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Rusiñol L, Puig L. Multi-Omics Approach to Improved Diagnosis and Treatment of Atopic Dermatitis and Psoriasis. Int J Mol Sci 2024; 25:1042. [PMID: 38256115 PMCID: PMC10815999 DOI: 10.3390/ijms25021042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/07/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Psoriasis and atopic dermatitis fall within the category of cutaneous immune-mediated inflammatory diseases (IMIDs). The prevalence of IMIDs is increasing in industrialized societies, influenced by both environmental changes and a genetic predisposition. However, the exact immune factors driving these chronic, progressive diseases are not fully understood. By using multi-omics techniques in cutaneous IMIDs, it is expected to advance the understanding of skin biology, uncover the underlying mechanisms of skin conditions, and potentially devise precise and personalized approaches to diagnosis and treatment. We provide a narrative review of the current knowledge in genomics, epigenomics, and proteomics of atopic dermatitis and psoriasis. A literature search was performed for articles published until 30 November 2023. Although there is still much to uncover, recent evidence has already provided valuable insights, such as proteomic profiles that permit differentiating psoriasis from mycosis fungoides and β-defensin 2 correlation to PASI and its drop due to secukinumab first injection, among others.
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Affiliation(s)
- Lluís Rusiñol
- Department of Dermatology, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Institut de Recerca Sant Pau (IR SANT PAU), 08041 Barcelona, Spain
- Unitat Docent Hospital Universitari Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain
| | - Lluís Puig
- Department of Dermatology, Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain;
- Institut de Recerca Sant Pau (IR SANT PAU), 08041 Barcelona, Spain
- Unitat Docent Hospital Universitari Sant Pau, Universitat Autònoma de Barcelona, 08025 Barcelona, Spain
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Łuczaj W, Gęgotek A, Skrzydlewska E. Analytical approaches to assess metabolic changes in psoriasis. J Pharm Biomed Anal 2021; 205:114359. [PMID: 34509137 DOI: 10.1016/j.jpba.2021.114359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 12/18/2022]
Abstract
Psoriasis is one of the most common human skin diseases, although its development is not limited to one tissue, but is associated with autoimmune reactions throughout the body. Overproduction of pro-inflammatory cytokines and growth factors systemically stimulates the proliferation of skin cells, which manifests as excessive exfoliation of the epidermis, and/or arthritis, as well as other comorbidities such as insulin resistance, metabolic syndrome, hypertension, and depression. Thus, there is a great need for a thorough analysis of the pathophysiology of psoriatic patients, including classical methods, such as spectrophotometry, chromatography, or Western blot, and also novel omics approaches such as lipidomics and proteomics. Moreover, the extensive pathophysiology forces increased research examining biological changes in both skin cells, and systemically. A wide range of techniques involved in lipidomic research based on a combination of mass spectrometry and different types of chromatography (RP-LC-QTOF-MS/MS, HILIC-QTOF-MS/MS or RP-LC-QTRAP-MS/MS), have allowed comprehensive assessment of lipid modification in psoriatic skin and provided new insight into the role of lipids and their mechanism of action in psoriasis. Moreover, proteomic analysis using gel-nanoLC-OrbiTrap-MS/MS, as well as MALDI-TOF/TOF techniques facilitates the description of panels of enzymes involved in lipidome modifications, and the response of the endocannabinoid system to metabolic changes. Psoriasis is known to alter the expression of proteins that are involved in the inflammatory and antioxidant response, as well as protein biosynthesis, degradation, as well as cell proliferation and apoptosis. Knowledge of changes in the lipidomic and proteomic profile will not only allow the understanding of psoriasis pathophysiology, but also facilitate proper and early diagnosis and effective pharmacotherapy.
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Affiliation(s)
- Wojciech Łuczaj
- Department of Analytical Chemistry, Medical University of Bialystok, Mickiewicza 2d, 15-222, Bialystok, Poland
| | - Agnieszka Gęgotek
- Department of Analytical Chemistry, Medical University of Bialystok, Mickiewicza 2d, 15-222, Bialystok, Poland
| | - Elżbieta Skrzydlewska
- Department of Analytical Chemistry, Medical University of Bialystok, Mickiewicza 2d, 15-222, Bialystok, Poland.
