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

Lin Y, Lin S, Baxter MD, Lin L, Kennedy SM, Zhang Z, Goodfellow PJ, Chapman WC, Davidson NO - Genome Med (2015)

Bottom Line: 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.These 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, Washington University School of Medicine, St. Louis, Missouri USA.

ABSTRACT

Background: 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.

Methods: We 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.

Results: We 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.

Conclusions: These 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.

No MeSH data available.


Related in: MedlinePlus

Second-generation sequencing across theAPClocus revealed an ~11 kb heterozygous deletion. Affected individual IV-4 of kindred 0124 (red bar) was subjected to second-generation sequencing across the APC locus including the promoter, exons and introns. A heterozygous deletion approximately 44 kb upstream of APC exon 1A was found between coordinates chr5:112,034,824 and chr5:112,045,845 (GRCh37/hg19) which encompasses exon and promoter 1B (Genbank D13981.1). Other studies (Snow et al., Rohlin et al., and Kadiyska et al.) have reported larger promoter deletions in this region [6,8-10] (blue bars).
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Fig2: Second-generation sequencing across theAPClocus revealed an ~11 kb heterozygous deletion. Affected individual IV-4 of kindred 0124 (red bar) was subjected to second-generation sequencing across the APC locus including the promoter, exons and introns. A heterozygous deletion approximately 44 kb upstream of APC exon 1A was found between coordinates chr5:112,034,824 and chr5:112,045,845 (GRCh37/hg19) which encompasses exon and promoter 1B (Genbank D13981.1). Other studies (Snow et al., Rohlin et al., and Kadiyska et al.) have reported larger promoter deletions in this region [6,8-10] (blue bars).

Mentions: To search for a non-coding mutation at the APC locus of the affected individual IV-4 of kindred 0124, we used the ColoSeq™ assay to capture and sequence exonic, intronic, and promoter regions of the APC gene [12]. This assay identified an ~11 kb heterozygous deletion 44 kb upstream of the first exon of APC between coordinates chr5:112,034,824-112,045,845 (Figure 2). This deletion contains exon and promoter 1B (Genbank D13981.1) and represents the smallest promoter deletion currently described in an FAP family.Figure 2


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

Lin Y, Lin S, Baxter MD, Lin L, Kennedy SM, Zhang Z, Goodfellow PJ, Chapman WC, Davidson NO - Genome Med (2015)

Second-generation sequencing across theAPClocus revealed an ~11 kb heterozygous deletion. Affected individual IV-4 of kindred 0124 (red bar) was subjected to second-generation sequencing across the APC locus including the promoter, exons and introns. A heterozygous deletion approximately 44 kb upstream of APC exon 1A was found between coordinates chr5:112,034,824 and chr5:112,045,845 (GRCh37/hg19) which encompasses exon and promoter 1B (Genbank D13981.1). Other studies (Snow et al., Rohlin et al., and Kadiyska et al.) have reported larger promoter deletions in this region [6,8-10] (blue bars).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4418073&req=5

Fig2: Second-generation sequencing across theAPClocus revealed an ~11 kb heterozygous deletion. Affected individual IV-4 of kindred 0124 (red bar) was subjected to second-generation sequencing across the APC locus including the promoter, exons and introns. A heterozygous deletion approximately 44 kb upstream of APC exon 1A was found between coordinates chr5:112,034,824 and chr5:112,045,845 (GRCh37/hg19) which encompasses exon and promoter 1B (Genbank D13981.1). Other studies (Snow et al., Rohlin et al., and Kadiyska et al.) have reported larger promoter deletions in this region [6,8-10] (blue bars).
Mentions: To search for a non-coding mutation at the APC locus of the affected individual IV-4 of kindred 0124, we used the ColoSeq™ assay to capture and sequence exonic, intronic, and promoter regions of the APC gene [12]. This assay identified an ~11 kb heterozygous deletion 44 kb upstream of the first exon of APC between coordinates chr5:112,034,824-112,045,845 (Figure 2). This deletion contains exon and promoter 1B (Genbank D13981.1) and represents the smallest promoter deletion currently described in an FAP family.Figure 2

Bottom Line: 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.These 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, Washington University School of Medicine, St. Louis, Missouri USA.

ABSTRACT

Background: 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.

Methods: We 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.

Results: We 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.

Conclusions: These 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.

No MeSH data available.


Related in: MedlinePlus