Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer

Introduction

Next-generation sequencing (NGS) is currently widely used for biomarker studies and molecular profiling to identify concurrent alterations that can lead to the better characterization of a tumor's molecular landscape. However, further evaluation of technical aspects related to the detection of gene rearrangements and copy number alterations is warranted.

Methods

There were 12 ALK rearrangement-positive tumor specimens from patients with non-small cell lung cancer (NSCLC) previously detected via fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and an RNA-based NGS assay, and 26 MET high gene copy number (GCN) cases detected by FISH, selected for this retrospective study. All 38 pre-characterized cases were reassessed utilizing the PGDx™ elio™ tissue complete assay, a 505 gene targeted NGS panel, to evaluate concordance with these conventional diagnostic techniques.

Results

The detection of ALK rearrangements using the DNA-based NGS assay demonstrated excellent sensitivity with the added benefit of characterizing gene fusion partners and genomic breakpoints. MET copy number alterations were also detected; however, some discordances were observed likely attributed to differences in algorithm, reporting thresholds and gene copy number state. TMB was also assessed by the assay and correlated to the presence of NSCLC driver alterations and was found to be significantly lower in cases with NGS-confirmed canonical driver mutations compared with those without (p=0.0019).

Discussion

Overall, this study validates NGS as an accurate approach for detecting structural variants while also highlighting the need for further optimization to enable harmonization across methodologies for amplifications.

11 Convergence insufficiency: are we making a difference in patients' lives or is it a waste of time!

Convergence insufficiency (CI) is a common condition that can impair visual performance and comfort during close visual work. This prospective study evaluated the effectiveness of interventions on clinical outcomes and quality-of-life using the adult strabismus quality-of-life questionnaire (AS20) in patients with CI.Data was extracted from a database collected at first consultation from 2015 to 2022. Demographics, interventions and outcomes of 84 patients with CI (mean age 47.0±24.9 years) were analysed.Orthoptic exercises were prescribed to 56% of patients, 32% received prisms, 15% received no treatment, with 3 discharged on the same day. At latest follow-up review, 22.6% were recommended to continue exercises, 28.6% had prisms, 1 underwent bimedial resection and 2 had botox. The median follow-up was 5.5(5.0-55)months, 88.1% were discharged with 29.8% following failure to attend and 9.5% deceased. Near-point of convergence (NPC) improved from a median of 15(6-50)cm to 10(6-30)cm. The median AS20 score at presentation were 100(30-100) and 47.5(0-100), and post-intervention were 100(80-100) and 77.5(12.5-97.5) for psychosocial and functional components, respectively.At the latest follow-up, the attendance failure rate was higher for exercises (36%) than for prisms (15%). Improvement was noted in NPC (33%) and mean AS20 scores was 9% higher psychosocially and 32.8% functionally, highlighting the benefits of intervention on patients' quality-of-life.This cohort provides valuable insights into the clinical management of CI, as evidenced by improvements in NPC and AS20 scores. However, the study also found that long-term compliance with treatment is intrinsically challenging, emphasising the importance of disease education.

Social Justice and Equity: Why Older Adults With Cancer Belong-A Life Course Perspective

The population of older adults with cancer in the United States is rapidly increasing, which will have a substantial impact on the oncology and public health workforces across the cancer continuum, from prevention to end of life. Unfortunately, inequities in existing social structures that cause increased psychosocial stressors have led to disparities in the incidence of cancer and the morbidity and mortality of cancer for individuals from marginalized backgrounds. It is imperative that older adults, especially those from historically marginalized backgrounds, be adequately represented in all stages of cancer research to address health inequities. Continued efforts and progress toward achieving social justice and health equity require a deeper commitment to and better understanding of the impact of social determinants of health within the cancer domain. Undoubtedly, a more holistic and integrated view that extends beyond the biologic and genetic factors of health must be adopted for health entities to recognize the critical role of environmental, behavioral, and social determinants in cancer health disparities. Against this backdrop, this paper uses a life course approach to present a multifactorial framework for understanding and addressing cancer disparities in an effort to advance social justice and health equity for racially and ethnically diverse older adults.

Validation of a Circulating Tumor DNA-Based Next-Generation Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing

BACKGROUND

Characterization of circulating tumor DNA (ctDNA) has been integrated into clinical practice. Although labs have standardized validation procedures to develop single locus tests, the efficacy of on-site plasma-based next-generation sequencing (NGS) assays still needs to be proved.

MATERIALS AND METHODS

In this retrospective study, we profiled DNA from matched tissue and plasma samples from 75 patients with cancer. We applied an NGS test that detects clinically relevant alterations in 33 genes and microsatellite instability (MSI) to analyze plasma cell-free DNA (cfDNA).

RESULTS

The concordance between alterations detected in both tissue and plasma samples was higher in patients with metastatic disease. The NGS test detected 77% of sequence alterations, amplifications, and fusions that were found in metastatic samples compared with 45% of those alterations found in the primary tumor samples (p = .00005). There was 87% agreement on MSI status between the NGS test and tumor tissue results. In three patients, MSI-high ctDNA correlated with response to immunotherapy. In addition, the NGS test revealed an FGFR2 amplification that was not detected in tumor tissue from a patient with metastatic gastric cancer, emphasizing the importance of profiling plasma samples in patients with advanced cancer.

CONCLUSION

Our validation experience of a plasma-based NGS assay advances current knowledge about translating cfDNA testing into clinical practice and supports the application of plasma assays in the management of oncology patients with metastatic disease. With an in-house method that minimizes the need for invasive procedures, on-site cfDNA testing supplements tissue biopsy to guide precision therapy and is entitled to become a routine practice.

