Using population-scale transcriptomic and genomic data to map 3' UTR alternative polyadenylation quantitative trait loci.
Using population-scale transcriptomic and genomic data to map 3' UTR alternative polyadenylation quantitative trait loci.
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DOI：
10.1016/j.xpro.2022.101566
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发表时间：
2022-09-16
期刊：
影响因子：
--
通讯作者：
Li, Lei
中科院分区：
文献类型：
--
作者：
Zou, Xudong;Ding, Ruofan;Chen, Wenyan;Wang, Gao;Cheng, Shumin;Wang, Qin;Li, Wei;Li, Lei
3‘非编码区交替多聚腺苷酸化(APA)数量性状基因座(3’aQTL)可解释约16.1%的性状相关非编码变异，与其他分子QTL有很大区别。在这里，我们描述了一种生物信息学协议，用于通过标准的RNA-seq和匹配的基因组数据来识别3‘aQTL。该方案允许用户分析动态APA事件，识别与差异3‘非编码区使用相关的常见遗传变异，并预测影响APA的潜在因果变异。有关本议定书的使用和执行的完整细节，请参阅。跨多个RNA-SEQ样本识别和量化APA事件3aQTL-PIPE有助于识别APA相关的遗传变异通过精细作图识别可能导致动态APA事件的SNP出版者注：执行任何实验方案都需要遵守当地实验室安全和伦理的机构指南。3‘非编码区交替多聚腺苷酸化(APA)数量性状基因座(3’aQTL)可解释约16.1%的性状相关非编码变异，与其他分子QTL有很大区别。在这里，我们描述了一种生物信息学协议，用于通过标准的RNA-seq和匹配的基因组数据来识别3‘aQTL。该方案允许用户分析动态APA事件，识别与差异3‘非编码区使用相关的常见遗传变异，并预测影响APA的潜在因果变异。
3′ UTR alternative polyadenylation (APA) quantitative trait loci (3′aQTL) can explain approximately 16.1% of trait-associated non-coding variants and is largely distinct from other molecular QTLs. Here, we describe a bioinformatic protocol for identifying 3′aQTLs through standard RNA-seq and matched genomic data. This protocol allows users to analyze dynamic APA events, identify common genetic variants associated with differential 3′ UTR usage, and predict the potential causal variants that affect APA. For complete details on the use and execution of this protocol, please refer to. Identification and quantification of APA events across multiple RNA-seq samples 3aQTL-pipe facilitates identification of APA-associated genetic variants Identification of potential causal SNPs for dynamics APA events by fine mapping Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 3′ UTR alternative polyadenylation (APA) quantitative trait loci (3′aQTL) can explain approximately 16.1% of trait-associated non-coding variants and is largely distinct from other molecular QTLs. Here, we describe a bioinformatic protocol for identifying 3′aQTLs through standard RNA-seq and matched genomic data. This protocol allows users to analyze dynamic APA events, identify common genetic variants associated with differential 3′ UTR usage, and predict the potential causal variants that affect APA.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
14.9
作者：
Feng X;Li L;Wagner EJ;Li W
通讯作者：
Li W
影响因子：
30.8
作者：
Li, Lei;Huang, Kai-Lieh;Li, Wei
通讯作者：
Li, Wei
影响因子：
9.2
作者：
Danecek P;Bonfield JK;Liddle J;Marshall J;Ohan V;Pollard MO;Whitwham A;Keane T;McCarthy SA;Davies RM;Li H
通讯作者：
Li H