The association of the <i>UHRF1BP1</i> gene with systemic lupus erythematosus was replicated in a Han Chinese population from mainland China

Wen, Leilei; Liu, Lu; Shen, Xue; Li, Hui; Zhu, Zhengwei; Huang, He; Cai, Minglong; Qian, Danfeng; Shen, Songke; Qiu, Ying; Cui, Yong; Sheng, Yujun

doi:10.1111/ahg.12362

Cited by 2 publications

(2 citation statements)

References 37 publications

(56 reference statements)

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“…6c ). Previous studies 37 , 38 had considered the UHRF1BP1 gene as candidate causal gene because of its strong eQTL effect. The present analysis indicated the SNRPC gene as another candidate gene, because it had a strong i 2 -rQTL effect with protein structural changes.…”

Section: Resultsmentioning

confidence: 99%

Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci

et al. 2022

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Splicing quantitative trait loci (sQTLs) are one of the major causal mechanisms in genome-wide association study (GWAS) loci, but their role in disease pathogenesis is poorly understood. One reason is the complexity of alternative splicing events producing many unknown isoforms. Here, we propose two approaches, namely integration and selection, for this complexity by focusing on protein-structure of isoforms. First, we integrate isoforms with the same coding sequence (CDS) and identify 369-601 integrated-isoform ratio QTLs (i2-rQTLs), which altered protein-structure, in six immune subsets. Second, we select CDS incomplete isoforms annotated in GENCODE and identify 175-337 isoform-ratio QTL (i-rQTL). By comprehensive long-read capture RNA-sequencing among these incomplete isoforms, we reveal 29 full-length isoforms with unannotated CDSs associated with GWAS traits. Furthermore, we show that disease-causal sQTL genes can be identified by evaluating their trans-eQTL effects. Our approaches highlight the understudied role of protein-altering sQTLs and are broadly applicable to other tissues and diseases.

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Section: Resultsmentioning

confidence: 99%

Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci

et al. 2022

View full text Add to dashboard Cite

show abstract

“…6c). Previous studies 38,39 had considered the UHRF1BP1 gene as candidate causal gene because of its strong eQTL effect. The present analysis indicated the SNRPC gene as another candidate gene, because it had a strong i 2 -rQTL effect with protein structural changes.…”

Section: Resultsmentioning

confidence: 99%

Splicing QTL analysis focusing on coding sequences reveals pathogenicity of disease susceptibility loci

Yamaguchi

Ishigaki

Suzuki

et al. 2022

Preprint

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Splicing QTL (sQTL) are one of the major causal mechanisms in GWAS loci, but their role in disease pathogenesis is poorly understood. One reason is the huge complexity of alternative splicing events producing many unknown isoforms. Here, we proposed two novel approaches, namely integration and selection, for this complexity by focusing on protein-structure of isoforms. First, we integrated isoforms with the same coding sequence (CDS) and identified 369-601 integrated-isoform ratio QTLs (i2-rQTLs), which altered protein-structure, in six immune subsets. Second, we selected CDS incomplete isoforms annotated in GENCODE and identified 175-337 isoform-ratio QTL (i-rQTL). By comprehensive long-read capture RNA-seq among these incomplete isoforms, we revealed 29 full-length isoforms with novel CDSs associated with GWAS traits. Furthermore, we have shown that disease-causal sQTL genes can be identified by evaluating their trans-eQTL effects. Our approaches highlight the understudied role of protein-altering sQTLs and are broadly applicable to other tissues and diseases.

show abstract

The association of the UHRF1BP1 gene with systemic lupus erythematosus was replicated in a Han Chinese population from mainland China

Cited by 2 publications

References 37 publications

Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci

Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci

Splicing QTL analysis focusing on coding sequences reveals pathogenicity of disease susceptibility loci

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