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Alcántara-Ortigoza MA, Rodríguez-Lozano AL, Estandía-Ortega B, González-del Angel A, Díaz-García L, Rivas-Larrauri FE, Nájera-Velázquez RG. Does the esv3587290 Copy Number Variation in the VANGL1 Gene Differ as a Genetic Factor for Developing Nephritis in Mexican Childhood-Onset Systemic Lupus Erythematosus Patients? CHILDREN (BASEL, SWITZERLAND) 2024; 11:712. [PMID: 38929291 PMCID: PMC11201895 DOI: 10.3390/children11060712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
A ~3-kb deletion-type DNA copy number variation (CNV, esv3587290) located at intron 7 of the VANGL1 gene (1p13.1, MIM*610132) has been proposed as a genetic factor in lupus nephritis (LN) development in adult systemic lupus erythematosus (SLE) patients across European-descent populations, but its replication in other ethnicities has been inconsistent and its association with LN in childhood-onset SLE (cSLE) remains unknown. Here, we performed an exploratory association study in a sample of 66 unrelated cSLE Mexican patients (11 males, 55 females; ages 7.8 to 18.6 years). Two stratified groups were compared: cSLE patients with (N = 39) or without (N = 27) LN, as diagnosed by renal biopsy (N = 17), proteinuria (N = 33), urinary protein-creatinine ratio > 0.2 (N = 34), and erythrocyturia and/or granular casts in urinary sediment (N = 16). For esv3587290 CNV genotyping, we performed an end-point PCR assay with breakpoint confirmation using Sanger sequencing. We also determined the allelic frequencies of the esv3587290 CNV in 181 deidentified ethnically matched individuals (reference group). The obtained genotypes were tested for Hardy-Weinberg equilibrium using the χ2 test. Associations between LN and esv3587290 CNV were tested by calculating the odds ratio (OR) and using Pearson's χ2 tests, with a 95% confidence interval and p ≤ 0.05. The esv3587290 CNV allele (OR 0.108, 95% CI 0.034-0.33, p = 0.0003) and the heterozygous genotype (OR 0.04, 95% CI 0.119-0.9811, p = 0.002) showed a significant protective effect against LN development. Finally, we characterized the precise breakpoint of the esv3587290 CNV to be NG_016548.1(NM_138959.3):c.1314+1339_1315-897del in our population. This report supports the notion that a broad genetic heterogeneity underlies the susceptibility for developing LN.
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Affiliation(s)
- Miguel Angel Alcántara-Ortigoza
- Laboratorio de Biología Molecular, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; (B.E.-O.); (A.G.-d.A.)
| | - Ana Luisa Rodríguez-Lozano
- Servicio de Inmunología, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; (A.L.R.-L.); (F.E.R.-L.); (R.G.N.-V.)
| | - Bernardette Estandía-Ortega
- Laboratorio de Biología Molecular, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; (B.E.-O.); (A.G.-d.A.)
| | - Ariadna González-del Angel
- Laboratorio de Biología Molecular, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; (B.E.-O.); (A.G.-d.A.)
| | - Luisa Díaz-García
- Departamento de Metodología de la Investigación, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico;
| | | | - Ruth Guadalupe Nájera-Velázquez
- Servicio de Inmunología, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; (A.L.R.-L.); (F.E.R.-L.); (R.G.N.-V.)
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2
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Smyk W, Adrych K, Krawczyk M. Artificial replication cohort: Leveraging AI-fabricated data for genetic studies. Liver Int 2024; 44:1286-1289. [PMID: 38426626 DOI: 10.1111/liv.15890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Recent advancements in artificial intelligence (AI) present both opportunities and challenges within the scientific community. This study explores the capability of AI to replicate findings from genetic research, focusing on findings from prior work. Using an AI model without exposing any raw data, we created a dataset that closely mirrors the results of our original study, illustrating the ease of fabricating datasets with authenticity. This approach highlights the risks associated with AI misuse in scientific research. The study emphasizes the critical importance of maintaining the integrity of scientific inquiry in an era increasingly influenced by advanced AI technologies.
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Affiliation(s)
- Wiktor Smyk
- Department of Gastroenterology and Hepatology, Medical University of Gdansk, Gdansk, Poland
| | - Krystian Adrych
- Department of Gastroenterology and Hepatology, Medical University of Gdansk, Gdansk, Poland
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany
- Laboratory of Metabolic Liver Diseases, Center for Preclinical Research, Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
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3
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Chatziparasidis G, Chatziparasidi MR, Kantar A, Bush A. Time-dependent gene-environment interactions are essential drivers of asthma initiation and persistence. Pediatr Pulmonol 2024; 59:1143-1152. [PMID: 38380964 DOI: 10.1002/ppul.26935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/27/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
Asthma is a clinical syndrome caused by heterogeneous underlying mechanisms with some of them having a strong genetic component. It is known that up to 82% of atopic asthma has a genetic background with the rest being influenced by environmental factors that cause epigenetic modification(s) of gene expression. The interaction between the gene(s) and the environment has long been regarded as the most likely explanation of asthma initiation and persistence. Lately, much attention has been given to the time frame the interaction occurs since the host response (immune or biological) to environmental triggers, differs at different developmental ages. The integration of the time variant into asthma pathogenesis is appearing to be equally important as the gene(s)-environment interaction. It seems that, all three factors should be present to trigger the asthma initiation and persistence cascade. Herein, we introduce the importance of the time variant in asthma pathogenesis and emphasize the long-term clinical significance of the time-dependent gene-environment interactions in childhood.
