Abstract 6687: Prevalence of four major gene mutation classes in a survey of ctDNA recovery from early and advanced stage NSCLC

Introduction: Circulating tumor DNA (ctDNA) has emerged as a powerful biomarker with many applications in oncology including early and late-stage disease prognosis and in treatment decision making. Liquid biopsies have become critical in non-small cell lung cancer (NSCLC) given the patient risks associated with biopsies. It is well established that circulating nucleic acid levels representative of all solid tumors are increased in advanced stages of the disease. Less well characterized is the status of cfDNA levels in the earliest stages of solid tumor progression. We used validated methods for quantitative fluorometry and a high sensitivity amplicon based NGS method to survey cfDNA recovery and prevalence for the four major mutation classes (copy number amplifications (CNAs), single nucleotide variations (SNVs), fusions, and insertions/deletions (INDELs)) from patients previously diagnosed with NSCLC.

Methods: Cell-free nucleic acid was extracted from 1,139 late-stage and 185 early-stage NSCLC plasma specimens. cfDNA was quantified using fluorometry, and the 52 gene GeneStrat NGS Test was used for the detection of CNAs, SNVs, fusions and INDELs. We evaluated cfDNA concentration (normalized to plasma input volume), quantity in circulation, and the prevalence of the four classes of mutations in early-stage (I-IIIA) versus late-stage (IIIB-IV) NSCLC.

Results: We observed significantly lower average concentrations of cf nucleic acids in plasma recovered from early versus late-stage NSCLC specimens (early-stage: 13.7 ng/mL; range (3.14, 118.65); n = 185; late-stage: 18.3 ng/mL; range (0.67, 187.2); n =1,139; p=0.00176). We also evaluated total cfDNA recovered for the sample set and observed significantly lower average measurements for early-stage specimens versus late-stage (early-stage: 101.4 ng; range (18.38, 652.6); n=185; late-stage: 140.5 ng; range (9.802, 1534); n=1,139; p=0.00692). We do note that there were overlaps at the low end of the ranges. Also significant was the finding that all mutation classes were more prevalent in late versus early-stage NSCLC. Specifically, 56 of 58 CNAs (96.6%); 737 of 805 SNVs (91.6%); 42 of 43 INDELs (97.3%) and 12 fusions (100%) were associated with late-stage specimens.

Conclusion: In this observational study cohort, cfDNA yields were significantly higher in late-stage NSCLC patients compared to early-stage. We also observed significantly more and varied mutations in plasma from late-stage patients. These initial findings need to be extended to additional cancers and refined by stage at diagnosis. We are currently expanding our study to include additional technologies and panels to assess ctDNA mutations especially for the early-stage patients. Quantitative cfDNA data may be of utility in diagnosis, monitoring and recurrence of cancer.

Citation Format: Claire Gould, Leisa Jackson, Colin Cochran, Audrey Audetat, Brittany D'Alessio, Amanda Weaver, Janice Riley, Gary A. Pestano. Prevalence of four major gene mutation classes in a survey of ctDNA recovery from early and advanced stage NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6687.

Safety and efficacy of tenecteplase in patients with wake-up stroke assessed by non-contrast CT (TWIST): a multicentre, open-label, randomised controlled trial

BACKGROUND

Current evidence supports the use of intravenous thrombolysis with alteplase in patients with wake-up stroke selected with MRI or perfusion imaging and is recommended in clinical guidelines. However, access to advanced imaging techniques is often scarce. We aimed to determine whether thrombolytic treatment with intravenous tenecteplase given within 4·5 h of awakening improves functional outcome in patients with ischaemic wake-up stroke selected using non-contrast CT.

METHODS

TWIST was an investigator-initiated, multicentre, open-label, randomised controlled trial with blinded endpoint assessment, conducted at 77 hospitals in ten countries. We included patients aged 18 years or older with acute ischaemic stroke symptoms upon awakening, limb weakness, a National Institutes of Health Stroke Scale (NIHSS) score of 3 or higher or aphasia, a non-contrast CT examination of the head, and the ability to receive tenecteplase within 4·5 h of awakening. Patients were randomly assigned (1:1) to either a single intravenous bolus of tenecteplase 0·25 mg per kg of bodyweight (maximum 25 mg) or control (no thrombolysis) using a central, web-based, computer-generated randomisation schedule. Trained research personnel, who conducted telephone interviews at 90 days (follow-up), were masked to treatment allocation. Clinical assessments were performed on day 1 (at baseline) and day 7 of hospital admission (or at discharge, whichever occurred first). The primary outcome was functional outcome assessed by the modified Rankin Scale (mRS) at 90 days and analysed using ordinal logistic regression in the intention-to-treat population. This trial is registered with EudraCT (2014-000096-80), ClinicalTrials.gov (NCT03181360), and ISRCTN (10601890).

FINDINGS

From June 12, 2017, to Sept 30, 2021, 578 of the required 600 patients were enrolled (288 randomly assigned to the tenecteplase group and 290 to the control group [intention-to-treat population]). The median age of participants was 73·7 years (IQR 65·9-81·1). 332 (57%) of 578 participants were male and 246 (43%) were female. Treatment with tenecteplase was not associated with better functional outcome, according to mRS score at 90 days (adjusted OR 1·18, 95% CI 0·88-1·58; p=0·27). Mortality at 90 days did not significantly differ between treatment groups (28 [10%] patients in the tenecteplase group and 23 [8%] in the control group; adjusted HR 1·29, 95% CI 0·74-2·26; p=0·37). Symptomatic intracranial haemorrhage occurred in six (2%) patients in the tenecteplase group versus three (1%) in the control group (adjusted OR 2·17, 95% CI 0·53-8·87; p=0·28), whereas any intracranial haemorrhage occurred in 33 (11%) versus 30 (10%) patients (adjusted OR 1·14, 0·67-1·94; p=0·64).

INTERPRETATION

In patients with wake-up stroke selected with non-contrast CT, treatment with tenecteplase was not associated with better functional outcome at 90 days. The number of symptomatic haemorrhages and any intracranial haemorrhages in both treatment groups was similar to findings from previous trials of wake-up stroke patients selected using advanced imaging. Current evidence does not support treatment with tenecteplase in patients selected with non-contrast CT.

FUNDING

Norwegian Clinical Research Therapy in the Specialist Health Services Programme, the Swiss Heart Foundation, the British Heart Foundation, and the Norwegian National Association for Public Health.

POS1147 CHALLENGES IN CONDUCTING PRAGMATIC CARE STRATEGY STUDIES IN OSTEOPOROSIS: PATIENT PERCEPTIONS

Background

Large pragmatic osteoporosis studies to improve outcomes are needed. Direct-to-patient studies have highest generalizability but achieving sufficient sample size is difficult; recruitment challenges represent an important consideration given limited participant eligibility and interest. The Fracture Liaison Service (FLS), a team approach to post-fracture care, is a secondary fracture prevention method that has significantly improved outcomes internationally.

Objectives

Our goal was to evaluate the interest, barriers, and lessons learned in recruiting participants for a future trial assessing remote FLS approaches for post-fracture care.

Methods

We used ICD10 fracture codes to identify patients > 50 years of age with a documented hip/pelvis, spine, humerus, or wrist fracture in the previous 1 year. We excluded patients with i) prescriptions for osteoporosis medications (e.g., bisphosphonates, parathyroid hormone analogs, denosumab, romosozumab, raloxifene) in the prior 1 year; ii) an ICD10 code for end-stage renal disease, non-osteoporotic metabolic bone disease, malignant neoplasm, or motor vehicle accident. In December 2021, research assistants reviewed electronic health records (EHR) of potentially eligible patients for evidence of additional serious illness limiting life expectancy to < 1 year or non-ambulatory status prior to fracture. Research assistants called preliminary eligible patients that met inclusion and exclusion criteria and asked them to complete a survey by phone. Interest in a FLS future clinical trial was evaluated using a Likert scale (1=“Definitely would not volunteer”, to 5=“Definitely would volunteer”). We used descriptive statistics to analyze baseline demographic, clinical characteristics, and interest. This pilot was approved by the UAB Institutional Review Board (IRB-300008310-005).

