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Emerging technologies for detection of circulating tumour DNA (ctDNA) are expanding the possibilities for clinical impact to patients with localized, potentially curable cancer. For such patients, ctDNA analysis could aid in prognostication, prediction of treatment response, longitudinal monitoring for adaptive treatment, and evaluation of minimal residual disease. Radiation oncologists currently have few tools at their disposal for predicting or rapidly assessing treatment efficacy. By reflecting the genetic and epigenetic makeup of tumours as well as dynamic changes with treatment, ctDNA as a biomarker for radiation response could enable new personalized treatment approaches. In this review, we will discuss recent advances in ctDNA technologies and potential clinical applications of ctDNA analysis throughout the therapeutic course. Furthermore, we will consider how ctDNA analysis could someday guide radiotherapy prescriptions by revealing differences in tumour radiophenotype.

Clinical studies have shown plasma Epstein-Barr virus (EBV) DNA level to be an independent prognostic biomarker for nasopharyngeal carcinoma (NPC). However, the proportion of NPC patients whose tumors are associated with EBV vary with geographic location, and there are a variety of assays for plasma EBV. To develop the level of evidence needed to demonstrate the clinical utility of plasma EBV DNA detection for NPC patients and encourage widespread adoption of this biomarker test in clinical laboratories, validated harmonized assays are needed. In 2015, the National Cancer Institute (NCI) convened a Workshop on Harmonization of EBV Testing for Nasopharyngeal Cancer, where experts in head and neck oncology and laboratory medicine addressed the limitations of currently available polymerase chain reaction-based EBV DNA quantitation assays and discussed strategies for advancing the development of harmonized EBV DNA assays and their appropriate clinical use. This article presents the key recommendations to direct future efforts in assay harmonization and validation.

Osteoradionecrosis (ORN) of the mandible is a late toxicity affecting patients treated with radiotherapy for head and neck malignancies. To the authors' knowledge, ORN has no standardized grading system and its reporting is based on retrospective findings in heterogeneous patient populations. The rate of ORN in the era of intensity-modulated radiotherapy (IMRT) still is unknown.The authors report the incidence of ORN from prospectively collected data regarding 1196 patients who were diagnosed with squamous cell carcinoma of the oropharynx and treated with curative-intent IMRT, with or without concomitant systemic treatment, from January 2005 to December 2014. Each case of ORN was graded according to its severity. Clinical and dosimetric comparisons were performed between patients with ORN and a matched control cohort of patients without ORN.The actuarial rate of ORN of the mandible was 3% at 1 year, 5% at 3 years, and 7% at 5 years. On multivariable analysis, smoking (hazard ratio, 1.9; 95% confidence interval, 1.07-3.4 [P = .03]) and T classification (hazard ratio, 1.78; 95% confidence interval, 1.02-3.1 [P = .041]) were found to be statistically significant risk factors. The presence of cardiovascular comorbidities, use of bisphosphonates, and pre-IMRT dental extractions were found to be different between the matched cohorts. The mandibular volume receiving 50 grays (Gy) (in cmORN is relatively uncommon among patients with oropharyngeal carcinoma who are treated with IMRT, but continues to occur beyond 5 years after treatment. Modifiable risk factors that are associated with higher rates of ORN include smoking and the use of bisphosphonates. Minimizing the volumes of the mandible receiving50 Gy or 60 Gy also may have an effect on the ORN rate. Cancer 2017;123:3691-3700. © 2017 American Cancer Society.

Epstein-Barr virus (EBV) DNA analysis has been shown to be useful for early detection, prognostication, and monitoring of treatment response of nasopharyngeal carcinoma (NPC), and the recent literature provides growing evidence of the clinical utility of EBV DNA testing, particularly to inform treatment decisions for NPC patients. Despite the fact that NPC is a rare disease, the NRG Oncology cooperative group has successfully activated a phase 2/3 randomized clinical trial for NPC with international partners and in that process has discovered that the development of a harmonized EBV DNA test is absolutely critical for integration into clinical trials and for future deployment in clinical and central laboratories. In November 2015, the National Cancer Institute (NCI) convened a workshop of international experts in the treatment of NPC and EBV testing to provide a forum for discussing the state of EBV DNA testing and its clinical utility, and to stimulate consideration of future studies and clinical practice guidelines for EBV DNA. This review provides a summary of that discussion.

We aimed to investigate the impact of lymph node ratio (LNR, number of positive nodes/total number of excised nodes) on regional-only-failure, distant-only-failure and overall survival (OS) in oral squamous cell carcinoma (OSCC).Retrospective review of pN0-2 OSCC-patients (1994-2012) treated with curative-surgery with neck dissection±postoperative radiotherapy (PORT)±concurrent chemotherapy. LNR was subjected to multivariable analysis (MVA) of regional-only-failure, distant-only-failure and OS.Overall 914 patients were identified; median follow-up: 51months (1-189); pN0: 482 (52.7%), pN1: 128 (14%), pN2a: 6 (0.7%); pN2b: 225 (24.6%); pN2c: 73 (8%); median number of dissected nodes: 36 (6-125); median number of pN+: 2 (1-49); median LNR for pN+ patients: 6%; extranodal extension: 187 (20.5%). Bilateral neck dissection: 368 (40.3%); PORT: 452 (49.5%); and concurrent chemotherapy: 80 (8.8%). High grade, lymphovascular invasion perineural invasion and pT3-4 were associated with high LNR. On MVA, LNR was associated with regional-only-failure (HR=1.06; 95%CI: 1.04-1.08; p0.001), distant-only-failure (HR=1.03; 95%CI: 1.02-1.05; p=0.004) and lower OS (HR=1.03; 95%CI: 1.02-1.05; p0.001). Similarly, in pN2-subgroup: LNR was associated with regional-only-failure (HR=1.04; 95%CI: 1.02-1.06; p0.001), distant-only-failure (HR=1.03; 95%CI: 1.01-1.06; p=0.045) and lower OS (HR=1.03; 95%CI: 1.02-1.04; p0.001).High LNR is associated with higher regional-only-failure/distant-only-failure and lower OS. LNR should be assessed in future prospective trials for selection of adjuvant therapy.

Individuals with Down syndrome (DS) are at elevated risk for acute leukemia, whereas solid tumors are uncommon, and most types, including breast cancers, have significantly lower-than-expected age-adjusted incidence rates. This article reports on a man with DS and breast cancer, thought to be the first in the literature, and presents the management of his cancer. The literature on malignancies in patients with DS is reviewed and the major epidemiologic studies that have examined the spectrum of cancer risk in individuals with DS are summarized. Potential environmental and genetic determinants of cancer risk are discussed, and the potential role of chromosomal mosaicism in cancer risk among patients with DS is explored. Trisomy of chromosome 21, which causes DS, provides an extra copy of genes with tumor suppressor or repressor functions. Recent studies have leveraged mouse and human genetics to uncover specific candidate genes on chromosome 21 that mediate these effects. In addition, global perturbations in gene expression programs have been observed, with potential effects on proliferation and self-renewal.

