Title: ELUSIVE: Early-stage LUng and Second primary cancer non-invasIVE detection by analysis of trace amounts of tumour DNA in liquid biopsy specimens
Funder: Cancer Research UK

Abstract: Background: Diagnosing non-small cell lung cancer (NSCLC) at an earlier stage can save lives. Circulating tumour DNA (ctDNA) can be detected in plasma of patients with early-stage cancer, but it is unclear how early it can be detected, or what analytical sensitivity is required to detect the majority of stage I-II cancers. Ideally, performance should be assessed in samples collected prior to diagnosis; however prospective collection in the general population is costly and complex. Previous studies collected plasma from patients at or after diagnosis, analysed few mutated loci, and detected ctDNA in only a minority of stage I cancer patients. We hypothesize that multiplexed analysis of 100s-1000s of somatic mutations, combined with other molecular biomarkers, could detect early-stage cancer months or years ahead of clinical diagnosis in a high-risk population. Aims: 1) Measure ctDNA at diagnosis of NSCLC and in the months and years prior to diagnosis of early-stage disease. 2) Establish a prospective “Second Primary cohORT” (SPORT) following lung cancer survivors who are at high risk of developing second primary cancers, to collect samples prior to diagnosis. 3) Assess the utility of ultra-sensitive analysis for detecting pre-symptomatic, residual and recurrent disease in early-stage NSCLC. 4) Combine ctDNA with cell-free DNA methylation and other markers into a multi-modal assay for non-invasive cancer detection. Methods: We will analyse samples from SPORT and LUCID cohorts. In LUCID, we have collected plasma samples from 100 patients with early-stage NSCLC at diagnosis, treatment and follow-up/relapse. We will detect ctDNA at unprecedented sensitivity by analysing 100s-1000s of tumour-mutated loci with patient-specific sequencing panels, with resolution to parts per million. We will integrate ctDNA sequencing panels, cell-free DNA methylation and immune receptor repertoires to create a sensitive multi-modal assay for cancer detection. We will design a prospective study to deploy screening assays in high-risk populations. How the results of this research will be used: By determining the distribution of ctDNA levels at diagnosis of early-stage NSCLC and prior to diagnosis of second primary cancers, this study will clarify the potential and limitations of ctDNA for cancer screening. We will assess the utility of ultra-sensitive ctDNA analysis for earlier detection of pre-symptomatic, residual or relapsed disease. Our results will be critical for designing future trials, to validate our multi-modal assay and other emerging methods. In addition, samples we will collect prior to diagnosis will provide a unique resource to evaluate future assays for earlier detection of cancer.

Lay abstract: Background: Diagnosing non-small cell lung cancer (NSCLC) at an earlier stage can save lives. Circulating tumour DNA (ctDNA) can be detected in plasma of patients with early-stage cancer, but it is unclear how early it can be detected, or what analytical sensitivity is required to detect the majority of stage I-II cancers. Ideally, performance should be assessed in samples collected prior to diagnosis; however prospective collection in the general population is costly and complex. Previous studies collected plasma from patients at or after diagnosis, analysed few mutated loci, and detected ctDNA in only a minority of stage I cancer patients. We hypothesize that multiplexed analysis of 100s-1000s of somatic mutations, combined with other molecular biomarkers, could detect early-stage cancer months or years ahead of clinical diagnosis in a high-risk population. Aims: 1) Measure ctDNA at diagnosis of NSCLC and in the months and years prior to diagnosis of early-stage disease. 2) Establish a prospective “Second Primary cohORT” (SPORT) following lung cancer survivors who are at high risk of developing second primary cancers, to collect samples prior to diagnosis. 3) Assess the utility of ultra-sensitive analysis for detecting pre-symptomatic, residual and recurrent disease in early-stage NSCLC. 4) Combine ctDNA with cell-free DNA methylation and other markers into a multi-modal assay for non-invasive cancer detection. Methods: We will analyse samples from SPORT and LUCID cohorts. In LUCID, we have collected plasma samples from 100 patients with early-stage NSCLC at diagnosis, treatment and follow-up/relapse. We will detect ctDNA at unprecedented sensitivity by analysing 100s-1000s of tumour-mutated loci with patient-specific sequencing panels, with resolution to parts per million. We will integrate ctDNA sequencing panels, cell-free DNA methylation and immune receptor repertoires to create a sensitive multi-modal assay for cancer detection. We will design a prospective study to deploy screening assays in high-risk populations. How the results of this research will be used: By determining the distribution of ctDNA levels at diagnosis of early-stage NSCLC and prior to diagnosis of second primary cancers, this study will clarify the potential and limitations of ctDNA for cancer screening. We will assess the utility of ultra-sensitive ctDNA analysis for earlier detection of pre-symptomatic, residual or relapsed disease. Our results will be critical for designing future trials, to validate our multi-modal assay and other emerging methods. In addition, samples we will collect prior to diagnosis will provide a unique resource to evaluate future assays for earlier detection of cancer.

Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS