Guide Therapy Decisions Research Articles

Abstract 572: The liquid biopsy Guardant360 CDx has robust performance at low inputs allowing for high rate of returning patient results

Abstract Background Liquid biopsy tests capable of tumor profiling with NGS have recently received FDA approval for companion diagnostic treatment selection and tumor profiling, demonstrating the clinical validity of the identification of druggable variants with such information. As the amount of cfDNA per volume of plasma varies greatly from patient to patient, and whole blood/plasma volumes from advanced cancer patients are often limited, it would be advantageous for a liquid biopsy to be able to operate with minimal input, providing robust results across a broad spectrum of blood sample volumes and resultant cfDNA input. In this study, we evaluate the performance of Guardant360 CDx with as little as 3 mL whole blood and 5 ng cfDNA input. Methods The primary concern with low input like 3 mL whole blood is excess preservative in a blood collection tube (BCT) relative to whole blood. In a simulated short draw experiment, the same advanced cancer patient provided whole blood in BCTs with standard, elevated (2X), and high (3.3X) preservatives. We evaluated the molecule coverage across the panel at key exons and positions of interest, across genes evaluated for copy number amplifications, and at frequent fusion gene breakpoint positions. Precision and limit of detection (LoD) have been demonstrated at 5 ng input (P200010B) the lowest allowable input. For clinical utility of a liquid biopsy with low cfDNA input, we also assessed the cfDNA input of 87,305 samples tested with Guardant360 CDx or LDT from a single 10mL BCT. Results and Discussion Differences in molecule coverage between the high preservative and standard preservative were found to fall within expected technical variation (the median of log10 differences in exon-level DNA molecule coverage between short draw and reference conditions fell within +/- 0.125), indicating no meaningful loss of sensitivity for detecting somatic variants. Among the 87,305 clinical samples tested by Guardant360 CDx or LDT, median cfDNA yield was 25ng, with 98.5% yielding at least 5 ng, 88.4% at least 10ng, 73.5% at least 15 ng, and 17.9% at least 60ng. Clinically actionable biomarkers are detectable in low input samples. Of the Guardant360 CDx samples yielding 5-15ng cfDNA input, an average of 0.64 clinically significant variants was reported per sample. With the robust analytical performance demonstrated at low inputs, Guardant360 CDx (a 5ng cutoff) may provide tumor profiling results to guide therapy decisions for about 34% more patients compared to some liquid biopsies that use 2 BCTs for minimal 30ng cfDNA yield (a 15 ng cutoff). Retrospective studies for pharma research are often performed with as little as 2mL of plasma, meaning Guardant360 CDx can return results on 88.4% of such samples whereas other technologies may only be able to address 17.9% (extrapolated from the cfDNA yield distribution for 10mL whole blood yielding 4mL plasma). Citation Format: Aaron O. Richardson, Aaron Hardin, Soni Shukla, Jing Zhao, Catalin Barbacioru, Hilda Beas, Carin Espenschied, Adrian Bubie, Jamie Hutchins, Han-Yu Chuang, Tingting Jiang, Darya Chudova. The liquid biopsy Guardant360 CDx has robust performance at low inputs allowing for high rate of returning patient results [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 572.

Baseline Disease Characteristics and Diagnostic Patterns for NDMM of the Connect® MM Registry: Observations over Time in Cohort 1 (2009-2011) and Cohort 2 (2012-2016)

