▸ About
FORGE2 |
| FORGE2 standalone was developed by Charles Breeze at UCL as part of the EpiTrain Initial Training Network. |
| The system is the latest iteration of the FORGE tool originally developed by Ian Dunham. |
| The web interface was originally developed by Javier Herrero from the Bill Lyons Informatics Centre team and updated by Alex Reynolds from the Altius Institute for Biomedical Sciences in Seattle. |
| The example data set corresponds to a set of PR associated SNPs from the GWAS catalog. |
(last updated on Fri Dec 6 03:05:53 2024) |
System |
| FORGE2 is currently running on a virtual machine provided by the Altius Institute for Biomedical Sciences. |
Contact |
| Email Charles Breeze: c.breeze(at)ucl.ac.uk |
Citation |
| If you use FORGE2 in your work, please cite the FORGE2 paper below: Breeze CE, Haugen E, Reynolds A, Teschendorff A, van Dongen J, Lan Q, et al. Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations. Genome Biology. 2022;23:13. https://doi.org/10.1186/s13059-021-02560-3 If you use FORGEdb in your work, please cite the FORGEdb paper below: Breeze CE, Haugen E, Gutierrez-Arcelus M, Yao X, Teschendorff A, Beck S, Dunham I, et al. FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome Biology. 2024;25:3. https://doi.org/10.1186/s13059-023-03126-1 |
Some of the papers that use or cite FORGE2 |
| Papers that use or cite FORGE2 (as of 30 November 2024, for a more updated list see Google Scholar): Zheng Z, Liu S, Sidorenko J, Wang Y, Lin T, Yengo L, et al. Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries. Nature Genetics. 2024;56:767-77 Shi J, Shiraishi K, Choi J, Matsuo K, Chen T-Y, Dai J, et al. Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population. Nature Communications. 2023;14:3043 Biddie SC, Weykopf G, Hird EF, Friman ET, Bickmore WA. DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants. Genome Biology. 2024;25:208 Pushkarev O, van Mierlo G, Kribelbauer JF, Saelens W, Gardeux V, Deplancke B. Non-coding variants impact cis-regulatory coordination in a cell type-specific manner. Genome Biology. 2024;25:190 Winkler TW, Wiegrebe S, Herold JM, Stark KJ, Kuchenhoff H, Heid IM. Genetic-by-age interaction analyses on complex traits in UK Biobank and their potential to identify effects on longitudinal trait change. Genome Biology. 2024;25:300 Rahman ML, Breeze CE, Shu X-O, Wong JYY, Blechter B, Cardenas A, et al. Epigenome-wide association study of lung cancer among never smokers in two prospective cohorts in Shanghai, China. Thorax. 2024;79:735-44 Chen W, Wang Z, Lin J, Chen S, Chen H, Ma X, et al. Enhancer RNA transcriptome-wide association study reveals an atlas of pan-cancer susceptibility eRNAs. medRxiv. 2024;2024-02 Berndt SI, Vijai J, Benavente Y, Camp NJ, Nieters A, Wang Z, et al. Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes. Leukemia. 2022;1-10 Hughes O, Bentley AR, Breeze CE, Aguet F, Xu X, Nadkarni G, et al. Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas. Cell Genomics. 2023;0 Horimoto ARVR, Sun Q, Lash JP, Daviglus ML, Cai J, Haack K, et al. Admixture mapping screening of CKD traits and risk factors in U.S. Hispanic/Latino individuals from Central America country-of-origin. medRxiv; 2022. p. 2022.06.17.22276554 Lee M, Huan T, McCartney DL, Chittoor G, de Vries M, Lahousse L, et al. Pulmonary Function and Blood DNA Methylation: A Multi-Ancestry Epigenome-Wide Association Meta-Analysis. Am J Respir Crit Care Med. 2022 Breeze CE, Batorsky A, Lee MK, Szeto MD, Xu X, McCartney DL, et al. Epigenome-wide association study of kidney function identifies trans-ethnic and ethnic-specific loci. Genome Medicine. 