We are analyzing https://link.springer.com/article/10.1186/1471-2164-14-627.

Title:
The splice site variant rs11078928 may be associated with a genotype-dependent alteration in expression of GSDMB transcripts | BMC Genomics
Description:
Background Many genetic variants have been associated with susceptibility to complex traits by genome wide association studies (GWAS), but for most, causal genes and mechanisms of action have yet to be elucidated. Using bioinformatics, we identified index and proxy variants associated with autoimmune disease susceptibility, with the potential to affect splicing of candidate genes. PCR and sequence analysis of whole blood RNA samples from population controls was then carried out for the 8 most promising variants to determine the effect of genetic variation on splicing of target genes. Results We identified 31 splice site SNPs with the potential to affect splicing, and prioritised 8 to determine the effect of genotype on candidate gene splicing. We identified that variants rs11078928 and rs2014886 were associated with altered splicing of the GSDMB and TSFM genes respectively. rs11078928, present in the asthma and autoimmune disease susceptibility locus on chromosome 17q12-21, was associated with the production of a novel Δ exon5-8 transcript of the GSDMB gene, and a separate decrease in the percentage of transcripts with inclusion of exon 6, whereas the multiple sclerosis susceptibility variant rs2014886, was associated with an alternative TFSM transcript encompassing a short cryptic exon within intron 2. Conclusions Our findings demonstrate the utility of a bioinformatic approach in identification and prioritisation of genetic variants effecting splicing of their host genes, and suggest that rs11078928 and rs2014886 may affect the splicing of the GSDMB and TSFM genes respectively.
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Keywords {🔍}

gsdmb, expression, splicing, pubmed, article, splice, google, scholar, gene, tsfm, snps, cas, autoimmune, site, transcript, variants, allele, identified, disease, figure, exon, central, variant, genotype, diseases, nature, transcripts, file, inflammatory, reverse, genes, sequence, minor, individuals, susceptibility, additional, forward, analysis, snp, isoforms, data, effect, asthma, information, significance, showing, traits, blood, sequences, found,

Topics {✒️}

kif5a-cyp27b1-mettl1-fam119b locus genome-wide association studies open access article nonsense-mediated mrna decay genome-wide eqtl associations article download pdf genome-wide association loci conserved leucine-rich motifs long-range chromatin interactions harries genetics real-time quantitative pcr genome-wide association study immunity-related gtpase family highly tissue-specific manner real-time rt-pcr allele-specific chromatin remodeling human protein-encoding transcriptomes rna secondary structure tissue-specific genetic control nonsense-mediated decay long-range interaction landscape org/mpg/snap/ldsearch anna murray & tim frayling pre-mrna splicing identify genotype-specific alternations past medical history genetic association studies secondary structure change exeter medical school isoform-specific expression cohort genome wide significance privacy choices/manage cookies alternative splice product real-time pcr genome-wide analysis biomed central zpbp2/gsdmb/ormdl3 locus cryptic splice site chromatin state dynamics single nucleotide polymorphisms splicing control elements full size image respective pcr primers endogenous control rplpo custom taqman assays strong acceptor site splice site enrichment verlaan dj intronic splicing enhancers acceptor splice site

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         headline:The splice site variant rs11078928 may be associated with a genotype-dependent alteration in expression of GSDMB transcripts
         description:Many genetic variants have been associated with susceptibility to complex traits by genome wide association studies (GWAS), but for most, causal genes and mechanisms of action have yet to be elucidated. Using bioinformatics, we identified index and proxy variants associated with autoimmune disease susceptibility, with the potential to affect splicing of candidate genes. PCR and sequence analysis of whole blood RNA samples from population controls was then carried out for the 8 most promising variants to determine the effect of genetic variation on splicing of target genes. We identified 31 splice site SNPs with the potential to affect splicing, and prioritised 8 to determine the effect of genotype on candidate gene splicing. We identified that variants rs11078928 and rs2014886 were associated with altered splicing of the GSDMB and TSFM genes respectively. rs11078928, present in the asthma and autoimmune disease susceptibility locus on chromosome 17q12-21, was associated with the production of a novel Δ exon5-8 transcript of the GSDMB gene, and a separate decrease in the percentage of transcripts with inclusion of exon 6, whereas the multiple sclerosis susceptibility variant rs2014886, was associated with an alternative TFSM transcript encompassing a short cryptic exon within intron 2. Our findings demonstrate the utility of a bioinformatic approach in identification and prioritisation of genetic variants effecting splicing of their host genes, and suggest that rs11078928 and rs2014886 may affect the splicing of the GSDMB and TSFM genes respectively.
         datePublished:2013-09-17T00:00:00Z
         dateModified:2013-09-17T00:00:00Z
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            Asthma
            Autoimmune disease
            GWAS
            SNP
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            general
            Microarrays
            Proteomics
            Animal Genetics and Genomics
            Microbial Genetics and Genomics
            Plant Genetics and Genomics
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      headline:The splice site variant rs11078928 may be associated with a genotype-dependent alteration in expression of GSDMB transcripts
      description:Many genetic variants have been associated with susceptibility to complex traits by genome wide association studies (GWAS), but for most, causal genes and mechanisms of action have yet to be elucidated. Using bioinformatics, we identified index and proxy variants associated with autoimmune disease susceptibility, with the potential to affect splicing of candidate genes. PCR and sequence analysis of whole blood RNA samples from population controls was then carried out for the 8 most promising variants to determine the effect of genetic variation on splicing of target genes. We identified 31 splice site SNPs with the potential to affect splicing, and prioritised 8 to determine the effect of genotype on candidate gene splicing. We identified that variants rs11078928 and rs2014886 were associated with altered splicing of the GSDMB and TSFM genes respectively. rs11078928, present in the asthma and autoimmune disease susceptibility locus on chromosome 17q12-21, was associated with the production of a novel Δ exon5-8 transcript of the GSDMB gene, and a separate decrease in the percentage of transcripts with inclusion of exon 6, whereas the multiple sclerosis susceptibility variant rs2014886, was associated with an alternative TFSM transcript encompassing a short cryptic exon within intron 2. Our findings demonstrate the utility of a bioinformatic approach in identification and prioritisation of genetic variants effecting splicing of their host genes, and suggest that rs11078928 and rs2014886 may affect the splicing of the GSDMB and TSFM genes respectively.
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         Rs11078928
         Asthma
         Autoimmune disease
         GWAS
         SNP
         Alternative mRNA splicing
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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      name:Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK
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      name:RNA mediated mechanisms of disease group, University of Exeter Medical School, Exeter, UK

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