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Tekin B, Xie F, Lehman JS. Lichen Planus: What is New in Diagnosis and Treatment? Am J Clin Dermatol 2024:10.1007/s40257-024-00878-9. [PMID: 38982032 DOI: 10.1007/s40257-024-00878-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2024] [Indexed: 07/11/2024]
Abstract
Lichen planus (LP), an idiopathic, multifaceted chronic inflammatory disease with a heterogeneous clinical presentation, affects approximately 0.5-1% of the population. The various clinical manifestations of LP fall into three broad categories, namely cutaneous, appendageal, and mucosal, with further subclassification depending on the morphology and distribution patterns of individual lesions. There is mounting evidence that LP has systemic associations, including autoimmune conditions, glucose intolerance, dyslipidemia, and cardiovascular disorders. Cutaneous hypertrophic and mucosal forms of LP are at a heightened risk for malignant transformation. Familiarity with these potential associations in conjunction with long-term follow-up and regular screening could lead to a timely diagnosis and management of concomitant conditions. In addition, the frequent quality of life (QoL) impairment in LP underscores the need for a comprehensive approach including psychological evaluation and support. Several treatment strategies have been attempted, though most of them have not been adopted in clinical practice because of suboptimal benefit-to-risk ratios or lack of evidence. More recent studies toward pathogenesis-driven treatments have identified Janus kinase inhibitors such as tofacitinib, phosphodiesterase-4 inhibitors such as apremilast, and biologics targeting the interleukin-23/interleukin-17 pathway as novel therapeutic options, resulting in a dramatic change of the treatment landscape of LP. This contemporary review focuses on the diagnosis and management of LP, and places emphasis on more recently described targeted treatment options.
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Affiliation(s)
- Burak Tekin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
- Department of Dermatology, Mayo Clinic, Rochester, MN, USA
| | - Fangyi Xie
- Department of Dermatology, Mayo Clinic, Rochester, MN, USA
- Department of Dermatology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Julia S Lehman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
- Department of Dermatology, Mayo Clinic, Rochester, MN, USA.
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2
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Assarsson M, Söderman J, Seifert O. Significant Correlation Between Cutaneous Abundance of Streptococcus and Psoriasis Severity in Patients with FBXL19 Gene Variants. Acta Derm Venereol 2024; 104:adv34892. [PMID: 38898675 PMCID: PMC11210493 DOI: 10.2340/actadv.v104.34892] [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: 12/13/2023] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Psoriasis results from both genetic predisposition and environmental triggers, such as Streptococcal infections. This study aimed to explore the correlation between the abundance of the Streptococcus genus on the skin and psoriasis severity in individuals carrying specific psoriasis-associated genetic variants. Studying 39 chronic plaque psoriasis patients, the elbow skin microbiome and 49 psoriasis-related single nucleotide polymorphisms (SNPs) were analysed using a MiSeq instrument for 16S rDNA sequencing, and CLC Genomic Workbench for processing and analysis. Through multivariate linear regression analysis, a positive correlation was found between Streptococcus genus abundance and psoriasis severity in patients with certain FBXL19 gene-related heterozygous SNPs (rs12924903, rs10782001, rs12445568). Conversely, a negative association was observed in patients with homozygous genotypes. Moreover, we identified an association between Streptococcus abundance and psoriasis severity in patients with genetic variants related to IL-22, ERAP1, NOS2, and ILF3. This is the first study highlighting a positive association between Streptococcus skin colonization and psoriasis severity in patients with heterozygous genotypes within the FBXL19 gene region. FXBL19 targets the IL-33/IL1RL1 axis, crucial in infectious diseases and innate immunity promotion. These novel results suggests an intricate interaction among host genetics, Streptococcus skin colonization, and psoriasis inflammation, offering potential avenues for novel treatment approaches.
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Affiliation(s)
- Malin Assarsson
- Department of Biomedical and Clinical Sciences, Faculty of Health Sciences, Linköping University, Linköping, Sweden; Division of Dermatology and Venereology, Region Jönköping County, Jönköping, Sweden.
