1. Zhernakova,A., Van Diemen,C.C. and Wijmenga,C. (2009) Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet, 10, 43–55.
2. Weatherburn,C.J., Guthrie,B., Mercer,S.W. and Morales,D.R. (2017) Comorbidities in adults with asthma: population‐based cross‐sectional analysis of 1.4 million adults in Scotland. Clinical & Experimental Allergy, 47, 1246–1252.
3. Bousquet,J., Anto,J., Auffray,C., Akdis,M., Cambon‐Thomsen,A., Keil,T., Haahtela,T., Lambrecht,B.N., Postma,D.S. and Sunyer,J. (2011) MeDALL (Mechanisms of the Development of ALLergy): an integrated approach from phenotypes to systems medicine. Allergy, 66, 596–604.
4. Roberts,K.C., Rao,D.P., Bennett,T.L., Loukine,L. and Jayaraman,G.C. (2015) Prevalence and patterns of chronic disease multimorbidity and associated determinants in Canada. Health Promot Chronic Dis Prev Can, 35, 87.
5. Caughey,G.E., Vitry,A.I., Gilbert,A.L. and Roughead,E.E. (2008) Prevalence of comorbidity of chronic diseases in Australia. BMC Public Health, 8, 1–13.
6. Haider,S., Simpson,A. and Custovic,A. Genetics of Asthma and Allergic Diseases. In. Springer Berlin Heidelberg, Berlin, Heidelberg, pp. 1–17.
7. Demenais,F., Margaritte-Jeannin,P., Barnes,K.C., Cookson,W.O.C., Altmüller,J., Ang,W., Barr,R.G., Beaty,T.H., Becker,A.B. and Beilby,J. (2018) Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks. Nat Genet, 50, 42–53.
8. Fadason,T., Farrow,S., Gokuladhas,S., Golovina,E., Nyaga,D., O’Sullivan,J.M. and Schierding,W. (2021) Assigning function to SNPs: Considerations when interpreting genetic variation. In Seminars in Cell & Developmental Biology. Elsevier.
9. Martin,P., McGovern,A., Orozco,G., Duffus,K., Yarwood,A., Schoenfelder,S., Cooper,N.J., Barton,A., Wallace,C. and Fraser,P. (2015) Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci. Nat Commun, 6, 1–7.
10. Dekker,J. and Misteli,T. (2015) Long-range chromatin interactions. Cold Spring Harb Perspect Biol, 7, a019356.
11. Ardlie,K.G., DeLuca,D.S., Segrè,A. V., Sullivan,T.J., Young,T.R., Gelfand,E.T., Trowbridge,C.A., Maller,J.B., Tukiainen,T., Lek,M., et al. (2015) The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science (1979), 348.
12. Schierding,W., Farrow,S., Fadason,T., Graham,O.E.E., Pitcher,T.L., Qubisi,S., Davidson,A.J., Perry,J.K., Anderson,T.J. and Kennedy,M.A. (2020) Common variants Coregulate expression of GBA and modifier genes to delay Parkinson’s disease onset. Movement Disorders, 35, 1346–1356.
13. Fadason,T., Schierding,W., Kolbenev,N., Liu,J., Ingram,J.R. and O’Sullivan,J.M. (2020) Reconstructing the blood metabolome and genotype using long-range chromatin interactions. Metabol Open, 6, 100035.
14. Sharma,A., Menche,J., Huang,C.C., Ort,T., Zhou,X., Kitsak,M., Sahni,N., Thibault,D., Voung,L. and Guo,F. (2015) A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma. Hum Mol Genet, 24, 3005–3020.
15. Sharma,A., Kitsak,M., Cho,M.H., Ameli,A., Zhou,X., Jiang,Z., Crapo,J.D., Beaty,T.H., Menche,J. and Bakke,P.S. (2018) Integration of molecular interactome and targeted interaction analysis to identify a COPD disease network module. Sci Rep, 8, 1–14.
16. Maiorino,E., Baek,S.H., Guo,F., Zhou,X., Kothari,P.H., Silverman,E.K., Barabási,A.-L., Weiss,S.T., Raby,B.A. and Sharma,A. (2020) Discovering the genes mediating the interactions between chronic respiratory diseases in the human interactome. Nat Commun, 11, 1–14.
17. Goh,K.-I., Cusick,M.E., Valle,D., Childs,B., Vidal,M. and Barabási,A.-L. (2007) The human disease network. Proceedings of the National Academy of Sciences, 104, 8685–8690.
18. Menche,J., Sharma,A., Kitsak,M., Ghiassian,S.D., Vidal,M., Loscalzo,J. and Barabási,A.-L. (2015) Uncovering disease-disease relationships through the incomplete interactome. Science (1979), 347.