IMPLICATIONS FOR PRACTICE

This study proposes a solution for decentralized liquid biopsy testing based on validation of a next-generation sequencing (NGS) test that detects four classes of genomic alterations in blood: sequence mutations (single nucleotide substitutions or insertions and deletions), fusions, amplifications, and microsatellite instability (MSI). Although there are reference labs that perform single-site comprehensive liquid biopsy testing, the targeted assay this study validated can be established locally in any lab with capacity to offer clinical molecular pathology assays. To the authors' knowledge, this is the first report that validates evaluating an on-site plasma-based NGS test that detects the MSI status along with common sequence alterations encountered in solid tumors.

Abstract CT251: MEDOCC-CrEATE trial in progress: effectiveness of adjuvant chemotherapy in stage II colon cancer patients with positive circulating tumor DNA

Background Accurate detection of patients with minimal residual disease (MRD) after resection of localized colon cancer remains an unmet clinical need as these patients might benefit from adjuvant chemotherapy (ACT). For stage II colon cancer, ACT is only indicated in patients with a pT4 tumor without a deficient mismatch repair system (dMMR), according to Dutch guidelines. However, recurrence rate (RR) in stage II colon cancer is still 15-20%. Circulating tumor DNA (ctDNA), consisting of small fragments of DNA containing tumor-specific mutations, has been shown to be a promising biomarker for MRD and a strong predictor for recurrent disease when detectable after resection. The MEDOCC-CrEATE trial investigates how many stage II colon cancer patients with detectable ctDNA after surgery will accept ACT and whether ACT reduces RR in these patients.

Methods The MEDOCC-CrEATE study follows the ‘trials within cohorts' (TwiCs) design. Patients with colorectal cancer are included in the Prospective Dutch ColoRectal Cancer (PLCRC) cohort study and give informed consent for collection of clinical data and biomaterials, including tissue and blood samples. Additionally, patients are invited to give their consent for future randomization without being informed when allocated to the control group receiving standard of care. In MEDOCC-CrEATE 1320 stage II colon cancer patients without an indication for ACT will be included and randomized 1:1 into an experimental and a control arm. In the experimental arm, tissue and blood samples are analyzed after surgery for tissue-informed detection of plasma ctDNA, using the PGDx elio™ Platform. Patients with detectable ctDNA after surgery will be offered ACT consisting of 8 cycles of capecitabine plus oxaliplatin. Patients in the experimental arm without detectable ctDNA and patients in the control arm receive standard follow-up. The primary endpoint is the proportion of patients accepting ACT when ctDNA is detectable after resection. Most important secondary endpoint is 2-year RR, but also includes 5-year RR, disease free and overall survival, time to recurrence, quality of life and cost-effectiveness of the ctDNA-based treatment strategy. Data will be analyzed by intention to treat. To our knowledge, MEDOCC-CrEATE is the first trial in which a ctDNA guided strategy for adjuvant chemotherapy in colon cancer is investigated. The first patient was enrolled in August 2020. MEDOCC-CrEATE is now open for inclusion in 8 hospitals in the Netherlands. So far, 9 patients have been randomized. The number of participating hospitals will be expanded to 20-25 hospitals to include all 1320 patients within 3 years. MEDOCC-CrEATE has been registered in the Netherlands Trial Register: NL6281/NTR6455.

Citation Format: Suzanna J. Schraa, Karlijn L. Van Rooijen, Dave E. Van Der Kruijssen, Carmen Rubio Alarcón, Jillian Phallen, John Simmons, Sam Angiuoli, Amy E. Greer, Veerle M. Coupé, Helma M. Van Grevenstein, Sjoerd Elias, Helena M. Verkooijen, Miranda M. Van Dongen, Linda J. Bosch, Daan Van Den Broek, Gerrit A. Meijer, Victor E. Velculescu, Remond J. Fijneman, Geraldine R. Vink, Miriam Koopman. MEDOCC-CrEATE trial in progress: effectiveness of adjuvant chemotherapy in stage II colon cancer patients with positive circulating tumor DNA [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 CT251.

Impact of sample scaling on shear strength: coupled effects of grains size and shape

Size limitations of geotechnical testing equipment often require that samples of coarse granular materials have to be scaled in order to be tested in the laboratory. Scaling implies a convenient modification of the particle size distribution (PSD) to reduce particle sizes. However, it is well known that particle size and shape may be correlated in nature, due to geological factors (as an example). By means of two-dimensional contact dynamics simulations, we analyzed the effect of altering the size span on the shear strength of granular materials when particle size and shape are correlated. Two different systems were considered: one made of only circular particles, and the second made of size-shape correlated particles. By varying systematically the size span we observed that the resulting alteration of material strength is not due to the change in particle sizes. It results instead from the variation of the particle shapes induced by the modification of the PSD, when particle size and particle shape are correlated. This finding suggests that particle shape distribution is a higher order factor than PSD for the shear strength of granular materials. It also highlights the importance of particle shape quantification in soil classification and the case for its consideration in activities such as sampling, subsampling, and scaling of coarse materials for geotechnical testing

Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC's Analytical Variables Working Group

Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC's Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors' presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.

Circulating tumor DNA guided adjuvant chemotherapy in stage II colon cancer (MEDOCC-CrEATE): study protocol for a trial within a cohort study

BACKGROUND

Accurate detection of patients with minimal residual disease (MRD) after surgery for stage II colon cancer (CC) remains an urgent unmet clinical need to improve selection of patients who might benefit form adjuvant chemotherapy (ACT). Presence of circulating tumor DNA (ctDNA) is indicative for MRD and has high predictive value for recurrent disease. The MEDOCC-CrEATE trial investigates how many stage II CC patients with detectable ctDNA after surgery will accept ACT and whether ACT reduces the risk of recurrence in these patients.

