After carefully matching cases and controls using genome-wide genotyping data and removing outliers, we calculated a genomic inflation factor (λ) of 1.14. While there is no consensus regarding a maximum value for CNV studies - in fact, few CNV studies have addressed this issue – our value is slightly above that generally accepted for genome-wide association studies (74). To protect against potential liability for Type I error, we looked for residual population structure in any putative positive associations arising from our case-control analyses and identified that this likely played a role in the observed FHIT finding (Figure S7 in Supplement 1).