2021;13:74 Horimoto ARVR, Xue D, Cai J, Lash JP, Daviglus ML, Franceschini N, et al. Genome-Wide Admixture Mapping of Estimated Glomerular Filtration Rate and Chronic Kidney Disease Identifies European and African Ancestry-of-Origin Loci in Hispanic and Latino Individuals in the United States. J Am Soc Nephrol. 2022;33:77-87 Meduri E, Breeze C, Marando L, Richardson SE, Huntly BJP. The RNA editing landscape in Acute Myeloid Leukaemia reveals associations with disease mutations and clinical outcome. iScience. 2022;105622 Coltell O, Asensio EM, Sorli JV, Ortega-Azorin C, Fernandez-Carrion R, Pascual EC, et al. Associations between the New DNA-Methylation-Based Telomere Length Estimator, the Mediterranean Diet and Genetics in a Spanish Population at High Cardiovascular Risk. Antioxidants (Basel, Switzerland). 2023;12 Chu P-L, Gigliotti JC, Cechova S, Bodonyi-Kovacs G, Wang YT, Chen L, et al. Collectrin (Tmem27) deficiency in proximal tubules causes hypertension in mice and a TMEM27 variant associates with blood pressure in males in a Latino cohort. Am J Physiol Renal Physiol. 2023;324:F30-42 Breeze CE, Haugen E, Gutierrez-Arcelus M, Yao X, Teschendorff A, Beck S, et al. FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome Biology. 2024;25:3 Ma Z, Zhao M, Zhao H, Qu N. Causal role of immune cells in generalized anxiety disorder: Mendelian randomization study. Front Immunol. 2023;14:1338083 Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci. 2024;81:178 Allen PC, Smith S, Wilson RC, Wirth JR, Wilson NH, Baker Frost D, et al. Distinct genome-wide DNA methylation and gene expression signatures in classical monocytes from African American patients with systemic sclerosis. Clin Epigenetics. 2023;15:25 Ma R, Chen C, Wang Z, Guo H, Zhang W. Causal relationship between plasma lipidome and four types of pancreatitis: a bidirectional Mendelian randomization study. Front Endocrinol (Lausanne). 2024;15:1415474 Liu X, Wang M, Qin J, Liu Y, Chai Z, Peng W, et al. Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information. Animals (Basel). 2023;13:1470 Yang N, Li C, Liu R, Qi X, Qian X. Causality between immunocytes and polymyositis: A Mendelian randomization analysis. Medicine (Baltimore). 2024;103:e40254 Liu X, Chai Z, Peng W, Kangzhu Y, Zhong J, Wang J. pCMLM: Genome Wide Association Study of Body Size Traits in Multiple Regions of Yak Based on the Provided Compressed Mixed Linear Model. bioRxiv; 2022. p. 2022.09.26.509454 Lin Z, Wu Z, Duan X. The Causal Nexus of Immune Cells and Vitiligo: A Genetic Perspective. medRxiv; 2024. p. 2024.11.03.24316683 Yu X, Xiao J, Cai M, Jiao Y, Wan X, Liu J, et al. PALM: a powerful and adaptive latent model for prioritizing risk variants with functional annotations. Bioinformatics. 2023;39:btad068 Nott A, Holtman IR. Genetic insights into immune mechanisms of Alzheimer's and Parkinson's disease. Front Immunol. 2023;14:1168539 Reynolds KM, Horimoto ARVR, Lin BM, Zhang Y, Kurniansyah N, Yu B, et al. Ancestry-driven metabolite variation provides insights into disease states in admixed populations. Genome Medicine. 2023;15:52 |
Some of the papers that use or cite FORGEdb |