METHODS/DESIGN

MEDOCC-CrEATE follows the 'trial within cohorts' (TwiCs) design. Patients with colorectal cancer (CRC) are included in the Prospective Dutch ColoRectal Cancer cohort (PLCRC) and give informed consent for collection of clinical data, tissue and blood samples, and consent for future randomization. MEDOCC-CrEATE is a subcohort within PLCRC consisting of 1320 stage II CC patients without indication for ACT according to current guidelines, who are randomized 1:1 into an experimental and a control arm. In the experimental arm, post-surgery blood samples and tissue are analyzed for tissue-informed detection of plasma ctDNA, using the PGDx elio™ platform. Patients with detectable ctDNA will be offered ACT consisting of 8 cycles of capecitabine plus oxaliplatin while patients without detectable ctDNA and patients in the control group will standard follow-up according to guideline. The primary endpoint is the proportion of patients receiving ACT when ctDNA is detectable after resection. The main secondary outcome is 2-year recurrence rate (RR), but also includes 5-year RR, disease free survival, overall survival, time to recurrence, quality of life and cost-effectiveness. Data will be analyzed by intention to treat.

DISCUSSION

The MEDOCC-CrEATE trial will provide insight into the willingness of stage II CC patients to be treated with ACT guided by ctDNA biomarker testing and whether ACT will prevent recurrences in a high-risk population. Use of the TwiCs design provides the opportunity to randomize patients before ctDNA measurement, avoiding ethical dilemmas of ctDNA status disclosure in the control group.

TRIAL REGISTRATION

Netherlands Trial Register: NL6281/NTR6455 . Registered 18 May 2017, https://www.trialregister.nl/trial/6281.

Abstract B029: Comparison of a comprehensive NGS profiling assay and conventional molecular testing approaches for detection of clinically relevant alterations in NSCLC

Introduction: Genomic analysis using next-generation sequencing (NGS) enables simultaneous detection of targetable alterations and biomarkers with emerging clinical utility in non-small cell lung cancer (NSCLC) patients. Importantly, many of these alterations are mutually exclusive and tumor tissue for molecular testing is often limited. As such, we developed PGDx elioTM tissue complete (ETC) as a comprehensive NGS assay capable of detecting somatic single nucleotide variants (SNVs), insertions and deletions (indels), amplifications, and rearrangements, as well as microsatellite stability (MSI) and tumor mutational burden (TMB). Here, we present the performance of this assay in detecting key clinical variants in NSCLC. Methods: Studies comprising >300 NSCLC specimens (FFPE tissue and characterized cell lines) were analyzed using ETC, a 500+ gene assay (under development), across key clinically relevant variants in NSCLC, including tumor mutation burden (TMB). Accuracy of the results were compared to orthogonal methods (e.g. whole-exome sequencing (WES), IHC, FISH) and analyzed for the overall percent agreement (OPA). Additionally, archival FFPE samples from 46 NSCLC patients previously found to harbor ALK translocations, MET amplifications, MET exon 14 skipping mutations, EGFR mutations, and/or ROS1 translocations were also analyzed. The results were compared to orthogonal methods and the overall genomic landscape evaluated. Results: Clinical FFPE and characterized cell line specimens were evaluated for the following alterations: EGFR mutations (L858R, T790M, and Exon 19 deletions), BRAF V600E mutations, and ALK and ROS1 translocations. Compared to orthogonal methods, the NGS assay demonstrated >93% OPA across all variants. Comparison of TMB results to WES data demonstrated high accuracy and precision, across a range of DNA inputs (50-200 ng) and tumor purities (10-30%). In the 46 retrospective NSCLC cases, the NGS assay identified 15 ALK translocations, 6 MET amplifications, 1 MET exon 14 skipping mutation, and 5 EGFR mutations, with most being mutually exclusive. The majority of cases were confirmed by orthogonal assays, with the few apparent discordances likely due to tumor heterogeneity, assay distinctions, or analyte input. Higher TMB was found in cases without targetable alterations. Conclusions: ETC provides accurate and reproducible results for the detection of clinically relevant alterations in NSCLC. Further verification and validation studies of this gene panel are ongoing. Overall NGS showed excellent concordance with orthogonal variant detection methods. Importantly, ETC demonstrated added value in assessing all genomic alteration types in a single assay, as well as reporting composite genomic scores, suggesting that NGS may offer a comprehensive solution to molecular testing.

Citation Format: Elizabeth Weingartner, Kelly M.R. Gerding, Gustavo Cerquiera, Christopher Gault, James Hernandez, Kenneth Valkenburg, Laurel Keefer, Eileen Sagini, Dorhyun Johng, Caitlin Gilley, Colby Ganey, Leila Ettehadieh, Diandra Denier, Christina Oliveras, Kartikeya Joshi, Eric Kong, Eniko Papp, Amy Greer, James R. White, Donna Nichol, John Simmons. Comparison of a comprehensive NGS profiling assay and conventional molecular testing approaches for detection of clinically relevant alterations in NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B029. doi:10.1158/1535-7163.TARG-19-B029

Abstract B027: Analytical validation of a 500+ gene comprehensive NGS assay to detect genomic alterations across 35 tumor types