19. Fadason,T., Schierding,W., Lumley,T. and O’Sullivan,J.M. (2018) Chromatin interactions and expression quantitative trait loci reveal genetic drivers of multimorbidities. Nat Commun, 9.
20. Rao,S.S.P., Huntley,M.H., Durand,N.C., Stamenova,E.K., Bochkov,I.D., Robinson,J.T., Sanborn,A.L., Machol,I., Omer,A.D., Lander,E.S., et al. (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159.
21. Buniello,A., MacArthur,J.A.L., Cerezo,M., Harris,L.W., Hayhurst,J., Malangone,C., McMahon,A., Morales,J., Mountjoy,E., Sollis,E., et al. (2019) The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res, 47, D1005–D1012.
22. Szklarczyk,D., Gable,A.L., Lyon,D., Junge,A., Wyder,S., Huerta-Cepas,J., Simonovic,M., Doncheva,N.T., Morris,J.H., Bork,P., et al. (2019) STRING v11: Protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res, 47.
23. Johnson,K.L., Qi,Z., Yan,Z., Wen,X., Nguyen,T.C., Zaleta-Rivera,K., Chen,C.-J., Fan,X., Sriram,K., Wan,X., et al. (2021) Revealing protein-protein interactions at the transcriptome scale by sequencing. Mol Cell, 81, 4091-4103.e9.
24. Piñero,J., Ramírez-Anguita,J.M., Saüch-Pitarch,J., Ronzano,F., Centeno,E., Sanz,F. and Furlong,L.I. (2020) The DisGeNET knowledge platform for disease genomics: 2019 update. Nucleic Acids Res, 48.
25. Muiños,F., Martínez-Jiménez,F., Pich,O., Gonzalez-Perez,A. and Lopez-Bigas,N. (2021) In silico saturation mutagenesis of cancer genes. Nature, 596.
26. Gutierrez-Sacristan,A., Grosdidier,S., Valverde,O., Torrens,M., Bravo,A., Piñero,J., Sanz,F. and Furlong,L.I. (2015) PsyGeNET: A knowledge platform on psychiatric disorders and their genes. Bioinformatics, 31.
27. Rehm,H.L., Berg,J.S., Brooks,L.D., Bustamante,C.D., Evans,J.P., Landrum,M.J., Ledbetter,D.H., Maglott,D.R., Martin,C.L., Nussbaum,R.L., et al. (2015) ClinGen — The Clinical Genome Resource. New England Journal of Medicine, 372.
28. Davis,A.P., Grondin,C.J., Johnson,R.J., Sciaky,D., Wiegers,J., Wiegers,T.C. and Mattingly,C.J. (2021) Comparative Toxicogenomics Database (CTD): Update 2021. Nucleic Acids Res, 49.
29. Apweiler,R., Bateman,A., Martin,M.J., O’Donovan,C., Magrane,M., Alam-Faruque,Y., Alpi,E., Antunes,R., Arganiska,J., Casanova,E.B., et al. (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res, 42.
30. Weinreich,S.S., Mangon,R., Sikkens,J.J., Teeuw,M.E. en and Cornel,M.C. (2008) [Orphanet: a European database for rare diseases]. Ned Tijdschr Geneeskd, 152.
31. Martin,A.R., Williams,E., Foulger,R.E., Leigh,S., Daugherty,L.C., Niblock,O., Leong,I.U.S., Smith,K.R., Gerasimenko,O., Haraldsdottir,E., et al. (2019) PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat Genet, 51.
32. Gutiérrez-Sacristán,A., Bravo,À., Giannoula,A., Mayer,M.A., Sanz,F. and Furlong,L.I. (2018) comoRbidity: an R package for the systematic analysis of disease comorbidities. Bioinformatics, 34, 3228–3230.
33. Golovina,E., Fadason,T., Jaros,R.K., Kumar,H., John,J., Burrowes,K., Tawhai,M. and O’Sullivan,J.M. (2022) De novo discovery of traits co-occurring with chronic obstructive pulmonary disease. bioRxiv.
34. Watanabe,K., Taskesen,E., Van Bochoven,A. and Posthuma,D. (2017) Functional mapping and annotation of genetic associations with FUMA. Nat Commun, 8.
35. Pividori,M., Schoettler,N., Nicolae,D.L., Ober,C. and Im,H.K. (2019) Shared and distinct genetic risk factors for childhood-onset and adult-onset asthma: genome-wide and transcriptome-wide studies. Lancet Respir Med, 7, 509–522.
36. Moffatt,M.F., Gut,I.G., Demenais,F., Strachan,D.P., Bouzigon,E., Heath,S., von Mutius,E., Farrall,M., Lathrop,M. and Cookson,W.O.C.M. (2010) A Large-Scale, Consortium-Based Genomewide Association Study of Asthma. New England Journal of Medicine, 363, 1211–1221.
