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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

Exome sequencing inAPCmutation-negative kindred 0124 revealed positive LOD scores at theAPClocus. (A) Affected members of kindred 0124 have classical FAP phenotypes with highly-penetrant, autosomal dominant inheritance across the family. Extra-colonic malignancies were unusually common in this kindred, including duodenal adenocarcinoma (in two members), pancreas adenocarcinoma, gastric adenocarcinoma, breast cancer, leukemia, ovarian adenocarcinoma, endometrioid carcinoma, and neuroendocrine carcinoma. The proband (III-5, arrow) underwent standard genetic testing and no known FAP-causing mutation was identified. Asterisks indicate the eight individuals who underwent exome sequencing. Analysis did not reveal a credible causal mutation within the exonic sequences. Parametric linkage analysis using a rare autosomal dominant model with SNPs identified from the exome sequencing data was then performed. (B) LOD scores are plotted across somatic chromosomes, with positive LOD score regions marked in red and negative scores marked in blue. The maximum LOD of 2.408 occurred at 5q22, which contains the APC locus.
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Fig1: Exome sequencing inAPCmutation-negative kindred 0124 revealed positive LOD scores at theAPClocus. (A) Affected members of kindred 0124 have classical FAP phenotypes with highly-penetrant, autosomal dominant inheritance across the family. Extra-colonic malignancies were unusually common in this kindred, including duodenal adenocarcinoma (in two members), pancreas adenocarcinoma, gastric adenocarcinoma, breast cancer, leukemia, ovarian adenocarcinoma, endometrioid carcinoma, and neuroendocrine carcinoma. The proband (III-5, arrow) underwent standard genetic testing and no known FAP-causing mutation was identified. Asterisks indicate the eight individuals who underwent exome sequencing. Analysis did not reveal a credible causal mutation within the exonic sequences. Parametric linkage analysis using a rare autosomal dominant model with SNPs identified from the exome sequencing data was then performed. (B) LOD scores are plotted across somatic chromosomes, with positive LOD score regions marked in red and negative scores marked in blue. The maximum LOD of 2.408 occurred at 5q22, which contains the APC locus.

Mentions: 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. Analysis of the exome data revealed one non-synonymous heterozygous mutation which segregated in the affected family members and did not appear in dbSNP132 or an in-house exome sequence database. This was a c.G512A (p.R171Q) mutation in the gene Proline Rich Protein BstNI Subfamily 2 (PRB2) at coordinate chr12:11,546,500. PRB2 is a member of a class of genes located on chromosome 12p13.2 which code for abundant proteins in salivary excretion [19]. Of note, this SNP has appeared in dbSNP as of version 135 and has a minor allele frequency of 0.009 in dbSNP 137. The significance of this non-synonymous mutation remains unclear in relation to the FAP phenotype.Figure 1


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)

Exome sequencing inAPCmutation-negative kindred 0124 revealed positive LOD scores at theAPClocus. (A) Affected members of kindred 0124 have classical FAP phenotypes with highly-penetrant, autosomal dominant inheritance across the family. Extra-colonic malignancies were unusually common in this kindred, including duodenal adenocarcinoma (in two members), pancreas adenocarcinoma, gastric adenocarcinoma, breast cancer, leukemia, ovarian adenocarcinoma, endometrioid carcinoma, and neuroendocrine carcinoma. The proband (III-5, arrow) underwent standard genetic testing and no known FAP-causing mutation was identified. Asterisks indicate the eight individuals who underwent exome sequencing. Analysis did not reveal a credible causal mutation within the exonic sequences. Parametric linkage analysis using a rare autosomal dominant model with SNPs identified from the exome sequencing data was then performed. (B) LOD scores are plotted across somatic chromosomes, with positive LOD score regions marked in red and negative scores marked in blue. The maximum LOD of 2.408 occurred at 5q22, which contains the APC locus.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Exome sequencing inAPCmutation-negative kindred 0124 revealed positive LOD scores at theAPClocus. (A) Affected members of kindred 0124 have classical FAP phenotypes with highly-penetrant, autosomal dominant inheritance across the family. Extra-colonic malignancies were unusually common in this kindred, including duodenal adenocarcinoma (in two members), pancreas adenocarcinoma, gastric adenocarcinoma, breast cancer, leukemia, ovarian adenocarcinoma, endometrioid carcinoma, and neuroendocrine carcinoma. The proband (III-5, arrow) underwent standard genetic testing and no known FAP-causing mutation was identified. Asterisks indicate the eight individuals who underwent exome sequencing. Analysis did not reveal a credible causal mutation within the exonic sequences. Parametric linkage analysis using a rare autosomal dominant model with SNPs identified from the exome sequencing data was then performed. (B) LOD scores are plotted across somatic chromosomes, with positive LOD score regions marked in red and negative scores marked in blue. The maximum LOD of 2.408 occurred at 5q22, which contains the APC locus.
Mentions: 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. Analysis of the exome data revealed one non-synonymous heterozygous mutation which segregated in the affected family members and did not appear in dbSNP132 or an in-house exome sequence database. This was a c.G512A (p.R171Q) mutation in the gene Proline Rich Protein BstNI Subfamily 2 (PRB2) at coordinate chr12:11,546,500. PRB2 is a member of a class of genes located on chromosome 12p13.2 which code for abundant proteins in salivary excretion [19]. Of note, this SNP has appeared in dbSNP as of version 135 and has a minor allele frequency of 0.009 in dbSNP 137. The significance of this non-synonymous mutation remains unclear in relation to the FAP phenotype.Figure 1

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