Introduction: Advances in precision medicine for solid tumors have led to an increase in the number of molecular biomarkers and signatures associated with clinical decisions and clinical trial eligibility. In advanced disease settings, timely clinical decision making informed by robust and accurate molecular biomarker testing is increasingly important. As such, there is a need for a comprehensive, decentralized and rigorously validated diagnostic test. To address this need, we developed and analytically validated PGDx elioTM tissue complete (ETC) assay, which reports somatic single nucleotide variants (SNVs), insertions and deletions (indels), amplifications, and rearrangements, as well as microsatellite stability (MSI) and tumor mutational burden (TMB). Methods: >500 FFPE tumor tissue specimens, across 35 tumor types and 9 organ systems, were analyzed using our 500+ gene targeted panel, ETC (assay in development). Accuracy of the results was compared to orthogonal methods, such as whole exome sequencing (WES), IHC, FISH, NGS, and other on-market IVD assays. Results for all variant types were analyzed for overall percent agreement (OPA). Additional analytical studies were performed to assess precision/repeatability for detection of somatic variants, evaluated across multiple operators, instruments and days. Results: 112 unique samples were evaluated for SNVs and indels by ETC and accuracy assessed via orthogonal validated NGS assays, demonstrating an OPA >99.9%. Detection of amplification events was assessed in 176 samples and concordance with orthogonal FISH and IHC assays demonstrated >93.0 % OPA. Rearrangement accuracy was evaluated across several clinically relevant translocations, with an >94.0 % OPA when compared to FISH and an RNA-based sequencing method (n=270). 115 pan cancer samples were analyzed for microsatellite status and accuracy with PCR was determined, with an overall agreement of 100.0%. Lastly, TMB was determined in 118 samples and results compared to WES-derived TMB, displaying a high level of concordance (Pearson correlation, p=0.903) across a range of TMB scores (0.2-89.7 muts/Mbp). Conclusions: The PGDx elio tissue complete assay system, including proprietary, automated bioinformatics, provides accurate and reproducible results for the detection of clinically relevant genetic alterations across tumor types. Further verification and validation studies of this gene panel are ongoing. The PGDx elio tissue complete assay will employ a decentralized, kitted model, increasing clinical accessibility to NGS and allow for delivery of highly accurate and timely results.

Citation Format: Kelly M.R. Gerding, Kenneth C Valkenburg, Christina Oliveras, James R. White, Leila Ettehadieh, Gustavo Cerquiera, Christopher Gault, James Hernandez, Eric Kong, Samuel Angiuoli, John Simmons, Isabell Loftin, Abigail McElhinny. Analytical validation of a 500+ gene comprehensive NGS assay to detect genomic alterations across 35 tumor types [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B027. doi:10.1158/1535-7163.TARG-19-B027

Randomized Phase II Study of Paclitaxel plus Alisertib versus Paclitaxel plus Placebo as Second-Line Therapy for SCLC: Primary and Correlative Biomarker Analyses

INTRODUCTION

We assessed the Aurora A kinase inhibitor, alisertib, plus paclitaxel (henceforth referred to as alisertib/paclitaxel) as second-line treatment for SCLC.

METHODS

In this double-blind study, patients with relapsed or refractory SCLC were stratified by relapse type (sensitive versus resistant or refractory) and brain metastases and randomized 1:1 to alisertib/paclitaxel or placebo plus paclitaxel (henceforth referred to as placebo/paclitaxel) in 28-day cycles. The primary end point was progression-free survival (PFS). Associations of c-Myc expression in tumor tissue (prespecified) and genetic alterations in circulating tumor DNA (retrospective) with clinical outcome were evaluated.

RESULTS

A total of 178 patients were enrolled (89 in each arm). The median PFS was 3.32 months with alisertib/paclitaxel versus 2.17 months with placebo/paclitaxel (hazard ratio [HR] = 0.77, 95% confidence limit [CI]: 0.557-1.067, p = 0.113 in the intent-to-treat population versus HR = 0.71, 95% CI: 0.509-0.985, p = 0.038 with corrected analysis applied). Among 140 patients with genetic alternations, patients with cell cycle regulator mutations (cyclin-dependent kinase 6 gene [CDK6], retinoblastoma-like 1 gene [RBL1], retinoblastoma-like 2 gene [RBL2], and retinoblastoma 1 gene [RB1]) had significantly improved PFS with alisertib/paclitaxel versus with placebo/paclitaxel (3.68 versus 1.80 months, respectively [HR = 0.395, 95% CI: 0.239-0.654, p = 0.0003]), and overall survival (7.20 versus 4.47 months, respectively [HR = 0.427, 95% CI: 0.259-0.704, p = 0.00085]). A subset of patients with c-Myc expression showed significantly improved PFS with alisertib/paclitaxel. The incidence of grade 3 or higher drug-related adverse events was 67% (58 patients) with alisertib/paclitaxel versus 22% (25 patients) with placebo/paclitaxel. Twelve patients (14%) versus 11 (12%) died on study, including four versus zero treatment-related deaths.

CONCLUSIONS

Efficacy signals were seen with alisertib/paclitaxel in relapsed or refractory SCLC. c-Myc expression and mutations in cell cycle regulators may be potential predictive biomarkers of alisertib efficacy; further prospective validations are warranted.

Characterization of tumor mutational burden (TMB), PD-L1, and DNA repair genes to assess correlation with immune checkpoint inhibitors (ICIs) response in metastatic renal cell carcinoma (mRCC)

e16079

Background: ICIs have revolutionized treatment for mRCC; however there are limited predictive biomarkers for response to ICIs. PD-L1 status is still controversial, demonstrating little predictive utility in mRCC. TMB is predictive for response to ICIs in melanoma and non-small cell lung cancer (NSCLC), but has not been validated in mRCC. Here, we assess the correlations between TMB and PD-L1 status with outcomes to ICI treatment in mRCC. Methods: 34 patients (pts) with mRCC who had previously received ICIs at Duke Cancer Institute were identified. Tumor samples were retrospectively evaluated using a Personal Genome Diagnostics Assay for somatic variants across > 500 genes, as well as TMB and microsatellite status. PD-L1 status was tested via the Dako 28-8 PD-L1 IHC assay. Deidentified clinical information was extracted from the medical record and tumor response was evaluated based on RECIST criteria. Results: Pts were grouped by overall response following ICI therapy into either progressive disease (“PD”, n = 18) or disease control group (“DC”, n = 16), defined as either stable disease, partial response, or complete response. Pts displayed a TMB range from 0.36 to 12.24 mutations/Mb with a mean score of 2.83 muts/Mb, with no significant difference between the PD and DC groups (mean 3.01 muts/Mb vs. 2.63 muts/Mb, p > 0.05). 9 of 32 evaluable samples were PD-L1 positive, with 4 in the PD group and 5 in the DC group. Notably, the DC group displayed a significant enrichment of mutations in genes affiliated with DNA repair (including BRCA1, BRCA2, FANCA, FANCB, FANCG, FANCM, MSH3, MSH6, RAD50, RAD51C, RAD51D, RAD54B, RECQL4, and SLX4; p = 0.0444). DNA damage gene mutations were found in 8/10 (80%) metastatic tumor specimens and 14/24 (58%) primary tumors. Conclusions: Overall, in this mRCC cohort, neither TMB nor PD-L1 correlated with patient outcomes or with ICI response. Furthermore, high TMB was not significantly associated with PD-L1 expression within the samples. The higher frequency of mutations in DNA repair genes in the DC group suggests potential use as a predictive signature for ICI response, warranting future prospective studies. Further studies with matched primary-metastatic samples would be beneficial to determine if DNA repair mutations occur more frequently in metastatic versus primary tumor specimens.