Purpose: Radiotherapy can result in lymphopenia, which has been linked to poorer survival. Here, we test the hypothesis that radiotherapy-induced lymphopenia is mediated by a tumor-secreted factor, Galectin-1 (Gal-1), which possesses T-cell proapoptotic activities. Experimental Design: Matched Gal-1 wild-type (WT) or null mice were implanted with Lewis lung carcinoma (LLC-1) that either expressed Gal-1 or had Gal-1 stably downregulated. Tumors were irradiated locally and circulating Gal-1 and T cells were measured. Tumor growth, lung metastasis, intratumoral T-cell apoptosis, and microvessel density count were quantified. Thiodigalactoside (TDG), a Gal-1 inhibitor, was used to inhibit Gal-1 function in another group of mice to validate the observations noted with Gal-1 downregulation. Lymphocyte counts, survival, and plasma Gal-1 were analyzed in cohorts of radiotherapy-treated lung [non–small cell lung cancer (NSCLC)] and head and neck cancer patients. Results: LLC irradiation increased Gal-1 secretion and decreased circulating T cells in mice, regardless of host Gal-1 expression. Inhibition of tumor Gal-1 with either shRNA or thiodigalactoside ablated radiotherapy-induced lymphopenia. Irradiated shGal-1 tumors showed significantly less intratumoral CD8+ T-cell apoptosis and microvessel density, which led to marked tumor growth delay and reduced lung metastasis compared with controls. Similar observations were made after thiodigalactoside treatment. Radiotherapy-induced lymphopenia was associated with poorer overall survival in patients with NSCLC treated with hypofractionated radiotherapy. Plasma Gal-1 increased whereas T-cell decreased after radiation in another group of patients. Conclusions: Radiotherapy-related systemic lymphopenia appeared to be mediated by radiotherapy-induced tumor Gal-1 secretion that could lead to tumor progression through intratumoral immune suppression and enhanced angiogenesis. Clin Cancer Res; 20(21); 5558–69. ©2014 AACR.

Summary: For practical and robust de novo identification of genomic fusions and breakpoints from targeted paired-end DNA sequencing data, we developed Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm (FACTERA). Our method has minimal external dependencies, works directly on a preexisting Binary Alignment/Map file and produces easily interpretable output. We demonstrate FACTERA’s ability to rapidly identify breakpoint-resolution fusion events with high sensitivity and specificity in patients with non-small cell lung cancer, including novel rearrangements. We anticipate that FACTERA will be broadly applicable to the discovery and analysis of clinically relevant fusions from both targeted and genome-wide sequencing datasets. Availability and implementation: http://factera.stanford.edu. Contact: arasha@stanford.edu or diehn@stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Currently, only patients with HER2-positive tumors are candidates for HER2-targeted therapies. However, recent clinical observations suggest that the survival of patients with HER2-low breast cancers, who lack HER2 amplification, may benefit from adjuvant therapy that targets HER2. In this study, we explored a mechanism through which these benefits may be obtained. Prompted by the hypothesis that HER2/HER3 signaling in breast tumor-initiating cells (TIC) promotes self-renewal and survival, we obtained evidence that neuregulin 1 (NRG1) produced by TICs promotes their proliferation and self-renewal in HER2-low tumors, including in triple-negative breast tumors. Pharmacologic inhibition of EGFR, HER2, or both receptors reduced breast TIC survival and self-renewal in vitro and in vivo and increased TIC sensitivity to ionizing radiation. Through a tissue microarray analysis, we found that NRG1 expression and associated HER2 activation occurred in a subset of HER2-low breast cancers. Our results offer an explanation for why HER2 inhibition blocks the growth of HER2-low breast tumors. Moreover, they argue that dual inhibition of EGFR and HER2 may offer a useful therapeutic strategy to target TICs in these tumors. In generating a mechanistic rationale to apply HER2-targeting therapies in patients with HER2-low tumors, this work shows why these therapies could benefit a considerably larger number of patients with breast cancer than they currently reach. Cancer Res; 74(1); 341–52. ©2013 AACR.

IntroductionCarcinomas of unknown primary site (CUP) of the head and neck have historically been worked up and managed heterogeneously. Failure to identify a primary site may result in large radiotherapy mucosal volumes. Transoral approaches such as Transoral Robotic Surgery (TORS) may improve the yield of identifying hidden primaries. We aim to assess the oncological and functional outcomes of a combined treatment approach with TORS and tailored radiotherapy.Methods and analysisTwenty-five patients with metastatic squamous cell carcinoma to the neck without clinical or radiographic evidence of a primary site will be enrolled in a phase II trial. Patients will undergo a diagnostic or therapeutic approach with TORS based on specific algorithms incorporating tailored radiotherapy according to the location and laterality of the primary tumour. The primary outcome is to evaluate the out-of-field failure rate over a 2-year period. Secondary outcomes include identification rates, survival outcomes, patient reported outcomes and functional swallowing outcomes.Ethics and disseminationThe University Health Network Research Ethics Board approved this study (ID 15–9767). The results will be published in an open access journal.Trial registration numberNCT03281499.

Introduction: Although induction chemotherapy results in a complete remission (CR) in ~70% of newly diagnosed AML patients, post-remission therapies are needed to eliminate minimal residual disease (MRD) and prevent relapse. Consolidation chemotherapy, either as definitive therapy or bridge to bone marrow transplantation (BMT), is currently the most common form of post-remission therapy. Yet, our understanding of its impact on MRD remains limited. In this study, we investigated the effects of consolidation chemotherapy on molecular MRD (mMRD) burden using ultra-deep next generation sequencing (NGS) and correlated treatment response with disease characteristics and survival outcomes in AML patients. Patients and Methods: 91 newly diagnosed AML patients who achieved CR following standard induction chemotherapy were evaluated. Targeted conventional NGS using a 54-gene panel was performed on whole blood (PB) or bone marrow samples collected at diagnosis. PB samples were collected during remission at two consecutive time points (T1 and T2), before and after 1 (n=79) or 2 (n=12) cycles of consolidation chemotherapy, for each patient. To detect mMRD, we used a custom 37-gene hybrid-capture panel and error-corrected NGS based on the duplex sequencing approach with a variant allele frequency (VAF) detection limit of ~1x10-4. For 10 patients, we also performed duplex sequencing analysis on their relapsed samples. Results: NGS of the diagnostic samples identified a total of 298 putative oncogenic mutations in 92% (n=84) of the 91 patients. Ninety percent of these mutations (n=267) were trackable by the custom hybrid-capture panel. Duplex sequencing detected persistence of 56% (n=149) of the trackable mutations in T1 samples; 34% (n=50) of which were clonal hematopoiesis-associated DTA mutations (those involving DNMT3A, TET2, or ASXL1), and the remaining 66% (n=99) were non-DTA mutations. Analysis of T2 samples showed that consolidation chemotherapy reduced the VAF of non-DTA mutations by a median of 73% and cleared 27% (n=27) of them at T2. In contrast, the burden of DTA mutations increased by 0.5% (P < 0.0001 by Mann-Whitney test), and only 2% (n=1) of the mutations was cleared (P = 0.0001 by Fisher's exact test). These findings are consistent with prior studies demonstrating that non-DTA mutations are more reliable markers of leukemic burden than DTA mutations. To study the impact of consolidation chemotherapy at the level of individual patients, the mean VAF of all persistent non-DTA mutations was calculated for each sample and used as a composite measure of mMRD burden (henceforth referred to as "cmMRD"). Analysis of the 10 patients with relapsed samples showed that cmMRD levels tracked well with achievement of remission and disease progression (Fig. 1). In the subset of patients with persistent non-DTA mutations at T1 (n=61), consolidation chemotherapy decreased cmMRD levels by a median of 36% at T2. However, we observed high interpatient variability (Fig. 2); 36% (n=22) of the patients experienced an increase in cmMRD burden after consolidation chemotherapy, and 36% (n=22) had less than a 1 log reduction. Only 28% (n=17) of the patients achieved a log reduction of greater than 1. The likelihood and magnitude of cmMRD response were significantly associated with cytogenetic risk (P = 0.026 by 3x3 Chi-square test; Fig. 3). The proportion of patients with favorable, intermediate, and poor-risk cytogenetics who experienced cmMRD expansion was 17%, 27%, and 71%, respectively. Consistent with these findings, a suboptimal response (defined as cmMRD ratio [T2/T1] > 0.4) was associated with inferior overall survival (HR = 3.29, P = 0.007 by log-rank test; Fig. 4). Conclusions: Our analysis showed that mMRD response to consolidation chemotherapy was highly variable among patients. Although consolidation chemotherapy was effective in deepening the remission for a subset of patients, it failed to lower MRD levels for a substantial proportion of patients, especially those with poor risk cytogenetics. These findings challenge the practice of using consolidation chemotherapy to achieve a deeper remission prior to BMT for high-risk patients and indicate that the opposite outcome may occur instead. NGS-based monitoring of mMRD can potentially be used to distinguish between patients who can remain on consolidation chemotherapy as definitive therapy and those who require a switch in post-remission therapy. Disclosures Gupta: Sierra Oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Incyte: Honoraria, Research Funding. Maze:Pfizer Inc: Consultancy; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees. McNamara:Novartis Pharmaceutical Canada Inc.: Consultancy. Minden:Trillium Therapetuics: Other: licensing agreement. Schimmer:Medivir Pharmaceuticals: Research Funding; Jazz Pharmaceuticals: Consultancy; Novartis Pharmaceuticals: Consultancy; Otsuka Pharmaceuticals: Consultancy. Schuh:Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees; Jazz: Honoraria, Membership on an entity's Board of Directors or advisory committees; Agios: Honoraria; Astellas: Honoraria, Membership on an entity's Board of Directors or advisory committees; Teva Canada Innovation: Honoraria, Membership on an entity's Board of Directors or advisory committees; AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees. Yee:Novartis, Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astellas, Celgene, Otsuka, Shire, Takeda: Membership on an entity's Board of Directors or advisory committees; Agensys, Astex, Hoffman La Roche, MedImmune, Merck, Millenium, Roche/Genentech: Research Funding. Bratman:SVB: Other: is co-inventor of a patent relating to circulating tumor DNA detection technology, which has been licensed to Roche Molecular Diagnostics.. Chan:Agios: Honoraria; AbbVie Pharmaceuticals: Research Funding; Celgene: Honoraria, Research Funding.