Results

We identified 1,577 patients > 50 years of age with a fracture. After applying exclusion criteria, we identified 869 preliminary eligible patients. Over 3 weeks, we screened the medical records of a random sample of half of the preliminary eligible patient cohort (n=414), of whom we contacted 271 patients determined potentially eligible, and successfully reached 141 (52% of those contacted) by phone. A total of 108 (77% of those reached) persons, mean (SD) age 69.5 (11.5) years, 40% men, 21% Black or non-white Hispanics completed the survey. Among those contacted, 68 (63%, interest rate) said they would be very or highly interested in participating in a future clinical trial evaluating FLS approaches. Among the 40 (37%) people who said they were not sure, unlikely or very unlikely to volunteer the most common reasons cited were “I don’t want to participate in a study” (33%); “I don’t feel well enough to participate” (10%); “I don’t understand what the study is for” (3%). From this pilot, we calculated a refined eligibility/interest rate of 9.1% among those patients preliminarily identified as eligible using administrative data alone.

Conclusion

Based on our pilot, we estimate that approximately 9% of eligible patients with fractures will be interested in enrolling in a future comparative effectiveness study to prevent recurrent fragility fractures. We identified several potential modifiable barriers to clinical trial recruitment. Patient perceptions collected from this pilot will inform enrollment strategies, which can be incorporated early when planning direct-to-patient pragmatic osteoporosis studies to achieve recruitment goals.

Disclosure of Interests

Lesley Jackson: None declared, Ellen McNeeley: None declared, Norma C. Techarukpong: None declared, Faith Mugeta: None declared, Kiara Aaron: None declared, Amy Mudano: None declared, Jeanne Merchant: None declared, Kellie Warren: None declared, Jeff Foster: None declared, Kenneth Saag Grant/research support from: Amgen, Horizon, LG Chem, Radius, SOBI, Maria Danila Grant/research support from: Pfizer, Horizon

POS1171 TRIPLE THE RATE OF EMERGENCY ROOM VISITS AND HOSPITALIZATIONS FOR GOUT AMONG US BLACKS VS WHITES – 2019 NATIONWIDE ANALYSIS

Background

Gout is a highly prevalent inflammatory arthritis with increasing global disease burden in recent years.1,2 Gout prevalence has been reported to be higher among Blacks compared to Whites,3 and that they are less likely to receive allopurinol in outpatient care.4 The potential nationwide impact of these racial disparities on emergency department (ED) visits and hospitalizations is unknown.

Objectives

To examine the contemporary racial disparities in ED visits and hospitalizations with a primary discharge diagnosis of gout in the US (2019).

Methods

We compared ED visits and hospitalizations between Blacks and Whites in the latest data (2019) from the US National Emergency Department Sample (NEDS) and National Inpatient Sample (NIS). We focused on encounters for which the primary diagnosis was gout based on ICD codes (M1A.xx, M10.xx). We calculated annual population rates of ED visits and hospitalizations for gout (per 100,000 US adults) using the 2019 US census adult population (>18 years) according to race.

Results

There were a total of 160,759 ED visits and 9,560 hospitalizations among White and Blacks with a gout diagnosis in the US in 2019. The mean age (58.2 years vs. 56.5 years) and male proportion (78.0% vs. 74.8%) tended to be higher among Whites, while more Blacks tended to live in the South (40.7% vs. 66.5%) and reported a median household income of < $50,000 (30.7% vs. 57.1%). Compared to Whites, Blacks had 2.7- and 3.2-fold higher rates of gout ED visits and hospitalizations, respectively, after adjusting for age, sex, payer, region, and household income (Table 1 & Figure 1). Black women, in particular, had 3.4- and 4.0-fold higher rates of ED visits and hospitalizations compared to White women, while the corresponding rate ratios for men were 2.5 and 2.8, respectively. The mean costs per gout ED visit were similar for Blacks compared to Whites (adjusted difference, -$7.6 [95% CI, -25.4 to 1.0]), while hospitalizations were more costly (adjusted difference, $1,055.3 [95% CI, 553.1 to 1557.5]). The duration of ED visits and hospitalizations was also higher among Blacks than Whites (adjusted difference of 0.41 days [95% CI, 0.19 to 0.63] and 0.59 days [95% CI, 0.25 to 0.94], respectively).

Table 1.

Racial Disparities in Emergency Department Visits and Hospitalizations with Primary Diagnosis of Gout in 2019

Emergency Department VisitsHospitalizationsRaceWhiteBlackWhiteBlackAll6801196524521330198510434519150Visits, N888107194962003360Rate per 100,000130.6293.431.274.4Rate Ratio (95% CI)*1.0 (ref)2.81 (2.63, 3.00)1.0 (ref)3.08 (2.79, 3.40)Rate Ratio (95% CI)**1.0 (ref)2.66 (2.50, 2.82)1.0 (ref)3.17 (2.86, 3.50)Women3785136914363031110390932647105Visits, N195671816317701145Rate per 100,00051.7126.516.043.3Rate Ratio (95% CI)*1.0 (ref)3.68 (3.39, 3.99)1.0 (ref)4.01 (3.40, 4.73)Rate Ratio (95% CI)**1.0 (ref)3.36 (3.11, 3.62)1.0 (ref)4.02 (3.39, 4.78)Men301561011015657388098151871620Visits, N692285378344302215Rate per 100,000229.6529.550.3118.3Rate Ratio (95% CI)*1.0 (ref)2.59 (2.42, 2.78)1.0 (ref)2.66 (2.36, 3.00)Rate Ratio (95% CI)**1.0 (ref)2.47 (2.32, 2.64)1.0 (ref)2.77 (2.45, 3.14)

*Adjusted for age and sex for all, adjusted for age for sex-specific rate ratios

**Adjusted for age, sex, payment, region, and household income

Conclusion

These latest national data indicate that ED visits and hospitalization due to gout are both 3 times higher among Blacks than Whites; this disparity was particularly prominent among women with gout. Higher risk of developing gout3 and suboptimal care4 both translate to these avoidable costly healthcare utilizations, calling for improved primary prevention and gout care.

References

[1]Safiri et al., PMID 32755051

[2]Xia et al., PMID 31624843

[3]Chen-Xu et al., PMID 30618180

[4]Krishnan et al., PMID 18260174

Disclosure of Interests

Chio Yokose: None declared, Natalie McCormick: None declared, Na Lu: None declared, Amit Joshi: None declared, Lesley Jackson: None declared, Minna Kohler Speakers bureau: Lilly, Consultant of: Mymee, Novartis, Grant/research support from: Setpoint Medical, Janeth Yinh: None declared, Yuqing Zhang: None declared, Kenneth Saag Consultant of: Arthrosi, Atom Bioscience, Horizon Therapeutics, LG Pharma, Mallinkrodt, SOBI, Takeda, Grant/research support from: Horizon Therapeutics, SOBI, Shanton, Hyon Choi Consultant of: Ironwood, Selecta, Horizon, Takeda, Kowa, and Vaxart, Grant/research support from: Ironwood and Horizon

Long-term cancer surveillance: results from the Forteo Patient Registry Surveillance Study

The Forteo Patient Registry estimated the incidence of osteosarcoma in US patients treated with teriparatide and enrolled in the study between 2009 and 2019. No incident cases of osteosarcoma were identified among patients registered, and the crude incidence rate was 0 (95% confidence interval [CI], 0-10.2) cases per million person-years.

PURPOSE

The prospective, voluntary Forteo Patient Registry was established to estimate the incidence of osteosarcoma in patients who have received treatment with teriparatide (Forteo).

