Cis -nonPro peptides, a very rare feature in protein structures, are of considerable importance for two opposite reasons. On one hand, their genuine occurrences are mostly found at sites critical to biological function, from the active sites of carbohydrate enzymes to rare adjacent-residue disulfide bonds. On the other hand, a cis -nonPro can easily be misfit into weak or ambiguous electron density, which has led to a high incidence of unjustified cis -nonPro over the last decade. This paper uses the greatly expanded crystallographic data and newly stringent quality-filtering to identify the genuine occurrences and survey both individual examples and broad patterns of their functionality. The accompanying paper describes the problem of cis -nonPro over-use, including its causes, validation, and correction.We explain the procedure developed to identify genuine cis -nonPro examples with almost no false positives, including the new observation that peptides with a glycine on one side or the other need extra care to avoid mis-assignment as cis -nonPro. We then survey a sample of the varied functional roles and structural contexts of cis -nonPro, emphasizing aspects not previously covered systematically: the preferred occurrence at β-strand ends in TIM barrel structures, the concentration of occurrence in proteins that process, bind, or contain carbohydrates, and the resulting complications in defining a simple occurrence frequency.

Study objectiveThis study aimed to (1) develop and validate a natural language processing model to identify the presence of pulmonary embolism (PE) based on real-time radiology reports and (2) identify low-risk PE patients based on previously validated risk stratification scores using variables extracted from the electronic health record at the time of diagnosis. The combination of these approaches yielded an natural language processing-based clinical decision support tool that can identify patients presenting to the emergency department (ED) with low-risk PE as candidates for outpatient management.MethodsData were curated from all patients who received a PE-protocol computed tomography pulmonary angiogram (PE-CTPA) imaging study in the ED of a 3-hospital academic health system between June 1, 2018 and December 31, 2020 (n=12,183). The “preliminary” radiology reports from these imaging studies made available to ED clinicians at the time of diagnosis were adjudicated as positive or negative for PE by the clinical team. The reports were then divided into development, internal validation, and temporal validation cohorts in order to train, test, and validate an natural language processing model that could identify the presence of PE based on unstructured text. For risk stratification, patient- and encounter-level data elements were curated from the electronic health record and used to compute a real-time simplified pulmonary embolism severity (sPESI) score at the time of diagnosis. Chart abstraction was performed on all low-risk PE patients admitted for inpatient management.ResultsWhen applied to the internal validation and temporal validation cohorts, the natural language processing model identified the presence of PE from radiology reports with an area under the receiver operating characteristic curve of 0.99, sensitivity of 0.86 to 0.87, and specificity of 0.99. Across cohorts, 10.5% of PE-CTPA studies were positive for PE, of which 22.2% were classified as low-risk by the sPESI score. Of all low-risk PE patients, 74.3% were admitted for inpatient management.ConclusionThis study demonstrates that a natural language processing-based model utilizing real-time radiology reports can accurately identify patients with PE. Further, this model, used in combination with a validated risk stratification score (sPESI), provides a clinical decision support tool that accurately identifies patients in the ED with low-risk PE as candidates for outpatient management.

Background: Beta-blockers (BB) and non-dihydropyridine calcium channel blockers (CCB) are first-line therapies for hypertrophic cardiomyopathy (HCM) used both upon symptom onset and for pre-symptomatic patients. However, there is limited evidence supporting their efficacy, particularly from randomized controlled trials. Aims: In this study we assessed the prevalence, discontinuation rates, and effectiveness of BB/CCB for NYHA class I HCM patients. Methods: Utilizing data from a real world cohort spanning 4 centers, we evaluated BB/CCB effectiveness in NYHA class I patients with HCM. The effectiveness analysis for a composite endpoint (NYHA class worsening and cardiovascular-related hospitalization) was performed independently at each center and an aggregated analysis was performed. NT-proBNP level analysis was performed where longitudinal data was available. Patients initiating therapy during follow-up were compared to untreated controls, adjusting for confounders (duration since HCM diagnosis, left atrial volume index (LAVi), E/e' lateral ratio, medical history, NT-ProBNP levels) using inverse probability weighting and Stürmer trimming. The association between treatment and the risk of composite endpoint was assessed through Cox regression, while mixed models for repeated measures were used for NT-proBNP levels. Results: Among the 735 patients, 64% initiated BB/CCB therapy with a 33% discontinuation rate at 4 years. A total of 222 patients with extreme propensity scores were excluded. As shown in Table 1., no benefit from BB/CCB in reducing the composite endpoint risk (HR=1.08, p=0.79) was observed. This was consistent across the different components of the endpoint. Additionally, no benefit in reducing NT-proBNP levels after 1 year was detected (Least Means Square difference=0.02, p=0.79). Conclusion: Initiation of BB/CCB for NYHA I HCM patients did not appear to reduce the risk of progression measured by the functional capacity, CV hospitalization and NT-proBNP. Despite the inherent limitation of observational studies, these findings together with the high discontinuation rate of the therapy, underscore the need for further research to validate optimal treatment strategies for pre-symptomatic HCM patients.

