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

Overview of attention for article published in Genome Medicine, May 2015
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Title
Novel APC promoter and exon 1B deletion and allelic silencing in three mutation-negative classic familial adenomatous polyposis families
Published in
Genome Medicine, May 2015
DOI 10.1186/s13073-015-0148-0
Pubmed ID
Authors

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

Abstract

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. 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. 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. 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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 21 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 21 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 6 29%
Student > Ph. D. Student 4 19%
Student > Master 2 10%
Student > Bachelor 1 5%
Other 1 5%
Other 1 5%
Unknown 6 29%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 6 29%
Medicine and Dentistry 4 19%
Agricultural and Biological Sciences 2 10%
Pharmacology, Toxicology and Pharmaceutical Science 1 5%
Immunology and Microbiology 1 5%
Other 1 5%
Unknown 6 29%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 03 May 2015.
All research outputs
#18,409,030
of 22,803,211 outputs
Outputs from Genome Medicine
#1,370
of 1,440 outputs
Outputs of similar age
#192,558
of 264,425 outputs
Outputs of similar age from Genome Medicine
#28
of 28 outputs
Altmetric has tracked 22,803,211 research outputs across all sources so far. This one is in the 11th percentile – i.e., 11% of other outputs scored the same or lower than it.
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We're also able to compare this research output to 28 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.