Characterization of genomic alterations as biomarkers of immune checkpoint inhibitor (ICI) response in metastatic urothelial carcinoma (mUC)

400

Background: ICIs have expanded therapeutic options for mUC patients (pts); however, biomarkers such as PD-L1 have not served as reliable predictors of treatment efficacy. High tumor mutation burden (TMB) has been previously described as a potential biomarker for predicting ICI response in several indications, but its utility is still being explored in mUC. Here, we compare the genomic landscapes and clinical outcomes of mUC pts following ICI therapy using an investigational solid tissue-based next-generation sequencing assay to assess TMB and identify genetic correlates of ICI response. Methods: 20 pts with mUC treated with ICIs at Duke Cancer Institute were identified. Tumor samples were retrospectively evaluated with a Personal Genome Diagnostics Assay for somatic variants across > 500 genes, as well as TMB and microsatellite status. Tumor samples were also stained for PD-L1 status using the Dako 22C3 IHC assay. Deidentified clinical information was extracted from the medical record and tumor response was evaluated using RECIST 1.1 criteria. Results: Pts were grouped by overall response following ICI therapy as either responders (“R”, n = 6) or non-responders (“NR”, n = 13). Pts exhibited a wide range of TMB scores (0.7 to 30.4 mutations/Mb), with a mean TMB score of 9.60 vs. 3.87 mut/Mb in R vs NR groups, respectively; however, this difference was not statistically significant ( p = 0.284). 18 pts were evaluated for PD-L1 status, with only 2 positive samples (one in each group). Rs had significantly more mutations in histone methylation genes (KDM6A, KMT2C, and KMT2D), (67% vs 15% in NRs, p = 0.0039). FGFR3 mutations were also more frequent in R vs NR (67% vs 5%, p = 0.0339). Finally, there was a higher frequency of mutations in TP53 and BRCA1 in the NRs. Conclusions: In this mUC cohort, neither TMB nor PD-L1 correlated with response to ICI therapy. Histone modifying genes and FGFR3 mutations were more frequent in responders, whereas BRCA1 and TP53 mutations were enriched in non-responders, warranting future prospective studies to understand underlying mechanisms of ICI response and resistance in mUC.

Characterization of tumor mutational burden (TMB), PD-L1, and DNA repair genes to assess correlation with immune checkpoint inhibitors (ICIs) response in metastatic renal cell carcinoma (mRCC)

589

Background: ICIs have revolutionized treatment for mRCC; however there are limited predictive biomarkers for response to ICIs. PD-L1 status is still controversial demonstrating little predictive utility in mRCC. TMB is predictive for response to ICIs in melanoma and non-small cell lung cancer (NSCLC), but has not been validated in mRCC. Here, we assess the correlations between TMB and PD-L1 status with outcomes to ICI treatment in mRCC. Methods: 34 patients (pts) with mRCC who had previously received ICI therapy at Duke Cancer Institute were identified. Tumor samples were retrospectively evaluated using a Personal Genome Diagnostics Assay for somatic variants across > 500 genes, as well as TMB and microsatellite status. Tumor samples were also analyzed with the Dako 28-8 PD-L1 IHC assay. Deidentified clinical information was extracted from the medical record and tumor response was evaluated based on RECIST criteria. Results: Pts were grouped by overall response following ICI therapy into either progressive disease (“PD”, n = 18) or disease control group (“DC”, n = 16), defined as either stable disease, partial response, or complete response. Pts displayed a TMB range from 0.36 to 12.24 mutations/Mb with a mean score of 2.83 muts/Mb, with no significant difference between the PD and DC groups (mean 3.01 muts/Mb vs. 2.63 muts/Mb, p > 0.05). 9 of 32 evaluable samples were PD-L1 positive, with 4 in the PD group and 5 in the DC group. Notably, the DC group displayed a significant enrichment of mutations in genes affiliated with DNA repair (including BRCA1, BRCA2, FANCA, FANCB, FANCG, FANCM, MSH3, MSH6, RAD50, RAD51C, RAD51D, RAD54B, RECQL4, and SLX4; p = 0.0444). Conclusions: Overall, in this mRCC cohort, neither TMB nor PD-L1 correlated with patient outcomes or with ICI response. Furthermore, high TMB was not significantly associated with PD-L1 expression within the samples. The higher frequency of mutations in DNA repair genes in the DC group suggests potential use as a predictive signature for ICI response, warranting future prospective studies.

