Only a single gene, fragile histidine triad (FHIT), reached statistical significance based on this corrected p-value threshold of 7.5 × 10-4 (Table 3; Figure S6 in Supplement 1). However, a detailed inspection of this locus showed that the majority of CNVs in this interval had highly similar start and stop coordinates, despite the absence of flanking segmental duplications. In addition, one affected individual was homozygous for what appeared to be the identical CNV (Figure S6 in Supplement 1). These observations raised the prospect of residual population stratification. Consequently, we further evaluated ancestral clustering in cases and controls (59, 60) (see Methods in Supplement 1) and found that all carriers of the identical FHIT CNV (N=17), showed significant ancestral clustering, compared to a randomly chosen control sample of equal size (p=0.028) (Figure S7 in Supplement 1). Interestingly, when FHIT CNV carriers were grouped based on affected status, the TS carriers (N=12) were more similar in ancestry than a random sample of non-carriers (p=0.002) while control carriers (N=5) were not (p=0.58). While this last observation deserves further scrutiny, overall these results suggest that the FHIT association with TS identified in our cohort is most likely the result of population stratification.