Background Limited data exist in the clonal dynamics of serial ctDNA as a predictive biomarker in advanced solid tumor pts receiving immune checkpoint blockade. Methods Pts with mixed solid tumors received single agent P (anti-PD-1) 200mg IV Q3wks in the investigator-initiated phase II INSPIRE trial (NCT02644369). ctDNA was assayed at baseline (B) and start of cycle 3 (C3) using a pt-specific amplicon-based NGS assay (Signatera™). Samples were considered ctDNA positive if≥2 of 16pt-specific targets met the qualifying confidence score threshold.Table: 113PTable: 113PEndpointORR N=72*CBR N=72*EndpointPFS N=73*OS N=73*SubgroupCR/PR N=15SD/PD N=57CR/PR/SD≥6 cycles N=22CR/PR/SD Results Of 94 pts are presented. Demographics: male 38%; median age=55 yrs (range 21–81); triple negative breast (19%), ovarian (19%) and head and neck (17%) cancers comprised the major malignancies. Median no. of P cycles=3 (range 1–35); follow up was 14m (range 0.6-35.4); RECIST responses: CR 3.2% (n=3), PR 14% (n=13), CBR (CR+PR+SD>6 cycles) 28% (n=26), RECIST/clinical PD (n=61/18; 65%/19%). Median PFS=2.5m and median OS=14m. In all 94 pts, ctDNAB correlated with PFS (adjusted HR 0.53, 95% CI 0.34-0.84, p=0.01) and OS (adjusted HR 0.47, 95% CI 0.28-0.8, p=0.01). Among 74 pts with both ctDNAB and ctDNAC3, the change (ΔctDNA) correlated with clinical efficacy parameters (Table). Conclusions Strong correlations exist between both ctDNAB and ΔctDNA with clinical outcome, suggesting both prognostic and predictive values in pts with mixed solid tumors. Clinical trial identification NCT02644369, December 31, 2015. Legal entity responsible for the study University Health Network, Toronto. Funding Merck, Netera, Terry Fox Research Institute, Princess Margaret Cancer Foundation. Disclosure S. Dashner: Shareholder / Stockholder / Stock options, Full / Part-time employment: Netera. A.R. Hansen: Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Merck; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): GlaxoSmithKline; Research grant / Funding (institution): Genentech/Roche; Research grant / Funding (institution): Bristol-Myers Squibb; Research grant / Funding (institution): Novartis; Research grant / Funding (institution): Boston Biomedical; Research grant / Funding (institution): Boehringer-Ingelheim; Research grant / Funding (institution): AstraZeneca/Medimmune; Research grant / Funding (institution): Janssen; Research grant / Funding (institution): Karyopharm. P. Bedard: Honoraria (institution), Advisory / Consultancy: Sanofi; Advisory / Consultancy, Research grant / Funding (institution): Roche/Genentech; Advisory / Consultancy, Research grant / Funding (institution): Bristol-Myers Squibb; Advisory / Consultancy, Research grant / Funding (institution): Pfizer; Research grant / Funding (institution): Novartis; Research grant / Funding (institution): GlaxoSmithKline; Research grant / Funding (institution): AstraZeneca/Medimmune; Research grant / Funding (institution): Merck; Research grant / Funding (institution): Nektar Therapeutics; Research grant / Funding (institution): Servier; Research grant / Funding (institution): Seattle Genetics; Research grant / Funding (institution): PTC Therapeutics; Research grant / Funding (institution): Oncothyreon. S. Lheureux: Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Merck; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca/Medimmune; Research grant / Funding (institution): Roche/Genentech; Research grant / Funding (institution): Tesaro. A. Spreafico: Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Merck; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Bristol-Myers Squibb; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Novartis; Honoraria (self), Advisory / Consultancy: Oncorus; Research grant / Funding (institution): Symphogen; Research grant / Funding (institution): AstraZeneca/Medimmune; Research grant / Funding (institution): Bayer; Research grant / Funding (institution): Surface Oncology; Research grant / Funding (institution): Northern Biologics; Research grant / Funding (institution): Janssen; Research grant / Funding (institution): Oncology/Johnson & Johnson; Research grant / Funding (institution): Array Biopharma. A.A. Razak: Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Boehringer Ingelheim; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Eli Lilly; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Merck; Research grant / Funding (institution): CASI Pharmaceuticals; Research grant / Funding (institution): Novartis; Research grant / Funding (institution): Deciphera; Research grant / Funding (institution): Karyopharm Therapeutics; Research grant / Funding (institution): Pfizer; Research grant / Funding (institution): Roche/Genentech; Research grant / Funding (institution): Boston Biomedical; Research grant / Funding (institution): Bristol-Myers Squibb; Research grant / Funding (institution): AstraZeneca/Medimmune; Research grant / Funding (institution): Amgen; Research grant / Funding (institution): GlaxoSmithKline; Research grant / Funding (institution): Blueprint Medicines; Research grant / Funding (institution): Merck; Research grant / Funding (institution): Abbvie; Research grant / Funding (institution): Adaptimmune. H. Wu: Shareholder / Stockholder / Stock options, Full / Part-time employment: Netera. S. Shchegrova: Shareholder / Stockholder / Stock options, Full / Part-time employment: Netera. P.S. Ohashi: Honoraria (self), Advisory / Consultancy: Symphogen Inc; Honoraria (self), Advisory / Consultancy: Providence Therapeutics. M. Louie: Shareholder / Stockholder / Stock options, Full / Part-time employment: Netera. H. Sethi: Shareholder / Stockholder / Stock options, Full / Part-time employment: Netera. A. Aleshin: Shareholder / Stockholder / Stock options, Full / Part-time employment: Netera. L.L. Siu: Honoraria (self), Advisory / Consultancy: Merck; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Pfiser; Honoraria (self), Advisory / Consultancy: Celgene; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca/Medimmune; Honoraria (self), Advisory / Consultancy: Morphosys; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Roche/Genentech; Honoraria (self), Advisory / Consultancy: GeneSeeq; Honoraria (self), Advisory / Consultancy: Loxo; Honoraria (self), Advisory / Consultancy: Oncorus; Honoraria (self), Advisory / Consultancy, Research grant / Funding (institution): Symphogen; Honoraria (self), Advisory / Consultancy: Seattle Genetics; Research grant / Funding (institution): Novartis; Research grant / Funding (institution): Bristol-Myers Squibb; Research grant / Funding (institution): Boerhinger-Ingelheim; Research grant / Funding (institution): GlaxoSmithKline; Research grant / Funding (institution): Karyopharm; Research grant / Funding (institution): Astellas; Research grant / Funding (institution): Bayer; Research grant / Funding (institution): Abbvie; Research grant / Funding (institution): Amgen; Research grant / Funding (institution): Intensity Therapeutics; Research grant / Funding (institution): Mirati; Research grant / Funding (institution): Shattucks; Spouse / Financial dependant: Agios. S. Bratman: Research grant / Funding (self): Nektar Therapeutics; Licensing / Royalties, Co-inventor of a patent relating to circulating tumor DNA detection technology: Roche Molecular Diagnostics. T.J. Pugh: Honoraria (self): Merck; Honoraria (self): Prosigna; Honoraria (self): Chrysalis Medical Advisors; Advisory / Consultancy: DynaCare; Research grant / Funding (self): Boehringer Ingelheim. All other authors have declared no conflicts of interest.