Abstract 5850: Nrf2-mediated oxidative stress response is altered during acquired resistance to the proteasome inhibitor, oprozomib, in multiple myeloma

Multiple myeloma (MM) is a hematologic neoplasm characterized by malignant proliferation of plasma cells in the bone marrow. Proteasome inhibitors are widely used in treatment regimens for MM. Although initial responses to PI (e.g., bortezomib, carfilzomib) treatments have been promising, patients often develop resistance and become refractory to disease. Understanding molecular alterations in signaling cascades influenced by proteasome inhibitors and mechanisms underlying acquired resistance is needed. In this study, we have established a clinically relevant oproxomib-resistant subline (KMS28BMONYX) of the MM cell line KMS28BM. The KMS28BMONYX cell line is pan-resistant to PIs with a 10-fold increase in IC50 for oprozomib as compared to the parental line. To identify genes involved in modulating drug resistance, we analyzed gene expression profiles of both parental and resistant cell lines using the Affymetrix GeneChip Human Genome U133 Plus 2.0 array. Ingenuity Pathway Analysis of microarray data comparing the parental and resistant cells revealed an acute dependence on stress response proteins to maintain PI-resistance. Activation of nuclear factor-erythroid 2 (NF-E2)-related factor 2 (Nrf2; gene symbol NFE2L2) coupled with elevated levels of sequestosome 1/p62 (SQSTM1/p62) were prominent features of the KMS28BMONYX cell line. Altered levels of SQSTM1 correlated with resistance to oprozomib in several MM cell lines. Simultaneously, the KMS28BMONYX cell line showed increased expression of MYC and MCL1. Oprozomib treatment stabilized c-Myc expression in the KMS28BMONYX line. The Champion ChiP Transcription Factor Search Portal database DECODE predicted two c-Myc transcription factor binding sites in the SQSTM1 promoter. CHIP-seq data for MYC in MM1s cells also indicates strong binding in the promoter region of SQSTM1. Our data suggest that therapies targeting the SQSTM1/p62-Nrf2 pathway may help overcome proteasome inhibitor resistance in refractory MM patients.

Citation Format: Snehal M. Gaikwad, Adriana Zingone, Aleksandra Michalowski, Susana Najera, Anaisa Quintanilla-Artega, Sayeh Gorjifard, John Simmons, Nick Watson, Ola Landgren, Jing Huang, Beverly Mock. Nrf2-mediated oxidative stress response is altered during acquired resistance to the proteasome inhibitor, oprozomib, in multiple myeloma [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 5850.

Computer-Based Exercises in Anemia Diagnosis (PlanAlyzer)

PlanAlyzer is a microcomputer-based, event-driven system for instructional research in medical education. Aimed at the second year medical student, PlanAlyzer elicits and critiques a student´s approach to the diagnosis of a common medical disorder. In this paper we discuss the concept, development, implementation and formative evaluation of the PlanAlyzer system for the evaluation of anemia.

Abstract P2-02-20: Withdrawn

This abstract was withdrawn by the authors.

Pan-Cancer assessment of tumor mutational burden using a comprehensive genomic profiling assay

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Background: Checkpoint inhibitors (CPIs) have been approved for frontline or subsequent therapies in several indications over the last few years. While patient response can be remarkably durable, many patients do not benefit. Current clinical biomarkers of response to CPIs include microsatellite instability (MSI) and PD-L1 expression. While a proportion of many solid tumors display microsatellite instability, the prevalence is often very low. Similarly, while clinically informative, PD-L1 expression alone is not sufficient to predict therapeutic outcomes with high accuracy. The lack of predictive biomarkers for response highlights the need for improved biomarkers with greater prevalence across tumor types to predict response to CPIs. Multiple clinical studies have revealed that high tumor mutational burden (TMB) is associated with improved clinical response. Methods: Here, we describe the development of a method that can be used to accurately infer mutational burden from a discrete set of targeted regions of interest across the exome. Initially, we performed an assessment of the accuracy across multiple bioinformatics methods for identification of individual sequence mutations (SBS/indels) using orthogonally validated data together with publicly available TCGA whole-exome sequencing data. The targeted regions were then isolated from these datasets to demonstrate analytical performance across several different solid tumor types. Finally, we evaluated independent non-small cell lung cancer (NSCLC) and colorectal carcinoma (CRC) cohorts to demonstrate the analytical accuracy of the assay and bioinformatics approach for determination of mutational burden when compared to whole exome sequencing. Results: In summary, high concordance was observed across a large dynamic range of mutations per megabase of coding sequence. Conclusions: Our data indicate that the assay can be used to accurately determine mutational burden in a range of tumor types, across a spectra of potential mutational burden cut-offs using automated, complex mutation identification algorithms.

Abstract 4954: Clinical validation of a cell-free DNA liquid biopsy approach for noninvasive molecular profiling

Clinical molecular profiling of advanced cancers enables the identification of actionable genomic alterations to guide therapeutic decisions. Although profiling of tissue samples is considered the gold standard, specimens may be unavailable or unsuitable for testing due to limited tumor purity or specimen quality. Further, genetically informed treatment decisions are increasingly necessary after disease progression and re-biopsy in this setting may not be feasible. Circulating tumor DNA (ctDNA) approaches for identification of genetic alterations in cancer patients may be more informative as the alterations reflect the current status of the tumor. ctDNA is representative of multiple tumor sites within a patient and may aid in the detection of alterations throughout the course of therapy. However, the fraction of ctDNA obtained from a blood sample is often very low (<1.0%) and difficult to detect. Additionally, many methods to evaluate ctDNA interrogate single hotspot or a few mutations. The next generation of ctDNA assays must identify clinically actionable genetic alterations and novel biomarkers with high precision and accuracy. To address these issues, we have developed and validated PlasmaSelect64, a ctDNA approach to comprehensively detect genetic alterations at low allele frequencies in the circulation of cancer patients. Utilizing digital genomic approaches, we demonstrated robust sensitivity and specificity in our CLIA laboratory in 64 well-established cancer genes that were identified based on clinical actionability. In addition to the evaluation of exons in 58 genes that are frequently mutated in cancer for sequence mutations, we performed a comprehensive genomic analysis of translocations in 18 genes and copy number analyses in 19 genes. We have also developed a novel approach for identification of microsatellite instability (MSI) using these error correction methodologies. To evaluate the PlasmaSelect64 approach, we developed and optimized the pre-analytical conditions for sample collection and processing with K2EDTA and Streck blood collection tubes. Analytical validation studies were performed with clinical samples and contrived cell-line mixtures containing known alterations determined by orthogonal methods. We robustly identified sequence mutations at 0.50% mutant allele frequency (MAF) with a limit of detection of 0.05% MAF, corresponding to a per-base specificity of 99.9997% and a sensitivity of 99.4%. For detection of focal amplifications and translocations, analytical method validation studies demonstrated sensitivity of 97.2% and 94.4% and specificity of >99% at MAFs of ≥20% and ≥0.50%, respectively. PlasmaSelect64 provides a non-invasive platform to enable detection of clinically relevant genetic alterations across a large number of genomic regions to aid in the therapeutic management of cancer patients.