Children with single ventricle physiology (SV) are at high risk of in-hospital morbidity and mortality. Identifying children at risk for deterioration may allow for earlier escalation of care and subsequently decreased mortality.We conducted a retrospective chart review of all admissions to the pediatric cardiology non-ICU service from 2014 to 2018 for children < 18 years old. We defined clinical deterioration as unplanned transfer to the ICU or inpatient mortality. We selected children with SV by diagnosis codes and defined infants as children < 1 year old. We compared demographic, vital sign, and lab values between infants with and without a deterioration event. We evaluated vital sign and medical therapy changes before deterioration events.Among infants with SV (129 deterioration events over 225 admissions, overall 25% with hypoplastic left heart syndrome), those who deteriorated were younger (p = 0.001), had lower baseline oxygen saturation (p = 0.022), and higher baseline respiratory rate (p = 0.022), heart rate (p = 0.023), and hematocrit (p = 0.008). Median Duke Pediatric Early Warning Score increased prior to deterioration (p < 0.001). Deterioration was associated with administration of additional oxygen support (p = 0.012), a fluid bolus (p < 0.001), antibiotics (p < 0.001), vasopressor support (p = 0.009), and red blood cell transfusion (p < 0.001).Infants with SV are at high risk for deterioration. Integrating baseline and dynamic patient data from the electronic health record to identify the highest risk patients may allow for earlier detection and intervention to prevent clinical deterioration.

Background Surveillance in 2020-2021 showed that seasonal respiratory illnesses were below levels seen during prior seasons, with the exception of interseasonal respiratory syncytial virus (RSV). Methods Electronic health record data of infants aged <1 year visiting the Duke University Health System from 4 October 2015 to 28 March 2020 (pre-COVID-19) and 29 March 2020 to 30 October 2021 (COVID-19) were assessed. International Classification of Diseases-Tenth Revision (ICD-10) codes for RSV (B97.4, J12.1, J20.5, J21.0) and bronchiolitis (RSV codes plus J21.8, J21.9) were used to detail encounters in the inpatient (IP), emergency department (ED), outpatient (OP), urgent care (UC), and telemedicine (TM) settings. Results Pre-COVID-19, 88% of RSV and 92% of bronchiolitis encounters were seen in ambulatory settings. During COVID-19, 94% and 93%, respectively, occurred in ambulatory settings. Pre-COVID-19, the highest RSV proportion was observed in December-January (up to 38% in ED), while the peaks during COVID-19 were seen in July-September (up to 41% in ED) across all settings. RSV laboratory testing among RSV encounters was low during pre-COVID-19 (IP, 51%; ED, 51%; OP, 41%; UC, 84%) and COVID-19 outside of UC (IP, 33%; ED, 47%; OP, 47%; UC, 87%). Full-term, otherwise healthy infants comprised most RSV encounters (pre-COVID-19, up to 57% in OP; COVID-19, up to 82% in TM). Conclusions With the interruption of historical RSV epidemiologic trends and the emergence of interseasonal disease during COVID-19, continued monitoring of RSV is warranted across all settings as the changing RSV epidemiology could affect the distribution of health care resources and public health policy.