| | - Jan Söderman
- Department of Biomedical and Clinical Sciences, Faculty of Health Sciences, Linköping University, Linköping, Sweden; Laboratory Medicine, Region Jönköping County, Jönköping, Sweden
| | - Oliver Seifert
- Department of Biomedical and Clinical Sciences, Faculty of Health Sciences, Linköping University, Linköping, Sweden; Division of Dermatology and Venereology, Region Jönköping County, Jönköping, Sweden
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3
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Vinay K, Kamat D, Narayan R V, Minz RW, Singh J, Bishnoi A, Chatterjee D, Parsad D, Kumaran MS. Major histocompatibility complex (MHC) gene frequency in acquired dermal macular hyperpigmentation: a case control study. Int J Dermatol 2024; 63:773-779. [PMID: 38263574 DOI: 10.1111/ijd.17017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/12/2023] [Accepted: 12/28/2023] [Indexed: 01/25/2024]
Abstract
BACKGROUND Human leukocyte antigen (HLA) allele frequencies have a known association with the pathogenesis of various autoimmune diseases. METHODS We recruited 31 Indian patients of acquired dermal macular hyperpigmentation (ADMH) and 60 unrelated, age-and-gender-matched healthy controls. After history and clinical examination, 5 ml of blood in EDTA vials was collected. These samples were subjected to DNA extraction and the expression of HLA A, B, C, DR, DQ-A, and DQ-B was studied. RESULTS There was a predominance of females with a gender ratio of 23 : 8 and the most common phototype was Fitzpatrick type IV (83.9%). There was a significant association of HLA A*03:01 (OR: 5.8, CI: 1.7-17.0, P = 0.005), HLA B*07:02 (OR: 5.3, CI: 1.9-14.6, P = 0.003), HLA C*07:02 (OR: 4.3, CI: 1.8-9.6, P = 0.001), HLA DRB1*10:01 (OR: 7.6, CI: 1.7-38.00, P = 0.022), and HLA DRB1*15:02 (OR: 31.0, CI: 4.4-341.8, P < 0.001) with patients compared to controls, whereas HLA DQB*03:01 was less associated with patients compared to controls (OR: 0.2, CI: 0.0-0.6, P = 0.009). CONCLUSION Patients with ADMH are more likely to have the HLA A*03:01, HLA B 07*02, HLA C*07:02, HLA DRB1*10:01, HLA DRB1*15:02 and less likely to have the HLA DQB*03:01 allele. Larger cohort studies may thus be conducted studying these specific alleles.
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Affiliation(s)
- Keshavamurthy Vinay
- Department of Dermatology, Venereology & Leprology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Divya Kamat
- Department of Dermatology, Venereology & Leprology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Vignesh Narayan R
- Department of Dermatology, Venereology & Leprology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ranjana W Minz
- Department of Immunopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Jagdeep Singh
- Department of Immunopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Anuradha Bishnoi
- Department of Dermatology, Venereology & Leprology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Debajyoti Chatterjee
- Department of Histopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Davinder Parsad
- Department of Dermatology, Venereology & Leprology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Muthu S Kumaran
- Department of Dermatology, Venereology & Leprology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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4
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Manchanda Y, Rathi SK, Joshi A, Das S. Oral Lichen Planus: An Updated Review of Etiopathogenesis, Clinical Presentation, and Management. Indian Dermatol Online J 2024; 15:8-23. [PMID: 38283029 PMCID: PMC10810384 DOI: 10.4103/idoj.idoj_652_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 07/17/2023] [Accepted: 07/26/2023] [Indexed: 01/30/2024] Open
Abstract
Lichen planus (LP) is a chronic idiopathic immune-mediated inflammatory condition. LP is a heterogeneous disease with varied clinical presentations having different natural history, prognosis, sequelae, and outcomes. It can affect skin, hair, nails, and mucosae. Mucosal LP (including oral LP) tends to be persistent and resistant to treatment, compared to cutaneous LP. Oral LP (OLP) is broadly divided into two main categories: hyperkeratotic (usually asymptomatic) and erosive (commonly symptomatic). It can present with symptoms including odynophagia, dysphagia, dysgeusia, and sensitivity to hot spicy foods. Apart from the superficial epidermal changes, which vary with the type of clinical presentation, histopathologically oral LP shows a unifying similar and consistent feature of a lichenoid interface dermatitis. Recently, researchers have highlighted the critical role played by IL-17 in the pathogenesis of OLP. World Health Organization has categorized oral LP as one of the oral potentially malignant disorders (OPMD), albeit with a low risk of malignant transformation. Also, in the last couple of years there have been various reports on the usage of newer drugs like anti-IL17, anti-IL12/23, anti-IL 23, PDE4 inhibitors, and JAK inhibitors in the management of refractory OLP. The principal aim of treatment still remains to resolve the symptoms, prolong the symptoms free period, and reduce the risk of potential malignant transformation. We have described many new revelations made in recent times regarding the etiopathogenesis, associated conditions as well as management of OLP. Thus, the objective of this review is to present a comprehensive up-to-date knowledge including the recent advances made regarding OLP.
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Affiliation(s)
| | | | - Arun Joshi
- Consultant, Department of Dermatology, Farwaniya Hospital, Kuwait
| | - Sudip Das
- Head of the Department National Medical College, Kolkata, India
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5
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Mustafa R, Ghanbari M, Karhunen V, Evangelou M, Dehghan A. Phenome-wide association study on miRNA-related sequence variants: the UK Biobank. Hum Genomics 2023; 17:104. [PMID: 37996941 PMCID: PMC10668386 DOI: 10.1186/s40246-023-00553-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Genetic variants in the coding region could directly affect the structure and expression levels of genes and proteins. However, the importance of variants in the non-coding region, such as microRNAs (miRNAs), remain to be elucidated. Genetic variants in miRNA-related sequences could affect their biogenesis or functionality and ultimately affect disease risk. Yet, their implications and pleiotropic effects on many clinical conditions remain unknown. METHODS Here, we utilised genotyping and hospital records data in the UK Biobank (N = 423,419) to investigate associations between 346 genetic variants in miRNA-related sequences and a wide range of clinical diagnoses through phenome-wide association studies. Further, we tested whether changes in blood miRNA expression levels could affect disease risk through colocalisation and Mendelian randomisation analysis. RESULTS We identified 122 associations for six variants in the seed region of miRNAs, nine variants in the mature region of miRNAs, and 27 variants in the precursor miRNAs. These included associations with hypertension, dyslipidaemia, immune-related disorders, and others. Nineteen miRNAs were associated with multiple diagnoses, with six of them associated with multiple disease categories. The strongest association was reported between rs4285314 in the precursor of miR-3135b and celiac disease risk (odds ratio (OR) per effect allele increase = 0.37, P = 1.8 × 10-162). Colocalisation and Mendelian randomisation analysis highlighted potential causal role of miR-6891-3p in dyslipidaemia. CONCLUSIONS Our study demonstrates the pleiotropic effect of miRNAs and offers insights to their possible clinical importance.