6045 Background: The ROMA LA-OPSCC ( NCT03759730) study prospectively evaluated the oral and gut microbiota in a single-centre cohort of LA-OPSCC patients (pts) receiving chemoradiotherapy (CRT). Methods: LA-OPSCC pts treated with definitive CRT (IMRT plus single-agent cisplatin) were eligible. Oral swabs over the tumor site and stool samples were collected at baseline and end of CRT (EOT). Taxonomic profiles were generated by 16S rRNA sequencing. ANOSIM/Kruskal-Wallis tests were used to identify differences between baseline and EOT samples. Results: A total of 96 samples were collected from 24 evaluable pts (100% compliance). Baseline characteristics: median age = 61 (range, 50-71); smoking status current/former/never = 5/11/8; HPV+/- = 23/1; stage I/II/III/IVA = 7/7/9/1; use of antibiotics = 12 pts. In oral swabs, decreased Shannon diversity ( p< 0.01) and changes in abundance (adjusted p value: q< 0.05) of multiple taxa including Prevotella, Veillonella, and Streptococcuswere observed at EOT vs baseline. Stool diversity did not differ between baseline and EOT ( p= 0.42), but abundance of Ruminoccocus and Roseburia decreased ( q< 0.05). CRT-associated changes remained significant when controlled for stage, smoking, antibiotics, cisplatin dose and mucositis grade ( p< 0.01). In HPV+ pts, stage I-II baseline oral swabs had higher relative abundance of Clostridium IV ( p= 0.02) and Escherichia ( p= 0.04) than stage III, which had higher Fusobacterium ( p =0.03) and Gemella ( p< 0.01). Relative abundance of Actinobacteria (p < 0.01), Proteobacteria (p < 0.01) and Firmicutes (p = 0.03) was higher in stool from stage III pts . Akkermansia muciniphila was present in 57% of the stage I-II stool samples, and 11% in stage III ( p= 0.04). Conclusions: CRT in LA-OPSCC is associated with increases in potentially pathogenic genera in the oropharynx. HPV+ stage III disease was associated with higher Fusobacterium in the oropharynx, which has been implicated in tumor metastases, and with decreased prevalence of the immunotherapy-response-associated species Akkermansia in stool. These preliminary observations suggest an opportunity for the evaluation of IO based therapies or manipulation of the gut microbiota in this patient population. Clinical trial information: NCT03759730.

2542 Background: Limited data exist in the clonal dynamics of serial ctDNA as a predictive biomarker in advanced solid tumor pts receiving immune checkpoint blockade. Methods: Pts with mixed solid tumors received single agent P (anti-PD-1) 200 mg IV Q3wks in the investigator-initiated phase II INSPIRE trial (NCT02644369). ctDNA was assayed at baseline (B) and start of cycle 3 (C3) using a pt-specific amplicon-based NGS assay (Signatera™). Samples were considered ctDNA positive if ≥2 of 16 pt-specific targets met the qualifying confidence score threshold. Results: Results of 70 pts are presented. Demographics: male 46%; median age=60 yrs (range 21–82); head and neck (20%), triple negative breast (14%) and ovarian (14%) cancers comprised the major malignancies. Median no. of P cycles=4 (range 2–35); follow up was 14m (range 2–29); RECIST responses: CR 2.9% (n=2), PR 17% (n=12), CBR (CR+PR+SD≥6 cycles) 31% (n=22), RECIST/clinical PD (n=43/10; 65%/15%). Median PFS=3.3m and median OS=17.8m. 68/70 pts had ctDNA detected at baseline (median=16/16 variants) demonstrating 97% sensitivity. Table shows correlation of ΔctDNA (ctDNAB compared to ctDNAC3) with clinical efficacy parameters, whereas ctDNAB values did not reach statistical significance. Conclusions: A strong correlation exists between ΔctDNA with OS, PFS, CBR and ORR with P, suggesting it is a potential predictive biomarker in pts with mixed solid tumors. Clinical trial information: NCT02644369. [Table: see text]

6085 Background: We developed and validated a prediction-score for distant metastases (DM) in major salivary gland carcinoma (SGC). Methods: Patients with SGC treated with curative-intent surgery +/- postoperative radiation therapy (PORT) at 4 tertiary cancer centers were divided into discovery (institution A&B) and validation (institution C&D) cohorts. Multivariable analysis using competing risk regression was used to identify predictors of DM in the discovery cohort and create a prediction score. The optimal score cut-off for high vs low-DM risk was determined using a minimal p-value approach. The results were subsequently evaluated in the validation cohort. The cumulative incidence and Kaplan-Meier methods were used to analyze DM and overall survival (OS), respectively. Results: Overall, 1035 patients were included (Table). In the discovery cohort, DM predictors (risk score coefficient) were: positive margin (0.6), pT3-4 (0.7), pN+ (0.7), lymphovascular invasion (LVI; 0.8), and high risk histology* (1.2). High DM-risk SGC was defined by sum of coefficients greater than 2. In the discovery cohort, the 5-year cumulative incidence of DM for high vs low risk SGC was 50% vs 8%; p < 0.01; these results were similar in the validation cohort (44% vs 4% at 5 years; p < 0.01). In the combined cohorts, this model predicted distant-only failure (40% vs 6%, p < 0.01) and late ( > 2yr post surgery) DM (22% vs 4%; p < 0.01). Patients with high DM-risk SGC had an increased incidence of DM in the subgroup receiving PORT (46% vs 8%; p < 0.01) or concurrent chemotherapy (71% vs 34%; p < 0.01). The 5-yr OS for high vs low risk SGC was 48% vs 92% (p < 0.01). Conclusions: This validated prediction score model may be used to identify SGC patients at increased risk for DM and select those who may benefit from prospective evaluation of treatment intensification and/or surveillance strategies. Baseline characteristics. [Table: see text]