METHODS

Information on US adults prescribed teriparatide and enrolled in the Forteo Patient Registry 2009-2019 was linked with data from participating state cancer registries annually (2010-2019) to identify incident osteosarcoma cases using a standardized linkage algorithm. Teriparatide exposure was ascertained from self-reported data that included teriparatide initiation and demographics necessary to complete linkage. Osteosarcoma cases diagnosed on or after January 1, 2009, were identified by participating state cancer registries. The crude incidence rate (IR) and standardized incidence ratio (SIR) of observed cases to the expected number of cases adjusted to the background rate (3 per million person-years) and corresponding 95% CIs for the occurrence of osteosarcoma were calculated whereby the cumulative amount of person-time observed was adjusted for mortality.

RESULTS

Data for 75,247 enrolled patients (representing 361,763 cumulative person-years) were linked to each of 42 participating state cancer registries (covering 93% of the US population), which included information on 6180 cases of osteosarcoma. No matches with incident cases of osteosarcoma following registry enrollment were found. The crude IR was 0 (95% CI, 0-10.2) cases per million person-years and the SIR was 0 (95% CI, 0-3.0).

CONCLUSIONS

The ability to draw conclusions about the incidence of osteosarcoma among patients participating in the registry was limited due to the smaller than expected amount of patient follow-up time and the fact that no cases were identified.

70 Improving the Documentation of DNACPR Decisions Following the Transition to Electronic Record Keeping

Background

This quality improvement project was based at The Royal Bolton Hospital across our four Complex Care wards.

Introduction

We have recently transferred to electronic record keeping. At these points of transition there may be an adverse impact on the quality of patient care and safety. We recognised on our own ward there were inaccuracies between the required paper form and electronic documentation of DNACPR decisions. Consequently, we wanted to review and improve the accuracy of our DNACPR documentation to ensure safe and effective patient care.

Methods

To gauge the scope of the problem we audited 87 patient’s electronic and paper notes, with no exclusion criteria. We reviewed whether each patient had a formal resuscitation decision, and if a DNACPR decision had been made whether we met our hospital policy by having:

93% of the 87 patient’s had an active decision regarding resuscitation, with a DNACPR decision documented for 50 patients. Of these 50 patients only 11 had all three forms of documentation. More worryingly, there were discrepancies in the documented DNACPR decisions for 11 patients across paper and electronic records.

Interventions

We escalated our concerns to the Clinical Governance team who sent out a trust wide SBAR highlighting this as an urgent clinical issue. On a directorate level we incorporated DNACPR decision documentation into our afternoon safety huddle and arranged informal teaching for medical, nursing and administrative staff.

Results

Reassuringly, the subsequent re-audit of 90 patient’s notes showed only one patient to have a discrepancy between paper and electronic documentation. We saw an improvement to 98% having paper forms in the right bedside notes and 100% having a documented electronic DNACPR decision.

Conclusion

Through local education and trust-wide dissemination of our expected standards we have seen some improvement. We recognise the importance of maintaining this, and importantly that there is still work to be done. The electronic “Resuscitation and treatment escalation plan” is still rarely completed and provides important information on escalation of care and thus will be the focus of a further educational intervention.

Targeted Next-Generation Sequencing of Liquid Biopsy Samples from Patients with NSCLC

Liquid biopsy tests have become an integral part of the molecular diagnosis of patients with non-small cell lung cancer (NSCLC). We describe a new test panel that uses very low input (20 ng) of cell-free nucleic acids extracted from human plasma, which is designed to yield results in less than 72 h. In this study, we performed novel amplicon-based targeted next-generation sequencing with a semiconductor-based system, the Ion GeneStudio S5 Prime. The analytic performance of the assay was evaluated using contrived and retrospectively collected clinical specimens. The cumulative percent coefficient of variation for the new test process was very precise at 8.4% for inter-day, 4.0% for inter-operator and 3.4% for inter-instrument. We also observed significant agreement (95.7-100%) with an orthogonal, high-sensitivity droplet digital™ Polymerase Chain Reaction (ddPCR) test. This method offers a valuable supplement to assessing targeted mutations from blood while conserving specimens and maintaining sensitivity, with rapid turn-around times to actionable results.

Utilization of P16 in Head and Neck Cytology and Surgical Specimens After the Release of CAP Guidelines

Introduction/Objective

HPV-positive oropharyngeal squamous cell carcinoma is biologically and clinically unique and has a survival advantage over other head and neck squamous cell carcinomas. In December 2017 College of American Pathologist published guidelines for testing HPV status in head and neck cancer. It was recommended that pathologists perform HR-HPV testing on head and neck squamous cell carcinomas from all patients with known oropharyngeal SCC not previously tested for HR-HPV, with suspected oropharyngeal SCC, or with metastatic SCC of unknown primary. The aim of this study was to determine the compliance of pathologists following the CAP guidelines.

Methods

Cases that underwent HPV testing using p16 immunohistochemistry for the years 2017 and 2019 were retrieved. Based on the guidelines, p16 testing was designated as “indicated” or “not indicated”.

Results

There were 196 cases in which p16 testing was performed in a period of 3 consecutive years. Of these, 175 were FNA/ biopsies and 21 were surgical resections. In 69 cases (56 FNAs and 13 biopsies) the biopsy was performed on neck masses with unknown primary. The compliance for p16 testing in OPC and Lymph nodes with metastatic SCC of unknown primary was 100%. In 34 (17.3%) cases p16 testing was not indicated, the most common reason being wrong site (85%) including the larynx, oral tongue, the floor of the mouth, buccal mucosa, and nasal mass. Of the unindicated p16s, 20 (58%) were received in consultation for continuity of care.

Conclusion

Not being clear about the site of the tumor is the most common reason for unindicated p16 testing. A clear designation of biopsy site and proper communication between pathologist and surgeon can improve utilization of p16 testing in head and neck carcinomas.

Abstract 3101: Utility of a new targeted next generation sequencing test for liquid biopsy samples from patients with NSCLC

Blood-based methods for profiling tumor-sourced nucleic acids have become increasingly important in the diagnostic workup for cancer patients, particularly in non-small cell lung cancer (NSCLC). Blood-based assays address several limitations of tissue-based testing approaches such as inaccessible lesions, limited tissue, extended time to results, and invasive specimen collection procedures. Broad-profiling next-generation sequencing (NGS) methods are used to detect rare variants in blood samples. Here we describe the utility of a newly developed 52 gene NGS test, which uses the GeneStudio S5 Prime platform. We report on performance verification of the assay using contrived specimens as well as studies which evaluated clinical specimens at diagnosis and during monitoring. Thirty-eight cell-free nucleic acid (cfNA) specimens were evaluated from donors previously diagnosed with NSCLC. Specimens were collected in blood collection tubes containing preservatives (Streck cfDNA BCT) and shipped at ambient temperature to our central testing Laboratory. cfNA was isolated from plasma and reverse transcribed. The sequencing metrics for these studies included an average of 15 million mapped reads, 94.4% of on target reads, and a mean sequencing depth of 52,000. Additionally, the average molecular coverage was 2400 reads per amplicon with 99.9% uniformity at 500x coverage. Detected variants and their allelic frequencies were compared with reference results from a validated ddPCR method. Eleven variants (6 EGFR and 5 KRAS) were detected in the cohort with allele frequencies ranging from 0.90 - 96.16%. Results were highly concordant between the two methods (R2=0.992) with 90.3% sensitivity and 100% specificity. In addition, we present a case study to further demonstrate clinical utility of NGS for longitudinal monitoring over 540 days for clearance followed by re-emergence of EGFR positive cfNA harboring the EGFR C797S resistance mutation. These studies add to the growing body of knowledge supporting the utility of molecular detection for actionable and emerging biomarkers in liquid biopsy.

Citation Format: Jordan Reese, Victoria Maxwell, Leisa Jackson, Gary Pestano, Hestia S. Mellert. Utility of a new targeted next generation sequencing test for liquid biopsy samples from patients with NSCLC [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3101.