Introduction: Children with single ventricle physiology (SV) are at high risk of in-hospital morbidity and mortality, with much of that increased risk coming in the first year of life. Understanding which children are at the highest risk for clinical deterioration may allow for increased monitoring and earlier escalation of care, with associated decreased mortality. Methods: We conducted a retrospective chart review of all admissions to the pediatric cardiology non-ICU inpatient service from 2014 - 2018 for children < 18 years old. Clinical deterioration was defined as an unplanned transfer to the ICU or inpatient mortality. Children with SV were selected by diagnosis codes. Results: From the entire cohort of 1612 pediatric cardiology admissions (56 % male, 25% SV), 288 admissions had a deterioration event including 26 deaths. Infants less than one year with SV (n = 197 admissions) were significantly more likely to have a deterioration event (107 events over 62 admissions with an event) than the overall pediatric cardiology cohort (OR 2.11, 95% CI 1.52-2.93). Among infants with SV, those with a deterioration event were significantly younger (median 1.7 v 4.3 months, p < 0.001). Further, at baseline they had significantly lower oxygen saturation (84% v 87%, p < 0.01), lower systolic blood pressure (85mmHg v 90mmHg, p< 0.02), higher respiration rate (48 v 44, p < 0.01), and higher hematocrit (44.0 v 40.2, p < 0.005) compared to those who remained stable. Mean Pediatric Early Warning Scores (PEWS) were significantly higher for infants with SV who had a deterioration event (1.4 v 0.9, p < 0.001) and PEWS scores significantly increased in the 48 hours prior to an event (p < 0.001). Of the 104 non-death events, 61 required an increase in oxygen support and 51 required a fluid bolus prior to the event (p < 0.001). Conclusions: Infants with SV are at high risk for clinical deterioration. There are baseline differences in vital signs and lab work between those that remain stable and those that have a deterioration event. PEWS scores and oxygen and fluid treatment significantly increase prior to deterioration events. Leveraging data from the Electronic Medical Record to identify the highest risk patients may allow for earlier detection and intervention to prevent clinical deterioration.

PURPOSE: Next-generation sequencing (NGS) gene panels are frequently completed for patients with advanced non–small-cell lung cancer (NSCLC). Patients with highly actionable gene variants have improved outcomes and reduced toxicities with the use of corresponding targeted agents. We sought to identify barriers to targeted agent use within the Veterans Health Affairs' National Precision Oncology Program (NPOP). METHODS: A retrospective evaluation of patients with NSCLC who underwent NGS multigene panels through NPOP between July 2015 and February 2019 was conducted. Patients who were assigned level 1 or 2A evidence for oncogenic gene variants by an artificial intelligence offering (IBM Watson for Genomics [WfG]) and NPOP staff were selected. Antineoplastic drug prescriptions and provider notes were reviewed. Reasons for withholding targeted treatments were categorized. RESULTS: Of 1,749 patients with NSCLC who successfully underwent NGS gene panel testing, 112 (6.4%) patients were assigned level 1 and/or 2A evidence for available targeted treatments by WfG and NPOP staff. All highly actionable gene variants were within ALK, BRAF, EGFR, ERBB2, MET, RET, and ROS1. Of these, 36 (32.1%) patients were not prescribed targeted agents. The three most common reasons were (1) patient did not carry a diagnosis of metastatic disease (33.3%), (2) treating provider did not comment on the NGS results (25.0%), and (3) provider felt that patient could not tolerate therapy (19.4%). No patients were denied access to level 1 or 2A targeted drugs because of rejection of a nonformulary drug request. CONCLUSION: A substantial minority of patients with NSCLC bearing highly actionable gene variants are not prescribed targeted agents. Further provider- and pathologist-directed educational efforts and implementation of health informatics systems to provide real-time decision support for test ordering and interpretation are needed.