6046 Background: Total cumulative cisplatin dose (CDDP-D) (concurrent/induction/adjuvant) in multimodality therapy for LA-NPC has been associated with survival at centers in Asia. We evaluated the survival impact of adjuvant chemotherapy (adj chemo) and total CDDP-D in a large, single institution Canadian cohort of LA-NPC. Methods: Patients (Pts) withWHO type II and III LA-NPC treated with concurrent IMRT with high-dose CDDP and adj chemo with CDDP/Carboplatin and 5-FU (maximum total/adjuvant CDDP-D= 540/240 mg/m2) between 2003-2016 were analyzed. EBER status was tested by ISH. Staging was classified by UICC/AJCC7thedition TNM. Kaplan-Meier 5-year (5y) for overall survival (OS) and recurrence-free survival (RFS) were calculated and compared by log-rank test betweenstage, adj chemo (yes vs no) and total CDDP-D (>300 vs ≤300mg/m2). Multivariable analysis (MVA) identified survival predictors. Results: A total of 312 pts were evaluated: median age = 49.8 (range 17.4-75.9); EBER+/-/unknown=67%/1%/32%; stage II/III/IV=2%/51%/47%; T4=36%; N3=17%; adj chemo=83% (21% switched to carboplatin); median total/adjuvant CDDP-D=380/160 mg/m2; median follow-up 7.6 years (range 0.6-14.9). 5y OS differed by stage II-III vs IV (95% vs 80%, p300 vs ≤300mg/m2 (89% vs 83%, p=0.02). Adj chemo and total CDDP-D impacted 5y OS in stage IV (table). 5y RFS was higher in stage IV with total CDDP-D >300 vs ≤300mg/m2 (74% vs 59%, p=0.03), with a trend in locoregional control (LRC) (91% vs 80%, p=0.05) but not significant on distant control (DC) (78% vs 72%, p=0.36). Conclusions: Total CDDP-D >300 mg/m2 impacts OS in the overall cohort. The benefit of adj chemo and total CDDP-D on OS and RFS is significant in stage IV but not stage II-III LA-NPC, mainly due to higher LRC rather than DC. [Table: see text]

Purpose To report the outcome of ipsilateral radiation therapy (RT) in human papillomavirus (HPV)-positive (HPV+) patients and HPV-negative (HPV−) patients with T1-T2N0-N2b tonsillar cancer treated 25 years after our initial historical cohort. Methods and Materials Patients with T1-T2N0-N2b tonsillar cancer who received ipsilateral RT or bilateral RT between 1999 and 2014 were reviewed. Overall survival (OS), local control (LC), regional control (RC), and grade 3 to 4 late toxicity (LT) were compared between ipsilateral RT and bilateral RT within HPV+ and HPV− patients, separately. Results HPV status was ascertained in 379/427 (88%) consecutive patients (ipsilateral RT: 62 HPV+, 34 HPV−; bilateral RT: 240 HPV+ 240, 41 HPV−). The proportion of ipsilateral RT by N category for HPV+ and HPV− patients were as follows: N0: 24/37 (65%) versus 28/48 (74%); N1: 21/49 (43%) versus 4/9 (44%); N2a: 10/39 (26%) versus 1/4 (25%); and N2b: 7/177 (4%) versus 1/24 (4%), respectively. Of the patients receiving ipsilateral RT, 94/96 (98%) were treated with RT alone. The median follow-up time was 5.03 years. The respective 5-year rates of OS, LC, RC, and LT were similar between ipsilateral RT and bilateral RT for the HPV+ patients (OS: 89% vs 87%, P =.55; LC: 97% vs 98%, P =.65; RC: 98% vs 97%, P =.27; LT: 17% vs 12%, P =.83) and HPV− patients (OS: 63% vs 48%, P =.27; LC: 90% vs 80%, P =.19; RC: 94% vs 83%, P =.14; LT: 15% vs 22%, P =.36). Of the 96 patients receiving ipsilateral RT, contralateral neck failure (CNF) occurred in 1/52 HPV+ patients and 1/34 HPV− patients. The 5-year CNF rates were 2% (95% CI: 1-9) (HPV+: 2% [0-14]; HPV−: 3% [0-21], P =.66). Five local failures (2 HPV+; 3 HPV−) and no distant failures were seen. The 5-year rates of LC, RC, and LT were 97% versus 90% ( P =.24), 98% versus 94% ( P =.25), and 18% versus 15% ( P =.75) for the HPV+ and HPV− cohorts, respectively. Osteoradionecrosis occurred in 9 patients: 6/47 (13%) treated with conventional RT and 3/49 (6%) with intensity modulated RT ( P =.32). Conclusion Ipsilateral radiation to selected patients with T1-T2N0-N2b tonsillar cancer results in equally excellent outcomes regardless of tumor HPV status.

Importance Transoral robotic surgery– or transoral laser microsurgery–assisted lingual tonsillectomy may improve the identification rate of hidden base-of-tongue (BOT) carcinoma presenting as head or neck carcinoma of unknown primary (CUP) site. Objective To evaluate the potential impact of lingual tonsillectomy in CUP site by comparing differences in radiotherapy volumes, dosimetry, and clinical outcomes for CUP site and T1-category BOT carcinoma. Design, Setting, and Participants Retrospective study of 115 patients treated at a tertiary cancer center between January 1, 2005, and December 31, 2013, that included patients with BOT carcinoma (category T1N1-3M0) and CUP site (category T0N1-3M0) with known p16 status. Fifty-four patients with T1-category BOT carcinoma (50 [92.6%] p16-positive) were treated with definitive intensity-modulated radiotherapy (IMRT), including 34 (63%) who received concurrent chemotherapy. Sixty-one patients with CUP site (38 [62.3%] p16-positive) received definitive (42 [68.9%]) or postoperative (19 [31.1%]) IMRT, including 22 (36%) who received concurrent chemotherapy. Interventions Definitive or postoperative IMRT, with or without concurrent chemotherapy. Main Outcomes and Measures Characteristics of mucosal clinical target volume (CTV-T), nodal CTV, and organ-at-risk dosimetry; local, regional, and distant control; cause-specific and overall survival; and Radiation Therapy Oncology Group grade 3 or higher late toxic effects. Results Of 115 participants, 104 (90.4%) were male; mean (SD) age was 59 (10) years. High-dose CTV-T was prescribed in all 54 patients with BOT carcinoma and 23 (37.7%) with CUP site (effect size [Δ], 62%; 95% CI, 50%-74%). Low-dose CTV-T included mucosal pharyngeal sites outside the oropharynx in no patients with BOT carcinoma and 26 (42.6%) (95% CI, 30%-54%) with CUP site, with greater low-dose CTV-T volume in CUP site than BOT carcinoma (113 vs 84 cm 3 ; Δ, 30 cm 3 ; 95% CI, 10-49 cm 3 ). Bilateral neck irradiation was used in 53 of 54 patients (98.1%) with BOT carcinoma and 46 of 61 (75.4%) with CUP site (Δ, 23%; 95% CI, 12% to 34%). Patients with BOT carcinoma received a higher maximum dose to the mandible (71 vs 67.2 Gy; Δ, 3.8 Gy; 95% CI, 1.6 to 6 Gy), with a nonsignificantly higher maximum dose (66.1 vs 62.8 Gy; 3.2 Gy; 95% CI, −0.1 to 6.5 Gy) and lower mean dose to the larynx (43.8 vs 47.1 Gy; 3.3 Gy; 95% CI, −0.3 to 6.9 Gy). There were no significant differences in local control, regional control, distant control, cause-specific survival, and overall survival between the BOT carcinoma and CUP site groups stratified by p16 status. Grade 3 Radiation Therapy Oncology Group late toxic effects occurred in 2 patients (3.3%) with CUP site (both neck fibrosis) and 5 (9.3%) with BOT carcinoma (2 neck fibrosis, 2 osteoradionecrosis, and 1 dysphagia). Conclusions and Relevance Intensity-modulated radiotherapy for CUP site or T1-category BOT carcinoma had similar clinical outcomes. Identifying hidden BOT primary carcinoma with novel approaches (eg, transoral robotic surgery and transoral laser microsurgery) may lead to changes in the radiotherapy target volume and dose prescription. Studies are needed to investigate the effect of these differences on quality of life and functional outcomes.