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Affiliation(s)
- Grigorios Chatziparasidis
- Faculty of Nursing, University of Thessaly, Volos, Greece
- School of Physical Education, Sport Science & Dietetics, University of Thessaly, Volos, Greece
| | | | - Ahmad Kantar
- Pediatric Asthma and Cough Centre, Instituti Ospedalieri Bergamashi, Bergamo, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Andrew Bush
- Departments of Paediatrics and Paediatric Respiratory Medicine, Royal Brompton Harefield NHS Foundation Trust and Imperial College, London, UK
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Zhang S, Jiang Z, Zeng P. Incorporating genetic similarity of auxiliary samples into eGene identification under the transfer learning framework. J Transl Med 2024; 22:258. [PMID: 38461317 PMCID: PMC10924384 DOI: 10.1186/s12967-024-05053-6] [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: 01/27/2023] [Accepted: 03/01/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND The term eGene has been applied to define a gene whose expression level is affected by at least one independent expression quantitative trait locus (eQTL). It is both theoretically and empirically important to identify eQTLs and eGenes in genomic studies. However, standard eGene detection methods generally focus on individual cis-variants and cannot efficiently leverage useful knowledge acquired from auxiliary samples into target studies. METHODS We propose a multilocus-based eGene identification method called TLegene by integrating shared genetic similarity information available from auxiliary studies under the statistical framework of transfer learning. We apply TLegene to eGene identification in ten TCGA cancers which have an explicit relevant tissue in the GTEx project, and learn genetic effect of variant in TCGA from GTEx. We also adopt TLegene to the Geuvadis project to evaluate its usefulness in non-cancer studies. RESULTS We observed substantial genetic effect correlation of cis-variants between TCGA and GTEx for a larger number of genes. Furthermore, consistent with the results of our simulations, we found that TLegene was more powerful than existing methods and thus identified 169 distinct candidate eGenes, which was much larger than the approach that did not consider knowledge transfer across target and auxiliary studies. Previous studies and functional enrichment analyses provided empirical evidence supporting the associations of discovered eGenes, and it also showed evidence of allelic heterogeneity of gene expression. Furthermore, TLegene identified more eGenes in Geuvadis and revealed that these eGenes were mainly enriched in cells EBV transformed lymphocytes tissue. CONCLUSION Overall, TLegene represents a flexible and powerful statistical method for eGene identification through transfer learning of genetic similarity shared across auxiliary and target studies.
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Affiliation(s)
- Shuo Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Zhou Jiang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Xuzhou Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Jiangsu Engineering Research Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
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Pugsley K, Namipashaki A, Bellgrove MA, Hawi Z. Evaluating the regulatory function of non-coding autism-associated single nucleotide polymorphisms on gene expression in human brain tissue. Autism Res 2024; 17:467-481. [PMID: 38323502 DOI: 10.1002/aur.3101] [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: 09/11/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Common variants account for most of the estimated heritability associated with autism spectrum disorder (autism). Although several replicable single nucleotide polymorphisms (SNPs) for the condition have been detected using genome-wide association study (GWAS) methodologies, their pathophysiological relevance remains elusive. Examining this is complicated, however, as all detected loci are situated within non-coding regions of the genome. It is therefore likely that they possess roles of regulatory function as opposed to directly affecting gene coding sequences. To bridge the gap between SNP discovery and mechanistic insight, we applied a comprehensive bioinformatic pipeline to functionally annotate autism-associated polymorphisms and their non-coding linkage disequilibrium (i.e., non-randomly associated) partners. We identified 82 DNA variants of probable regulatory function that may contribute to autism pathogenesis. To validate these predictions, we measured the impact of 11 high-confidence candidates and their GWAS linkage disequilibrium partners on gene expression in human brain tissue from Autistic and non-Autistic donors. Although a small number of the surveyed variants exhibited measurable influence on gene expression as determined via quantitative polymerase chain reaction, these did not survive correction for multiple comparisons. Additionally, no significant genotype-by-diagnosis effects were observed for any of the SNP-gene associations. We contend that this may reflect an inability to effectively capture the modest, neurodevelopmental-specific impact of individual variants on biological dysregulation in available post-mortem tissue samples, as well as limitations in the existing autism GWAS data.