BACKGROUND:Epidermal growth factor receptor (EGFR) mutation testing is recommended in metastatic non-small cell lung cancer (NSCLC). The objective of this study was to assess changes in EGFR mutation testing patterns and tyrosine kinase inhibitor (TKI) use in US veterans with stage III-IV NSCLC between 2013 and 2017.PATIENTS AND METHODS:Retrospective study using linked data from Department of Veterans Affairs (VA) Cancer Registry System, Corporate Data Warehouse, commercial laboratories, and clinical notes. Generalized linear mixed models accounting for clustering by VA facility were used to determine factors associated with EGFR mutation testing.RESULTS:From 2013 to 2017, EGFR mutation testing increased from 29.5% to 38.4% among veterans with stage III-IV NSCLC and from 47.0% to 57.4% among veterans with stage IV non-squamous disease. Factors associated with increased odds of testing included being married, Medicare enrollment, and adenocarcinoma histology. Factors associated with decreased odds of testing included Medicaid eligibility, stage III disease, increasing age, being a current or former smoker, increasing Charlson-Deyo comorbidity score, and receiving cancer care in the South. Appropriate use of a TKI rose from 2013 to 2017 (17.2% to 74.1%).CONCLUSION:EGFR mutation testing rates increased to almost 60% in the stage IV non-squamous NSCLC population in 2017, with residual opportunity for further increase. Several sociodemographic characteristics, comorbidities, and geographic regions were associated with EGFR mutation testing suggestive of inequitable testing decisions. Appropriate use of TKI improved drastically from 2013 to 2017 demonstrating rapidly changing practice patterns through the adoption phase of new treatment options.

PURPOSE Next-generation sequencing (NGS) multigene panel testing has become widespread, including the Veterans Affairs (VA), through the VA National Precision Oncology Program (NPOP). The interpretation of genomic alterations remains a bottleneck for realizing precision medicine. We sought to examine the concordance for pathogenicity determination and clinical actionability of annotation services in NPOP. METHODS Unique gene variants were generated from NGS gene panel results using two sequencing services. For each unique gene variant, annotations were provided through N-of-One (NoO), IBM Watson for Genomics (WfG), and OncoKB. Annotations for pathogenicity (all three sources) and actionability (WfG and OncoKB) were examined for concordance. Cohen's kappa statistic was calculated to measure agreement between annotation services. RESULTS Among 1,227 NGS results obtained between 2015 and 2017, 1,388 unique variants were identified in 117 genes. The genes with the largest number of variants included TP53 (270), STK11 (92), and CDKN2A (81). The most common cancer type was lung adenocarcinoma (440), followed by colon adenocarcinoma (113). For pathogenic and likely pathogenic variants, there was 30% agreement between WfG and NoO (kappa, -0.26), 76% agreement between WfG and OncoKB (kappa, 0.22), and 42% agreement between NoO and OncoKB (kappa, -0.07). For level 1 drug actionability of gene variant-diagnosis combinations, there was moderate agreement between WfG and OncoKB (96.9%; kappa, 0.44), with 27 combinations identified as level 1 by both services, 58 by WfG alone, and 6 variants by OncoKB alone. CONCLUSION There is substantial variability in pathogenicity assessment of NGS variants in solid tumors by annotation services. In addition, there was only moderate agreement in level 1 therapeutic actionability recommendations between WfG and OncoKB. Improvement in the precision of NGS multigene panel annotation is needed.

2005 Background: Next-Generation Sequencing (NGS) gene panels are often completed to guide therapeutic decisions for patients with advanced stage non-small cell lung cancer (NSCLC). Patients with highly-actionable gene variants may experience improved therapeutic treatments and reduced toxicities with use of targeted agents. Ensuring appropriate prescription of targeted therapies is therefore of high importance. We sought to identify barriers to targeted agent use within the Veterans Health Affairs’ (VHA) National Precision Oncology Program (NPOP). Methods: A retrospective evaluation examined the cohort of NSCLC patients who underwent NGS multi-gene panels through NPOP between July 2015 and February 2019. A level of evidence for drug actionability was assigned to each observed oncogenic gene variant using an artificial intelligence offering (IBM Watson for Genomics: WfG). WfG level 1 and 2A evidence was reviewed by NPOP staff to exclude gene variants that did not conform to NPOP level 1 and 2A definitions. Anti-neoplastic drug prescriptions and oncology provider notes were obtained for all included patients from the VHA Corporate Data Warehouse. Review of clinical notes of patients who did not receive targeted agents was performed to categorize the reason(s). Results: Of 1764 NSCLC patients who successfully underwent NGS gene panel testing, 156 (8.9%) received therapeutic level 1 (7.3%) or 2A (1.6%) options for targeted agents based on WfG evidence analysis. In total, 117 (6.6%) patients had NPOP level 1 and 2A gene variants, all within ALK, BRAF, EGFR, ERBB2, MET, and RET. Of these, 49 (41.2%) patients were not prescribed available targeted agents. The three most common reasons were: (1) treating provider did not comment on NGS results (30.7%), (2) patient did not carry a diagnosis of advanced stage disease (18.4%), and (3) patient had begun an alternative systemic therapy prior to completion of sequencing (16.3%). No patient was denied access to a level 1 or 2A targeted drug due to utilization-management review. Conclusions: A substantial minority of patients with advanced NSCLC bearing highly-actionable gene variants are not prescribed available targeted agents. Further provider- and pathologist-directed educational effort are needed, as well as implementation of health informatics systems to provide near real-time decision support for test ordering and interpretation.