To explore the impact of tumor human papillomavirus (HPV) status, comorbidity, polypharmacy, and treatment intensity on overall survival (OS) of elderly oropharyngeal cancer (OPC) patients.All elderly (70 years) OPC patients receiving definitive (chemo-) radiation therapy in 2000 to 2013 were reviewed. Charlson comorbidity index (CCI, comorbidity alone) and the comorbidity-polypharmacy score (CPS, comorbidity and medication) were calculated. Overall survival was compared between HPV-positive (HPV+) and HPV-negative (HPV-) cohorts. Multivariable analyses (MVA) incorporating either the CCI (MVA-CCI) or the CPS (MVA-CPS) identified survival predictors.Among 231 of 287 patients (80%) with p16 staining, 117 were HPV+ and 114 HPV-. Systemic treatments were administered in 48 patients (21%) (chemotherapy 17; epidermal growth factor receptor inhibitor 31). The distribution of CCI (P=.59), CPS (P=.23), and age (P=.50) were similar between HPV+ versus HPV- cohorts. Median follow-up was 4.3 years. The HPV+ patients had better 5-year OS (57% vs 32%, P.001) versus HPV- patients. Multivariable analysis adjusted for T-/N-category confirmed that HPV+ status (MVA-CCI: hazard ratio [HR] 0.58, P=.01; MVA-CPS: HR 0.60, P=.02), Zubrod scale score (0-1) (MVA-CCI: HR 0.44, P.001; MVA-CPS: HR 0.43, P.001), and higher radiation therapy dose (MVA-CCI: HR 0.97, P=.001; MVA-CPS: HR 0.96, P.001) were correlated with higher OS. A marginal inverse correlation between CPS and OS was observed in the entire cohort (HR 1.05, P=.05) and was stronger for the HPV+ cohort (HR 1.11, P=.02). Nonsignificant higher OS was also found with ≤20 pack-years of smoking (MVA-CCI: P=.10; MVA-CPS: P=.15) and with systemic treatments (MVA-CCI: P=.13; MVA-CPS: P=.19). No association with OS was found for CCI (P=.46).Elderly HPV+ OPC patients have longer survival than their HPV- counterparts. Lower Zubrod scale score and higher radiation therapy dose are associated with longer OS, whereas fewer smoking pack-years and systemic agents have nonsignificant associations. Comorbidity-polypharmacy score, but not CCI, is correlated with OS, especially in HPV+ patients, suggesting the potential importance of assessing polypharmacy in addition to comorbidity burden in this population.

Despite the identification of circulating tumor cells (CTCs) and cell-free DNA (cfDNA) as potential blood-based biomarkers capable of providing prognostic and predictive information in cancer, they have not been incorporated into routine clinical practice. This resistance is due in part to technological limitations hampering CTC and cfDNA analysis, as well as a limited understanding of precisely how to interpret emergent biomarkers across various disease stages and tumor types. In recognition of these challenges, a group of researchers and clinicians focused on blood-based biomarker development met at the Canadian Cancer Trials Group (CCTG) Spring Meeting in Toronto, Canada on 29 April 2016 for a workshop discussing novel CTC/cfDNA technologies, interpretation of data obtained from CTCs versus cfDNA, challenges regarding disease evolution and heterogeneity, and logistical considerations for incorporation of CTCs/cfDNA into clinical trials, and ultimately into routine clinical use. The objectives of this workshop included discussion of the current barriers to clinical implementation and recent progress made in the field, as well as fueling meaningful collaborations and partnerships between researchers and clinicians. We anticipate that the considerations highlighted at this workshop will lead to advances in both basic and translational research and will ultimately impact patient management strategies and patient outcomes.

Introduction:Induction chemotherapy debulks the leukemic burden in AML patients. Blood count recovery usually occurs during the fourth week of starting chemotherapy in patients who achieve a morphologic remission in bone marrow. However, a subset of patients experience significantly delayed recovery. The relevance of delayed recovery on long-term clinical outcomes and its contributing factors have not been well studied. Specifically, the association between recurrent mutations in AML and hematologic recovery is unknown. Methods:We studied a total of 262 newly diagnosed adult AML patients treated between September 2014 and December 2017 at Princess Margaret Cancer Centre who achieved a complete remission (CR) or CR with incomplete count recovery (CRi) after one cycle of induction chemotherapy. The regimens consisted of 3+7 (N=194) and FLAG-IDA (N=68). We collected information on disease characteristics and blood count results at baseline and during chemotherapy. Mutation profiling of diagnostic samples was performed using a 54-gene next generation sequencing panel (TruSight Myeloid Sequencing Panel, Illumina). Detection of persistent mutations in remission samples was performed using a custom 37-gene duplex sequencing platform with a lower detection limit of ~0.05% variant allele frequency (VAF). Results:Of the cohort of 262 patients, 256 patients (97.7%) achieved neutrophil recovery (defined as > 1x109/L), with time to recovery ranging from 17 to 84 days. Two hundred forty-four (93.1%) patients achieved platelet recovery (defined as > 100x109/L); time to recovery ranged from 17 to 117 days. The percentage of patients who achieved neutrophil and platelet count recovery before day 35 was 82.4% and 84.0% respectively (Fig. 1). To evaluate the prognostic significance of delayed recovery, we categorized patients who achieved CR into two groups, "normal" or "delayed" recovery, according to whether they achieved recovery before or after day 35, respectively. Relapse-free survival (RFS) of patients with delayed recovery was significantly worse than those with normal recovery and only marginally better than those with CRi (P=0.02; Fig. 2). Analysis restricted to 3+7 treated patients showed the same trend (P=0.02), excluding the possibility that the inferior outcome was due to treatment of higher risk patients with more intensive regimens. To study the factors associated with delayed recovery, we performed multivariable Cox regression analysis that included clinical factors and mutations identified at the time of diagnosis as covariates. Four factors were found to be independently correlated with delayed recovery: treatment with FLAG-IDA, truncating ASXL1mutations, SRSF2mutations, and DNMT3AR882 mutations (Table 1). Because FLAG-IDA is the preferred frontline regimen for higher risk patients at our institution, we performed a secondary analysis restricted to patients treated with 3+7 to exclude chemotherapy regimen as a potential confounding variable. This analysis identified six independent factors: AML with myelodysplasia-related changes, lower hemoglobin levels at presentation, truncating ASXL1mutations, TET2mutations, CEBPAmutations, and DNMT3AR882 mutations (Table 1). Somatic mutations in DNMT3A, TET2, ASXL1, and SRSF2(DTAS) mutations are associated with preleukemic conditions, such as myelodysplastic syndrome and age-related clonal hematopoiesis, and frequently persist in remission. These mutations are acquired in hematopoietic stem cells resulting in their propagation to progenitors and terminally differentiated blood cells. We hypothesized that the persistence of DTAS mutations in progenitors might compromise their capacity for reconstitution of normal hematopoiesis resulting in delayed recovery. To test this hypothesis, we performed duplex sequencing on peripheral blood DNA samples collected from a random subset of 43 patients during remission. The detection of DTAS mutations in remission above a VAF of 2% was strongly associated with delayed recovery (P=0.0004; Fig. 3). Conclusion:Delayed hematologic recovery in AML patients after induction chemotherapy is associated with inferior RFS and persistence of preleukemic mutations (i.e., DTAS mutations). Our results support a model in which progenitors harboring DTAS mutations have reduced repopulation capacity leading to delayed hematologic recovery after induction chemotherapy. Disclosures Gupta: Incyte: Research Funding; Novartis: Consultancy, Honoraria, Research Funding. Schimmer:Otsuka Pharmaceuticals: Consultancy; Jazz Pharmaceuticals: Consultancy; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Medivir AB: Research Funding. Yee:Agensys, Astex, GSK, Onconova, Genentech/Roche: Research Funding; Celgene, Novartis, Otsuka: Membership on an entity's Board of Directors or advisory committees. Maze:Novartis: Consultancy, Honoraria. Bratman:Roche: Other: SVB is a co-inventor on a patent describing methods for circulating tumor DNA analysis, which has been licensed to Roche Molecular Diagnostics.. Schuh:Shire: Consultancy; Jazz: Consultancy; Novartis: Consultancy; Otsuka: Consultancy; Teva: Consultancy; Pfizer: Consultancy; Celgene: Consultancy; Amgen Inc.: Consultancy.

