EAGLE is a population-based study of newly diagnosed lung cancer cases and matched controls from the Italian region of Lombardy, as described elsewhere.15 EAGLE participants, aged 35 to 79 years old, were genotyped on the Illumina HumanHap550v3 BeadChip array, as part of the GENEVA (Gene Environment Association Studies Initiative).20 We obtained their genome-wide SNP genotypes, overall FTND score and other phenotype data via the database of Genotypes and Phenotypes (dbGaP; accession number phs000093.v2.p2). Additional analyses were conducted using the specific FTND item scores by the original study investigators. We began by applying all participant-level and SNP-level QC procedures that were recommended as part of the dbGaP release and then applied our own standard set of QC procedures (Supplementary Information). There were 3006 EAGLE participants included in our study.
