SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine.
SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine.
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DOI：
10.1093/nar/gky399
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发表时间：
2018-07-02
影响因子：
14.9
通讯作者：
Chelala C
中科院分区：
文献类型：
--
作者：
Dayem Ullah AZ;Oscanoa J;Wang J;Nagano A;Lemoine NR;Chelala C
遗传变异的更广泛的功能注释是在进一步的疾病研究和大规模基因分型项目中优先考虑表型重要变异的有价值的手段。我们开发了SNPnexus，通过评估已知和新型SNP对主要转录组、蛋白质组、调节和结构变异模型的潜在意义来满足这一需求。自2012年发布以来，我们对注释类别进行了重大改进，并更新了查询和数据查看系统。最显著的变化包括非编码变体的更广泛的功能注释和对最新人类基因组组装GRCh 38/hg 38的扩展注释。SNPnexus现已整合了ENCODE和Roadmap Epigenomics Consortium的丰富资源，将非编码变体映射和注释到不同类别的调控区和非编码RNA上，并通过八种流行的非编码变体评分算法和计算方法提供其预测的功能影响。现在提供的一种新功能是支持来自领先工具的新表位预测，以促进其在免疫学应用中的使用。SNPnexus的这些更新是为了将来扩展到一个完全全面的计算工作流程，用于从测序数据中确定疾病相关变异的优先级，使其用户处于转化研究的最前沿。SNPnexus可在http://www.snp-nexus.org上免费获得。
Broader functional annotation of genetic variation is a valuable means for prioritising phenotypically-important variants in further disease studies and large-scale genotyping projects. We developed SNPnexus to meet this need by assessing the potential significance of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models. Since its previous release in 2012, we have made significant improvements to the annotation categories and updated the query and data viewing systems. The most notable changes include broader functional annotation of noncoding variants and expanding annotations to the most recent human genome assembly GRCh38/hg38. SNPnexus has now integrated rich resources from ENCODE and Roadmap Epigenomics Consortium to map and annotate the noncoding variants onto different classes of regulatory regions and noncoding RNAs as well as providing their predicted functional impact from eight popular non-coding variant scoring algorithms and computational methods. A novel functionality offered now is the support for neo-epitope predictions from leading tools to facilitate its use in immunotherapeutic applications. These updates to SNPnexus are in preparation for its future expansion towards a fully comprehensive computational workflow for disease-associated variant prioritization from sequencing data, placing its users at the forefront of translational research. SNPnexus is freely available at http://www.snp-nexus.org.
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影响因子：
12.3
作者：
McLaren W;Gil L;Hunt SE;Riat HS;Ritchie GR;Thormann A;Flicek P;Cunningham F
通讯作者：
Cunningham F
影响因子：
30.8
作者：
Kircher, Martin;Witten, Daniela M.;Jain, Preti;O'Roak, Brian J.;Cooper, Gregory M.;Shendure, Jay
通讯作者：
Shendure, Jay
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
一种预测非编码和编码序列变化的功能效应的综合方法。
DOI：
10.1093/bioinformatics/btv009
发表时间：
2015-05-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Shihab HA;Rogers MF;Gough J;Mort M;Cooper DN;Day IN;Gaunt TR;Campbell C
通讯作者：
Campbell C
非编码序列变体的功能注释。
影响因子：
48
作者：
Ritchie, Graham R. S.;Dunham, Ian;Zeggini, Eleftheria;Flicek, Paul
通讯作者：
Flicek, Paul