Introduction The limited improvement of acute myeloid leukemia (AML) patient survival rates over the last few decades reveals that the strategy of targeting AML after diagnosis provides limited success. In many solid cancers, early detection leads to decreased morbidity and improved survival suggesting that a similar approach may benefit AML patients. Recently, we showed that the initial genomic events that drive AML can be detected years before diagnosis and that individuals at increased risk share distinct features that differentiate them from those with benign age related clonal hematopoiesis (ARCH). However, the relative high incidence of ARCH and the low incidence of AML, along with the fact that ARCH is recurrently being driven by mutations that occur in genes associated with AML, impedes complete discrimination. High sequencing costs for the relative large number of mutated genes implicated with the disease further hinders clinical adaptation. Therefore, a better strategic approach that is focussed on the most informative mutations and the development of accurate tools for data mining would better estimate the risk for AML development and create applicable and cost-efficient screens for early detection of AML. Methods We hypothesize that the majority of the power to accurately predict the development of AML can be derived by a minimal number of pre-leukemic hotspot mutations (pLHM) and that improved accuracy of mutation calling algorithms will increase the discrimination between high and low risk cases. We developed a novel approach to differentiate technical errors from true mutations by accounting for local sequence features to derive contextual error signatures. We demonstrate that Error Correction by Signatures Integration (ECSI) detects mutations at a higher sensitivity and specificity when compared to other techniques. 320 blood samples taken years before AML diagnosis and 856 controls were interrogated for the presence of pLHM. This data was used to construct an AML prediction model that was tuned to achieve 100% positive predictive value. To estimate the frequency of individuals at the highest risk for AML development in the general population, we applied the model to a total of 42,838 individuals whose blood was sequenced in four independent ARCH studies. Results ECSI revealed that some pLHM lie within signatures with particularly high error rates. For example, DNMT3A-R882H is defined by the signature G[C>T]G that has the highest sequencing error rate of all. Our analysis suggests that this mutation and others might be over reported when error signatures are not being considered. As compared with other mutation calling techniques, our analysis unbiasedly increased the discrimination between cases and controls by accurately indicating the presence of mutations in pre-AML cases and flagging others that are not significantly above their corresponding signature's error-rate in the controls. We show that a highly specific AML prediction model can be generated by targeting a small number of genomic loci corresponding to changes in only 46 amino-acids previously reported to define AML with poor outcome. Testing our model on the four ARCH datasets pointed to 103 individuals who are at the highest risk for AML development. At least 6 could have been confirmed to developed hematological cancer after sampling. Conclusions The development of a technically simple tool for data mining that is reliable and has a rapid turnaround is a critical step for clinical adaptation of sequencing-based screens for early cancer detection. We present a novel mutation calling method that fulfills such criteria and provides an improved analytical sensitivity and specificity. We found that a minimal group of pLHM carries most of the information needed to accurately predict AML development. Focusing on such a small yet an informative number of mutations provides a 'two birds, one stone' strategic approach that enables better discrimination between pre-AML and benign ARCH at reduced costs. Implementing a highly effective and affordable genomic assay is an important step enabling a wider population screen to identify the portion of individuals at the highest risk for pre-malignant cell transformation with minimal false discovery rate. Populations targeted by our prediction model should be prioritized for frequent follow-up, clinical studies and further research to elucidate additional risk-parameters. Disclosures No relevant conflicts of interest to declare.

Purpose: Radiotherapy (RT) is the foundation of curative treatment regimens for many cancer types and is often delivered with drugs to produce synergistic effects. The “precision medicine” paradigm in which genomic biomarkers guide therapeutic decisions has eluded RT. To support preclinical discovery of biomarker-directed RT dose and drug combinations, we built a computational platform for integrating and interrogating radiogenomics data sets. Methods: RadioGx integrates in vitro cancer cell line survival data with multimodal molecular profiles from the NCI-60 and Cancer Cell Line Encyclopedia (CCLE) cell line panels. We fit published radiation response data from both clonogenic and high-throughput viability assays to established radiobiologic models of clonogenic survival. We assessed the concordance of radiation response profiles across different survival endpoints (i.e., surviving fraction at 2Gy [SF2] and Area Under the Curve of the radiobiologic model [AUC]). By comparing radiation response with transcriptomic data, we examined indicators of radiosensitivity at the pathway level. We integrated drug response data from Cancer Therapeutics Response Portal (CTRP v2) using an interface between RadioGx and our previously published pharmacogenomics platform, PharmacoGx. Using the oxygen modification factor in established radiobiologic models, we identified pathways that are enriched under hypoxic conditions. Results: RadioGx includes 600 radiation dose response data, 511 gene expression data sets, and 504 drug dose response data for chemotherapeutic compounds. Goodness-of-fit (given by R2 value) of the linear-quadratic radiobiologic model ranged from 0.927 to 0.99 (median=0.998, n=57) for the clonogenic assay and from 0.043 to 0.99 (median=0.952, n=535) for the viability assay. The concordance between SF2 and AUC using the clonogenic assay and the viability assay was 0.79 (n=12) and 0.82 (n=15), respectively. Among cell lines with survival data from both assays (n=28) across two different studies, the concordance of SF2 and AUC was 0.68 and 0.62, respectively. By interrogating the 504 cell lines that were profiled using the viability assay, we found drugs that behaved similar to RT were enriched in three pharmacologic classes, namely, drugs that impact mitosis, DNA replication, or cytoskeleton. Pathway analysis of radiation response under hypoxia revealed two key DNA repair pathways, namely, DNA double-strand break repair by NHEJ and DNA damage-induced 14-3-3, to be enriched compared to normoxic conditions. Conclusions: Our work is a major step towards analyzing preclinical models of radiation response using in vitro survival and transcriptomic data. RadioGx coupled with PharmacoGx lays the foundation for the identification of synergistic drug-RT combinations, which can further push the boundaries of translational research towards precision radiation medicine. Citation Format: Venkata S. Manem, Meghan Lambie, Petr Smirnov, Mark Freeman, Victor Kofia, Mohamed E. Abazeed, Scott V. Bratman, Benjamin Haibe-Kains. Therapeutic effects of radiotherapy on cancer cell lines using RadioGx computational platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3211.

Purpose: High-dose radiotherapy (RT) is a standard treatment for locally advanced head and neck squamous cell carcinoma (HNSCC). Despite known molecular prognostic biomarkers in HNSCC, such as the presence of human papillomavirus (HPV) within tumor tissues, RT regimens remain one-size-fits-all without any patient-specific individualization. We hypothesize that rapid release of circulating tumor DNA (ctDNA) can act as a biomarker of treatment response in HNSCC by reflecting tumor cell death in response to RT. Methods: Four HNSCC cell lines, two HPV- (Cal33, FaDu) and two HPV+ (HMS-001, 93-Vu147T), were evaluated for ctDNA release following single dose RT in vitro. Quantification of ctDNA was performed by quantitative polymerase chain reaction (qPCR) with primers amplifying the human long interspersed nuclear element 1 (hLINE1). RT-induced apoptosis was measured using a luminometric caspase 3/7 assay, and RT-induced senescence was evaluated using a fluorometric senescence associated β-galactocidase (SA-β-Gal) assay. The pan-caspase inhibitor, z-vad-fmk, was used to block RT-induced apoptosis. Subcutaneous cell-line xenografts were established in Nod-Scid-Gamma (NSG) mice, where plasma from serial blood draws was purified and quantified for ctDNA release using hLINE1 qPCR. Endpoint tumors were evaluated for mechanisms of cell death by histological staining. Results: HNSCC cell lines exhibited variable magnitude and timing of ctDNA release and apoptosis. Maximal ctDNA release occurred between 72 and 144 hours post-RT. The release of ctDNA was not correlated with HPV status nor with apoptosis occurring following RT. To further interrogate the contribution of apoptosis to ctDNA release, we treated cells with a pan-caspase inhibitor and evaluated ctDNA release and caspase activity following RT. Although caspase inhibition resulted in a near complete reduction in RT-induced caspase activity (84.0% ±8.1%), a comparatively minor reduction in ctDNA release (28.9%±8.9%) was observed. To evaluate the impact of senescence on RT-induced ctDNA release, we measured SA-β-Gal activity post-RT. The degree of senescence following RT was inversely associated with ctDNA release. In cell line xenografts, maximal ctDNA release into mouse plasma occurred 96 hours following RT. Staining patterns of endpoint tumors for caspase-3, TUNEL, p21, and Ki67 are currently under analysis. Conclusions: Our results demonstrate a robust and sensitive method for longitudinal evaluation of ctDNA release and cell death post-RT both in vitro and in vivo. Timing of ctDNA release demonstrate peaks around 72-96 hours post-RT, highlighting the potential for ctDNA to depict early response to therapy. Ongoing studies aimed at further investigating ctDNA release in association with mechanisms of cell death in vivo will help further elucidate the potential for ctDNA as a biomarker of treatment response. Citation Format: Ariana Rostami, Caberry Yu, Marco A. Di Grappa, Scott V. Bratman. Rapid release of ctDNA as a biomarker of treatment response in preclinical models of head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 583.