Abstract B54: Profiling the TCR beta repertoire in liquid biopsies from NSCLC donors

Introduction: During infection and in cancer, the immune system’s response to antigen leads to changes in the T-cell repertoire. T-cell clonal expansions can be measured by sequencing the antigen-specific loci in the T-Cell Receptor Beta gene (TCRβ). In oncology research, TCRβ sequencing is being explored as a predictor for response to immunotherapy as well as IRAE (immune-related adverse events) post-immunotherapy. Recent studies have focused on two metrics, T-cell clonality and TCR convergence, as potential biomarkers. Noninvasive testing for these markers can be achieved using peripheral blood lymphocytes (PBL). In this study, PBL specimens from donors previously diagnosed with NSCLC were evaluated using TCRβ sequencing. Additionally, to model T-cell repertoire changes due to antigen stimulation, primary PBL were challenged in vitro with cytomegalovirus (CMV) antigen.

Methods: Peripheral blood mononuclear cells (PBMC) from 4 healthy donors were challenged with a 1-week exposure to whole-cell lysate from CMV-infected cells or CMV pp65495-503 peptide (NLVPMVATV). T-cell repertoire perturbations were assessed using the Oncomine TCR Beta-SR Assay and Ion GeneStudio S5 Sequencer. A pp65 tetramer flow cytometry assay was used as an orthogonal method to assess clonal expansion of a subset of CMV-specific T cells. For evaluation of the assay in PBL from NSCLC donors, five whole-blood specimens were evaluated using the same sequencing workflow.

Results: The TCR Beta assay identified 6,683-61,936 unique clones from 1-2 million reads per sample, and an average of 80% of the total reads were usable for TCR profiling. In the NSCLC donors, TCR convergence and clonality values were consistent with published results and ranged from 0.016-0.033 for convergence and 0.09-0.48 for clonality. In the CMV study, TCR sequencing detected the expansion of a common family of clones in 3 samples in response to pp65 peptide stimulation. This expansion corresponded to an increase in pp65 tetramer staining by flow cytometry. Interestingly, this family was not detected in the 4th sample, and an increase in tetramer staining was not observed with pp65 challenge. However, TCRβ clonality increased significantly in the CMV lysate condition for this sample. A single clonotype increased from 6.5% to 76% frequency, and this shift corresponded to increased pp65 tetramer staining by flow cytometry. Baseline TCR convergence scores ranged from 0.009-0.041 and increased 5-fold in one sample as a result of pp65 antigen stimulation.

Conclusions: These data demonstrate that the TCRβ assay can detect repertoire features with high resolution using PBMC isolated from liquid biopsies. Profiling of the TCRβ repertoire using the Ion Torrent platform represents a valuable new solution given the technology’s relatively low substitution error rate. Additional studies are being pursued to evaluate the clinical utility of sequencing the immune repertoire in NSCLC patients receiving immunotherapy.

Citation Format: Leisa Jackson, Benjamin Tjoa, Hestia Mellert, Gary Pestano. Profiling the TCR beta repertoire in liquid biopsies from NSCLC donors [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B54.

An investigation of targeted inhibition of transcription factor activity with pyrrole imidazole polyamide (PA) in chronic myeloid leukemia (CML) blast crisis cells

Tyrosine kinase inhibitor (TKI) therapy is the standard treatment for chronic phase (CP)-chronic myeloid leukemia (CML), yet patients in blast crisis (BC) phase of CML are unlikely to respond to TKI therapy. The transcription factor E2F1 is a down-stream target of the tyrosine kinase BCR-ABL1 and is up-regulated in TKI-resistant leukemia stem cells (LSC). Pyrrole imidazole polyamides (PA) are minor groove binders which can be programmed to target DNA sequences in a gene-selective manner. This manuscript describes such an approach with a PA designed to down-regulate E2F1 controlled gene expression by targeting a DNA sequence within 100 base pairs (bp) upstream of the E2F1 consensus sequence. Human BC-CML KCL22 cells were assessed after treatment with PA, TKI or their combination. Our PA inhibited BC-CML cell expansion based on cell density analysis compared to an untreated control after a 48-hour time-course of PA treatment. However, no evidence of cell cycle arrest was observed among BC-CML cells treated with PA, with respect to their no drug control counterparts. Thus, this work demonstrates that PAs are effective in inhibiting E2F1 TF activity which results in a temporal reduction in BC-CML cell number. We envisage that PAs could be used in the future to map genes under E2F1 control in CML LSCs.

Abstract 411: Rapid and sensitive detection of EGFR C797S mutations using a blood-based droplet digital PCR assay

The adoption of third-generation tyrosine kinase inhibitors (TKIs) to treat non-small cell lung cancer (NSCLC) for EGFR positive patient cases has led to the emergence of acquired resistance pathways. Approximately 40% of EGFRT790M-positive NSCLC cases display an acquired mutation of amino acid 797 (C797S) that mediates this resistance, which can develop after a median of 10 months following treatment. The effectiveness of treatment for patients with EGFRC797S may depend on whether the mutation is present in cis or trans with EGFRT790M, the type of sensitizing mutation (EGFRdel19 or EGFRL858R), and previous treatment(s). Patients with EGFRdel19 or EGFRL858R in conjunction with EGFRT790M and EGFRC797S remain resistant to all current targeted therapies. Several fourth-generation inhibitors are in development but have yet to be validated in clinical trials. We have developed a blood-based test that can detect two of the most common C797S nucleotide mutations (T&gt;A and G&gt;C) in cis or trans with EGFRT790M using the droplet digital PCR (ddPCR) technology and assays. Analytic sensitivity and specificity were assessed using synthetic DNA designed to mimic the EGFRC797S variants and their locus detected in the assay. Normal healthy donors as well as reference ddPCR positive and negative NSCLC donor samples were assessed for clinical specificity and sensitivity. Finally, the precision of the assay was evaluated with both clinical and analytical samples. Specifically, we evaluated the assay at high, medium, and low mutation frequencies over three consecutive days, including repeat runs on one day, and with multiple operators. This assay is capable of accurately and precisely detecting multiple EGFRC797S variants and their locus from blood specimens in the clinical laboratory. Consistent with other ddPCR blood-based EGFR variant assays we have developed, the limit of detection was 0.02%for C797S variants detected in both cis and trans with the T790M mutation. Once validated, the EGFR C797S assay described here may be of utility in diagnosing patients who have developed resistance to osimertinib.

Citation Format: Victoria Edwards, Leisa Jackson, Jordan Reese, Hestia S. Mellert, Gary Pestano. Rapid and sensitive detection of EGFR C797S mutations using a blood-based droplet digital PCR assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 411.

Abstract 3980: Molecular profiling of cell-free DNA and RNA in the blood of patients with non-small cell lung cancer

Lung cancer is the leading cause of cancer-related deaths in the United States with Non-Small Cell Lung Cancer (NSCLC) being the most commonly diagnosed subtype. However, up to 30% of advanced NSCLC patients are not eligible for tissue biopsy. As a result, liquid biopsies are becoming increasingly utilized in clinical testing as they are non-invasive and have an overall decreased risk to patients. This approach also addresses other challenges associated with tissue-based profiling, including tumor heterogeneity and low yield of quality nucleic acid for the identification of actionable targets of treatment. In this study, cell-free total nucleic acid (cfTNA) was isolated from donor patient plasma samples collected and shipped at ambient temperatures in blood collection tubes to the Biodesix CAP/CLIA laboratory in Boulder, CO. cfTNA was profiled with a targeted cancer NGS (next generation sequencing) panel, using the Ion Torrent GeneStudio S5 Plus System. Variant analyses were conducted using a threshold of ≥0.3% percent variant allele frequency to assess concordance in the patient donor specimens. A high level of concordance (R2=0.99) was observed between inter-laboratory/inter-instrument NGS runs using 6 clinical samples. In the 0.1% single nucleotide variant (SNV) positive control sample which encompasses 23 hotspots, there was slightly lower concordance (R2=0.90) due to low variant allele frequency (0.06-0.3%). Validation studies are in progress and include RNA fusions and additional variants present in blood from patients diagnosed with NSCLC.