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Proteomic Profiling Change and Its Implies in the Early Mycosis Fungoides (MF) Using Isobaric Tags for Relative and Absolute Quantification (iTRAQ). BIOMED RESEARCH INTERNATIONAL 2020; 2020:9237381. [PMID: 33299887 PMCID: PMC7707953 DOI: 10.1155/2020/9237381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/01/2020] [Accepted: 10/31/2020] [Indexed: 11/17/2022]
Abstract
Purpose Mycosis fungoides (MF) is the most common T-cell lymphoma, with indolent biologic behavior in the early stage and features of invasive in the tumor stage. The diagnosis of MF is still ambiguous and difficult. We focused on the proteomic profiling change in the pathogenesis of early MF and identified candidate biomarkers for early diagnosis. Methods We collected peripheral blood samples of MF patients and healthy individuals (HI) performed proteomic profiling analysis using isobaric tags for relative and absolute quantification (iTRAQ) platform. Differently expressed proteins (DEPs) were filtered, and involved biological functions were analyzed through Gene Ontology (GO) and Ingenuity Pathway Analysis (IPA) software. Results We identified 78 DEPs including fifty proteins were upregulated and 28 proteins were downregulated in the MF group with HI as a control. Total DEPs were analyzed according to the biological regulation and metabolic process through GO analysis. The pathways of LXR/RXR activation and FXR/RXR activation were significantly activated, in which APOH, CLU, and ITIH4 were involved. The top annotated disease and function network was (Cancer, Organismal Injury and Abnormalities, Reproductive System Disease), with a key node CLU. These DEPs were involved in cancer, including thyroid carcinoma, head and neck carcinoma, and cancer of secretory structure, in which CLU, GNAS, and PKM played an indirect role in the occurrence and development of cancer. Relevant causal network was IL12 (family), which is related to GNAS, PKM, and other DEPs. Conclusion Proteomic profiling of early-stage MF provided candidate protein biomarkers such as CLU, GNAS, and PKM, which benefit the early diagnosis and understanding of the mechanism of MF development. Besides, lipid metabolism may be one of the pathogenesis of MF, and IL12 was a potential marker for the diagnosis and treatment of early MF.
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Stafford IS, Kellermann M, Mossotto E, Beattie RM, MacArthur BD, Ennis S. A systematic review of the applications of artificial intelligence and machine learning in autoimmune diseases. NPJ Digit Med 2020; 3:30. [PMID: 32195365 PMCID: PMC7062883 DOI: 10.1038/s41746-020-0229-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 01/17/2020] [Indexed: 02/07/2023] Open
Abstract
Autoimmune diseases are chronic, multifactorial conditions. Through machine learning (ML), a branch of the wider field of artificial intelligence, it is possible to extract patterns within patient data, and exploit these patterns to predict patient outcomes for improved clinical management. Here, we surveyed the use of ML methods to address clinical problems in autoimmune disease. A systematic review was conducted using MEDLINE, embase and computers and applied sciences complete databases. Relevant papers included "machine learning" or "artificial intelligence" and the autoimmune diseases search term(s) in their title, abstract or key words. Exclusion criteria: studies not written in English, no real human patient data included, publication prior to 2001, studies that were not peer reviewed, non-autoimmune disease comorbidity research and review papers. 169 (of 702) studies met the criteria for inclusion. Support vector machines and random forests were the most popular ML methods used. ML models using data on multiple sclerosis, rheumatoid arthritis and inflammatory bowel disease were most common. A small proportion of studies (7.7% or 13/169) combined different data types in the modelling process. Cross-validation, combined with a separate testing set for more robust model evaluation occurred in 8.3% of papers (14/169). The field may benefit from adopting a best practice of validation, cross-validation and independent testing of ML models. Many models achieved good predictive results in simple scenarios (e.g. classification of cases and controls). Progression to more complex predictive models may be achievable in future through integration of multiple data types.
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Affiliation(s)
- I. S. Stafford
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - M. Kellermann
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - E. Mossotto
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - R. M. Beattie
- Department of Paediatric Gastroenterology, Southampton Children’s Hospital, Southampton, UK
| | - B. D. MacArthur
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - S. Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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Proteomics in Psoriasis. Int J Mol Sci 2019; 20:ijms20051141. [PMID: 30845706 PMCID: PMC6429319 DOI: 10.3390/ijms20051141] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/21/2019] [Accepted: 03/02/2019] [Indexed: 12/14/2022] Open
Abstract
Psoriasis has been thought to be driven primarily by innate and adaptive immune systems that can be modified by genetic and environmental factors. Complex interplay between inflammatory cytokines and T-cells, especially Th1 and Th17 cells, leads to abnormal cell proliferation and psoriatic skin lesions. Nevertheless, such mechanisms do not entirely represent the pathogenesis of psoriasis. Moreover, earlier and better biomarkers in diagnostics, prognostics, and monitoring therapeutic outcomes of psoriasis are still needed. During the last two decades, proteomics (a systematic analysis of proteins for their identities, quantities, and functions) has been widely employed to psoriatic research. This review summarizes and discusses all of the previous studies that applied various modalities of proteomics technologies to psoriatic skin disease. The data obtained from such studies have led to (i) novel mechanisms and new hypotheses of the disease pathogenesis; (ii) biomarker discovery for diagnostics and prognostics; and (iii) proteome profiling for monitoring treatment efficacy and drug-induced toxicities.