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Affiliation(s)
- Rima Mustafa
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- UK Dementia Research Institute, Imperial College London, London, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ville Karhunen
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | | | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
- UK Dementia Research Institute, Imperial College London, London, UK.
- MRC Centre for Environment and Health, Imperial College London, London, UK.
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6
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Ye Z, Mayer J, Leary EJ, Kitchner T, Dart RA, Brilliant MH, Hebbring SJ. Estimating the efficacy of pharmacogenomics over a lifetime. Front Med (Lausanne) 2023; 10:1006743. [PMID: 38020121 PMCID: PMC10645151 DOI: 10.3389/fmed.2023.1006743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 07/10/2023] [Indexed: 12/01/2023] Open
Abstract
It is well known that common variants in specific genes influence drug metabolism and response, but it is currently unknown what fraction of patients are given prescriptions over a lifetime that could be contraindicated by their pharmacogenomic profiles. To determine the clinical utility of pharmacogenomics over a lifetime in a general patient population, we sequenced the genomes of 300 deceased Marshfield Clinic patients linked to lifelong medical records. Genetic variants in 33 pharmacogenes were evaluated for their lifetime impact on drug prescribing using extensive electronic health records. Results show that 93% of the 300 deceased patients carried clinically relevant variants. Nearly 80% were prescribed approximately three medications on average that may have been impacted by these variants. Longitudinal data suggested that the optimal age for pharmacogenomic testing was prior to age 50, but the optimal age is greatly influenced by the stability of the population in the healthcare system. This study emphasizes the broad clinical impact of pharmacogenomic testing over a lifetime and demonstrates the potential application of genomic medicine in a general patient population for the advancement of precision medicine.
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Vičić M, Hlača N, Kaštelan M, Brajac I, Sotošek V, Prpić Massari L. Comprehensive Insight into Lichen Planus Immunopathogenesis. Int J Mol Sci 2023; 24:ijms24033038. [PMID: 36769361 PMCID: PMC9918135 DOI: 10.3390/ijms24033038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Lichen planus is a chronic disease affecting the skin, appendages, and mucous membranes. A cutaneous lichen planus is a rare disease occurring in less than 1% of the general population, while oral illness is up to five times more prevalent; still, both forms equally impair the patient's quality of life. The etiology of lichen planus is not entirely understood. Yet, immune-mediated mechanisms have been recognized since environmental factors such as hepatitis virus infection, mechanical trauma, psychological stress, or microbiome changes can trigger the disease in genetically susceptible individuals. According to current understanding, lichen planus immunopathogenesis is caused by cell-mediated cytotoxicity, particularly cytotoxic T lymphocytes, whose activity is further influenced by Th1 and IL-23/Th-17 axis. However, other immunocytes and inflammatory pathways complement these mechanisms. This paper presents a comprehensive insight into the actual knowledge about lichen planus, with the causal genetic and environmental factors being discussed, the immunopathogenesis described, and the principal effectors of its inflammatory circuits identified.
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Affiliation(s)
- Marijana Vičić
- Department of Dermatovenereology, Medical Faculty, University of Rijeka, Clinical Hospital Center Rijeka, Krešimirova 42, 51000 Rijeka, Croatia
| | - Nika Hlača
- Department of Dermatovenereology, Medical Faculty, University of Rijeka, Clinical Hospital Center Rijeka, Krešimirova 42, 51000 Rijeka, Croatia
| | - Marija Kaštelan
- Department of Dermatovenereology, Medical Faculty, University of Rijeka, Clinical Hospital Center Rijeka, Krešimirova 42, 51000 Rijeka, Croatia
| | - Ines Brajac
- Department of Dermatovenereology, Medical Faculty, University of Rijeka, Clinical Hospital Center Rijeka, Krešimirova 42, 51000 Rijeka, Croatia
| | - Vlatka Sotošek
- Department of Anesthesiology, Reanimation and Intensive Care, Medical Faculty, University of Rijeka, Clinical Hospital Center Rijeka, Tome Strižića 3, 51000 Rijeka, Croatia
| | - Larisa Prpić Massari
- Department of Dermatovenereology, Medical Faculty, University of Rijeka, Clinical Hospital Center Rijeka, Krešimirova 42, 51000 Rijeka, Croatia
- Correspondence:
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8
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HLA-disease association and pleiotropy landscape in over 235,000 Finns. Hum Immunol 2022; 83:391-398. [DOI: 10.1016/j.humimm.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/31/2022] [Accepted: 02/09/2022] [Indexed: 01/10/2023]
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9
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Kim C, Kim YJ, Choi W, Jang HM, Hwang MY, Jung S, Lim H, Hong SB, Yoon K, Kim BJ, Park HY, Han B. Phenome-wide association study of the major histocompatibility complex region in the Korean population identifies novel association signals. Hum Mol Genet 2022; 31:2655-2667. [PMID: 35043955 DOI: 10.1093/hmg/ddac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Human leukocyte antigen (HLA) gene variants in the major histocompatibility complex (MHC) region are associated with numerous complex human diseases and quantitative traits. Previous phenome-wide association studies (PheWAS) for this region demonstrated that HLA association patterns to the phenome have both population-specific and population-shared components. We performed MHC PheWAS in the Korean population by analyzing associations between phenotypes and genetic variants in the MHC region using the Korea Biobank Array project data samples from the Korean Genome and Epidemiology Study (KoGES) cohorts. Using this single-population dataset, we curated and analyzed 82 phenotypes for 125 673 Korean individuals after imputing HLA using CookHLA, a recently developed imputation framework. More than one-third of these phenotypes showed significant associations, confirming 56 known associations and discovering 13 novel association signals that were not reported previously. In addition, we analyzed heritability explained by the variants in the MHC region and genetic correlations among phenotypes based on the MHC variants.