Citation Format: Jordan Reese, Leisa Jackson, Hestia S. Mellert, Gary Pestano. Molecular profiling of cell-free DNA and RNA in the blood of patients with non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3980.

Development and correlative analysis of a TML assay in specimens with reference MSI and somatic variant results

124

Background: Treatment of late-stage non-small cell lung cancer has been greatly impacted by the advances in immunotherapy. Molecular biomarkers such as tumor mutation load (TML or TMB) and micro-satellite instability (MSI) may identify patients with NSCLC that are more likely to respond to immune checkpoint inhibitors. In this report, we describe the development of and NGS-based assay for the robust detection of TML and somatic variants simultaneously using a targeted assay that covers 1.7 Mb of the genome. Methods: Initial feasibility included reference control cell-lines, HCC1143 and NIST8398, as well as FFPE (formalin-fixed, paraffin-embedded) samples from lung and colorectal tumors. In development, eight FFPE specimens from patients with late stage cancer and a reference MSI status were evaluated. FFPE slides were extracted using the MagMax FFPE DNA/RNA Ultra kit, and nucleic acid quality was assessed using qPCR. Extracted DNA was processed through the Oncomine TML Assay with a minimum input of 30 ng of DNA per specimen. Automated library and template preparation were performed followed by sequencing on the Ion GeneStudio S5 Plus system using replicate 540 chips. Eight samples with barcoded adapters were multiplexed per chip. Tumor mutation analysis and variant calling was performed using the Oncomine TML v2.0 workflow. Results: The time from FFPE extraction to result was 96 hours, and all samples passed QC metrics. TML scores ranged from 14.4-36.04 mutations/Mb for all samples with MSI-high reference results. A very high level of inter-chip concordance was also observed (R2=0.990). Additionally, the variant caller function within the TML workflow was used to detect BRAF V600E mutations with 100% concordance to reference testing results. Conclusions: The accurate quantification of somatic mutations paired with fast turn-around time and robust automated workflow is ideal for assessing the tumor mutation load as well as hotspot mutations from limited (FFPE) samples.

Abstract 5573: Highly multiplexed diagnostic test for the detection of extended EGFR del19 variants in patients with NSCLC

The detection of nucleic acids in circulation has become an increasingly important part of the clinical workup and testing for cancer patients, particularly those with non-small cell lung cancer (NSCLC). The utilization of blood-based PCR platforms for detection of somatic variant mutations addresses several limitations of previously established molecular testing approaches such as an inability to access tissue, insufficient tissue quantity or quality, and slow turnaround time for results. However, the number of variants detected may be limited by use of some rapid PCR technologies. We have focused in this study on the analytic and clinical development of a highly multiplexed assay for the detection of EGFR del19 while maintaining a rapid turn-around time. The test system includes the prospective collection of whole blood into a cfDNA BCT and the reproducible detection of del19 variants out of plasma using ddPCR-based technology. Analytic specificity and sensitivity was examined using in vitro DNA designed to mimic the EGFR del19 variants in the assay. Analytic sensitivity was performed and demonstrates that the theoretical limit of detection of the test was below 0.02% minor variant frequency when using high concentrations of synthetic standards. Precision studies were conducted with both analytic and clinical samples at high, medium and low mutation frequencies, over three consecutive days, three runs in one day and with two operators. All test parameters were successfully met. Normal healthy donor (n = 11) and reference ddPCR positive and negative NSCLC donor (n = 80) samples were tested. EGFR del19 variants were not identified in the plasma from the normal healthy donors or the EGFR del19 reference negative NSCLC donors. All reference positive cases were accurately detected above our required threshold of 2 variant copies with detection ranging from 14 to 1584. For all donor specimens the wild-type copies were well above the predefined clinical QC threshold of 300, ranging from 380 to 760 copies. Of note, no negative reference samples contained more than two mutant copies. We conclude that the developed test is highly suited for the sensitive and reproducible detection of multiple EGFR del19 variants from blood specimens in the clinical laboratory.

Citation Format: Hestia S. Mellert, Leisa Jackson, Kristin Alexander, Amanda Weaver, Dianna Maar, Dawne Shelton, Gary Pestano. Highly multiplexed diagnostic test for the detection of extended EGFR del19 variants in patients with NSCLC [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 5573.

Development and Clinical Utility of a Blood-Based Test Service for the Rapid Identification of Actionable Mutations in Non-Small Cell Lung Carcinoma

Nearly 80% of cancer patients do not have genetic mutation results available at initial oncology consultation; up to 25% of patients begin treatment before receiving their results. These factors hinder the ability to pursue optimal treatment strategies. This study validates a blood-based genome-testing service that provides accurate results within 72 hours. We focused on targetable variants in advanced non-small cell lung carcinoma-epidermal growth factor receptor gene (EGFR) variant L858R, exon 19 deletion (ΔE746-A750), and T790M; GTPase Kirsten ras gene (KRAS) variants G12C/D/V; and echinoderm microtubule associated protein like and 4 anaplastic lymphoma receptor tyrosine kinase fusion (EML4-ALK) transcripts 1/2/3. Test development included method and clinical validation using samples from donors with (n = 219) or without (n = 30) cancer. Clinical sensitivity and specificity for each variant ranged from 78.6% to 100% and 94.2% to 100%, respectively. We also report on 1643 non-small cell lung carcinoma samples processed in our CLIA-certified laboratory. Mutation results were available within 72 hours for 94% of the tests evaluated. We detected 10.5% mutations for EGFR sensitizing (n = 2801 samples tested), 13.8% mutations for EGFR resistance (n = 1055), 13.2% mutations in KRAS (n = 3477), and 2% mutations for EML4-ALK fusion (n = 304). This rapid, highly sensitive, and actionable blood-based assay service expands testing options and supports faster treatment decisions.

Performance verification of a plasma-based PD-L1 test that reliably measures mRNA expression from patients with NCSLC

156

Background: The detection of circulating nucleic acids using non-invasive blood-draws has become highly relevant to clinical testing. In this study we report on the development of a blood-based PD-L1 test for immunotherapy selection. Methods: We have previously reported on the analytic performance of a droplet digital™ PCR (ddPCR) assay for circulating cytokeratin 19 and PD-L1. Using a variable threshold based on a logistic regression score for the blood assay and a 1% IHC (immunohistochemistry) tissue cut-off, concordance was 80% (n = 16). Positive calls for the blood-based PD-L1 assay ranged from 2 to 124 copies. In this study we focused on variables that could impact concordance of the blood assay and tissue results. Criteria included droplet counts for tissue and blood mRNA transcripts and tumor proportion score (TPS) for the tissue IHC assay (22C3 pharmDx). Results: We examined the correlation between PD-L1 in formalin-fixed paraffin-embedded (FFPE) tissue by IHC, mRNA expression in serial cut FFPE sections, and in matched plasma samples collected at the time of tissue resection. Five cases were assayed to confirm PD-L1 positivity by tissue. We successfully recovered RNA from serial tissue sections for each case and detected PD-L1 levels ranging from 6 to 1272 copies. Plasma samples were available for four of the cases for circulating RNA evaluation, and we were successful in detecting PD-L1 in all cases (copy range 32-138). While all four cases contained detectible PD-L1 mRNA in tissue and circulation, we observed little concordance between these levels in tissue and blood. Conclusions: We have developed methods to measure the dynamic range of PD-L1 from plasma. We have shown feasibility of these methods by evaluating key immune and cancer-specific RNAs. The current study demonstrates that although the development of quantitative assays for mRNA in blood is possible, concordance with traditional clinical tissue assays such as IHC may not be a useful validation measure. We have initiated prospective validation studies that will continue to evaluate PD-L1 expression by IHC and in the blood-based assay, and will also monitor patient performance measures in response to immunotherapy.