Citation Format: Monica Nesselbush, Samuel Angiuoli, Luis A. Diaz, Andrew Georgiadis, Shannon Glynn, Siân Jones, Laurel Keefer, Peter LoVerso, Derek Murphy, Sonya Parpart-Li, David Riley, Naomi Sengamalay, Manish Shukla, John Simmons, Snehal Talati, Rebecca Steinberg, Laura Tucker, Victor E. Velculescu, Ellen Verner, Angela Villarta, Mark Sausen. Clinical validation of a cell-free DNA liquid biopsy approach for noninvasive molecular profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4954. doi:10.1158/1538-7445.AM2017-4954

Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium

The cancer community understands the value of blood profiling measurements in assessing and monitoring cancer. We describe an effort among academic, government, biotechnology, diagnostic, and pharmaceutical companies called the Blood Profiling Atlas in Cancer (BloodPAC) Project. BloodPAC will aggregate, make freely available, and harmonize for further analyses, raw datasets, relevant associated clinical data (e.g., clinical diagnosis, treatment history, and outcomes), and sample preparation and handling protocols to accelerate the development of blood profiling assays.

A Case of Early Neurosyphilis

INTRODUCTION

Neurosyphilis is an infection of the central nervous system by Treponema pallidum, which can occur after the initial syphilis infection. Although commonly associated with late stage disease, patients with early neurosyphilis may present with acute syphilitic meningitis, meningovascular syphilis, or uveitis.

CASE

A 28 year old man with a past medical history of HIV (CD4 364);, and recent diagnosis of uveitis presented to the Emergency Department with a positive RPR result. His visual acuity had been gradually declining over the past few months. He denied painless or painful ulcerating lesions on his penis, or scrotum, difficulty concentrating, dermatitis on the soles/palms, or difficulty with proprioception. Physical exam was notable for atrophic hyperpigmented polycyclic, annular plaques and patches along the hairline as well as several areas of confluent hyperpigmented polycyclic plaques and nodules on the patient's face, back, left arm, and right posterior leg. Fundoscopic exam revealed bilateral posterior uveitis and chorioretinitis. Evaluation of cerebrospinal fluid revealed a lymphocytic pleocytosis with a positive VDRL and FTA-ABS. Aqueous crystalline penicillin G was initiated for treatment of early neurosyphilis. Within six hours of beginning the infusion, the patient had a documented temperature of 101.8°F, heart rate of 128 beats per minute, blood pressure 142/84, with generalized malaise and headache. Fever and tachycardia resolved over the next 12 hours, with weakness and headache resolving within 1-2 days. His symptom complex was consistent with the Jarisch-Herxheimer reaction. Histopathology of skin biopsy of the back showed perivascular inflammation and rare spirochetes, consistent with secondary syphilis. The patient completed 14 days of aqueous crystalline penicillin G and was discharged after receiving the first of three benzathine penicillin injections.

DISCUSSION

The initial manifestations of syphilis in this patient were posterior uveitis and pruritic skin plaques. His diagnosis should be appropriately classified as secondary syphilis with concomitant symptomatic early neurosyphilis, requiring 14 days of aqueous crystalline penicillin G. This type of presentation is not specific to immunocompromised populations and must be considered even in the general population. Making the diagnosis of early neurosyphilis, regardless of stage, is critical, as it necessitates a longer duration of treatment. Furthermore, clinicians should be reminded of the profound immunologic reaction, Jarisch-Herxheimer, which may occur when treating any treponemal disease.

Study protocol for a natural experiment in a lower socioeconomic area to examine the health-related effects of refurbishment to parks including built-shade (ShadePlus)

INTRODUCTION

Parks in disadvantaged suburbs often have low quality and few amenities, which is likely to result in them being underutilised for recreation and physical activity. Refurbishment of parks, including shade, walking paths and other amenities, may have broad health-related benefits.

METHODS AND ANALYSIS

The study design, methods and planned analyses for a natural experiment examining the effects of refurbishments including built-shade added to parks in disadvantaged outer suburbs of Melbourne are described. Three intervention parks and three comparison parks matched for equivalence of park and neighbourhood characteristics were selected. Using mixed methods, the outcomes will be assessed during three consecutive spring-summer periods (T1: 2013-2014; T2: 2014-2015: T3: 2015-2016). Primary outcomes included: observed park use, physical activity and shade use. Self-reported social connectedness, community engagement and psychological well-being were assessed as secondary outcomes.