Introduction: Patients with multiple myeloma (MM) experience clinical manifestations of hypercalcemia, renal insufficiency, anemia, or bone lesions. The National Comprehensive Cancer Network (NCCN) recommends specific testing as part of the initial workup of patients suspected of having MM. Connect MM is the first and largest US-based, multicenter, prospective observational registry of patients with newly diagnosed MM (NDMM). This registry includes patients with NDMM treated in community, academic, and government practices, thus allowing a reasonable generalizability to diagnostic patterns for the US. Previous work characterized baseline characteristics for patients enrolled in the first cohort of the registry (Rifkin, Clin Lymph Myeloma Leuk, 2014). The primary objectives of this analysis were to describe the baseline demographic and disease characteristics and to analyze the completion of diagnostic work-up of NDMM patients enrolled from 2009 to 2016.Methods: Connect MM (NCT01081028) was initiated in September 2009 at 250 community and academic sites. Patients were enrolled sequentially in 2 cohorts. Cohort 1 enrolled 1493 patients with NDMM from September 2009 to December 2011, and Cohort 2 enrolled 1518 patients with NDMM from December 2012 to April 2016. This current analysis was conducted in the populations of treated patients in Cohort 1 (n = 1450) and Cohort 2 (n = 1462). Baseline demographics and disease characteristics for Cohorts 1 and 2 individually were evaluated. The usage of NCCN-suggested diagnostic work-up as part of the initial diagnostic characterization of NDMM was also examined.Results: Across both cohorts, most patients (84%) were treated at community sites, with some in academic (15%) and government (1%) centers. The data cutoff date was April 2017. The median follow-up for Cohort 1 is 39.3 months and for Cohort 2 is 21.4 months. Baseline characteristics are listed in the Table. Cohorts 1 and 2 were similar in age (median 67 years), sex (57% male), and race (83% white). Patients with a documented history of MGUS, smoldering myeloma, or asymptomatic myeloma were uncommon (<10%) in both cohorts. Notably, ISS staging at baseline was reported for 59% and 51% of patients in Cohorts 1 and 2, respectively. The Figure lists the completed NCCN recommended diagnostic procedures. Significant differences were detected between the two cohorts in five assessments. The assessment of β2-microglobulin was reported for 74% (1070 of 1450) of patients in Cohort 1 compared with 66% (961 of 1462) in Cohort 2. Protein electrophoresis was assessed more frequently in Cohort 2 (99%; 1447 of 1462) vs Cohort 1 (78%; 1131 of 1450). Likewise, the serum free light chain ratio was assessed more frequently in Cohort 2 (72%; 1050 of 1462) than Cohort 1 (62%; 900 of 1450). Conventional cytogenetic analysis and FISH analysis were performed more frequently in Cohort 2 than in Cohort 1: 75% vs 64% and 77% vs 60%, respectively.Conclusions: This analysis outlines the diagnostic patterns from a real-world, multi-institutional registry of NDMM in the US. Results from this analysis indicate that the baseline demographics were largely unchanged from Cohort 1 and Cohort 2, which supports the pooling of data for future analyses. The multicenter nature of these data may better reflect clinical practice compared with single-center databases. The baseline testing of key factors required for accurate diagnosis and assessment, and adequate monitoring of patients with NDMM to guide therapy decisions is variable. Missing baseline diagnostic work-up assessments may impact ISS staging and risk stratification. Our findings suggest a better adherence to guidelines and adoption of diagnostic testing as standard of care over time. [Display omitted] DisclosuresNarang:Celgene: Consultancy, Speakers Bureau; Janssen: Speakers Bureau. Abonour:Takeda: Other: Steering committee, Research Funding; Prothena: Research Funding; Celgene: Other: Steering committee, Research Funding. Durie:Takeda: Consultancy; Janssen: Consultancy. Gasparetto:Janssen, BMS, Celgene, Takeda: Honoraria; Celgene: Research Funding; Janssen, BMS, Celgene: Consultancy; Janssen, BMS, Celgene: Other: Travel, accommodations, or other expenses paid or reimbursed. Toomey:Myriad Genetics: Speakers Bureau; Dava Oncology: Other: Travel; Celgene: Consultancy. Hardin:Celgene: Consultancy. Jagannath:Medicom: Speakers Bureau; Novartis: Consultancy; MMRF: Speakers Bureau; Celgene: Consultancy; Merck: Consultancy; Bristol-Meyers Squibb: Consultancy. Terebelo:Janssen: Speakers Bureau; Takeda: Speakers Bureau; Pharmacyclics: Speakers Bureau; Celgene: Consultancy. Wagner:EveryFit: Consultancy; Gilead: Consultancy; Janssen: Consultancy. Srinivasan:Celgene: Employment. Flick:Celgene: Employment. Zafar:Celgene Corporation: Employment. Kitali:Celgene: Employment. Agarwal:Celgene Corporation: Employment. Rifkin:Celgene: Consultancy; EMD Serono: Consultancy; Sandoz: Consultancy; Takeda: Consultancy; McKesson: Other: Stock; Boehringer Ingelheim: Consultancy; Amgen: Consultancy.

Change in management based on actionable mutations in metastatic breast cancer in an ethnically diverse cohort: Single institution experience.

e13067 Background: Recently, next generation sequencing (NGS) has been used with increasing frequency to guide therapy decisions for patients with metastatic solid tumors. NGS is a DNA sequencing technology that detects somatically acquired mutations. If an actionable mutation is identified, it may affect prognosis and guide therapy. At our institution we serve a large proportion of minority and underserved patients and analyzed their NGS results to determine if there was a change in management. Methods: Patients with metastatic breast cancer treated at one of two sites at Baylor College of Medicine who underwent NGS via Tempus between 2018-2020 were included. Tempus provided access to the variant database for these patients. We analyzed the charts of 43 patients who underwent NGS via Tempus on tissue, blood or both. In those patients with clinically actionable mutations, we noted if there was a change in management. Utilizing Redcap, we extracted demographics, sites of metastasis, biomarker activity and site, genomic sequencing, and duration and sequencing of therapies given along with clinical trial information. Results: Of the 43 patients included in this analysis, the mean age was 55 years, 33% were African American, 30% were Hispanic, 21% were white/non-Hispanic, 12% were Asian, 4% were other. Two thirds of patients were treated in the Harris Health System (a safety net hospital with a unique and diverse population) while one third was treated at the Baylor St. Luke’s Medical Center (a private academically affiliated institution). Of the 43 patients, 14 had PIK3CA mutations and 3 had a change in management. 2 patients had microsatellite instability (MSI) and received immunotherapy, and 1 patient had a HER2 mutation and entered a clinical trial with Neratinib. Additionally, 2 patients were incidentally found to have MUTYH germline mutation which is associated with polyposis. Conclusions: With increasing frequency, patients with metastatic malignancy undergo NGS in order to determine if there is an actionable mutation that can guide their next line of treatment. However, this technology could be cost prohibitive for many underserved patients. Our study analyzes a unique and diverse population of patients, many of whom are underserved. We were able conduct this testing in our cohort, study the frequency of somatic mutations and monitor for change in treatment. Of the variants analyzed, PIK3CA mutations are actionable and patients can receive Alpelisib + Fulvestrant- however many did not. There was not a large shift in management based on the incorporation of this DNA sequencing technology which suggests that, unlike the case of other solid tumors, there aren’t yet as many actionable targets for patients with metastatic breast cancer. Shared decision making along with consideration of cost is paramount for these patients as we shift into an era of highly personalized medicine.

