F-SNP: computationally predicted functional SNPs for disease association studies

Abstract

The Functional Single Nucleotide Polymorphism (F-SNP) database integrates information obtained from 16 bioinformatics tools and databases about the functional effects of SNPs. These effects are predicted and indicated at the splicing, transcriptional, translational and post-translational level. As such, the database helps identify and focus on SNPs with potential deleterious effect to human health. In particular, users can retrieve SNPs that disrupt genomic regions known to be functional, including splice sites and transcriptional regulatory regions. Users can also identify non-synonymous SNPs that may have deleterious effects on protein structure or function, interfere with protein translation or impede post-translational modification. A web interface enables easy navigation for obtaining information through multiple starting points and exploration routes (e.g. starting from SNP identifier, genomic region, gene or target disease). The F-SNP database is available at http://compbio.cs.queensu.ca/F-SNP/.

Genetic variation in genes interacting with BRCA1/2 and risk of breast cancer in the Cypriot population

“…The rs769416 SNP causes an amino acid [47]. Our result on the association of rs769416 SNP and breast cancer needs to be interpreted with caution, since this is a rare SNP in our population and the most likely explanation for this association is chance.…”

“…The polymorphism results in an amino acid change at codon 73 from a hydrophobic isoleucine to a hydrophilic threonine residue. Bioinformatics analysis indicates that this SNP could be involved in splicing regulation [47]. However, further work is warranted since the exact roles of the PBOV1 protein as well as its functional domains are not well known at present.…”

DNA Mismatch Repair Gene Polymorphisms Affect Survival in Pancreatic Cancer

“…This intronic SNP is in linkage with a 3ЈUTR SNP Ex7-32GϾA. Bioinformatics has predicted that the latter SNP may confer a protein with altered solvent accessibility [22]. PMS2L3 has a similar function to that of PMS2 in MutL␣, which is to play a role in maintaining genome integrity via MMR and DNA damage-induced apoptosis [26].…”

“…The genes, nucleotide substitutions, functions (such as encoding amino acid changes), reference SNP identification numbers, and reported allele frequencies of the 102 SNPs evaluated in this study are summarized in supplemental online Table 1. The protein sequences, structures, homology models, mRNA transcripts, and predicted functions for the SNPs were evaluated using F-SNP software (Queen's University, Kingston, Ontario, Canada) [22]. For genotyping, we used the mass spectroscopy-based MassArray method (Sequenom, Inc., San Diego).…”

Association of single nucleotide polymorphisms in the USF1, GTF2A1L and OR2W3 genes with non-obstructive azoospermia in the Chinese population

“…The deficient transcription of USF1 would decrease the level of USF1 protein. During proliferation, low level of USF1 expression in Sertoli cells limited the USF recruitment to E-box motifs within the promoter regions of Nr5a1 and Shbg genes which were vital for Sertoli cell differentiation [12], therefore the progress of the spermatogenesis might be repressed as a result of the aberrant differentiation of Sertoli cells, NOA would take place; 2) We found that the minor allele C of the SNP rs2284922 located in the conserved region of USF1 gene by means of the F-SNP database [25], a web-based SNP analysis tool. Such an alteration in the gene might lead to an abnormality of gene expression or weaken the stability of gene [26]; 3) the variation of rs2516838 might relate to the initiation of spermiogenesis.…”