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Gęgotek A, Domingues P, Wroński A, Wójcik P, Skrzydlewska E. Proteomic plasma profile of psoriatic patients. J Pharm Biomed Anal 2018; 155:185-193. [DOI: 10.1016/j.jpba.2018.03.068] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/29/2018] [Accepted: 03/31/2018] [Indexed: 12/16/2022]
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Ion A, Popa IM, Papagheorghe LML, Lisievici C, Lupu M, Voiculescu V, Caruntu C, Boda D. Proteomic Approaches to Biomarker Discovery in Cutaneous T-Cell Lymphoma. DISEASE MARKERS 2016; 2016:9602472. [PMID: 27821903 PMCID: PMC5086377 DOI: 10.1155/2016/9602472] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 01/16/2023]
Abstract
Cutaneous T-cell lymphoma (CTCL) is the most frequently encountered type of skin lymphoma in humans. CTCL encompasses multiple variants, but the most common types are mycosis fungoides (MF) and Sezary syndrome (SS). While most cases of MF run a mild course over a period of many years, other subtypes of CTCL are very aggressive. The rapidly expanding fields of proteomics and genomics have not only helped increase knowledge concerning the carcinogenesis and tumor biology of CTCL but also led to the discovery of novel markers for targeted therapy. Although multiple biomarkers linked to CTCL have been known for a relatively long time (e.g., CD25, CD45, CD45RA, and CD45R0), compared to other cancers (lymphoma, melanoma, colon carcinoma, head and neck cancer, renal cancer, and cutaneous B-cell lymphoma), information about the antigenicity of CTCL remains relatively limited and no dependable protein marker for CTCL has been discovered. Considering the aggressive nature of some types of CTCL, it is necessary to identify circulating molecules that can help in the early diagnosis, differentiation from inflammatory skin diseases (psoriasis, nummular eczema), and aid in predicting the prognosis and evolution of this pathology. This review aims to bring together some of the information concerning protein markers linked to CTCL, in an effort to further the understanding of the convolute processes involved in this complex pathology.
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Affiliation(s)
- Alexandra Ion
- Department of Dermatology and Allergology, Elias Emergency University Hospital, 011461 Bucharest, Romania
| | - Iris Maria Popa
- Department of Plastic and Reconstructive Surgery, “Bagdasar Arseni” Clinical Emergency Hospital, 041915 Bucharest, Romania
| | | | - Cristina Lisievici
- Department of Dermatology and Allergology, Elias Emergency University Hospital, 011461 Bucharest, Romania
| | - Mihai Lupu
- Department of Dermatology and Allergology, Elias Emergency University Hospital, 011461 Bucharest, Romania
| | - Vlad Voiculescu
- Department of Dermatology and Allergology, Elias Emergency University Hospital, 011461 Bucharest, Romania
| | - Constantin Caruntu
- Department of Physiology, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Dermatology, “Prof. N. C. Paulescu” National Institute of Diabetes, Nutrition and Metabolic Diseases, 020475 Bucharest, Romania
| | - Daniel Boda
- Dermatology Research Laboratory, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Department of Dermatology, Carol Medical Center, 020915 Bucharest, Romania
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Znamenskaya LF, Znamenskaya LF. Proteome technologies in studying the pathogenesisof psoriasis. VESTNIK DERMATOLOGII I VENEROLOGII 2011. [DOI: 10.25208/vdv1013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Psoriasis is one of the most prevalent inflammatory dermatoses. At the same time, its pathogenesis has not been studied
in full. Proteome profiling is currently a promising method to study the biological mechanisms of developing different
diseases. Proteome technologies make it possible to detect changes in the skin protein profile in psoriatic patients and
identify the revealed proteins. The proteins serve as potential targets for drugs or biomarkers for assessing the patients
individual drug response. The article describes the key achievements in the field of studying the pathogenesis of psoriasis
using proteome technologies (two-dimensional electrophoresis and mass spectrometry) set out in the latest literature
sources, and also analyzes the results of the authors studies aimed at detecting proteins being markers of the patients
response to the infliximab therapy.
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Braconi D, Bernardini G, Santucci A. Post-genomics and skin inflammation. Mediators Inflamm 2010; 2010:364823. [PMID: 20886018 PMCID: PMC2945662 DOI: 10.1155/2010/364823] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 08/22/2010] [Indexed: 01/26/2023] Open
Abstract
Atopic dermatitis and psoriasis are two chronic skin inflammatory diseases that have so far received a greater attention within the scientific community through different post-genomic approaches; on the contrary, acne, which is undoubtedly one of the most common skin disorders involving inflammatory processes, seems to be still quite neglected under the post-genomic point of view. In this paper, we will review how post-genomic technologies have provided new fundamental tools for the analysis of these three conditions and we will cast light on their potential in addressing future research challenges.
