DeepPheWAS：用于表型生成和表型全基因组关联研究关联分析的 R 包。
DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies.
机构信息
Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
Leicester National Institute of Health and Care Research Biomedical Research Centre, Glenfield Hospital, Leicester LE5 4PW, UK.
出版信息
Bioinformatics. 2023 Apr 3;39(4). doi: 10.1093/bioinformatics/btad073.
Abstract
SUMMARY
DeepPheWAS is an R package for phenome-wide association studies that creates clinically curated composite phenotypes and integrates quantitative phenotypes from primary care data, longitudinal trajectories of quantitative measures, disease progression and drug response phenotypes. Tools are provided for efficient analysis of association with any genetic input, under any genetic model, with optional sex-stratified analysis, and for developing novel phenotypes.
AVAILABILITY AND IMPLEMENTATION
The DeepPheWAS R package is freely available under GNU general public licence v3.0 from at https://github.com/Richard-Packer/DeepPheWAS.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
摘要
DeepPheWAS 是一个用于全基因组关联研究的 R 包，它创建了经过临床整理的综合表型，并整合了来自初级保健数据的定量表型、定量测量的纵向轨迹、疾病进展和药物反应表型。该工具提供了与任何遗传输入、任何遗传模型、可选的性别分层分析以及开发新表型的关联的有效分析。
可用性和实现
DeepPheWAS R 包根据 GNU 通用公共许可证 v3.0 版免费提供，可在 https://github.com/Richard-Packer/DeepPheWAS 上获取。
补充信息
补充数据可在“Bioinformatics”在线获取。
相似文献
1
DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies.DeepPheWAS：用于表型生成和表型全基因组关联研究关联分析的 R 包。
Bioinformatics. 2023 Apr 3;39(4). doi: 10.1093/bioinformatics/btad073.
2
MorphoTools2: an R package for multivariate morphometric analysis.MorphoTools2：一个用于多元形态计量分析的 R 包。
Bioinformatics. 2022 May 13;38(10):2954-2955. doi: 10.1093/bioinformatics/btac173.
3
PheWAS analysis on large-scale biobank data with PheTK.使用PheTK对大规模生物样本库数据进行表型全基因组关联研究分析。
Bioinformatics. 2024 Dec 26;41(1). doi: 10.1093/bioinformatics/btae719.
4
Drug Targetor: a web interface to investigate the human druggome for over 500 phenotypes.药物靶点资源库：一个用于研究人类药物靶点与 500 多种表型关系的网络界面。
Bioinformatics. 2019 Jul 15;35(14):2515-2517. doi: 10.1093/bioinformatics/bty982.
5
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline.回声定位器：一个自动化的端到端统计和功能基因组精细映射管道。
Bioinformatics. 2022 Jan 3;38(2):536-539. doi: 10.1093/bioinformatics/btab658.
6
EvAM-Tools: tools for evolutionary accumulation and cancer progression models.EvAM-Tools：用于进化积累和癌症进展模型的工具。
Bioinformatics. 2022 Dec 13;38(24):5457-5459. doi: 10.1093/bioinformatics/btac710.
7
SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data.SPUTNIK：用于质谱成像数据中空间相关峰过滤的 R 包。
Bioinformatics. 2019 Jan 1;35(1):178-180. doi: 10.1093/bioinformatics/bty622.
8
NeoFox: annotating neoantigen candidates with neoantigen features.NeoFox：利用新抗原特征对新抗原候选物进行注释。
Bioinformatics. 2021 Nov 18;37(22):4246-4247. doi: 10.1093/bioinformatics/btab344.
9
qgg: an R package for large-scale quantitative genetic analyses.qgg：一个用于大规模数量遗传学分析的 R 包。
Bioinformatics. 2020 Apr 15;36(8):2614-2615. doi: 10.1093/bioinformatics/btz955.
10
CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements.CellWalkR：一个用于整合和可视化单细胞和批量数据以解析调控元件的 R 包。
Bioinformatics. 2022 Apr 28;38(9):2621-2623. doi: 10.1093/bioinformatics/btac150.
引用本文的文献
1
Single-cell transcriptome-wide Mendelian randomization and colocalization analyses uncover cell-specific mechanisms in atherosclerotic cardiovascular disease.单细胞转录组全基因组孟德尔随机化和共定位分析揭示动脉粥样硬化性心血管疾病中的细胞特异性机制。
Am J Hum Genet. 2025 Jul 3;112(7):1597-1609. doi: 10.1016/j.ajhg.2025.06.001. Epub 2025 Jun 23.
2
Genomic Locus Tagged by Lung Function GWAS SNV rs12477314 (2q37.3) Acts as a Regulatory Region for a Systemic Inflammatory Phenotype.由肺功能全基因组关联研究单核苷酸变异位点rs12477314（2q37.3）标记的基因组位点作为全身炎症表型的调控区域。
FASEB J. 2025 Jun 30;39(12):e70689. doi: 10.1096/fj.202403208R.
3
Genetically proxied HTRA1 protease activity and circulating levels independently predict risk of ischemic stroke and coronary artery disease.遗传相关性 HTRA1 蛋白酶活性和循环水平均可独立预测缺血性卒中和冠状动脉疾病风险。
Nat Cardiovasc Res. 2024 Jun;3(6):701-713. doi: 10.1038/s44161-024-00475-3. Epub 2024 May 20.
