U01: EFIRM-LIQUID BIOPSY (ELB): ULTRASENSITIVE CTDNA AND MIRNA DETECTION FOR EARLY ASSESSMENT OF LUNG CANCER

Computed tomography (CT) is currently the most sensitive test for detecting preclinical lung cancer, which typically presents as an indeterminate pulmonary nodule (IPN). The success of CT for early detection was sealed by the National Lung Screening Trial, in which lung cancer mortality was reduced by 20% relative to chest radiography. However, in the NLST, the screen positivity rate was 24% and 96% of positive screens were false positive. Although these percentages have been partially attenuated by new screening guidelines, it is axiomatic that LDCT screening is highly sensitive for detecting lung cancer, but non-specific, and not without harms. Furthermore, more individuals, both smokers and non-smokers, are diagnosed outside of screening based on the finding of an indeterminate nodule. Methods are urgently needed to better differentiate between individuals with benign disease and those should undergo invasive diagnostic testing. Liquid biopsy has found its way into the cancer lexicon as a reference to tumor biomarkers within blood or other readily accessible biospecimens that reflect the presence and biology of cancer. This precompetitive collaboration brings together academic and industrial partners across the cancer spectrum to advance liquid biopsy technologies for early detection that are viable as clinical tools. Our partnership interleaves the expertise of lung cancer biologists, clinicians, and biostatisticians with industry engineers, converging on a novel liquid biopsy technology "EFIRM-Liquid biopsy (eLB)" that has already shown high sensitivity detecting circulating DNA mutations in patients with EGFR-mutant lung cancers. To address early lung cancer detection, our academic researchers will develop and validate independent assays for 10 DNA mutations commonly observed in lung cancer as well as introduce a 6-biomarker panel of miRNA to complement and strengthen the blood-based molecular signal of lung cancer. Our industry partners will convert these individual assays to a single array while preserving high sensitivity and specificity. With our clinician scientists, this integrated platform will be validated in patients with screen- or incidentally- detected lung nodules in the size ranges that are most diagnostically challenging. Our overall research proposition is that blood-based biomarkers using the eLB-Lung Cancer Detection Panel (eLB-LCDP) will inform the accurate and robust classification of nodules as benign or malignant. Beyond contributing molecular and technological expertise, standard operating procedures, and annotated clinical materials, we will compare eLB- LCDP with other lung cancer-associated liquid biopsy platforms to be developed in this and related NCI consortia to determine the highest performing biomarkers and platforms that should move to clinical translation, alone or in combination with models that include clinical and imaging variables acquired as part of patient management. Using this orthogonal, multiparametric interrogation approach, we hypothesize that the eLB-LCDP can achieve a classification performance area under the receiver operating characteristic curve (AUC) > 0.85 in near real- time clinical practice.

UH2: ADVANCING EFIRM-LIQUID BIOPSY (ELB) TO A CLIA-CERTIFIED LABORATORY DEVELOPED TEST (ELB-LDT) FOR DETECTION OF ACTIONABLE EGFR MUTATIONS IN NSCLC PATIENTS

Malignant transformation of normal cells are driven by oncogenic mutations of key cellular genes where therapeutics are actively being developed to target these mutations for interventions that will improve morbidity and/or mortality. The current clinical practice to interrogate these "actionable mutations" is by tumor biopsy followed by genotyping which is invasive and at times access restrictive, challenging, subject to sampling errors and may simply not possible. Liquid biopsy is a rapidly emerging field to access actionable mutations in tumors minimal/non-invasively in bodily fluids based on circulating tumor DNA (ctDNA). This UH2/UH3 application is responsive to the PAR-15-095 to advance the translational and clinical development of a matured academic laboratory assay, the EFIRM-Liquid Biopsy (eLB) to a "Clinical Laboratory Improvement Amendment" (CLIA)-certified laboratory developed test (eLB-LDT), in the UCLA Molecular Diagnostic Laboratories (MDL), a CLIA-certified/ College of American Pathologists (CAP)-accredited Laboratory. The eLB- LDT will be evaluated in a clinical context of use to interrogate actionable mutations in the EGFR gene of NSCLC patients at the VA Greater Los Angeles Healthcare System (VA GLA). It is important to advance academic assays for cancer detection, diagnosis and treatment to regulated clinical assays that will provide novel capabilities to physicians to impact health of their patients. Our proposal is to advance a matured academic assay, EFIRM-Liquid Biopsy (eLB) that delivers the best performance technology to detect oncogenic mutations, to become a CLIA-certified laboratory developed test (LDT), the EFIRM-Liquid Biopsy laboratory developed test (eLB-LDT). eLB detects actionable EGFR mutations in NSCLC patients with 100% concordance with biopsy-based genotyping, outperforms current technologies for liquid biopsy. The clinical validation study will be conducted at the UCLA Medical Center and VA Greater Los Angeles Healthcare System (VA GLA) where 20% of patients with adenocarcinoma subtype of non-small cell lung carcinoma (NSCLC) harbor TKI-responsive mutations in the EGFR gene. The eLB-LDT technology if validated, may replace current practice of liquid biopsy for EGFR genotyping as it has the best performance, minimal or non-invasive, rapid, inexpensive and self-contained permitting the detection of the most common EGFR gene mutations that are treatable with TKI such as Gefitinib or Erlotinib to effectively extend the progression free survival of lung cancer patients. Two Specific Aims are in place to achieve these goals. Aim 1/UH2 is to adapt the academic EFIRM-Liquid Biopsy (eLB) technology to become a CLIA-certified assay in the UCLA Diagnostics Molecular Pathology Laboratory and to determine analytical and clinical performance. Aim 2/UH3 is to analytically and clinically validate eLB-LDT at the clinical sites (UCLA and VA GLA).