title: Detection of APC gene deletion by double competitive polymerase chain reaction in patients with familial adenomatous polyposis.
abstract: Familial adenomatous polyposis (FAP) is an autosomal dominant familial cancer syndrome caused by germline mutations of the tumor suppressor adenomatous polyposis coli (APC) gene. Heterozygous apc mutations have been identified in the majority of classical FAP patients who develop more than 100 colorectal adenomas. However, classical FAP patients often fail to display germline APC mutations detectable by routine mutation analysis. These apparently mutation-negative cases may be caused by heterozygous large genomic deletions. In the present study, FAP patients who showed no APC germline mutation detectable by the protein truncation assay and direct sequencing of protein coding exons were screened for APC gene deletion by a gene dose assay based on double competitive polymerase chain reaction. Gene dosage measurements within exon 15 of the APC gene identified two patients with gene deletion and one with possible gene duplication among 41 apparently mutation-negative patients. The deleted sequences in the two patients were determined by fine gene dose mapping around the APC gene and nucleotide sequencing of the deletion breakpoints. They were approximately 435-kilobase pair (kb) and 737-kb regions including the whole APC gene and flanked by a 4-base pair repeat and LINE-1 repetitive sequences, respectively. The chimeric LINE-1 element created at the breakpoint in the latter case also contained a short sequence derived from another LINE-1 element, suggesting a complex unequal homologous recombination event. These findings indicate that this gene dose assay is a useful technique to detect large gene deletions of the APC gene and to determine their genomic breakpoints.
authors.affiliation: Tumor Endocrinology Project, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan.
authors.forename: Maho
authors.initials: M
authors.lastname: Takahashi
authors.forename: Mariko
authors.initials: M
authors.lastname: Kikuchi
authors.forename: Naganari
authors.initials: N
authors.lastname: Ohkura
authors.forename: Hiroko
authors.initials: H
authors.lastname: Yaguchi
authors.forename: Yuko
authors.initials: Y
authors.lastname: Nagamura
authors.forename: Sumiko
authors.initials: S
authors.lastname: Ohnami
authors.forename: Mineko
authors.initials: M
authors.lastname: Ushiama
authors.forename: Teruhiko
authors.initials: T
authors.lastname: Yoshida
authors.forename: Kokichi
authors.initials: K
authors.lastname: Sugano
authors.forename: Takeo
authors.initials: T
authors.lastname: Iwama
authors.forename: Shinji
authors.initials: S
authors.lastname: Kosugi
authors.forename: Toshihiko
authors.initials: T
authors.lastname: Tsukada
mesh_terms: D011125:Adenomatous Polyposis Coli / Q000235:genetics*; D025601:Adenomatous Polyposis Coli Protein / Q000096:biosynthesis*; D001483:Base Sequence; D005091:Exons; D017353:Gene Deletion; D017491:Genes, APC; D020022:Genetic Predisposition to Disease; D006579:Heterozygote; D006801:Humans; D018895:Microsatellite Repeats; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D011995:Recombination, Genetic
chemical_list: D025601:Adenomatous Polyposis Coli Protein