ETHICS AND DISSEMINATION

This study was approved by Cancer Council Victoria's Human Research Ethics Committee. Studies such as ShadePlus can improve understanding of the broader effects of park refurbishments (including physical activity levels and sun protection behaviours, as well as social connectedness and psychological well-being). The study findings will be disseminated through established urban planning and parks and recreation networks, peer review publications and conference presentations.

mQC: A Heuristic Quality-Control Metric for High-Throughput Drug Combination Screening

Quality control (QC) metrics are critical in high throughput screening (HTS) platforms to ensure reliability and confidence in assay data and downstream analyses. Most reported HTS QC metrics are designed for plate level or single well level analysis. With the advent of high throughput combination screening there is a need for QC metrics that quantify the quality of combination response matrices. We introduce a predictive, interpretable, matrix-level QC metric, mQC, based on a mix of data-derived and heuristic features. mQC accurately reproduces the expert assessment of combination response quality and correctly identifies unreliable response matrices that can lead to erroneous or misleading characterization of synergy. When combined with the plate-level QC metric, Z', mQC provides a more appropriate determination of the quality of a drug combination screen. Retrospective analysis on a number of completed combination screens further shows that mQC is able to identify problematic screens whereas plate-level QC was not able to. In conclusion, our data indicates that mQC is a reliable QC filter that can be used to identify problematic drug combinations matrices and prevent further analysis on erroneously active combinations as well as for troubleshooting failed screens. The R source code of mQC is available at http://matrix.ncats.nih.gov/mQC.

Abstract A039: Accurate identification and prioritization of candidate neoantigens from cancer exome sequencing

Somatic, nonsynonymous genetic alterations present in cancer can lead to the formation of novel protein sequences and thus production of immunogenic “non-self” neoantigens. Those neoantigens with sufficient expression will be processed and presented on MHC molecules, subsequently inducing a tumor-specific T cell response. Emerging data from clinical studies suggest that neoantigen load and composition is associated with the efficacy of some immunotherapies. As neoantigens play central a role in the cancer-immunity cycle, it is critical to identify the most potent immunogenic neoantigens effectively and accurately. Here we have leveraged highly accurate cancer whole exome (WES) analyses from FFPE tumor tissue with a state-of-the-art analysis protocol to identify and prioritize candidate neoantigens most likely to promote an immune response. ImmunoSelect-R utilizes somatic variants from WES to ensure detection of true somatic peptides and minimize false positives, and provides accurate HLA typing from whole exome sequencing data with >99.9% sensitivity and specificity. When applied to a set of experimentally validated neoantigens, ImmunoSelect correctly classified 18 out of 19 as strong neoantigen candidates, suggesting a sensitivity of greater than 90%. Moreover, in a small set of 10 patients, ImmunoSelect consistently ranked experimentally validated neoantigens within top 20% of all neoantigen candidates derived from whole exome sequencing. In summary, ImmunoSelect is able to identify and prioritize candidate neoantigens from cancer exome sequencing results effectively and accurately, enabling personalized cancer vaccine development, adoptive T-cell transfer, and prediction of response to checkpoint inhibitors

Citation Format: James White, John Simmons, Sam Angiuoli, Mark Sausen, Sian Jones, Lisa Kann, Manish Shukla, Maria Sevdali, Victor Velculescu, Luis Diaz, Theresa Zhang. Accurate identification and prioritization of candidate neoantigens from cancer exome sequencing [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A039.

Improving the care of patients with severe open fractures of the tibia: the effect of the introduction of Major Trauma Networks and national guidelines

AIMS

The management of open lower limb fractures in the United Kingdom has evolved over the last ten years with the introduction of major trauma networks (MTNs), the publication of standards of care and the wide acceptance of a combined orthopaedic and plastic surgical approach to management. The aims of this study were to report recent changes in outcome of open tibial fractures following the implementation of these changes.

PATIENTS AND METHODS

Data on all patients with an open tibial fracture presenting to a major trauma centre between 2011 and 2012 were collected prospectively. The treatment and outcomes of the 65 Gustilo Anderson Grade III B tibial fractures were compared with historical data from the same unit.

RESULTS

The volume of cases, the proportion of patients directly admitted and undergoing first debridement in a major trauma centre all increased. The rate of limb salvage was maintained at 94% and a successful limb reconstruction rate of 98.5% was achieved. The rate of deep bone infection improved to 1.6% (one patient) in the follow-up period.

CONCLUSION

The reasons for these improvements are multifactorial, but the major trauma network facilitating early presentation to the major trauma centre, senior orthopaedic and plastic surgical involvement at every stage and proactive microbiological management, may be important factors.

TAKE HOME MESSAGE

This study demonstrates that a systemised trauma network combined with evidence based practice can lead to improvements in patient care.

Plastic surgical operative workload in major trauma patients following establishment of the major trauma network in England: A retrospective cohort study

INTRODUCTION

The introduction of major trauma centres (MTCs) in England has led to 63% reduction in trauma mortality.(1) The role of plastic surgeons supporting these centres has not been quantified previously. This study aimed to quantify plastic surgical workload at an urban MTC to determine the contribution of plastic surgeons to major trauma care.

METHODS

All Trauma Audit and Research Network (TARN)-recorded major trauma patients who presented to an urban MTC in 2013 and underwent an operation were identified retrospectively. Patients who underwent plastic surgery were identified and the type and date of procedure(s) were recorded. The trauma operative workload data of another tertiary surgical specialty and local historical plastics workload data from pre-MTC go-live were collected for comparison.

RESULTS

Of the 416 major trauma patients who required surgical intervention, 29% (n = 122) underwent plastic surgery. Of these patients, 43% had open lower limb fractures, necessitating plastic surgical involvement according to British Orthopaedic Association Standards for Trauma (BOAST) 4 guidance. The overall plastic surgery operative workload increased sevenfold post-MTC go-live. A similar proportion of the same cohort required neurosurgery (n = 115; p = 0.589).

DISCUSSION

This study quantifies plastic surgery involvement in major trauma and demonstrates that plastic surgical operative workload is at least on par with other tertiary surgical specialties. It also reports one centre's experience of a significant change in plastic surgery activity following designation of MTC status. The quantity of plastic surgical operative workload in major trauma must be considered when planning major trauma service design and workforce provision, and for plastic surgical postgraduate training.