Points to consider for laboratories reporting results from diagnostic genomic sequencing

Although NGS technologies are well-embedded in the clinical setting for identification of genetic causes of disease, guidelines issued by professional bodies are inconsistent regarding some aspects of reporting results. Most recommendations do not give detailed guidance about whether variants of uncertain significance (VUS) should be reported by laboratory personnel to clinicians, and give conflicting messages regarding whether unsolicited findings (UF) should be reported. There are also differences both in their recommendations regarding whether actively searching for secondary findings (SF) is appropriate, and in the extent to which they address the duty (or lack thereof) to reanalyse variants when new information arises. An interdisciplinary working group considered the current guidelines, their own experiences, and data from a recent qualitative study to develop a set of points to consider for laboratories reporting results from diagnostic NGS. These points to consider fall under six categories: (i) Testing approaches and technologies used, (ii) Approaches for VUS; (iii) Approaches for reporting UF, (iv) Approaches regarding SF; (v) Reanalysis of data & re-contact; and vi) Minors. While it is unclear whether uniformity in reporting across all laboratories is desirable, we hope these points to consider will be useful to diagnostic laboratories as they develop their processes for making decisions about reporting VUS and UF from NGS in the diagnostic context.

Abstract A033: Concordance of IHC and a new blood-based expression assay for the detection of PD-L1 in patients diagnosed with NSCLC

Introduction: Therapeutic options for patients with non-small cell lung cancer (NSCLC) continue to expand with the approval of immunotherapies. PD-L1 testing can be clinically challenging due to lack of tissue and complexities associated with immunohistochemistry (IHC) including multiple antibodies, various scoring methods, and heterogeneous expression. Moreover, various thresholds have been established for diagnostic tests being used in the context of different checkpoint inhibitors in order to direct clinical practice. Therefore, there is an unmet need for diagnostic tests that measure biomarkers in circulation. We hypothesized that a test that delivered PD-L1 results from plasma read out as continuous variables may be of increased utility in the selection of therapeutic options. Methods: We focused this test development on mechanisms of blood-based testing for sensitive measurement of circulating RNA using ddPCR. Specifically, we optimized methods for the detection of PD-L1 transcripts recovered from platelet-enriched plasma. Specimens for feasibility and development included tumor derived cell lines, activated and resting immune cells, normal donor plasma (n=38), and NSCLC (n = 79) donor plasma. To assess the potential for concordance with tissue testing we collected a total of 43 tissue and blood samples. Tissue results had been previously performed for PD-L1 using IHC (PharmDx 22c3). The analysis excluded samples that lacked detectable CK19 indicating that RNA of epithelial origin was not present in circulation (n=25), and two cases with exceptionally high PD-L1 expression in plasma, leaving 16 samples for further statistical analysis and concordance evaluation. Results: Assessing PD-L1 in circulation is complicated by its expression in both immune and cancer cells. Analytic performance was initially evaluated with cancer cell lines and lymphocytes and monocytes expressing variable levels of PD-L1. Of the 79 NSCLC donor specimens initially evaluated with the RNA blood test, we observed a frequency of 62% positive samples (n=49) with highly variable levels of plasma PD-L1 (2 - 774 copies). We then evaluated a subset of a sample cohort with an IHC tissue test result (n=16). Although there was poor concordance with a 50% positive IHC cut-off, when we used a variable threshold based on a logistic regression score for the blood assay and the 1% cut-off, concordance of up to 80% was observed between the two assays. Conclusions: We have developed sensitive and specific methods that measure the dynamic range of PD-L1 in circulation. This assay is capable of measuring PD-L1 in circulation that arises from activated immune cells and/or tumor cells. We have identified a preliminary threshold for the PD-L1 circulating blood test in development that shows concordance with tissue IHC when using the 22c3 clone at 1% cut-off.

Citation Format: Michael A. Pritchett, Jiaxin Niu, Leisa Jackson, Hestia Mellert, Gary A. Pestano. Concordance of IHC and a new blood-based expression assay for the detection of PD-L1 in patients diagnosed with NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A033.

Abstract 1784: Early feasibility and development of multiplexed, single-reaction assays for ALK, ROS1 and RET novel ddPCR RNA fusions

We have previously described a targeted genomic Laboratory Developed Test (LDT) that includes variant specific Droplet Digital™ PCR (ddPCR) testing for EGFR, KRAS and BRAF in plasma. This test supports the rapid delivery of molecular diagnostic test results, with &gt;95% of tests results delivered in 72 hours of receipt in our Laboratory. This test then meets the key clinical need for the delivery of results that can result in faster treatment decisions. Additionally, the test may be of utility for those patients who need mutation results quickly or for whom tissue may be unavailable or insufficient for molecular testing. This is especially true for patients diagnosed with non-small cell lung cancer (NSCLC). In this report we will update on new test concepts created using the recently available design software engine for ddPCR assays. Specifically, we will describe studies on the development of single-reaction, multiplexed assays for the respective detection of ROS1 (up to 11 variants), RET (up to 8 variants) and EML4-ALK (v1 - v3). Design considerations, specificity and sensitivity, as well as reproducibility and robustness studies for these complex assays will be reviewed. Similar studies were conducted for the development of the commercially available test for the EML4-ALK fusion variants. EML4-ALK concordance studies compared the fusions found in blood with known positives and negatives found using FISH and PCR based methods (n=24 evaluable matched pair samples). Clinical sensitivity, specificity and concordance were 85%, 100% and 92% respectively. In this study we also report on test performance of the ALK RNA fusion test over 3 consecutive months of testing. Of note, we have delivered greater than 95% of tests (n = 272 samples) with an observed positive sample frequency of 2%. The robust detection of rare variant, RNA fusions from plasma within 72 hours represents a molecular testing option of value to patients with NSCLC and their physicians.

Citation Format: Hestia Mellert, Kristin Alexander, Leisa Jackson, Galen Roda, Samantha Cooper, Dianna Marr, Stephen J. Jones, Nia Charrington, Gary Pestano. Early feasibility and development of multiplexed, single-reaction assays for ALK, ROS1 and RET novel ddPCR RNA fusions [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 1784. doi:10.1158/1538-7445.AM2017-1784

Abstract 5681: Utility of a targeted NSCLC genomic test for cfDNA variants in the community setting

Time to treatment can have significant impact on progression of cancer, and treatment decisions rely heavily upon genomic and proteomic testing. However, multiple factors can delay the availability of molecular diagnostic test results, including the use of tissue-based testing. Almost one third of patients with non-small cell lung cancer (NSCLC) are either not candidates for biopsies, or have insufficient tissue samples from their initial biopsy. Additionally, most physicians in the community setting want to initiate treatment quickly but do not have access to on-site molecular testing at their practice. As a result, physicians may delay their decision to commence treatment with specific targeted therapies or treat before the mutation status is known. The goal of this study was to assess the utility of a blood-based cell-free (cf) nucleic acid Laboratory Developed Test (LDT) in the community setting. The tests utilize Droplet Digital™ PCR (ddPCR) technology to detect the EGFR sensitizing mutations L858R and exon 19 deletion (E746 - A750), the EGFR resistance mutation (T790M), the KRAS mutations G12C, G12V and G12D, and the BRAF V600E mutation. Patient samples for testing were collected and shipped at ambient room temperature using a Biodesix® whole blood sample collection kit and processed at the Biodesix laboratory. Metrics were reviewed from the real-time measurement of established molecular diagnostic markers in the plasma of patients with NSCLC. For this study we analyzed results from greater than 4,000 patient cases (~24,000 individual variants). Greater than 70% of test orders were received from physician practices that self-identified as community based. Test mutation status results were reported within 72 hours of sample receipt from the physician’s office (95%). The percentage of tests requested that were positive for each variant category were 9% for EGFR sensitizing, 9% for EGFR resistance, 11% for KRAS, and 1% for BRAF. Notably, we generated test results successfully for 98% of tests submitted. We have developed fast, highly robust and sensitive blood-based assays to expedite time to treatment and expand the laboratory testing options for patients with NSCLC.