37. Almoguera,B., Vazquez,L., Mentch,F., Connolly,J., Pacheco,J.A., Sundaresan,A.S., Peissig,P.L., Linneman,J.G., McCarty,C.A. and Crosslin,D. (2017) Identification of four novel loci in asthma in European American and African American populations. Am J Respir Crit Care Med, 195, 456–463.
38. von Mutius,E. and Smits,H.H. (2020) Primary prevention of asthma: from risk and protective factors to targeted strategies for prevention. The Lancet, 396.
39. Finan,C., Gaulton,A., Kruger,F.A., Lumbers,R.T., Shah,T., Engmann,J., Galver,L., Kelley,R., Karlsson,A., Santos,R., et al. (2017) The druggable genome and support for target identification and validation in drug development. Sci Transl Med, 9.
40. Cotto,K.C., Wagner,A.H., Feng,Y.Y., Kiwala,S., Coffman,A.C., Spies,G., Wollam,A., Spies,N.C., Griffith,O.L. and Griffith,M. (2018) DGIdb 3.0: A redesign and expansion of the drug-gene interaction database. Nucleic Acids Res, 46.
41. Valette,K., Li,Z., Bon-Baret,V., Chignon,A., Bérubé,J.C., Eslami,A., Lamothe,J., Gaudreault,N., Joubert,P., Obeidat,M., et al. (2021) Prioritization of candidate causal genes for asthma in susceptibility loci derived from UK Biobank. Commun Biol, 4.
42. Mills,M.C. and Rahal,C. (2019) A scientometric review of genome-wide association studies. Commun Biol, 2, 1–11.
43. Aguet,F., Barbeira,A.N., Bonazzola,R., Brown,A., Castel,S.E., Jo,B., Kasela,S., Kim-Hellmuth,S., Liang,Y., Oliva,M., et al. (2020) The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science (1979), 369, 1318–1330.
44. Mims,J.W. (2015) Asthma: definitions and pathophysiology. In International forum of allergy & rhinology. Wiley Online Library, Vol. 5, pp. S2–S6.
45. Ober,C. (2016) Asthma genetics in the post-GWAS era. Ann Am Thorac Soc, 13, S85–S90.
46. Charoenngam,N., Ponvilawan,B., Wongtrakul,W. and Ungprasert,P. (2021) Patients with asthma have a higher risk of systemic lupus erythematosus: a systematic review and meta-analysis. Clin Rheumatol, 40.
47. Oliver,P.J., Arutla,S., Yenigalla,A., Hund,T.J. and Parinandi,N.L. (2021) Lipid Nutrition in Asthma. Cell Biochem Biophys, 79.
48. Diamant,Z., Aalders,W., Parulekar,A., Bjermer,L. and Hanania,N.A. (2019) Targeting lipid mediators in asthma: Time for reappraisal. Curr Opin Pulm Med, 25.
49. Denisenko,Y., Novgorodtseva,T. and Antonyuk,M. (2020) The Activity of Fatty Acids Desaturases in Mild and Moderate ASTHMA. In.
50. Chung,W.S., Lin,C.L., Ho,F.M., Li,R.Y., Sung,F.C., Kao,C.H. and Yeh,J.J. (2014) Asthma increases pulmonary thromboembolism risk: A nationwide population cohort study. European Respiratory Journal, 43.
51. Bich,T.C.T., Quoc,Q.L., Choi,Y., Yang,E.M., Trinh,H.K.T., Shin,Y.S. and Park,H.S. (2022) Serum Amyloid A1: A Biomarker for Neutrophilic Airway Inflammation in Adult Asthmatic Patients. Allergy Asthma Immunol Res, 14.
52. Manuyakorn,W., Mairiang,D., Sirachainan,N., Kadegasem,P., Kamchaisatian,W., Benjaponpitak,S. and Chuansumrit,A. (2016) Blood coagulation and asthma exacerbation in children. Int Arch Allergy Immunol, 170.
53. Carlson,S.M., Kim,J., Khan,D.A., King,K., Lucarelli,R.T., McColl,R., Peshock,R. and Brown,E.S. (2017) Hippocampal volume in patients with asthma: Results from the Dallas Heart Study. Journal of Asthma, 54.
54. Rosenkranz,M., Dean,D., Esnault,S., Evans,M., Davidson,R. and Busse,W. (2020) Co-Morbid Asthma and Depression as Risk Factors for Neurodegeneration. Biol Psychiatry, 87.