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Affiliation(s)
- Chanwoo Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Wanson Choi
- Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hye-Mi Jang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Sunwoo Jung
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyunjoon Lim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Bin Hong
- Department of Neurology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Kyungheon Yoon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Hyun-Young Park
- Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159, Republic of Korea
| | - Buhm Han
- Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
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10
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Kerley CI, Chaganti S, Nguyen TQ, Bermudez C, Cutting LE, Beason-Held LL, Lasko T, Landman BA. pyPheWAS: A Phenome-Disease Association Tool for Electronic Medical Record Analysis. Neuroinformatics 2022; 20:483-505. [PMID: 34981404 PMCID: PMC9250547 DOI: 10.1007/s12021-021-09553-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
Along with the increasing availability of electronic medical record (EMR) data, phenome-wide association studies (PheWAS) and phenome-disease association studies (PheDAS) have become a prominent, first-line method of analysis for uncovering the secrets of EMR. Despite this recent growth, there is a lack of approachable software tools for conducting these analyses on large-scale EMR cohorts. In this article, we introduce pyPheWAS, an open-source python package for conducting PheDAS and related analyses. This toolkit includes 1) data preparation, such as cohort censoring and age-matching; 2) traditional PheDAS analysis of ICD-9 and ICD-10 billing codes; 3) PheDAS analysis applied to a novel EMR phenotype mapping: current procedural terminology (CPT) codes; and 4) novelty analysis of significant disease-phenotype associations found through PheDAS. The pyPheWAS toolkit is approachable and comprehensive, encapsulating data prep through result visualization all within a simple command-line interface. The toolkit is designed for the ever-growing scale of available EMR data, with the ability to analyze cohorts of 100,000 + patients in less than 2 h. Through a case study of Down Syndrome and other intellectual developmental disabilities, we demonstrate the ability of pyPheWAS to discover both known and potentially novel disease-phenotype associations across different experiment designs and disease groups. The software and user documentation are available in open source at https://github.com/MASILab/pyPheWAS .
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Affiliation(s)
- Cailey I Kerley
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Shikha Chaganti
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Tin Q Nguyen
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Special Education, Peabody College of Education and Human Development, Nashville, TN, USA
| | - Camilo Bermudez
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Laurie E Cutting
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Special Education, Peabody College of Education and Human Development, Nashville, TN, USA.,Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
| | - Lori L Beason-Held
- Laboratory of Behavioral Neuroscience, National Institute On Aging, NIH, Baltimore, MD, USA
| | - Thomas Lasko
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bennett A Landman
- Department of Electrical Engineering, Vanderbilt University, Nashville, TN, USA.,Department of Computer Science, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.,Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
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11
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Boch K, Langan EA, Kridin K, Zillikens D, Ludwig RJ, Bieber K. Lichen Planus. Front Med (Lausanne) 2021; 8:737813. [PMID: 34790675 PMCID: PMC8591129 DOI: 10.3389/fmed.2021.737813] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
Lichen planus (LP) is a T cell-mediated disease affecting the stratified squamous epithelia of the skin and/or mucus membrane. Histologically, the disease is characterized by a lichenoid inflammatory infiltrate and vacuolar degeneration of the basal layer of the epidermis. LP has three major subtypes: Cutaneous, mucosal and appendageal LP. Rarely, it may affect the nails in the absence of skin and/or mucosal changes. LP may also be induced by several drugs, typically anti-hypertensive medication or be associated with infections, particularly viral hepatitis. The diagnosis is based on the clinical presentation and characteristic histological findings. Although the disease is often self-limiting, the intractable pruritus and painful mucosal erosions result in significant morbidity. The current first-line treatment are topical and/or systemic corticosteroids. In addition, immunosuppressants may be used as corticosteroid-sparing agents. These, however are often not sufficient to control disease. Janus kinase inhibitors and biologics (anti-IL-12/23, anti-IL17) have emerged as novel future treatment options. Thus, one may expect a dramatic change of the treatment landscape of LP in the near future.