PURPOSE The Veterans Health Administration (VHA) is the largest cancer care provider in the United States, with the added challenge of serving more than twice the percentage of patients with cancer in rural areas than the national average. The VHA established the National Precision Oncology Program in 2016 to implement and standardize the practice of precision oncology across the diverse VHA system. METHODS Tumor or peripheral blood specimens from veterans with advanced solid tumors who were eligible for treatment were submitted for next-generation sequencing (NGS) at two commercial laboratories. Annotated results were generated by the laboratories and independently using IBM Watson for Genomics. Levels-of-evidence treatment recommendations were based on OncoKB criteria. RESULTS From July 2016 to June 2018, 3,698 samples from 72 VHA facilities were submitted for NGS testing, of which 3,182 samples (86%) were successfully sequenced. Most samples came from men with lung, prostate, and colorectal cancers. Thirty-four percent of samples were from patients who lived in a rural area. TP53, ATM, and KRAS were among the most commonly mutated genes. Approximately 70% of samples had at least one actionable mutation, with clinical trials identified as the recommended option in more than 50%. Mutations in genes associated with a neuroendocrine prostate cancer phenotype were expressed at increased frequency among veterans than in the general population. The most frequent therapies prescribed in response to NGS testing were immune checkpoint inhibitors, EGFR kinase inhibitors, and PARP inhibitors. CONCLUSION Clinical implementation of precision oncology is feasible across the VHA health care system, including rural sites. Veterans have unique occupational exposures that might inform the nature of the mutational signatures identified here. Importantly, these results underscore the importance of increasing clinical trial availability to veterans.

193 Background: Progress in understanding molecular changes in advanced prostate cancer has led to promising precision oncology opportunities; to date, most have been concentrated at tertiary research centers and urban centers and unequally available to patients. The VHA is the largest integrated healthcare system in the U.S. and provides medical care to >6 million veterans (~40% living in rural areas). The VHA has implemented a system-wide National Precision Oncology Program (NPOP) to offer tumor NGS testing to veterans with cancer. Methods: VHA patients with advanced stage cancers were offered targeted NGS gene panels (Personalis ACE Extended Cancer Panel; PGDx CancerSELECT/PlasmaSELECT) as part of clinical care. Annotated sequence data is collected by NPOP. We report preliminary findings of the participating veterans with prostate cancer. Results: 372 veterans from 81 sites underwent NGS sequencing of their prostate tumors (n=311) or cfDNA (n=61). Tumors from 165 (44%) were found to have mutations (allelic ratio ≥5%) in 47 genes. Of 372, 62 harbored mutations in TP53 (17%), 9 in NOTCH1 (2%), 16 in PTEN (4%), 16 in AR (4%), 13 in ATM (4%), 11 in BRCA2 (3%), 2 in MSH2 (0.5%), 1 in NBN (0.3%), and 1 in PALB2 (0.3%). 7 men (1.8%) had adequate tumor, but no identifiable somatic mutations. NPOP findings were compared to the existing databases SU2C/PCF (of metastatic biopsies in metastatic castration resistant disease) and TCGA (of primary tumors in localized disease), see table. Findings will be updated at presentation. Conclusions: The VA NPOP has been successfully implemented, and prostate tumors from veterans were found to carry potentially actionable mutations, including BRCA2 and ATM, for which there are precision treatment trials. The program will be expanded and will facilitate more diverse and equitable distribution of access to precision oncology diagnostics and therapeutic opportunities, in alignment with the Cancer Moonshot Initiative. (e.g. VA-ABCD clinicaltrials.gov; NCT02985021). [Table: see text]