55. Bian,R., Zhang,Y., Yang,Y., Yin,Y., Zhao,X., Chen,H. and Yuan,Y. (2018) White Matter Integrity Disruptions Correlate With Cognitive Impairments in Asthma. Journal of Magnetic Resonance Imaging, 48.
56. Grosso,A., Pesce,G., Marcon,A., Piloni,D., Albicini,F., Gini,E., Marchetti,P., Battaglia,S., Ferrari,M., Fois,A., et al. (2019) Depression is associated with poor control of symptoms in asthma and rhinitis: A population-based study. Respir Med, 155.
57. Nicholson,A., Pollard,S.L., Lima,J.J., Romero,K.M., Tarazona-Meza,C., Malpartida-Guzmán,G., Mougey,E., Hansel,N.N. and Checkley,W. (2017) Serum folate concentrations, asthma, atopy, and asthma control in Peruvian children. Respir Med, 133.
58. Weiss,S.T. (1997) Diet as a risk factor for asthma. CIBA Foundation Symposia, 10.1002/9780470515334.ch16.
59. Pistelli,R., Forastiere,F., Corbo,G.M., Dell’Orco,V., Brancato,G., Agabiti,N., Pizzabiocca,A. and Perucci,C.A. (1993) Respiratory symptoms and bronchial responsiveness are relatd to dietary salt intake and urinary potassium excretion in male children. European Respiratory Journal, 6.
60. Tanizaki,Y., Hosokawa,M., Goda,Y., Akagi,K., Takeyama,H. and Kimura,I. (1982) Numerical changes in blood monocytes in bronchial asthma. Acta Med Okayama, 36.
61. Zhi,Y., Gao,P., Li,W., Gao,F., Zhang,J., Lin,H. and Zhang,J. (2018) Soluble cd163 levels and cd163+cd14+ monocyte/macrophage counts in patients with asthma. Iranian Journal of Immunology, 15.
62. de Souza,E.C.C., Pizzichini,M.M.M., Dias,M., Cunha,M.J., Matte,D.L., Karloh,M., Maurici,R. and Pizzichini,E. (2020) Body mass index, asthma, and respiratory symptoms: A population-based study. Jornal Brasileiro de Pneumologia, 46.
63. Jiang,L., Sun,Y.Q., Langhammer,A., Brumpton,B.M., Chen,Y., Nilsen,T. Il, Leivseth,L., Wahl,S.G.F. and Mai,X.M. (2021) Asthma and asthma symptom control in relation to incidence of lung cancer in the HUNT study. Sci Rep, 11.
64. Greten,F.R. and Grivennikov,S.I. (2019) Inflammation and cancer: triggers, mechanisms, and consequences. Immunity, 51, 27–41.
65. Burgstaller,G., Oehrle,B., Gerckens,M., White,E.S., Schiller,H.B. and Eickelberg,O. (2017) The instructive extracellular matrix of the lung: basic composition and alterations in chronic lung disease. European Respiratory Journal, 50.
66. Vignola,A.M., Kips,J. and Bousquet,J. (2000) Tissue remodeling as a feature of persistent asthma. Journal of Allergy and Clinical Immunology, 105, 1041–1053.
67. Huang,Q.Q., Tang,H.H.F., Teo,S.M., Mok,D., Ritchie,S.C., Nath,A.P., Brozynska,M., Salim,A., Bakshi,A., Holt,B.J., et al. (2020) Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk. Nat Commun, 11.
68. Lin,Y., Zhou,H. and Li,S. (2022) BTN3A2 Expression Is Connected With Favorable Prognosis and High Infiltrating Immune in Lung Adenocarcinoma. Front Genet, 13.
69. Kuenzig,M.E., Bishay,K., Leigh,R., Kaplan,G.G. and Benchimol,E.I. (2018) Co-occurrence of Asthma and the Inflammatory Bowel Diseases: A Systematic Review and Meta-analysis. Clin Transl Gastroenterol, 9.
70. Sun,Y., Yu,W., Huang,L., Hou,J., Gong,P., Zheng,Y., Zhao,M., Zhou,P. and Li,X. (2012) Is Asthma related to choroidal neovascularization? PLoS One, 7.
71. Kim,K.W., Kim,D.Y., Yoon,D., Kim,K., Jang,H., Schoettler,N., Kim,E.G., Kim,M.N., Hong,J.Y., Lee,J., et al. (2022) Genome‐wide association study identifies TNFSF15 associated with childhood asthma. Allergy, 77, 218–229.
72. Kadiyska,T., Tourtourikov,I., Popmihaylova,A.-M., Kadian,H. and Chavoushian,A. (2018) Role of TNFSF15 in the intestinal inflammatory response . World J Gastrointest Pathophysiol, 9.
73. R core team (2021) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing.
74. RStudio team (2020) RStudio: Integrated development environment for R.