4
PYPE: A pipeline for phenome-wide association and Mendelian randomization in investigator-driven biobank scale analysis.PYPE：一种用于在研究者驱动的生物样本库规模分析中进行全表型组关联研究和孟德尔随机化的流程。
Patterns (N Y). 2024 May 1;5(6):100982. doi: 10.1016/j.patter.2024.100982. eCollection 2024 Jun 14.
5
Genetics of chronic respiratory disease.慢性呼吸道疾病的遗传学
Nat Rev Genet. 2024 Aug;25(8):534-547. doi: 10.1038/s41576-024-00695-0. Epub 2024 Mar 6.
6
Targeting TRP Channels for Pain, Itch and Neurogenic Inflammation.靶向 TRP 通道治疗疼痛、瘙痒和神经源性炎症。
Int J Mol Sci. 2023 Dec 25;25(1):320. doi: 10.3390/ijms25010320.
7
Genome-wide association study of preserved ratio impaired spirometry (PRISm).全基因组关联研究中比值保留的气流受限（PRISm）。
Eur Respir J. 2024 Jan 4;63(1). doi: 10.1183/13993003.00337-2023. Print 2024 Jan.
8
Genetically proxied HTRA1 protease activity and circulating levels independently predict risk of ischemic stroke and coronary artery disease.基因代理的HTRA1蛋白酶活性和循环水平可独立预测缺血性中风和冠状动脉疾病的风险。
Res Sq. 2023 Nov 7:rs.3.rs-3523612. doi: 10.21203/rs.3.rs-3523612/v1.
9
Genome-wide association study of thyroid-stimulating hormone highlights new genes, pathways and associations with thyroid disease.全基因组关联研究甲状腺刺激素强调了新的基因、途径以及与甲状腺疾病的关联。
Nat Commun. 2023 Oct 23;14(1):6713. doi: 10.1038/s41467-023-42284-5.
10
Genome-wide association study as a powerful tool for dissecting competitive traits in legumes.全基因组关联研究作为剖析豆科植物竞争性状的有力工具。
Front Plant Sci. 2023 Aug 14;14:1123631. doi: 10.3389/fpls.2023.1123631. eCollection 2023.
本文引用的文献
1
Exome-wide analysis of copy number variation shows association of the human leukocyte antigen region with asthma in UK Biobank.外显子组拷贝数变异的全基因组分析显示人类白细胞抗原区域与英国生物库中哮喘的关联。
BMC Med Genomics. 2022 May 21;15(1):119. doi: 10.1186/s12920-022-01268-y.
2
A large multiethnic GWAS meta-analysis of cataract identifies new risk loci and sex-specific effects.一项关于白内障的大型多民族全基因组关联研究荟萃分析确定了新的风险位点和性别特异性效应。
Nat Commun. 2021 Jun 14;12(1):3595. doi: 10.1038/s41467-021-23873-8.
3
Pleiotropic associations of heterozygosity for the Z allele in the UK Biobank.英国生物银行中Z等位基因杂合性的多效性关联。
ERJ Open Res. 2021 May 10;7(2). doi: 10.1183/23120541.00049-2021. eCollection 2021 Apr.
4
Variants associated with expression have sex-differential effects on lung function.与表达相关的变异对肺功能有性别差异效应。
Wellcome Open Res. 2021 May 24;5:111. doi: 10.12688/wellcomeopenres.15846.2. eCollection 2020.
5
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.开放靶点遗传学：利用大规模遗传学和功能基因组学系统地识别与性状相关的基因。
Nucleic Acids Res. 2021 Jan 8;49(D1):D1311-D1320. doi: 10.1093/nar/gkaa840.
6
Carotid Intima-Media Thickness: Novel Loci, Sex-Specific Effects, and Genetic Correlations With Obesity and Glucometabolic Traits in UK Biobank.颈动脉内中膜厚度：英国生物库中肥胖和糖代谢特征的新基因座、性别特异性效应及遗传相关性
Arterioscler Thromb Vasc Biol. 2020 Feb;40(2):446-461. doi: 10.1161/ATVBAHA.119.313226. Epub 2019 Dec 5.
7
Use of Genetic Variants Related to Antihypertensive Drugs to Inform on Efficacy and Side Effects.利用与抗高血压药物相关的遗传变异来预测疗效和副作用。
Circulation. 2019 Jul 23;140(4):270-279. doi: 10.1161/CIRCULATIONAHA.118.038814. Epub 2019 Jun 25.
8
Active repurposing of drug candidates for melanoma based on GWAS, PheWAS and a wide range of omics data.基于 GWAS、PheWAS 和广泛的组学数据对候选药物进行主动再利用以治疗黑色素瘤。
Mol Med. 2019 Jun 20;25(1):30. doi: 10.1186/s10020-019-0098-x.
9
New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.新的肺功能遗传信号突出了多种血统中的途径和慢性阻塞性肺疾病的关联。
Nat Genet. 2019 Mar;51(3):481-493. doi: 10.1038/s41588-018-0321-7. Epub 2019 Feb 25.
10
Phenome-wide association studies across large population cohorts support drug target validation.全表型关联研究在大型人群队列中支持药物靶点验证。
Nat Commun. 2018 Oct 16;9(1):4285. doi: 10.1038/s41467-018-06540-3.
Zotero 插件