318 Background: ASCO Quality Oncology Practice Initiative (QOPI) encourages hospitals to determine if patients (pts) with stage IV NSCLC adenocarcinoma have activating EGFR mutations. Guidelines recommend tumor testing to identify ALK, BRAF, EGFR, ROS1 and other gene alterations before treatment. Studies have shown EGFR testing underutilization. We developed and tested a tool to identify EGFR tests in Veterans Affairs (VA) electronic health record (EHR). We examined whether Veterans with newly diagnosed NSCLC-IV underwent EGFR testing. We measured EGFR testing trends and analyzed differences by patient, VA Medical Center (VAMC) and region. Methods: VA EHR data identified Veterans with NSCLC-IV diagnosed 2013-2017, who survived 45+ days and had 2+ visits with a VA oncologist within 120 days of diagnosis. All NSCLC histologies were included. Demographics and VAMC were obtained from VA Corporate Data Warehouse. EGFR testing results performed outside VA were from commercial laboratory data. We deployed a natural language processing (NLP) tool to identify EGFR tests in VA EHR clinical notes. Testing rates and characteristics associated with testing were examined by descriptive analysis. Results: Of 3484 pts, 623 (18%) had evidence of EGFR testing. There was a 244% rise in testing. 54 (9%) pts diagnosed in 2013 were tested vs 186 (25%) diagnosed in 2017 ( χ2 82.3, p-value 0.00). No statistically significant differences by sex, race, or urban/rural address existed. Testing decreased as pts aged ( χ2 27, p-value 0.00). 35% of pts age ≤49 and 12% of pts age ≥80 were tested. Testing varied widely by VAMC and region (VAMC χ2 795.6, p-value 0.00; region χ2 90.3, p-value 0.00). 28% of pts in the Pacific were tested vs 10% of pts in the Southeast. The main contributor to regional variation was VAMC differences. VAMCs that conducted EGFR testing within their own laboratories (64% and 53%), or were co-located with the national precision oncology program (NPOP, 59%) tested the most pts. NPOP was temporally associated with increased testing nationally. 9% of pts diagnosed in 2017 were tested using NPOP. Conclusions: EGFR testing underutilization in the VA persists. QOPI and the NLP tool for this initiative will help system-wide quality improvement initiatives.

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

BACKGROUND:To support the rising need for testing and to standardize tumor DNA sequencing practices within the U.S. Department of Veterans Affairs (VA)'s Veterans Health Administration (VHA), the National Precision Oncology Program (NPOP) was launched in 2016. We sought to assess oncologists' practices, concerns, and perceptions regarding Next-Generation Sequencing (NGS) and the NPOP.MATERIALS AND METHODS:Using a purposive total sampling approach, oncologists who had previously ordered NGS for at least one tumor sample through the NPOP were invited to participate in semi-structured interviews. Questions assessed the following: expectations for the NPOP, procedural requirements, applicability of testing results, and the summative utility of the NPOP. Interviews were assessed using an open coding approach. Thematic analysis was conducted to evaluate the completed codebook. Themes were defined deductively by reviewing the direct responses to interview questions as well as inductively by identifying emerging patterns of data.RESULTS:Of the 105 medical oncologists who were invited to participate, 20 (19%) were interviewed from 19 different VA medical centers in 14 states. Five recurrent themes were observed: (1) Educational Efforts Regarding Tumor DNA Sequencing Should be Undertaken, (2) Pathology Departments Share a Critical Role in Facilitating Test Completion, (3) Tumor DNA Sequencing via NGS Serves as the Most Comprehensive Testing Modality within Precision Oncology, (4) The Availability of the NPOP Has Expanded Options for Select Patients, and (5) The Completion of Tumor DNA Sequencing through the NPOP Could Help Improve Research Efforts within VHA Oncology Practices.CONCLUSION:Medical oncologists believe that the availability of tumor DNA sequencing through the NPOP could potentially lead to an improvement in outcomes for veterans with metastatic solid tumors. Efforts should be directed toward improving oncologists' understanding of sequencing, strengthening collaborative relationships between oncologists and pathologists, and assessing the role of comprehensive NGS panels within the battery of precision tests.

12109 Background: Multigene NGS testing has become widespread, including through the VA healthcare system through the VA Precision Oncology Program (POP). Algorithms to interpret the pathogenicity of NGS-detected sequence variants and clinical actionability have been implemented as clinical services, but little is known about their relative performance in clinical practice. Methods: NGS testing results from patients who had NGS results from VA POP were included. NGS results were generated at Personal Genome Diagnostics and Personalis and annotated by a commercial annotation service (N-of-One) as well as through Watson for Genomics (WfG) and OncoKB. Comparison of annotation results consisted of two parts: determination of pathogenicity and treatment actionability recommendations. Cohen’s kappa statistic was calculated for agreement between annotation services. Results: Among 1228 NGS results, 1388 unique variants were observed in 117 genes (TP53 270, STK11 92, CDKN2A 81, ATM 67, PTEN 52). Cancer type was lung adenocarcinoma in 440 samples, colon adeno 113, lung squamous 111, unknown primary 88, prostate 62, melanoma 57, H&N 41, NSCLC 40. For pathogenic and likely pathogenic variants, there was 87% agreement between WfG and N-of-One (kappa 0.729), 76% agreement between WfG and OncoKB (kappa 0.227) and 42% agreement between N-of-One and OncoKB (kappa -0.078). For level 1 drug actionability recommendations (not available from N-of-One) there was 91% agreement between WfG and OncoKB (kappa 0.19) with 54 variants identified only by WfG as level 1 and 74 variants identified only by OncoKB as level 1. Conclusions: There is substantial variability in assessment of pathogenicity of NGS variants in solid tumors by clinically available annotation services. In addition, there was only slight agreement in level 1 therapeutic actionability recommendations. Improvement of the precision of oncology NGS annotation is needed.

e24274 Background: Immune checkpoint inhibitors (CPIs) induce prolonged tumor responses in a minority of patients with solid tumors including those with MSI-high, melanoma and NSCLC. Established predictive markers imperfectly identify patients most likely to respond. Multigene NGS testing has become widely available, including throughout the VA healthcare system, and may reveal associations with therapeutic benefit from CPIs. Methods: Patients who had NGS results from the VA Precision Oncology Program (POP) and were treated with a PD-1 or PD-L1 antibody were identified from VA POP and Corporate Data Warehouse databases. Clinical benefit (CB) was defined as having received CPI for ≥ 6 months vs no CB (NCB) completed < 6 mos of CPI. Pathogenic and likely pathogenic mutations of 18 individual genes, 4 composite pathways (MTOR/PI3K, MEK, PARP, CDK), MSI status, and a tumor molecular burden (TMB) algorithm were examined for association with CB using Fisher’s exact test. TMB was calculated based on the number of non-synonymous mutations after removing likely germline variants using 1% as a cutoff in any ethnic group in ExAC database. Results: Among 292 patients there were 22 tumor types (lung adeno 135, lung squamous 39, melanoma 25, unknown primary 19, H&N 15 NSCLC 14, other 45) who received one or more CPI (nivolumab 164, pembrolizumab 108, atezolizumab 12, > 1 CPI 8). 10 pts had > 1 NGS result. CB was seen in 94 and NCB in 113. Non-evaluable patients included 26 continuing CPI < 6 months and 59 treated for < 42 days. Only the presence of a PTEN mutation (PTENmut) was associated with CB: PTENmut 8 of 10 (80%) vs PTENwt 88/206 (43%) (p = 0.025; RR 0.35 (95% CI 0.10-1.21)). All PTENmut were also MSI-low and TMB-low. All 5 lung adeno with PTENmut had CB. Conclusions: In this real-world population of patients with solid tumors, PTEN mutation by NGS was associated with longer duration of treatment with CPIs. Further analysis, including PD-L1 IHC, is ongoing plus planned analysis in an independent validation cohort.