This study was conducted with support from the University of Toronto McLaughlin Centre (MC-2015-02), the Canadian Institutes of Health Research (CIHR FDN 148430 and CIHR New Investigator Salary award 201512MSH-360794-228629), Ontario Institute for Cancer Research (OICR) with funds from the province of Ontario, Canada Research Chair (950-231346), and the Princess Margaret Cancer Foundation to D.D.D.C. as well as Canadian Cancer Society (CCSRI 701717) to R.J.H., CCSRI 704716 to R.J.H. and D.D.D.C. and CCSRI 703827 to M.M.H. Recruitment of healthy individuals was supported by Cancer Care Ontario Chair of Population Health and CCSRI 020214 awarded to R.J.H. Collection of lung cancer samples was supported by the Alan B. Brown chair in molecular genomics and the Lusi Wong Lung Cancer Early Detection Program to G.L. We acknowledge the Princess Margaret Genomics Centre for carrying out the next-generation sequencing and the Bioinformatics and HPC Core, Princess Margaret Cancer Centre for their expertise in generating the next-generation sequencing data.

Reviewer information

Nature thanks E. Collisson, A. Teschendorff and the other anonymous reviewer(s) for their contribution to the peer review of this work.