Citation Format: Westen Hahn, Scott Thurston, Leisa Jackson, Amanda Weaver, Cherie Tschida, Brent Sage, Kristin Alexander, Tunee Pelletier, Nia Charrington, Samantha Cooper, Dianna Marr, Paul M. Bowling, Hestia Mellert, Gary Pestano. Utility of a targeted NSCLC genomic test for cfDNA variants in the community setting [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 5681. doi:10.1158/1538-7445.AM2017-5681

PDL1 test to assess the dynamic range of mRNA expression from platelet enriched plasma in patients with NSCLC

e23063

Background: Therapeutic options for patients with non-small cell lung cancer (NSCLC) continue to expand with the advent of immunotherapies. Lack of tissue and drawbacks with IHC have increased the need for blood-based diagnostics that measure continuous variables. Thus these tests are of increasing relevance for clinical testing. Methods: We focused on mechanisms of blood-based testing for the sensitive measurement of circulating RNA using ddPCR. Specifically, we optimized methods for the detection of PD-L1 and cytokeratin 19 (CK19) transcripts recovered from plasma. Specimens included tumor derived cell-lines, activated and resting immune cells, normal donor plasma and NSCLC (stages 1-4) donor plasma. Results: Assessing PD-L1 in circulation is complicated by its expression in both immune and cancer cells. Analytic performance was initially evaluated with cancer cell lines and activated lymphocytes and monocytes expressing variable levels of cytokeratins and PD-L1. A preliminary threshold was defined based on CK19 expression levels in normal donor plasma (n = 35). Of the 79 NSCLC donors tested 49% expressed CK19 above the threshold, indicating they contained sufficient circulating RNA derived from tumor. These donor samples tested either positive for EGFR del19 E746-A750 or L858R (n = 13), negative for EGFR (n = 10) or positive for KRAS G12C/V (n = 16). We found no differentiation in PD-L1 levels on the basis of EGFR sensitizing and EGFR wild-type status. We observed only three donors that expressed PD-L1 at high levels, and this was regardless of EGFR mutation status. In contrast, 30% of KRAS mutation-positive donor samples were above the pre-defined PDL1 threshold (n = 6 of 16 samples tested). These data are consistent with tissue-based studies that report trends of higher PD-L1 expression in KRAS positive NSCLC patients. Conclusions: We have developed sensitive and specific methods to measure the dynamic range of PD-L1 in circulation and have shown utility of these methods by evaluating key immune and cancer-specific RNAs.

Development of DDPCR blood-based diagnostic tests that simultaneously measure mRNA expression from immune and cancer cells

22

Background: Therapeutic options for patients with non-small cell lung cancer (NSCLC) continue to expand with the advent of immunotherapies. Lack of tissue and drawbacks with available IHC tests have increased the need for blood-based diagnostics. Thus, the detection of circulating nucleic acids has become highly relevant to clinical testing. Methods: We focused on extending the utility of blood-based testing for measurement of intra-cellular transcripts to multiplexed detection of gene expression. Specifically, we addressed maximizing the yield of quality circulating RNA for use in multiplexed droplet digital PCR (ddPCR) assays. Evaluation criteria included droplet counts for biomarkers of cancer and immunotherapy response. The markers evaluated were CD45, CD3, CK8, CK18, CK19, and PD-L1. Specimens included cell lines and prospectively collected samples from normal, healthy donors and donors with NSCLC. Results: Cell lines expressing variable levels of cytokeratins and PD-L1 were used to establish assay sensitivity. In these experiments, the test system could detect these markers in the equivalent of a single cell. We evaluated specificity using RNA from these same cell lines, resting and activated lymphocytes, and monocytes. With the exception of CK8, all assays demonstrated the expected specificities. Given the complexity of assessing PD-L1 in circulation because of its expression on immune cells, a threshold of 30 copies of PD-L1 was established using normal healthy donors (n = 9). Using this cut-off we then measured PD-L1 in circulating RNA from donors with NSCLC (n = 20). By these criteria, PD-L1 expression of sufficient copy number was restricted to a single EGFR wild-type donor (1/10). Previous reports have indicated that for EGFR wild-type patients, PD-L1 over expression may be considered a poor prognostic indicator of OS. Conclusions: We are developing sensitive and specific methods that can be applied to gene expression studies in blood. We have shown feasibility of these methods by evaluating key immune and cancer-specific RNAs. Evaluations are on-going with prospective sample collections to validate thresholds for this assay that may lead to its clinical utility.

Abstract 857: Diagnostic test system for sensitive, specific and reproducible detection of EML4-ALK RNA fusion transcripts in the blood of patients with NSCLC

Clinical testing for the detection of RNA fusions in tissue currently include FISH, IHC, PCR and NGS. However, approximately 30% of patients with advanced non-small cell lung cancer (NSCLC) are not candidates for tissue biopsies and in some cases where tissue is obtained, it is not always of sufficient quantity for molecular testing. For these reasons, the detection of nucleic acids in circulation has become increasingly relevant to clinical testing. In this study, we have focused on the development of an EML4-ALK diagnostic test system that includes the prospective collection of whole blood and the reproducible detection of mRNA fusion transcripts by a PCR-based technology. The focus was on the detection of EML4-ALK transcripts from donors with and without previously diagnosed NSCLC. Pre-analytic complexity was reduced by restricting the handling of samples to 72 hours from time of sample receipt to test result. Recovery methods for RNA extraction from donor plasma were then optimized to enrich for RNA recovered from both circulating-free, and RNA within blood vesicles, including platelets and exosomes. A two-step reverse transcription and Droplet Digital™ PCR (RT-ddPCR) method was evaluated in detection testing using a multiplexed EML4-ALK assay that includes variants 1, 2 and 3. Analytic assay specificity and sensitivity was examined for RT-ddPCR efficiency using a cell-line positive for EML4-ALK variant 1 and in vitro RNA designed to mimic variants 1, 2, and 3. Analytic sensitivity was determined to be 0.2% of fusion RNA spiked into a background of normal plasma. Precision studies were conducted with two different amounts of input RNA (high and low), over three consecutive days, three runs in one day and with two operators. The SD of detected fusion transcripts in this study did not exceed 25%. Finally, normal (n = 10) and FISH positive NSCLC donor (n = 9) plasma samples were processed for the recovery of RNA and tested for EML4-ALK fusions. All FISH positive cases were accurately detected by the RT-ddPCR test with EML4-ALK variant copies ranging from 13 to 150 copies. EML4-ALK fusion transcripts were not identified in normal donor plasma. We conclude that the developed test system is highly suited for a 72 hour test to result turnaround, reproducible and sensitive detection of diagnostic fusion RNA variants, including EML4-ALK in blood in the clinical laboratory.

Citation Format: Hestia Mellert, Leisa Jackson, Dianna Maar, Dawne Shelton, Gary Pestano. Diagnostic test system for sensitive, specific and reproducible detection of EML4-ALK RNA fusion transcripts in the blood of patients with NSCLC. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 857.

Cross-disciplinary research in cancer: an opportunity to narrow the knowledge-practice gap

Health services researchers have consistently identified a gap between what is identified as "best practice" and what actually happens in clinical care. Despite nearly two decades of a growing evidence-based practice movement, narrowing the knowledge-practice gap continues to be a slow, complex, and poorly understood process. Here, we contend that cross-disciplinary research is increasingly relevant and important to reducing that gap, particularly research that encompasses the notion of transdisciplinarity, wherein multiple academic disciplines and non-academic individuals and groups are integrated into the research process. The assimilation of diverse perspectives, research approaches, and types of knowledge is potentially effective in helping research teams tackle real-world patient care issues, create more practice-based evidence, and translate the results to clinical and community care settings. The goals of this paper are to present and discuss cross-disciplinary approaches to health research and to provide two examples of how engaging in such research may optimize the use of research in cancer care.

Global, multicenter, randomized, phase II trial of gemcitabine and gemcitabine plus AGS-1C4D4 in patients with previously untreated, metastatic pancreatic cancer

BACKGROUND

We evaluated AGS-1C4D4, a fully human monoclonal antibody to prostate stem cell antigen (PSCA), with gemcitabine in a randomized, phase II study of metastatic pancreatic cancer.