Fast lightweight accurate xenograft sorting

MotivationWith an increasing number of patient-derived xenograft (PDX) models being created and subsequently sequenced to study tumor heterogeneity and to guide therapy decisions, there is a similarly increasing need for methods to separate reads originating from the graft (human) tumor and reads originating from the host species’ (mouse) surrounding tissue. Two kinds of methods are in use: On the one hand, alignment-based tools require that reads are mapped and aligned (by an external mapper/aligner) to the host and graft genomes separately first; the tool itself then processes the resulting alignments and quality metrics (typically BAM files) to assign each read or read pair. On the other hand, alignment-free tools work directly on the raw read data (typically FASTQ files). Recent studies compare different approaches and tools, with varying results.ResultsWe show that alignment-free methods for xenograft sorting are superior concerning CPU time usage and equivalent in accuracy. We improve upon the state of the art sorting by presenting a fast lightweight approach based on three-way bucketed quotiented Cuckoo hashing. Our hash table requires memory comparable to an FM index typically used for read alignment and less than other alignment-free approaches. It allows extremely fast lookups and uses less CPU time than other alignment-free methods and alignment-based methods at similar accuracy. Several engineering steps (e.g., shortcuts for unsuccessful lookups, software prefetching) improve the performance even further.AvailabilityOur software xengsort is available under the MIT license at http://gitlab.com/genomeinformatics/xengsort. It is written in numba-compiled Python and comes with sample Snakemake workflows for hash table construction and dataset processing.

New Therapeutic Landscape in Neuromyelitis Optica.

Purpose of reviewThis review discusses the current treatment trends and emerging therapeutic landscape for patients with neuromyelitis optica spectrum disorder (NMOSD).Recent findingsConventional immune suppressive therapies, such as B cell depletion, have been used for long-term treatment. However, the availability of recent FDA-approved and investigational drugs has made therapeutic choices for NMOSD more complex.SummaryRecent randomized clinical trials have shown that eculizumab, inebilizumab, and satralizumab are efficacious therapies for AQP4 seropositive NMOSD. These therapies may not have the same benefit in patients with seronegative NMOSD, including MOG-associated disease, and further investigation is required in this population. Reliable biomarkers to guide therapy decisions are urgently needed. There is a plethora of promising investigational therapies currently in the pipeline with exciting and novel mechanisms of action.

Philadelphia chromosome positive chronic myeloid leukemia with 5q deletion at diagnosis

BackgroundAlthough, molecular genetic analyses became more and more important to guide therapy decisions in leukemia, banding cytogenetic analysis has retained its vital role in diagnosis and monitoring of chronic myeloid leukemia (CML), by quick and easy enabling identification of pathognomonic Philadelphia chromosome (Ph).Case presentationA 45 year old female presented with characteristic hematological features of CML in chronic phase; cytogenetic studies revealed the presence of the typical Ph and a deletion of almost entire long arm of a chromosome 5.Conclusion5q deletions have rarely been reported in CML. Those seen yet were either associated with tyrosine kinase inhibitor therapy or detected post allogeneic stem cell transplantation. To our knowledge, this is the first case of Ph positive CML accompanied by a 5q deletion.

Longitudinal Multi-Parametric Liquid Biopsy Approach Identifies Unique Features of Circulating Tumor Cell, Extracellular Vesicle, and Cell-Free DNA Characterization for Disease Monitoring in Metastatic Breast Cancer Patients.

