Planned CT scan for lung cancer screening

Objectives:

• To evaluate the sensitivity and specificity of the DELFI lung cancer screening test for detection of lung cancer, using the reference method of chest CT at enrollment with pathological diagnosis in the overall study population (primary) and in clinically relevant subgroups of interest (secondary) Endpoint:
• Presence or absence of pathologically confirmed lung cancer as determined by diagnostic resolution achieved from the time of the enrollment chest CT scan through follow-up CASCADE-LUNG: Validation of a blood-based assay that evaluates cell-free DNA fragmentation patterns to detect lung cancer

Julie A. Barta, Stephen Freedland, Peter J. Mazzone, Amy E. Isaacson, Alisa M. Hewitt, Debbie M. Jakubowski, Peter B. Bach, Victor E. Velculescu

Thomas Jefferson University, Philadelphia, PA; Cedars-Sinai Medical Center, Los Angeles, CA; Cleveland Clinic, Cleveland, OH; Delfi Diagnostics, Inc., Baltimore, MD; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD

1-3 4,5 BACKGROUND Despite longstanding national recommendations for lung cancer screening by low-dose computed tomography (LDCT), annual participation rates are below 15%. Cost, access, and uncertainty over individual-level benefits and harms of screening preclude greater uptake. The development of a low-cost initial blood test that detects lung cancer with high sensitivity could boost LDCT screening rates and improve screening efficiency, by identifying within the screening-eligible population those at relatively higher risk of lung cancer. DELFI (DNA evaluation of fragments for early interception) is a technology that uses low-coverage, whole-genome sequencing and machine learning to detect cancer signals in the blood. In an early study, DELFI demonstrated high sensitivity to detect stage I/II lung cancers. CASCADE-LUNG (NCT05306288) is an ongoing study to clinically validate a DELFI-based test to detect lung cancers that would be found by chest LDCT.

1. USPSTF, et al. JAMA. 2021;325(10):962-70. 2. Pham D, et al. Clin Lung Cancer. 2020;21(3):e206-11. 3. American Lung Association. State of Lung Cancer 2022 Report. 4. Wang GX, et al. Radiology. 2019;290(2):278-87. 5. Jonas DE, et al. JAMA. 2021;325(10):971-87. 6. Mathios D, et al. Nat Commun. 2021;12(1):5060. cfDNA isolation; Low-coverage, whole-genome, Genome-wide Machine learning Blood sample DELFI Score library preparation next-generation sequencing fragmentation profile predictive model

CASCADE-LUNG (NCT05306288): Cancer Screening Assay Using DELFI: A Clinical Validation Study in Lung

ELIGIBILITY CRITERIA CURRENTLY ENROLLING IN ACADEMIC AND COMMUNITY SITES ACROSS THE US

Inclusion criteria: ≥50 years of age Current or previous smoking history of ≥20 pack-years

• Age ≥50 years AK ME

Planned CT scan for lung cancer screening

• Current or previous smoking history of ≥20 pack-years WI VT NH a Blood sample collection

• Initial or annual follow-up lung cancer screening chest CT planned/scheduled within 30 days after enrollment WA ID MT ND MN IL MI NY MA CT scan within 30 days after enrollment Exclusion criteria:

b bOR NV WY SD IA IN OH PA NJ CT RI

• Evidence of any diagnosed cancer (including lung cancer) other than nonmelanoma skinSuspicious nodules No suspicious nodules cancer or carcinoma in situ within 2 years prior to enrollment CA UT CO NE MO KY WV VA MD DE

• Prior systemic therapy, definitive therapy, radiation, or surgical resection for any cancer diagnosis within 2 years prior to enrollment (except surgery for nonmelanoma skin Medical record review Medical record review cancer and biopsies) at 4 months at 12 months AZ NM KS AR TN NC SC DC after enrollment after enrollment

• Any history of hematologic malignancies or myelodysplasia within 2 years prior to enrollment, or organ tissue transplantation OBJECTIVES AND ENDPOINTS a N≈15000; Enrollment until 70 patients with pathologically confirmed lung cancer and blood sample acceptable for DELFI analysis, OK LA MS AL GA based on 0.6% estimated rate of lung cancer diagnosis Darker blue color indicates higher enrollment number

• Blood product transfusion within 120 days prior to enrollmentb Suspicious nodules defined as: LungRADS category of 4A or higher reported on enrollment chest CT scan; follow-up recommended within 3 months of the enrollment chest CT scan; LungRADS category not reported and ≥6 mm lung nodule(s) identified on the enrollment chest CT scan HI TX FL PR

Development and validation of a noninvasive, accurate, low-cost DELFI test has the potential to improve lung

cancer screening among high-risk individuals, by identifying those more likely to benefit from screening,

thereby reducing harms and boosting uptake of lung cancer screening.

ANALYSIS PLAN

Primary analysis:

• The sensitivity and specificity of the DELFI lung cancer screening test will be estimated. LDCT Positive for +

• Additional predictive performance metrics will be calculated: positive predictive value, Scan + Lung Cancer The DELFI test has the potential to— negative predictive value, positive likelihood ratio, and negative likelihood ratio. Current uptake 5%-15% –

• Stratify a heterogeneous screening-eligible population into 14M Biopsy Negative for –

• Two-sided 95% confidence intervals will be constructed for these metrics. groups with relatively higher and lower risk Individuals or CT Lung Cancer Subgroup analyses: Eligible for

• Provide genomic data to inform shared decision making Lung + Shared Annual

• Performance of the DELFI lung cancer screening test in clinical subgroups of interest will DELFI Cancer Decision Making Screening

• Promote more judicious use of LDCT in healthcare be evaluated, including, but are not limited to, the following: cancer stage; cancer – Screening resource-constrained settings histology (NSCLC vs SCLC; NSCLC histological subtypes); previous cancer history; family history of lung cancer; USPSTF lung cancer screening criteria (2013 vs 2021; eligible vs ineligible); smoking status; COPD status; age; sex; race and/or ethnicity; initial screen vs annual screen. POSTER #CT068 presented at the AACR Annual Meeting 2023; 14-19 April 2023; Orlando, FL. The poster content is the intellectual property of the authors. Contact Amy Isaacson at isaacson@delfidiagnostics.com to request permission to reuse or distribute. JAB has received grant funding from the Prevent Cancer Foundation and the Genentech Health Equity & Diversity in STEM Innovation Fund; and has served as a consultant for Delfi Diagnostics. SF has received funding from Delfi Diagnostics. PJM and his institution have received research support from Adela, Biodesix, Delfi Diagnostics, ECAMP, Exact Sciences, MagArray, the Moore Foundation, Nucleix, PCORI, and Veracyte. AEI, AMH, DMJ, and PBB are employees of and have stock ownership in Delfi Diagnostics. VEV is a founder of Delfi Diagnostics, serves as on the Board of Directors and as a consultant for this organization, and owns Delfi Diagnostics stock, which is subject to certain restrictions under University policy. Additionally, Johns Hopkins University owns equity in Delfi Diagnostics. VEV divested his equity in Personal Genome Diagnostics (PGDx) to LabCorp in February 2022. VEV is an inventor on patent applications submitted by Johns Hopkins University related to cancer genomic analyses and cell-free DNA for cancer detection that have been licensed to one or more entities, including Delfi Diagnostics, LabCorp, Qiagen, Sysmex, Agios, Genzyme, Esoterix, Ventana and ManaT Bio. Under the terms of these license agreements, the University and inventors are entitled to fees and royalty distributions. VEV is an advisor to Viron Therapeutics and Epitope.