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Affiliation(s)
- Katharina Boch
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Ewan A Langan
- Department of Dermatology, University of Lübeck, Lübeck, Germany.,Dermatological Sciences, University of Manchester, Manchester, United Kingdom
| | - Khalaf Kridin
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Ralf J Ludwig
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
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12
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Johansson T, Koskela S, Yohannes DA, Partanen J, Saavalainen P. Targeted RNA-Based Oxford Nanopore Sequencing for Typing 12 Classical HLA Genes. Front Genet 2021; 12:635601. [PMID: 33763116 PMCID: PMC7982845 DOI: 10.3389/fgene.2021.635601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/11/2021] [Indexed: 01/29/2023] Open
Abstract
Identification of human leukocyte antigen (HLA) alleles from next-generation sequencing (NGS) data is challenging because of the high polymorphism and mosaic nature of HLA genes. Owing to the complex nature of HLA genes and consequent challenges in allele assignment, Oxford Nanopore Technologies' (ONT) single-molecule sequencing technology has been of great interest due to its fitness for sequencing long reads. In addition to the read length, ONT's advantages are its portability and possibility for a rapid real-time sequencing, which enables a simultaneous data analysis. Here, we describe a targeted RNA-based method for HLA typing using ONT sequencing and SeqNext-HLA SeqPilot software (JSI Medical Systems GmbH). Twelve classical HLA genes were enriched from cDNA of 50 individuals, barcoded, pooled, and sequenced in 10 MinION R9.4 SpotON flow cell runs producing over 30,000 reads per sample. Using barcoded 2D reads, SeqPilot assigned HLA alleles to two-field typing resolution or higher with the average read depth of 1750x. Sequence analysis resulted in 99-100% accuracy at low-resolution level (one-field) and in 74-100% accuracy at high-resolution level (two-field) with the expected alleles. There are still some limitations with ONT RNA sequencing, such as noisy reads, homopolymer errors, and the lack of robust algorithms, which interfere with confident allele assignment. These issues need to be inspected carefully in the future to improve the allele call rates. Nevertheless, here we show that sequencing of multiplexed cDNA amplicon libraries on ONT MinION can produce accurate high-resolution typing results of 12 classical HLA loci. For HLA research, ONT RNA sequencing is a promising method due to its capability to sequence full-length HLA transcripts. In addition to HLA genotyping, the technique could also be applied for simultaneous expression analysis.
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Affiliation(s)
- Tiira Johansson
- Translational Immunology Research Program and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Finnish Red Cross Blood Service, Helsinki, Finland
| | - Satu Koskela
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - Dawit A Yohannes
- Translational Immunology Research Program and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | | | - Päivi Saavalainen
- Translational Immunology Research Program and Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Finnish Red Cross Blood Service, Helsinki, Finland
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13
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Rathi S, Joshi A, Manchanda Y. Childhood lichen planus. INDIAN JOURNAL OF PAEDIATRIC DERMATOLOGY 2021. [DOI: 10.4103/ijpd.ijpd_132_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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14
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Sinnott JA, Cai F, Yu S, Hejblum BP, Hong C, Kohane IS, Liao KP. PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies. J Am Med Inform Assoc 2019; 25:1359-1365. [PMID: 29788308 DOI: 10.1093/jamia/ocy056] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/23/2018] [Indexed: 12/24/2022] Open
Abstract
Objective Standard approaches for large scale phenotypic screens using electronic health record (EHR) data apply thresholds, such as ≥2 diagnosis codes, to define subjects as having a phenotype. However, the variation in the accuracy of diagnosis codes can impair the power of such screens. Our objective was to develop and evaluate an approach which converts diagnosis codes into a probability of a phenotype (PheProb). We hypothesized that this alternate approach for defining phenotypes would improve power for genetic association studies. Methods The PheProb approach employs unsupervised clustering to separate patients into 2 groups based on diagnosis codes. Subjects are assigned a probability of having the phenotype based on the number of diagnosis codes. This approach was developed using simulated EHR data and tested in a real world EHR cohort. In the latter, we tested the association between low density lipoprotein cholesterol (LDL-C) genetic risk alleles known for association with hyperlipidemia and hyperlipidemia codes (ICD-9 272.x). PheProb and thresholding approaches were compared. Results Among n = 1462 subjects in the real world EHR cohort, the threshold-based p-values for association between the genetic risk score (GRS) and hyperlipidemia were 0.126 (≥1 code), 0.123 (≥2 codes), and 0.142 (≥3 codes). The PheProb approach produced the expected significant association between the GRS and hyperlipidemia: p = .001. Conclusions PheProb improves statistical power for association studies relative to standard thresholding approaches by leveraging information about the phenotype in the billing code counts. The PheProb approach has direct applications where efficient approaches are required, such as in Phenome-Wide Association Studies.