Dynamics of mRNA from circulating tumor cells (CTCs), mRNA from extracellular vesicles (EVs), and cell-free DNA (cfDNA) were assessed to examine the relevance of a longitudinal multi-parametric liquid biopsy strategy. Eighteen milliliters of blood was drawn from 27 hormone receptor-positive and human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC) patients at disease progression and at two subsequent radiologic staging time points. CTC mRNA and EV mRNA were analyzed using multi-marker qPCR, and cfDNA was analyzed using targeted next-generation sequencing (NGS). The presence of ERBB2 or ERBB3 overexpression signals in CTCs significantly correlated with disease progression (87% specificity, 36% sensitivity, p-value = 0.023), and the presence of either ERBB3 signals in CTCs or EVs or cfDNA variants in ERBB3 also showed a significant association with progressive MBC. Fluctuations during treatment were detected in the EV fraction with the appearance of hitherto undetected ERCC1 signals correlating with progressive disease (97% specificity, 18% sensitivity, p-value = 0.030). Allele frequency development of ESR1 and PIK3CA variants detected at subsequent staging time points could be used as a predictor for therapy success and, importantly, might help guide therapy decisions. The three analytes, each with their own unique features for disease monitoring, were shown to be complementary, underlining the usefulness of the longitudinal multi-parametric liquid biopsy approach.

In vivo detection of teriflunomide-derived fluorine signal during neuroinflammation using fluorine MR spectroscopy.

Background: Magnetic resonance imaging (MRI) is indispensable for diagnosing neurological conditions such as multiple sclerosis (MS). MRI also supports decisions regarding the choice of disease-modifying drugs (DMDs). Determining in vivo tissue concentrations of DMDs has the potential to become an essential clinical tool for therapeutic drug monitoring (TDM). The aim here was to examine the feasibility of fluorine-19 (19F) MR methods to detect the fluorinated DMD teriflunomide (TF) during normal and pathological conditions.Methods: We used 19F MR spectroscopy to detect TF in the experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis (MS) in vivo. Prior to the in vivo investigations we characterized the MR properties of TF in vitro. We studied the impact of pH and protein binding as well as MR contrast agents.Results: We could detect TF in vivo and could follow the 19F MR signal over different time points of disease. We quantified TF concentrations in different tissues using HPLC/MS and showed a significant correlation between ex vivo TF levels in serum and the ex vivo 19F MR signal.Conclusion: This study demonstrates the feasibility of 19F MR methods to detect TF during neuroinflammation in vivo. It also highlights the need for further technological developments in this field. The ultimate goal is to add 19F MR protocols to conventional 1H MRI protocols in clinical practice to guide therapy decisions.

CD123 as a Biomarker in Hematolymphoid Malignancies: Principles of Detection and Targeted Therapies.

Simple SummaryCD123 is overexpressed in multiple hematologic malignancies. Advances in CD123-targeted therapies over the past decade have positioned this molecule as an integral biomarker in current practice. This review provides an overview of CD123 biology and in-depth discussion of clinical laboratory techniques used to determine CD123 expression in various hematolymphoid neoplasms. In addition, we describe various pharmacologic strategies and agents that are available or under evaluation for targeting CD123.CD123, the α chain of the interleukin 3 receptor, is a cytokine receptor that is overexpressed in multiple hematolymphoid neoplasms, including acute myeloid leukemia, blastic plasmacytoid dendritic cell neoplasm, acute lymphoblastic leukemia, hairy cell leukemia, and systemic mastocytosis. Importantly, CD123 expression is upregulated in leukemic stem cells relative to non-neoplastic hematopoietic stem cells, which makes it a useful diagnostic and therapeutic biomarker in hematologic malignancies. Varying levels of evidence have shown that CD123-targeted therapy represents a promising therapeutic approach in several cancers. Tagraxofusp, an anti-CD123 antibody conjugated to a diphtheria toxin, has been approved for use in patients with blastic plasmacytoid dendritic cell neoplasm. Multiple clinical trials are investigating the use of various CD123-targeting agents, including chimeric antigen receptor-modified T cells (expressing CD123, monoclonal antibodies, combined CD3-CD123 dual-affinity retargeting antibody therapy, recombinant fusion proteins, and CD123-engager T cells. In this review, we provide an overview of laboratory techniques used to evaluate and monitor CD123 expression, describe the strengths and limitations of detecting this biomarker in guiding therapy decisions, and provide an overview of the pharmacologic principles and strategies used in CD123-targeted therapies.

Efficacy and safety of sofosbuvir-based pangenotypic direct-acting antiviral agents for chronic hepatitis C patients without genotype determination: Real-world experience of a retrospective study.

