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Germline mutations in the tumor suppressor gene  APC  are associated with familial adenomatous polyposis (FAP). Here we applied whole-genome sequencing (WGS) to the DNA of a sporadic FAP patient in which we did not find any pathological  APC  mutations by direct sequencing. WGS identified a promoter deletion of approximately 10 kb encompassing promoter 1B and exon1B of  APC . Additional allele-specific expression analysis by deep cDNA sequencing revealed that the deletion reduced the expression of the mutated  APC  allele to as low as 11.2% in the total  APC  transcripts, suggesting that the residual mutant transcripts were driven by other promoter(s). Furthermore, cap analysis of gene expression (CAGE) demonstrated that the deleted promoter 1B region is responsible for the great majority of  APC  transcription in many tissues except the brain. The deletion decreased the transcripts of  APC-1B  to 39–45% in the patient compared to the healthy controls, but it did not decrease those of  APC-1A . Different deletions including promoter 1B have been reported in FAP patients. Taken together, our results strengthen the evidence that analysis of structural variations in promoter 1B should be considered for the FAP patients whose pathological mutations are not identified by conventional direct sequencing.

Reduced expression of APC-1B but not APC-1A by the deletion of promoter 1B is responsible for familial adenomatous polyposis