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Affiliation(s)
| | - Fiona Cai
- Stuyvesant High School, New York City, NY, USA
| | - Sheng Yu
- Center for Statistical Science, Tsinghua University, Beijing, China.,Department of Industrial Engineering, Tsinghua University, Beijing, China
| | - Boris P Hejblum
- Univ. Bordeaux, ISPED, Inserm BPH 1219, Inria SISTM, Bordeaux, France
| | - Chuan Hong
- Department of Biostatistics, Harvard University, Boston, MA, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Children's Hospital Boston, Boston, MA, USA
| | - Katherine P Liao
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
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15
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Wu P, Gifford A, Meng X, Li X, Campbell H, Varley T, Zhao J, Carroll R, Bastarache L, Denny JC, Theodoratou E, Wei WQ. Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation. JMIR Med Inform 2019; 7:e14325. [PMID: 31553307 PMCID: PMC6911227 DOI: 10.2196/14325] [Citation(s) in RCA: 256] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/03/2019] [Accepted: 09/24/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The phecode system was built upon the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) for phenome-wide association studies (PheWAS) using the electronic health record (EHR). OBJECTIVE The goal of this paper was to develop and perform an initial evaluation of maps from the International Classification of Diseases, 10th Revision (ICD-10) and the International Classification of Diseases, 10th Revision, Clinical Modification (ICD-10-CM) codes to phecodes. METHODS We mapped ICD-10 and ICD-10-CM codes to phecodes using a number of methods and resources, such as concept relationships and explicit mappings from the Centers for Medicare & Medicaid Services, the Unified Medical Language System, Observational Health Data Sciences and Informatics, Systematized Nomenclature of Medicine-Clinical Terms, and the National Library of Medicine. We assessed the coverage of the maps in two databases: Vanderbilt University Medical Center (VUMC) using ICD-10-CM and the UK Biobank (UKBB) using ICD-10. We assessed the fidelity of the ICD-10-CM map in comparison to the gold-standard ICD-9-CM phecode map by investigating phenotype reproducibility and conducting a PheWAS. RESULTS We mapped >75% of ICD-10 and ICD-10-CM codes to phecodes. Of the unique codes observed in the UKBB (ICD-10) and VUMC (ICD-10-CM) cohorts, >90% were mapped to phecodes. We observed 70-75% reproducibility for chronic diseases and <10% for an acute disease for phenotypes sourced from the ICD-10-CM phecode map. Using the ICD-9-CM and ICD-10-CM maps, we conducted a PheWAS with a Lipoprotein(a) genetic variant, rs10455872, which replicated two known genotype-phenotype associations with similar effect sizes: coronary atherosclerosis (ICD-9-CM: P<.001; odds ratio (OR) 1.60 [95% CI 1.43-1.80] vs ICD-10-CM: P<.001; OR 1.60 [95% CI 1.43-1.80]) and chronic ischemic heart disease (ICD-9-CM: P<.001; OR 1.56 [95% CI 1.35-1.79] vs ICD-10-CM: P<.001; OR 1.47 [95% CI 1.22-1.77]). CONCLUSIONS This study introduces the beta versions of ICD-10 and ICD-10-CM to phecode maps that enable researchers to leverage accumulated ICD-10 and ICD-10-CM data for PheWAS in the EHR.
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Affiliation(s)
- Patrick Wu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
- Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Aliya Gifford
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Xiangrui Meng
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Xue Li
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Varley
- Public Health and Intelligence Strategic Business Unit, National Services Scotland, Edinburgh, United Kingdom
| | - Juan Zhao
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Evropi Theodoratou
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh, United Kingdom
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
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16
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Abstract
RATIONALE Cystic fibrosis, like primary ciliary dyskinesia, is an autosomal recessive disorder characterized by abnormal mucociliary clearance and obstructive lung disease. We hypothesized that genes underlying the development or function of cilia may modify lung disease severity in persons with cystic fibrosis. OBJECTIVES To test this hypothesis, we compared variants in 93 candidate genes in both upper and lower tertiles of lung function in a large cohort of children and adults with cystic fibrosis with those of a population control dataset. METHODS Variants within candidate genes were tested for association using the SKAT-O test, comparing cystic fibrosis cases defined by poor (n = 127) or preserved (n = 127) lung function with population controls (n = 3,269 or 3,148, respectively). Associated variants were then tested for association with related phenotypes in independent datasets. RESULTS Variants in DNAH14 and DNAAF3 were associated with poor lung function in cystic fibrosis, whereas variants in DNAH14 and DNAH6 were associated with preserved lung function in cystic fibrosis. Associations between DNAH14 and lung function were replicated in disease-related phenotypes characterized by obstructive lung disease in adults. CONCLUSIONS Genetic variants within DNAH6, DNAH14, and DNAAF3 are associated with variation in lung function among persons with cystic fibrosis.
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17
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Tziotzios C, Lee JYW, Brier T, Saito R, Hsu CK, Bhargava K, Stefanato CM, Fenton DA, McGrath JA. Lichen planus and lichenoid dermatoses: Clinical overview and molecular basis. J Am Acad Dermatol 2019; 79:789-804. [PMID: 30318136 DOI: 10.1016/j.jaad.2018.02.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deriving from the Greek word λειχήν for "tree moss" and the Latin word planus for "planar," lichen planus is a relatively uncommon and heterogeneous cutaneous disorder that typically develops in middle-aged adults. Despite the significant clinical burden associated with the disorder, little well-conducted molecular research has been undertaken, possibly because of heterogeneity impeding consistent and confident phenotyping. The multiple variants of lichenoid disease bear overlapping clinical and pathologic features despite manifesting as distinct clinical disorders. The first article in this 2-part continuing medical education series provides a comprehensive overview of the clinical and pathologic characteristics of cutaneous lichenoid dermatoses and links these manifestations to recent advances in our understanding of the underlying pathobiology of such diseases.