Several new, pangenotypic direct-acting antiviral agents (DAAs) have been approved, may reduce the need for genotyping to guide therapy decisions for patients with chronic hepatitis C (CHC).This study aimed to investigate the efficacy and safety of Sofosbuvir (SOF)-based pangenotypic DAAs therapy for CHC patients without genotype (GT determination in the real-world practice.This retrospective cohort study included treatment-naïve CHC patients without GT determination, who received SOF-based DAAs therapy, including 400 mg SOF plus 60 mg daclatasvir (DCV) daily or 400 mg SOF plus 100 mg velpatasvir (VEL) daily for 12 or 24 weeks. Clinical and laboratory data, including sustained virologic response (SVR), were obtained at baseline, end of treatment (EOT), 12 weeks after EOT, and 48 weeks after EOT.A total of 95 CHC patients, including 30 (31.58%) had liver cirrhosis were enrolled. SVR rates after 12 weeks of treatment (SVR12) was 96.84% (92/95), including 96.20% (76/79) of patients receiving SOF plus DCV and 100% (16/16) of patients receiving SOF plus VEL. For 92 patients achieving an SVR12, no virological relapse was observed at 48 weeks after EOT. Furthermore, serum evaluation of liver fibrosis aspartate aminotransferase-to-platelet ratio index and Fibrosis-4 score were decreased significantly at EOT and 12 weeks after EOT, compared to pre-treatment values (both P < .05). Treatment was well-tolerated by our patients.SOF-based pangenotypic DAAs including SOF plus DCV and SOF plus VEL, were effective and safe for CHC patients without GT determination in this study. This may provide a potential simple strategy for CHC treatment without GT determination.

Early Prediction of Response to Neoadjuvant Chemotherapy in Breast Cancer Sonography Using Siamese Convolutional Neural Networks.

Early prediction of response to neoadjuvant chemotherapy (NAC) in breast cancer is crucial for guiding therapy decisions. In this work, we propose a deep learning based approach for the early NAC response prediction in ultrasound (US) imaging. We used transfer learning with deep convolutional neural networks (CNNs) to develop the response prediction models. The usefulness of two transfer learning techniques was examined. First, a CNN pre-trained on the ImageNet dataset was utilized. Second, we applied double transfer learning, the CNN pre-trained on the ImageNet dataset was additionally fine-tuned with breast mass US images to differentiate malignant and benign lesions. Two prediction tasks were investigated. First, a L1 regularized logistic regression prediction model was developed based on generic neural features extracted from US images collected before the chemotherapy (apriori prediction). Second, Siamese CNNs were used to quantify differences between US images collected before the treatment and after the first and second course of NAC. The proposed methods were evaluated using US data collected from 39 tumors. The better performing deep learning models achieved areas under the receiver operating characteristic curve of 0.797 and 0.847in the case of the a priori prediction and the Siamese model, respectively. The proposed approach was compared with a method based on handcrafted morphological features. Our study presents the feasibility of using transfer learning with CNNs for the NAC response prediction in US imaging.

Candidate protein biomarkers in pancreatic neuroendocrine neoplasms grade 3

Pancreatic neuroendocrine neoplasms (PanNENs) are rare tumours that compose 1–2% of all pancreatic tumours.Patients with metastatic grade 3 neoplasia are usually treated with chemotherapy but have a poor progression-free and overall survival. According to the WHO 2017 classification, they are divided into neuroendocrine tumours (NETs) G3 and neuroendocrine carcinomas (NECs). Despite the new classification, new diagnostic and prognostic biomarkers are needed to sub-categorise the patients and to help guide therapy decisions. Blood from 42 patients and 42 healthy controls were screened for the presence of 92 proteins with the Immuno-Oncology panel using the Proximity Extension Assay provided by Olink Biosciences. Immunohistochemical staining of FAS ligand (FASLG) was performed on 16 patient tumour specimens using a commercial antibody. Fifty-four out of 87 evaluable proteins differed significantly in concentration between blood from patients and blood from healthy controls. FASLG was the only protein for which the concentration in blood was significantly lower in patients compared to controls and the levels correlated negatively to Ki-67 index. Seven of 14 evaluable PanNEN G3 specimens showed FASLG immunoreactivity in the tumour cells while there was scattered immunoreactivity in immune cells. Positive FASLG immunoreactivity correlated to well-differentiated morphology.FASLG concentration in blood was significantly lower in patients with pancreatic NENs G3 compared to controls, and the expression in tumour tissue was variable. Furthermore, FASLG was negatively correlated to Ki-67 and was more frequently expressed in well-differentiated tumours. Taken together, these results may suggest a role of FASLG in PanNENs.

Abstract A51: Personalized monitoring of treatment response using Targeted Digital Sequencing of circulating tumor DNA