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Affiliation(s)
- Daniela Braconi
- Dipartimento di Biologia Molecolare, Università degli Studi di Siena, via Fiorentina 1, 53100 Siena, Italy
| | - Giulia Bernardini
- Dipartimento di Biologia Molecolare, Università degli Studi di Siena, via Fiorentina 1, 53100 Siena, Italy
| | - Annalisa Santucci
- Dipartimento di Biologia Molecolare, Università degli Studi di Siena, via Fiorentina 1, 53100 Siena, Italy
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BRATSEVA YEV, MOSHKOVSKY SA, ZNAMENSKAYA LF, KUBANOVA AA, KUBANOV AA. Search for potential biomarkers of inveterate dermatoses by means of proteomic analysis. VESTNIK DERMATOLOGII I VENEROLOGII 2010. [DOI: 10.25208/vdv887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The review covers the key achievements of proteome studies using mass spectrometry and two-dimensional electrophoresis methods in the field of dermatology Works studying the most prevalent chronic dermatoses such as psoriasis, atopic dermatitis, acne vulgaris and mycosis fungoidea are examined. Proteome analysis in dermatology is a promising technique today because it makes it possible to study molecular pathogenic mechanisms of skin chronic diseases in a greater detail. In addition, proteome technologies are aimed at searching for potential disease biomarkers and targets for drugs.
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Alexandroff A, Graham-Brown R. Report from the 67th Annual Meeting of the American Academy of Dermatology. Br J Dermatol 2009; 162:12-21. [DOI: 10.1111/j.1365-2133.2009.09395.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Lai X, Liangpunsakul S, Crabb DW, Ringham HN, Witzmann FA. A proteomic workflow for discovery of serum carrier protein-bound biomarker candidates of alcohol abuse using LC-MS/MS. Electrophoresis 2009; 30:2207-14. [PMID: 19544491 PMCID: PMC2756771 DOI: 10.1002/elps.200800775] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The diagnosis and care of patients with alcohol abuse and dependence is hampered by a lack of sensitive and specific screening and monitoring tests. Proteomics is a good approach to search for biomarkers of alcohol abuse. Serum carrier protein-bound proteins have attracted significant interest because they remain a relatively un-mined region of the proteome. In the present study, a proteomic workflow including LC-MS/MS with enrichment of serum carrier protein-bound biomarkers technique was applied to profile the changes in quality and quantity of serum carrier protein-bound proteins for the discovery of novel biomarker candidates of alcohol abuse. In total, 311 proteins identified with high confidence were discovered to be bound to serum carrier proteins. Complement isoforms, Ig fragments, and apolipoprotein family proteins are the main serum carrier-bound proteins. Protein quantification analysis with and without concern as to gender revealed that gender is a critical consideration for biomarker development in alcohol abuse. Identified proteins not previously associated with alcohol abuse include gelsolin, selenoprotein P, serotransferrin, tetranectin, hemopexin, histidine-rich glycoprotein, plasma kallikrein, and vitronectin. Altered abundance of these proteins suggests that they may be potential novel biomarkers for alcohol abuse.
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Affiliation(s)
- Xianyin Lai
- Department of Cellular & Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Suthat Liangpunsakul
- Department of Medicine – Division of Gastroenterology/Hepatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - David W. Crabb
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Heather N. Ringham
- Department of Cellular & Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Frank A. Witzmann
- Department of Cellular & Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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QUADOMICS: an adaptation of the Quality Assessment of Diagnostic Accuracy Assessment (QUADAS) for the evaluation of the methodological quality of studies on the diagnostic accuracy of '-omics'-based technologies. Clin Biochem 2008; 41:1316-25. [PMID: 18652812 DOI: 10.1016/j.clinbiochem.2008.06.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 06/23/2008] [Accepted: 06/25/2008] [Indexed: 01/23/2023]
Abstract
OBJECTIVES To adapt the Quality Assessment of Diagnostic Accuracy Assessment (QUADAS) to the particular methodological challenges posed by research on '-omics'-based diagnostic tests. DESIGN AND METHODS We generated new guidelines by appraising the suitability of each criterion from QUADAS to '-omics'-based diagnostic research, and by adding new items that addressed specific sources of error. In addition, we defined four phases in the evaluation of a diagnostic test. RESULTS Twelve of the 14 criteria from QUADAS were retained in the new tool. The items relating to selection criteria and the description of the test were reformulated, and the criteria about external validation and the availability of clinical data were applied only in studies in the last research phase. Four new items were incorporated to QUADOMICS related to pre-analytical conditions and methods to avoid overfitting. CONCLUSIONS QUADOMICS is an adaptation of QUADAS to the special nature of '-omics'-based diagnostic research. The tool adds new items that assess quality issues specific to this research, and may enhance the application of '-omics'-based discoveries to clinical \and public health practice.
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