Overall outcomes for HPV-negative head and neck squamous cell carcinoma (HNSCC) remain poor with 5-year overall survival rates of 50-60%. Oral squamous cell carcinoma (OSCC), the most common subtype of HPV-negative HNSCC, is typically treated with surgery, and clinico-pathologic features are used to identify patients in need of adjuvant therapies such as radiation therapy (RT), or radiation plus concurrent chemotherapy (CRT). It is clear from the rate of loco-regional or distant failures that more accurate methods of risk stratification would greatly improve outcomes for OSCC patients. This requires biomarkers to identify patients that will benefit from adjuvant RT or CRT but currently there are no validated molecular biomarkers that have been clinically implemented for the personalized treatment of OSCC. In addition to biomarkers for better risk stratification, there is also a need for novel therapeutic strategies leading to improved outcomes. Recently patient-derived xenografts (PDXs) have been shown to faithfully recapitulate human tumor biology and predict drug responses, supporting their relevance as preclinical models for new drug development. Upon subcutaneous implantation of HNSCC specimens into NOD/SCID/IL2Rγ-/- mice, 161 of 243 samples (66%) successfully formed patient-derived xenografts (PDX). Using univariable and multivariable analyses, the ability to form a PDX correlated significantly with adverse clinical outcomes, and specifically, patients with palpable PDX-formation within 8 weeks experienced particularly poor outcomes (hazard ratio for overall survival = 3.0). A cohort of engrafting and non-engrafting samples were sequenced using a targeted sequencing panel designed for both mutational and copy number alteration detection. The overall frequency of somatic genomic alterations detected was similar to The Cancer Genome Atlas cohort and interestingly, successful engraftment correlated to amplification of the CCND1 gene. Twelve PDX models were treated with the CDK4/6 inhibitor, abemaciclib; 5 of 6 models with CCND1 amplifications and/or CDKN2A mutations responded to abemaciclib treatment, whereas only 1 of 6 models lacking these alterations responded. These results demonstrate the potential of using PDX models to identify novel targeted therapies for HNSCC patients who have the poorest outcomes. In the future, PDX avatars could also be exploited to individualize treatment for patients at high risk of relapse following definitive treatment. Citation Format: Christina Karamboulas, Jeffrey P. Bruce, Andrew J. Hope, Jalna Meens, Shao Hui Huang, Jie Su, Fei-Fei Liu, Trevor J. Pugh, Scott V. Bratman, Wei Xu, Laurie E. Ailles. Patient-derived xenografts for prognostication and personalized treatment for head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1033.

Purpose: Radiotherapy (RT) is frequently used either alone or in combination with chemotherapy for curative treatment of squamous cell carcinomas (SCC) originating from the head and neck, lung, esophagus, and cervix. Treatment outcomes for SCCs are heterogeneous, in part due to variable degrees of resistance to ionizing radiation and modest benefit of existing radiosensitizing drugs. Preclinical research into intrinsic cancer cell radiosensitivity biomarkers and novel radiosensitizing drugs has been hampered by a lack of robust high throughput assays of radiation response. We sought to validate a recently published high throughput viability assay as a surrogate of clonogenic survival and extend its use to drug-radiation combinations. Experimental Methods: Clonogenic assays—the gold standard for assessing radiation survival in vitro—and viability assays were performed on 19 SCC cell lines (16 head and neck, 3 esophageal). The clonogenic assay was performed according to published procedures (Franken et al. Nat. Protoc, 2006) with colonies counted using ImageJ. The viability assay was adapted from Abazeed et al. (Cancer Res., 2013). Cells were seeded with a range of densities in 96 well plates then treated with a range of radiation doses (0, 2, 4, and 8 Gy); viability was measured using CellTitre Glo reagent after 9 days. Agreement between clonogenic and viability assays was measured using modified concordance index (C-index) and Pearson correlation. For the addition of drug, cells were allowed to adhere to plates for 2 hours before drug administration. Cells were irradiated 16 hours later again at a range of doses (0, 2, 4, and 6 Gy for drug analysis), and then quantified as above. All assays were performed with technical and biological triplicates. Results: There was a high degree of agreement between the area under the curve with the clonogenic assay and the viability assay (C-index = 0.80, p = 3.03x10-7; Pearson r = 0.70, p = 1.10x10–3). Significant concordance was also seen at 2 Gy and 4 Gy dose points (Pearson r = 0.62 and 0.73 respectively), however not at 8 Gy (Pearson r Conclusion: The proliferative assay recapitulates the clonogenic assay within our cohort of SCC cell lines. Novel higher throughput methods to analyze radiation response will allow for a more efficient measure of drug and radiation combinations. Citation Format: Meghan Lambie, Venkata S. Manem, Benjamin Haibe-Kains, Scott V. Bratman. Validation of a viability assay for assessing radiation response and investigating drug/radiation combinations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 854.

6044Background: CDDP-D ≤ 200 mg/m2 has been shown to have a detrimental impact on overall survival (OS) in HPV negative disease with a similar trend in T4/N3 HPV+ patients (pts). We evaluated the i...

Summary Background Microtubules (MTs) participate in the spatial regulation of actin-based processes such as cytokinesis and cell polarization [1]. The fission yeast Schizosaccharomyces pombe is a rod-shaped cell that exhibits polarized cell growth at cell tips. MT plus ends contact and shrink from the cell tips and contribute to polarity regulation. Results Here, we investigate the effects of changing cell shape on MTs and cell-polarization machinery. We physically bend fission yeast cells by forcing them into microfabricated femtoliter chambers. In these bent cells, MTs maintain a straight axis and contact and shrink from cortical sites at the sides of cells. At these ectopic sites, polarity factors such as bud6p, for3p (formin), and cdc42p are recruited and assemble actin cables in a MT-dependent manner. MT contact at the cortex induces the appearance of a bud6p dot within seconds. The accumulation of polarity factors leads to cell growth at these sites, when the MT-associated polarity factor tea1p is absent. This process is dependent on MTs, mal3p (EB1), moe1p (an EB1-binding protein), and for3p but, surprisingly, is independent of the tea1p-tea4p pathway. Conclusions These studies provide a direct demonstration for how MTs induce actin assembly at specific locations on the cell cortex and begin to identify a new pathway involved in this process. MT interactions with the cortex may be regulated by cortical-attachment sites. These findings highlight the crosstalk between cell shape, polarity mechanisms, and MTs responsible for cell morphogenesis.