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Affiliation(s)
- Christos Tziotzios
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, United Kingdom.
| | - John Y W Lee
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, United Kingdom
| | - Timothy Brier
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, United Kingdom
| | - Ryo Saito
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, United Kingdom
| | - Chao-Kai Hsu
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, United Kingdom
| | - Kapil Bhargava
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, United Kingdom
| | - Catherine M Stefanato
- Department of Dermatopathology, St. John's Institute of Dermatology, St. Thomas' Hospital, London, United Kingdom
| | - David A Fenton
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, United Kingdom
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London, Guy's Hospital, London, United Kingdom
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18
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Genomic and Phenomic Research in the 21st Century. Trends Genet 2018; 35:29-41. [PMID: 30342790 DOI: 10.1016/j.tig.2018.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023]
Abstract
The field of human genomics has changed dramatically over time. Initial genomic studies were predominantly restricted to rare disorders in small families. Over the past decade, researchers changed course from family-based studies and instead focused on common diseases and traits in populations of unrelated individuals. With further advancements in biobanking, computer science, electronic health record (EHR) data, and more affordable high-throughput genomics, we are experiencing a new paradigm in human genomic research. Rapidly changing technologies and resources now make it possible to study thousands of diseases simultaneously at the genomic level. This review will focus on these advancements as scientists begin to incorporate phenome-wide strategies in human genomic research to understand the etiology of human diseases and develop new drugs to treat them.
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19
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Schmidt T, Solimani F, Pollmann R, Stein R, Schmidt A, Stulberg I, Kühn K, Eming R, Eubel V, Kind P, Arweiler N, Sitaru C, Hertl M. T H1/T H17 cell recognition of desmoglein 3 and bullous pemphigoid antigen 180 in patients with lichen planus. J Allergy Clin Immunol 2018; 142:669-672.e7. [PMID: 29626572 DOI: 10.1016/j.jaci.2018.02.044] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/02/2018] [Accepted: 02/21/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Thomas Schmidt
- Department of Dermatology and Allergology, Philipps-University, Marburg, Germany
| | - Farzan Solimani
- Department of Dermatology and Allergology, Philipps-University, Marburg, Germany
| | - Robert Pollmann
- Department of Dermatology and Allergology, Philipps-University, Marburg, Germany
| | - Ronja Stein
- Department of Dermatology and Allergology, Philipps-University, Marburg, Germany
| | - Ansgar Schmidt
- Department of Pathology, Philipps-University, Marburg, Germany
| | - Inna Stulberg
- Department of Dermatology and Allergology, Philipps-University, Marburg, Germany
| | - Katja Kühn
- Department of Dermatology and Allergology, Philipps-University, Marburg, Germany
| | - Rüdiger Eming
- Department of Dermatology and Allergology, Philipps-University, Marburg, Germany
| | - Verena Eubel
- Department of Dermatology and Allergology, Philipps-University, Marburg, Germany
| | - Peter Kind
- Hautzentrum Offenbach, Offenbach, Germany
| | - Nicole Arweiler
- Department of Periodontology, Philipps-University, Marburg, Germany
| | - Cassian Sitaru
- Department of Dermatology, Albert-Ludwigs-University, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, Freiburg, Germany
| | - Michael Hertl
- Department of Dermatology and Allergology, Philipps-University, Marburg, Germany.
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20
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Dubey R, Fischer G. Vulvo-vaginal lichen planus: A focussed review for the clinician. Australas J Dermatol 2018; 60:7-11. [PMID: 29961956 DOI: 10.1111/ajd.12875] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 05/22/2018] [Indexed: 01/04/2023]
Abstract
Vulvo-vaginal lichen planus is a condition which imposes a significant burden of symptoms and sequale. There is a paucity of knowledge and evidenced-based management with significant diagnostic delay prior to appropriate treatment being common. There remains great variability in clinician practice in the context of limited knowledge. This clinical review presents current evidence on the clinicopathological features, practical assessment and management options. Learning points include characterization of this chronic, burdensome clinical entity that has no standardized diagnostic or management protocols. We provide practical clinical conclusions based on current knowledge and identify areas for future research to improve patient outcomes.
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Affiliation(s)
- Ritika Dubey
- Northern Sydney Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Gayle Fischer
- Northern Sydney Clinical School, University of Sydney, Sydney, New South Wales, Australia.,Royal North Shore Hospital, Sydney, New South Wales, Australia
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21
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Hackinger S, Zeggini E. Statistical methods to detect pleiotropy in human complex traits. Open Biol 2018; 7:rsob.170125. [PMID: 29093210 PMCID: PMC5717338 DOI: 10.1098/rsob.170125] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/29/2017] [Indexed: 12/13/2022] Open
Abstract
In recent years pleiotropy, the phenomenon of one genetic locus influencing several traits, has become a widely researched field in human genetics. With the increasing availability of genome-wide association study summary statistics, as well as the establishment of deeply phenotyped sample collections, it is now possible to systematically assess the genetic overlap between multiple traits and diseases. In addition to increasing power to detect associated variants, multi-trait methods can also aid our understanding of how different disorders are aetiologically linked by highlighting relevant biological pathways. A plethora of available tools to perform such analyses exists, each with their own advantages and limitations. In this review, we outline some of the currently available methods to conduct multi-trait analyses. First, we briefly introduce the concept of pleiotropy and outline the current landscape of pleiotropy research in human genetics; second, we describe analytical considerations and analysis methods; finally, we discuss future directions for the field.