Abstract Background: Accurate circulating biomarkers for detecting residual disease can help guide therapy decisions, particularly in early-stage cancer patients. However, currently available methods lack the sensitivity required to confidently assess the presence of residual disease in patients with low tumor burden. To address this need, we have developed TARDIS (Targeted Digital Sequencing), a personalized, multiplexed amplicon sequencing method capable of tracking as many as 100 or more mutations simultaneously. Methods: We obtained tumor biopsies and longitudinal plasma samples from patients with early-stage breast cancer, glioblastoma, and pancreatic cancer. Each tumor biopsy was analyzed whole-exome sequencing. Founder mutations were selected, accounting for copy number alterations (analyzed using sequenza) and a consensus allele fraction approach that combined pyclone and custom in-house methods. Patient-specific TARDIS primers were designed to detect these mutations in plasma cfDNA. Error suppression in TARDIS was achieved using a combination of unique molecular identifiers and fragment sizes to group sequencing reads into read families. Results: In 33 patients with early-stage breast cancer treated with neoadjuvant therapy, we targeted between 3 and 116 (mean 30) mutations per patient and analyzed between 1 and 4 longitudinal plasma samples using TARDIS. Prior to treatment, we detected ctDNA in 100% patients with Stage I-III breast cancer (n=32, 95% CI= 89%-100%). We detected tumor-specific mutations in 100% of baseline breast cancer plasma samples. After completion of neoadjuvant therapy and before surgery, ctDNA levels were significantly lower in patients with pathologic complete response (pathCR, no evidence of disease at surgery) compared to patients with residual disease (median tumor fractions 0.003% and 0.017%, respectively, p=0.0058, AUC=0.83). Conclusions: TARDIS enables highly sensitive detection of ctDNA in patients with nonmetastatic cancers. Analysis of longitudinal plasma samples using TARDIS holds promise for personalizing the extent of treatment in patients with curable disease. Multiple clinical validation studies across cancer types are ongoing to define quantitative thresholds for changes in ctDNA levels that could improve clinical decision making. Citation Format: Bradon R. McDonald, Tania Contente-Cuomo, Stephen-John Sammut, Michelle D. Stephens, Ahuva Odenheimer-Bergman, Brenda Ernst, Nieves Perdigones, Suet-Feung Chin, Maria Farooq, Rosa Mejia, Patricia A. Cronin, Karen S. Anderson, Heidi E. Kosiorek, Donald W. Northfelt, Ann E. McCullough, Bhavika K. Patel, Jeffrey N. Weitzel, Thomas P. Slavin, Carlos Caldas, Barbara A. Pockaj, Muhammed Murtaza. Personalized monitoring of treatment response using Targeted Digital Sequencing of circulating tumor DNA [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A51.

IGF-Child-Turcotte-Pugh score as a predictor of treatment outcome in Child-Pugh A, advanced hepatocellular carcinoma patients undergoing sorafenib therapy.

e16660 Background: Sorafenib is the first systemic therapy approved for advanced HCC treatment; with no accurate tool available to help predict survival and treatment outcome and to guide therapy decisions. Our novel blood-based insulin-like growth factor-1 (IGF)-Child-Turcotte-Pugh (CTP) score comprises levels of IGF-1, bilirubin, INR, and albumin. IGF-CP score significantly improved the prediction of HCC survival in our recently published studies. The current prospective study aimed to compare the overall survival (OS) and progression free survival (PFS) of 116 patients with CTP-A HCC treated with sorafenib whose score is reclassified as IGF-A (AA) to that of patients whose score is reclassified as IGF-B/C (AB/AC). Methods: After the approval of the institutional review boards and signing written informed consent, a total of 116 patients with HCC were prospectively enrolled and started on sorafenib and followed until progression or death. We calculated IGF-CTP scores, used Kaplan-Meier method and log rank test to estimate and compare time to event outcomes between subgroups of patients. Results: 116 patients were CTP class A, 87 of the patients with CTP class A were classified as IGF-CTP-A and had median OS of 13.16 ms (95% CI = 12.04 to 22.6 ms), and a median PFS of 5.82 months (ms) (95% CI = 4.34 to 9.14 ms), whereas 29 patients were reclassified as intermediate risk (IGF-CTP-B) and had had a higher risk of death with a shorter OS of 7.6 months (95% CI = 5.23 to 24.47 months) and shorter PFS of 3.49 months (95% CI = 2.53 to 5.26 months). There was higher overall rate of adverse events in the CTP-A patients reclassified as IGF-CTP B than IGF-CTP A especially in grade III-IV adverse events, upper GI Bleeding, lower GI Bleeding, nose bleeding, renal failure, liver failure, encephalopathy, fatigue, weight loss, anorexia, and vomiting. Conclusions: The results of this study support our biologically-driven hypothesis that among HCC patients with CTP-A class treated with sorafenib, those reclassified as IGF-CTP-B/C will have poorer prognosis in terms of shorter OS and PFS. Thus, our study provides an objective non-invasive strategy to better predict the outcome in HCC patients undergoing systemic therapy. Future validation of our IGF-1 score may lead to adopting it as a stratification tool in clinical trials as well as to predict HCC outcome and guide therapy decision in routine practice.

Isolation of Circulating Tumor Cells from Glioblastoma Patients by Direct Immunomagnetic Targeting

Glioblastoma (GBM) is the most common form of primary brain cancer in adults and tissue biopsies for diagnostic purposes are often inaccessible. The postulated idea that brain cancer cells cannot pass the blood–brain barrier to form circulating tumor cells (CTCs) has recently been overthrown and CTCs have been detected in the blood of GBM patients albeit in low numbers. Given the potential of CTCs to be analyzed for GBM biomarkers that may guide therapy decisions it is important to define methods to better isolate these cells. Here, we determined markers for immunomagnetic targeting and isolation of GBM-CTCs and confirmed their utility for CTC isolation from GBM patient blood samples. Further, we identified a new marker to distinguish isolated GBM-CTCs from residual lymphocytes.

