Novel APC promoter and exon 1B deletion and allelic silencing in three mutation-negative classic familial adenomatous polyposis families.

Yiing Lin,Susan M Kennedy,Paul J Goodfellow,Melanie D Baxter,Zhengyan Zhang,William C Chapman,Shin Lin,Nicholas O Davidson,Lawrence Lin

doi:10.1186/s13073-015-0148-0

Abstract

BackgroundThe overwhelming majority (approximately 80%) of individuals with classic familial adenomatous polyposis (FAP) exhibit mutations in the coding sequence of the adenomatous polyposis coli (APC) tumor suppressor gene. Families without detectable APC mutations are unable to benefit from the use of genetic testing for clinical management of this autosomal dominant syndrome.MethodsWe used exome sequencing and linkage analysis, coupled with second-generation sequencing of the APC locus including non-coding regions to investigate three APC mutation-negative classical FAP families.ResultsWe identified a novel ~11 kb deletion localized 44 kb upstream of the transcription start site of APC that encompasses the APC 1B promoter and exon. This deletion was present only in affected family members of one kindred with classical FAP. Furthermore, this same deletion with identical breakpoints was found in the probands of two additional APC mutation-negative classical FAP kindreds. Phasing analysis of single nucleotide polymorphisms (SNPs) around the deletion site in the three probands showed evidence of a shared haplotype, suggesting a common founder deletion in the three kindreds. SNP analysis within the coding sequence of APC, revealed that this ~11 kb deletion was accompanied by silencing of one of the APC alleles in blood-derived RNA of affected individuals.ConclusionsThese results support the causal role of a novel promoter deletion in FAP and suggest that non-coding deletions, identifiable using second-generation sequencing methods, may account for a significant fraction of APC mutation-negative classical FAP families.

Highlights

The overwhelming majority of individuals with classic familial adenomatous polyposis (FAP) exhibit mutations in the coding sequence of the adenomatous polyposis coli (APC) tumor suppressor gene
Exome sequencing of a classical FAP family reveals a logarithm of the odds (LOD) peak at the APC locus Kindred 0124 is a multi-generational family with a classical FAP phenotype (Figure 1A), including the presence of multiple extra-colonic malignancies but with no mutations in APC using standard genetic testing
To investigate the causal mutation accounting for FAP, we performed exome sequencing on eight individuals spanning three generations of the 0124 kindred

Summary

Introduction

The overwhelming majority (approximately 80%) of individuals with classic familial adenomatous polyposis (FAP) exhibit mutations in the coding sequence of the adenomatous polyposis coli (APC) tumor suppressor gene. Families without detectable APC mutations are unable to benefit from the use of genetic testing for clinical management of this autosomal dominant syndrome. The classical FAP phenotype results in the growth of hundreds to thousands of adenomas, caused in approximately 70% to 80% of affected families by germline mutations in the tumor suppressor gene adenomatous polyposis coli (APC) on chromosome 5q21-22 [1,2]. Hundreds of pathologic mutations in APC have been described which result in FAP, most by producing a truncated protein product [4]. The inability to determine a causal mutation of FAP in ‘APC mutationnegative’ families precludes the identification of unaffected

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Discussion

Conclusion