| Papers that use or cite FORGEdb (as of 30 November 2024, for a more updated list see Google Scholar): Chappell K, Colle R, El Asmar K, Gressier F, Bouligand J, Trabado S, et al. Association of the GRIK4 rs1954787 polymorphism with clinical response in antidepressant-treated depressed patients: results from a prospective cohort and meta-analysis. Mol Psychiatry. 2024;1-10 Nygard L, Valta M, Laine A-P, Toppari J, Knip M, Veijola R, et al. CXADR polymorphism rs6517774 modifies islet autoimmunity characteristics and exhibits sex disparity. Front Genet. 2023;14 Mingardo E, Kalanithy JC, Dworschak G, Ishorst N, Yilmaz O, Lindenberg T, et al. EZH2 specifically regulates ISL1 during embryonic urinary tract formation. Sci Rep. 2024;14:22909 Abbatangelo CL, Lona Durazo F, Wendt FR, Parra EJ, Novroski NMM. From Genetic Association to Forensic Prediction: Computational Methods and Tools for Identifying Phenotypically Informative Single Nucleotide Polymorphisms. Forensic Genomics. 2023;3:47-68 An Y-C, Hung K-S, Liang C-S, Tsai C-K, Tsai C-L, Chen S-J, et al. Genetic variants associated with response to anti-CGRP monoclonal antibody therapy in a chronic migraine Han Chinese population. J Headache Pain. 2024;25:149 Cai L, Zuo X, Ma L, Zhang Y, Xu F, Lu B. Associations of MMP9 polymorphism with the risk of severe pneumonia in a Southern Chinese children population. BMC Infect Dis. 2024;24:19 Campa D, Felici A, Corradi C, Peduzzi G, Gentiluomo M, Farinella R, et al. Long or short? Telomere length and pancreatic cancer and its precursor lesions, a narrative review. Mutagenesis. 2023;gead034 Chappell K. Novel strategies for pharmacogenetic and metabolomic analysis of antidepressant treatment response in depression [PhD Thesis]. Universite Paris-Saclay; 2023 Fang S. Dissecting causal relationships and molecular mechanisms in disease using genetic risk profiles [PhD Thesis]. University of Bristol He SL. Family History, Genetic Risk Factors, and Risk of Multiple Primary Cancers [PhD Thesis]. University of Maryland, Baltimore; 2023 He Y, Li B, Zhao X, Pan L, Liu Y, Lan C, et al. Association between CACNA1D polymorphisms and hypospadias in a southern Chinese population. J Pediatr Urol. 2024;20:438.e1-438.e11 Lirio AE. Understanding genetic determinants of obstructive respiratory diseases in cohort studies using diverse phenotypes [PhD Thesis]. University of Leicester; 2024 Coltell O, Asensio EM, Sorli JV, Ortega-Azorin C, Fernandez-Carrion R, Pascual EC, et al. Associations between the New DNA-Methylation-Based Telomere Length Estimator, the Mediterranean Diet and Genetics in a Spanish Population at High Cardiovascular Risk. Antioxid Basel Switz. 2023;12 Oomatia A. Investigating the genetic and epigenetic architecture of Mesoamerican nephropathy [PhD Thesis]. UCL (University College London); 2024 Szafron LA, Iwanicka-Nowicka R, Podgorska A, Bonna AM, Sobiczewski P, Kupryjanczyk J, et al. The Clinical Significance of CRNDE Gene Methylation, Polymorphisms, and CRNDEP Micropeptide Expression in Ovarian Tumors. Int J Mol Sci. 2024;25:7531 Wu T-R, Jiao C-N, Cui X, Wang Y-L, Zheng C-H, Liu J-X. Deep Self-Reconstruction Fusion Similarity Hashing for the Diagnosis of Alzheimer's Disease on Multi-Modal Data. IEEE J Biomed Health Inform. 2024 Li Z, Ji W, Dai B, Chen S, Wang F, Duan G, et al. Single nucleotide polymorphism of Notch1 gene rs3124599 allele is associated with the severity of CVA6-related HFMD in the Chinese Han population. BMC Infect Dis. 2024;24:750 |
Credits |
| Breeze CE, Haugen E, Reynolds A, Teschendorff A, van Dongen J, Lan Q, et al. Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations.
Genome Biology. 2022;23:13. https://doi.org/10.1186/s13059-021-02560-3 Breeze CE, Haugen E, Gutierrez-Arcelus M, Yao X, Teschendorff A, Beck S, Dunham I, et al. FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases. Genome Biology. 2024;25:3. https://doi.org/10.1186/s13059-023-03126-1 |