Integrating the immune microenvironment of prostate cancerinduced bone disease.

Prostate cancer (PCa) is the most frequently diagnosed cancer for men in the U.S. but does not impede patient survival until the disease is metastatic. Metastatic lesions most frequently occur in the bone, which exhibits a distinct microenvironment of immune and bone cell populations. Advances in the diagnosis and treatment of primary PCa allow for the use of tailored therapeutic approaches based on biomarkers, protein expression, and histopathology. Understanding the molecular and cellular characteristics of primary tumors has advanced therapeutic development and survival for patients with PCa. Personalized medicine has only recently emerged for the treatment of metastatic bone lesions. Tumorinduced bone disease (TIBD) in patients with PCa can be classified into lytic, blastic, or mixed pathologies, with most patients exhibiting the blastic phenotype. Progress has been made in treating TIBD, but metastatic PCa has yet to be cured. Immune checkpoint inhibitors have exhibited limited responses in immunosuppressive PCa tumors, but have yet to be assessed in metastatic sites which may be susceptible to an increased inflammatory response. Recent discoveries have uncovered distinct tumor microenvironments (TMEs) of blastic and lytic bone metastases from patients with PCa, identifying actionable targets for therapeutic applications, including immune checkpoint inhibitors and targeted therapeutics. Enrichment for macrophages and T cells in patient samples suggests metastatic sites may be reappraised as immunologically targetable, despite their immunologically "cold" primary tumors. The practice of performing bone biopsies will help identify unique cellular and protein targets in the bone TME that can guide therapy decisions.

The Diagnostic, Prognostic, and Therapeutic Potential of Adaptive Immune Receptor Repertoire Profiling in Cancer.

Lymphocytes play a critical role in antitumor immune responses. They are directly targeted by some therapies, and the composition and spatial organization of intratumor T-cell populations is prognostic in some cancer types. A better understanding of lymphocyte population dynamics over the course of disease and in response to therapy is urgently needed to guide therapy decisions and to develop new therapy targets. Deep sequencing of the repertoire of antigen receptor-encoding genes expressed in a lymphocyte population has become a widely used approach for profiling the population's immune status. Lymphocyte antigen receptor repertoire deep sequencing data can be used to assess the clonal richness and diversity of lymphocyte populations; to track clone members over time, between tissues, and across lymphocyte subsets; to detect clonal expansion; and to detect the recruitment of new clones into a tissue. Repertoire sequencing is thus a critical complement to other methods of lymphocyte and immune profiling in cancer. This review describes the current state of knowledge based on repertoire sequencing studies conducted on human cancer patients, with a focus on studies of the T-cell receptor beta chain locus. The review then outlines important questions left unanswered and suggests future directions for the field.

MammaPrint guides treatment decisions in breast Cancer: results of the IMPACt trial

BackgroundIncreased usage of genomic risk assessment assays suggests increased reliance on data provided by these assays to guide therapy decisions. The current study aimed to assess the change in treatment decision and physician confidence based on the 70-gene risk of recurrence signature (70-GS, MammaPrint) and the 80-gene molecular subtype signature (80-GS, BluePrint) in early stage breast cancer patients.MethodsIMPACt, a prospective, case-only study, enrolled 452 patients between November 2015 and August 2017. The primary objective population included 358 patients with stage I-II, hormone receptor-positive, HER2-negative breast cancer. The recommended treatment plan and physician confidence were captured before and after receiving results for 70-GS and 80-GS. Treatment was started after obtaining results. The distribution of 70-GS High Risk (HR) and Low Risk (LR) patients was evaluated, in addition to the distribution of 80-GS compared to IHC status.ResultsThe 70-GS classified 62.5% (n = 224/358) of patients as LR and 37.5% (n = 134/358) as HR. Treatment decisions were changed for 24.0% (n = 86/358) of patients after receiving 70-GS and 80-GS results. Of the LR patients initially prescribed CT, 71.0% (44/62) had CT removed from their treatment recommendation. Of the HR patients not initially prescribed CT, 65.1% (41/63) had CT added. After receiving 70-GS results, CT was included in 83.6% (n = 112/134) of 70-GS HR patient treatment plans, and 91.5% (n = 205/224) of 70-GS LR patient treatment plans did not include CT. For patients who disagreed with the treatment recommended by their physicians, most (94.1%, n = 16/17) elected not to receive CT when it was recommended. For patients whose physician-recommended treatment plan was discordant with 70-GS results, discordance was significantly associated with age and lymph node status.ConclusionsThe IMPACt trial showed that treatment plans were 88.5% (n = 317/358) in agreement with 70-GS results, indicating that physicians make treatment decisions in clinical practice based on the 70-GS result. In clinically high risk, 70-GS Low Risk patients, there was a 60.0% reduction in treatment recommendations that include CT. Additionally, physicians reported having greater confidence in treatment decisions for their patients in 72% (n = 258/358) of cases after receiving 70-GS results.Trial registration“Measuring the Impact of MammaPrint on Adjuvant and Neoadjuvant Treatment in Breast Cancer Patients: A Prospective Registry” (NCT02670577) retrospectively registered on Jan 27, 2016.