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22
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Verma A, Lucas A, Verma SS, Zhang Y, Josyula N, Khan A, Hartzel DN, Lavage DR, Leader J, Ritchie MD, Pendergrass SA. PheWAS and Beyond: The Landscape of Associations with Medical Diagnoses and Clinical Measures across 38,662 Individuals from Geisinger. Am J Hum Genet 2018; 102:592-608. [PMID: 29606303 PMCID: PMC5985339 DOI: 10.1016/j.ajhg.2018.02.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/20/2018] [Indexed: 01/23/2023] Open
Abstract
Most phenome-wide association studies (PheWASs) to date have used a small to moderate number of SNPs for association with phenotypic data. We performed a large-scale single-cohort PheWAS, using electronic health record (EHR)-derived case-control status for 541 diagnoses using International Classification of Disease version 9 (ICD-9) codes and 25 median clinical laboratory measures. We calculated associations between these diagnoses and traits with ∼630,000 common frequency SNPs with minor allele frequency > 0.01 for 38,662 individuals. In this landscape PheWAS, we explored results within diseases and traits, comparing results to those previously reported in genome-wide association studies (GWASs), as well as previously published PheWASs. We further leveraged the context of functional impact from protein-coding to regulatory regions, providing a deeper interpretation of these associations. The comprehensive nature of this PheWAS allows for novel hypothesis generation, the identification of phenotypes for further study for future phenotypic algorithm development, and identification of cross-phenotype associations.
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Affiliation(s)
- Anurag Verma
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Anastasia Lucas
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shefali S Verma
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yu Zhang
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Navya Josyula
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Anqa Khan
- Mount Holyoke College, South Hadley, MA 01075, USA
| | - Dustin N Hartzel
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Daniel R Lavage
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Joseph Leader
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah A Pendergrass
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA 17822, USA.
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23
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Fahy CM, Torgerson RR, Davis MD. Lichen planus affecting the female genitalia: A retrospective review of patients at Mayo Clinic. J Am Acad Dermatol 2017; 77:1053-1059. [DOI: 10.1016/j.jaad.2017.07.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022]
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24
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Abstract
PURPOSE OF REVIEW Over many decades, researchers have been designing studies to investigate the relationship between genotypes and phenotypes to gain an understanding about the effect of genetics on disease. Recently, a high-throughput approach called phenome-wide associations studies (PheWAS) have been extensively used to identify associations between genetic variants and many diseases and traits simultaneously. In this review, we describe the value of PheWAS along with methodological issues and challenges in interpretation for current applications of PheWAS. RECENT FINDINGS PheWAS have uncovered a paradigm to identify new associations for genetic loci across many diseases. The application of PheWAS have been effective with phenotype data from electronic health records, epidemiological studies, and clinical trials data. SUMMARY The key strength of a PheWAS is to identify the association of one or more genetic variants with multiple phenotypes, which can showcase interconnections among the phenotypes due to shared genetic associations. While the PheWAS approach appears promising, there are a number of challenges that need to be addressed to provide additional robustness to PheWAS findings.
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Affiliation(s)
- Anurag Verma
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Marylyn D Ritchie
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA
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25
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Karnes JH, Bastarache L, Shaffer CM, Gaudieri S, Xu Y, Glazer AM, Mosley JD, Zhao S, Raychaudhuri S, Mallal S, Ye Z, Mayer JG, Brilliant MH, Hebbring SJ, Roden DM, Phillips EJ, Denny JC. Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants. Sci Transl Med 2017; 9:eaai8708. [PMID: 28490672 PMCID: PMC5563969 DOI: 10.1126/scitranslmed.aai8708] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/27/2017] [Indexed: 12/22/2022]
Abstract
Although many phenotypes have been associated with variants in human leukocyte antigen (HLA) genes, the full phenotypic impact of HLA variants across all diseases is unknown. We imputed HLA genomic variation from two populations of 28,839 and 8431 European ancestry individuals and tested association of HLA variation with 1368 phenotypes. A total of 104 four-digit and 92 two-digit HLA allele phenotype associations were significant in both discovery and replication cohorts, the strongest being HLA-DQB1*03:02 and type 1 diabetes. Four previously unidentified associations were identified across the spectrum of disease with two- and four-digit HLA alleles and 10 with nonsynonymous variants. Some conditions associated with multiple HLA variants and stronger associations with more severe disease manifestations were identified. A comprehensive, publicly available catalog of clinical phenotypes associated with HLA variation is provided. Examining HLA variant disease associations in this large data set allows comprehensive definition of disease associations to drive further mechanistic insights.
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Affiliation(s)
- Jason H Karnes
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, AZ 85721, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Christian M Shaffer
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Silvana Gaudieri
- School of Anatomy, Physiology and Human Biology, University of Western Australia, Nedlands, Western Australia, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrew M Glazer
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jonathan D Mosley
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Shilin Zhao
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA
- Institute of Inflammation and Repair, University of Manchester, Manchester, UK
- Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Simon Mallal
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Zhan Ye
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - John G Mayer
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - Scott J Hebbring
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Elizabeth J Phillips
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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