PATIENTS AND METHODS

Patients with Eastern Cooperative Oncology Group (ECOG) performance status 0/1 and previously untreated, metastatic pancreatic adenocarcinoma were randomly assigned 1:2 to gemcitabine (1000 mg/m(2) weekly seven times, 1 week rest, weekly three times q4weeks) or gemcitabine plus AGS-1C4D4 (48 mg/kg loading dose, then 24 mg/kg q3weeks IV). The primary end point was 6-month survival rate (SR). Archived tumor samples were collected for pre-planned analyses by PSCA expression.

RESULTS

Between April 2009 and May 2010, 196 patients were randomly assigned to gemcitabine (n = 63) or gemcitabine plus AGS-1C4D4 (n = 133). The 6-month SR was 44.4% (95% CI, 31.9-57.5) in the gemcitabine arm and 60.9% (95% CI, 52.1-69.2) in the gemcitabine plus AGS-1C4D4 arm (P = 0.03), while the median survival was 5.5 versus 7.6 months and the response rate was 13.1% versus 21.6% in the two arms, respectively. The 6-month SR was 57.1% in the gemcitabine arm versus 79.5% in the gemcitabine plus AGS-1C4D4 arm among the PSCA-positive subgroup and 31.6% versus 46.2% among the PSCA-negative subgroup.

CONCLUSIONS

This randomized, phase II study achieved its primary end point, demonstrating an improved 6-month SR with addition of AGS-1C4D4 to gemcitabine among patients with previously untreated, metastatic pancreatic adenocarcinoma. ClinicalTrials.gov identifier: NCT00902291.

Safety of zoster vaccine in adults from a large managed-care cohort: a Vaccine Safety Datalink study

OBJECTIVES

The aim of this study was to examine a large cohort of adults who received the zoster vaccine for evidence of an increased risk of prespecified adverse events requiring medical attention.

DESIGN

Two self-comparison approaches, including a case-centred approach and a self-controlled case series (SCCS) analysis were used.

SETTING

Eight managed-care organizations participating in the Vaccine Safety Datalink project in the United States.

SUBJECTS

A total of 193 083 adults aged 50 and older receiving a zoster vaccine from 1 January 2007 to 31 December 2008 were included.

MAIN OUTCOME MEASURES

Prespecified adverse events were identified by aggregated International Classification of Diseases, Ninth Revision (ICD-9) codes in automated health plan datasets.

RESULTS

The risk of allergic reaction was significantly increased within 1-7 days of vaccination [relative risk = 2.13, 95% confidence interval (CI): 1.87-2.40 by case-centred method and relative rate = 2.32, 95% CI: 1.85-2.91 by SCCS]. No increased risk was found for the following adverse event groupings: cerebrovascular events; cardiovascular events; meningitis; encephalitis; and encephalopathy; and Ramsay-Hunt syndrome and Bell's palsy.

CONCLUSIONS

The results of this study support the findings from the prelicensure clinical trials, providing reassurance that the zoster vaccine is generally safe and well-tolerated with a small increased risk of allergic reactions in 1-7 days after vaccination.

Direct to consumer genetic testing: a systematic review of position statements, policies and recommendations

In healthcare settings, genetic tests to determine whether an individual had inherited a genetic mutation are ordered by a health professional, and the results are interpreted and conveyed to the patient by that person. However, direct to consumer genetic testing (DTCGT) has enabled individuals to purchase genetic tests and receive results without the intervention of a health professional. To inform a set of guidelines for consumers and health professionals, we undertook a systematic review of position statements, policies and recommendations on the use of DTCGT. We performed a search of seven databases and the Internet for relevant documents. The search terms were 'direct to consumer' and 'genetic test', and documents in English published from 2002 to 2011 were included. The search retrieved 314 items, of which 14 were eligible for review. Five themes were derived from thematic analysis: motivation for use, potential benefits, potential harms, recommendations to guide consumers and need for research. The authors of these documents described more potential harms than benefits, but, although some stated that direct to consumer testing should be actively discouraged, others supported consumer rights to make autonomous choices. Further research into the impact of direct to consumer testing on health services and consumers is required to inform policies.

P4-08-03: Serum Autoantibodies to Breast Cancer Associated Antigens Reflect Tumor Biology: An Opportunity for Early Detection & Prevention?

Autoantibodies (AABs) are produced as an immune response to abnormal ('non-self') cancer antigens. Previous studies have reported that AABs can be measured in the blood long before cancers are presently diagnosed, e.g., up to 4 years before screening mammography identified breast cancers and up to 5 years before screening CT detected lung cancers. EarlyCDT™-Lung is currently available as an aid to early detection of lung cancer in high risk patients and measures a panel of seven AABs to general cancer antigens and also lung cancer (LC) specific antigens. These AABs have previously been reported to be associated with the two main types of LC i.e., non-small cell and small cell LC. This study looked at AABs to 4 general cancer antigens to evaluate whether their levels reflected different biology in primary breast tumors.

Methods

770 patients presented with primary breast cancer to three centers (Nottingham, UK n=323; Munich, Germany n=320; Oklahoma, USA n=127); the median ages and ranges were 61 (26-82), 61 (20-88) & 65 (54-84) years, respectively. All had serum samples taken post-diagnosis and pre-treatment. The tumors were well characterized for histological grade, estrogen receptor (ER), progesterone receptor (PgR) and HER2 status. Serum samples were tested for AABs to four generic cancer antigens(Ags) (p53, SOX2, NY-ESO-1 and Annexin1) originally included as part of Oncimmune's EarlyCDT™-Lung assay. The AABs were measured by ELISA on the Oncimmune platform, and the EarlyCDT™-Lung cutoffs were used to determine positivity.

Results

131/770 (17%) of primary breast cancers showed elevated AAB levels to one or more of the limited panel of four generic antigens. Positivity for each AAB was correlated with histological grade, ER, PgR and HER2 status. The results, which were similar for each of the three centres, were combined, and the results are shown in Table 1 below.

Can we use medical examiners’ records for suicide surveillance and prevention research in Nova Scotia?

Introduction

Medical examiners’ records can contribute to our understanding of the extent of suicide in a population, as well as associated sociodemographic and other factors.

Methods

Using a mixed methods approach, the key objective of this pilot study was to determine the sources and types of information found in the Nova Scotia Medical Examiner Service (NSMES) records that might inform suicide surveillance and targeted prevention efforts. A secondary objective was to describe the one-year cohort of 108 individuals who died by suicide in 2006 in terms of available sociodemographic information and health care use in the year prior to death.

Results

Data extraction revealed inconsistencies both across and within files in terms of the types and amounts of sociodemographic and other data collected, preventing correlational analyses. However, linkage of the records to administrative databases revealed frequent health care use in the month prior to death.

Conclusion

The introduction of systematic data collection to NSMES investigations may yield a comprehensive dataset useful for policy development and population level research.

Can we use medical examiners' records for suicide surveillance and prevention research in Nova Scotia?

INTRODUCTION

Medical examiners' records can contribute to our understanding of the extent of suicide in a population, as well as associated sociodemographic and other factors.

METHODS

Using a mixed methods approach, the key objective of this pilot study was to determine the sources and types of information found in the Nova Scotia Medical Examiner Service (NSMES) records that might inform suicide surveillance and targeted prevention efforts. A secondary objective was to describe the one-year cohort of 108 individuals who died by suicide in 2006 in terms of available sociodemographic information and health care use in the year prior to death.

RESULTS

Data extraction revealed inconsistencies both across and within files in terms of the types and amounts of sociodemographic and other data collected, preventing correlational analyses. However, linkage of the records to administrative databases revealed frequent health care use in the month prior to death.

CONCLUSION

The introduction of systematic data collection to NSMES investigations may yield a comprehensive dataset useful for policy development and population level research.