A nomogram for individualized estimation of survival among adult patients with adrenocortical carcinoma after surgery: a retrospective analysis and multicenter validation study

BackgroundClinical outcome of adrenocortical carcinoma (ACC) varies because of its heterogeneous nature and reliable prognostic prediction model for adult ACC patients is limited. The objective of this study was to develop and externally validate a nomogram for overall survival (OS) prediction in adult patients with ACC after surgery.MethodsBased on the data from the Surveillance Epidemiology, and End Results (SEER) database, adults patients diagnosed with ACC between January 1988 and December 2015 were identified and classified into a training set, comprised of 404 patients diagnosed between January 2007 and December 2015, and an internal validation set, comprised of 318 patients diagnosed between January 1988 and December 2006. The endpoint of this study was OS. The nomogram was developed using a multivariate Cox proportional hazards regression algorithm in the training set and its performance was evaluated in terms of its discriminative ability, calibration, and clinical usefulness. The nomogram was then validated using the internal SEER validation, also externally validated using the Cancer Genome Atlas set (TCGA, 82 patients diagnosed between 1998 and 2012) and a Chinese multicenter cohort dataset (82 patients diagnosed between December 2002 and May 2018), respectively.ResultsAge at diagnosis, T stage, N stage, and M stage were identified as independent predictors for OS. A nomogram incorporating these four predictors was constructed using the training set and demonstrated good calibration and discrimination (C-index 95% confidence interval [CI], 0.715 [0.679–0.751]), which was validated in the internal validation set (C-index [95% CI], 0.672 [0.637–0.707]), the TCGA set (C-index [95% CI], 0.810 [0.732–0.888]) and the Chinese multicenter set (C-index [95% CI], 0.726 [0.633–0.819]), respectively. Encouragingly, the nomogram was able to successfully distinguished patients with a high-risk of mortality in all enrolled patients and in the subgroup analyses. Decision curve analysis indicated that the nomogram was clinically useful and applicable.ConclusionsThe study presents a nomogram that incorporates clinicopathological predictors, which can accurately predict the OS of adult ACC patients after surgery. This model and the corresponding risk classification system have the potential to guide therapy decisions after surgery.

Niraparib in metastatic pancreatic cancer after previous chemotherapy (NIRA-PANC): A phase 2 trial.

TPS4168 Background: Attempts to improve therapy for patients with pancreatic adenocarcinoma with traditional chemotherapy have largely failed to meaningfully improve survival. Therefore, there is a critical need for identification of specific molecular changes that define prognosis and potentially guide therapy decisions. Defective DNA damage response pathways in pancreatic cancer represent a targeted opportunity for treatment. PARP inhibitors exert activity in tumor cells that may not be effectively able to repair initially single-stranded and cumulatively double-stranded DNA breaks and can have a heightened susceptibility in tumor cells over normal tissue. This concept is referred to as synthetic lethality. Niraparib is an orally available, potent, highly selective PARP-1 and -2 inhibitor. We are studying the efficacy of Niraparib in pancreatic cancer patients that harbor DNA repair defects. Methods: This study is funded by a research grant from TESARO. Pre-screening of patients to find biomarker positive patients is funded by KU Cancer Center. This is a phase II open label single arm trial in metastatic pancreatic cancer patients with germline or somatic mutations, either already known, or tested after consent to pre-screening tumor tissue analysis in BRCA1/2, PALB2, ATM, NBN, ATR, BRIP1, IDH1/2, RAD51, RAD51B/C/D, RAD54L, CDK12, BARD1, FAM175A, BAP1, CHEK1/2, GEN1, MRE11A, XRCC2, SHFM1, FANCD2, FANCA, FANCC, FANCG, RPA1, ARID1A. Patients are being treated with Niraparib 300mg or 200mg by mouth daily for 28 days (1 cycle = 28 days) (200mg dose is for participants whose baseline weight is &lt; 77 kg [169.756 lbs] or baseline platelet count is &lt; 150,000 µL). The primary objective is to assess antitumor efficacy of niraparib using Objective Response Rate per RECIST 1.1. Secondary objectives include PFS, OS, DCR, DOR, and safety. Eligible patients received &gt; 1 line of therapy, no prior PARP inhibitor(s), have measurable disease, and ECOG PS 0-1. Accrual target enrollment of 18 patients over a period of 24 months with a study duration of 30 months. Correlative studies include assessment of pharmacokinetics, circulating tumor cells and storing samples for future research. The trial is currently enrolling. Clinical trial information: NCT03553004.