Format: Aleksandra Ras, Samantha Helm, Kevin Kelly, Vanessa Spotlow, Guruprasad Ananda, Gregory Tsongalis. Simultaneous isolation of genomic DNA and total RNA using the Qiagen AllPrep® method. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3634.