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Affiliation(s)
- Kealan Pugsley
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Atefeh Namipashaki
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Mark A Bellgrove
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Ziarih Hawi
- Turner Institute for Brain and Mental Health and School of Psychological Sciences, Monash University, Melbourne, Victoria, Australia
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6
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Kang HY, Choe EK. Clinical Strategies in Gene Screening Counseling for the Healthy General Population. Korean J Fam Med 2024; 45:61-68. [PMID: 38528647 DOI: 10.4082/kjfm.23.0254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 03/27/2024] Open
Abstract
The burgeoning interest in precision medicine has propelled an increase in the use of genome tests for screening purposes within the healthy population. Gene screening tests aim to pre-emptively identify those individuals who may be genetically predisposed to certain diseases. However, as genetic screening becomes more commonplace, it is essential to acknowledge the unique challenges it poses. A prevalent issue in this regard is the occurrence of falsepositive results, which can lead to unnecessary additional tests or treatments, and psychological distress. Additionally, the interpretation of genomic variants is based on current research evidence, and can accordingly change as new research findings emerge, potentially altering the clinical significance of these variants. Conversely, a further prominent concern regards false assurances in genetic testing, as genetic tests can yield false-negative results, potentially posing a significant clinical risk. Moreover, the results obtained for the same disease can vary among different genetic testing services, due to differences in the types of variants assessed, the scope of tests, analytical methods, and the algorithms used for predicting diseases. Consequently, whereas genetic testing holds significant promise for the future of medicine, it poses unique challenges. If conducted without a full understanding of its implications, genetic testing may fail to achieve its purpose potentially hindering effective health management. Therefore, to ensure a comprehensive understanding of the implications of genetic testing within the general population, sufficient discussion and careful consideration should be given to counseling based on gene test results.
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Affiliation(s)
- Hae Yeon Kang
- Department of Internal Medicine, Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
| | - Eun Kyung Choe
- Department of Surgery, Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, Korea
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7
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Bojarczuk A, Egorova ES, Dzitkowska-Zabielska M, Ahmetov II. Genetics of Exercise and Diet-Induced Fat Loss Efficiency: A Systematic Review. J Sports Sci Med 2024; 23:236-257. [PMID: 38455434 PMCID: PMC10915602 DOI: 10.52082/jssm.2024.236] [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: 01/08/2024] [Accepted: 02/21/2024] [Indexed: 03/09/2024]
Abstract
Physical exercise and dieting are well-known and effective methods for fat loss and improving cardiovascular health. However, different individuals often react differently to the same exercise regimen or dietary plan. While specific individuals may undergo substantial fat loss, others may observe only limited effects. A wide range of inter-individual variability in weight gain and changes in body composition induced by physical exercises and diets led to an investigation into the genetic factors that may contribute to the individual variations in such responses. This systematic review aimed at identifying the genetic markers associated with fat loss resulting from diet or exercise. A search of the current literature was performed using the PubMed database. Forty-seven articles met the inclusion criteria when assessing genetic markers associated with weight loss efficiency in response to different types of exercises and diets. Overall, we identified 30 genetic markers of fat-loss efficiency in response to different kinds of diets and 24 in response to exercise. Most studies (n = 46) used the candidate gene approach. We should aspire to the customized selection of exercise and dietary plans for each individual to prevent and treat obesity.
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Affiliation(s)
- Aleksandra Bojarczuk
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | - Emiliya S Egorova
- Laboratory of Genetics of Aging and Longevity, Kazan State Medical University, Kazan, Russia
| | | | - Ildus I Ahmetov
- Laboratory of Genetics of Aging and Longevity, Kazan State Medical University, Kazan, Russia
- Sports Genetics Laboratory, St Petersburg Research Institute of Physical Culture, St. Petersburg, Russia
- Center for Phygital Education and Innovative Sports Technologies, Plekhanov Russian University of Economics, Moscow, Russia
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
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8
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Jia K, Shen J. Transcriptome-wide association studies associated with Crohn's disease: challenges and perspectives. Cell Biosci 2024; 14:29. [PMID: 38403629 PMCID: PMC10895848 DOI: 10.1186/s13578-024-01204-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
Crohn's disease (CD) is regarded as a lifelong progressive disease affecting all segments of the intestinal tract and multiple organs. Based on genome-wide association studies (GWAS) and gene expression data, transcriptome-wide association studies (TWAS) can help identify susceptibility genes associated with pathogenesis and disease behavior. In this review, we overview seven reported TWASs of CD, summarize their study designs, and discuss the key methods and steps used in TWAS, which affect the prioritization of susceptibility genes. This article summarized the screening of tissue-specific susceptibility genes for CD, and discussed the reported potential pathological mechanisms of overlapping susceptibility genes related to CD in a certain tissue type. We observed that ileal lipid-related metabolism and colonic extracellular vesicles may be involved in the pathogenesis of CD by performing GO pathway enrichment analysis for susceptibility genes. We further pointed the low reproducibility of TWAS associated with CD and discussed the reasons for these issues, strategies for solving them. In the future, more TWAS are needed to be designed into large-scale, unified cohorts, unified analysis pipelines, and fully classified databases of expression trait loci.
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Affiliation(s)
- Keyu Jia
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Nephrology department, Shanghai Jiao Tong University, 1058 Huanzhen Northroad, Shanghai, 200444, China
| | - Jun Shen
- Laboratory of Medicine, Baoshan Branch, Ren Ji Hospital, School of Medicine, Nephrology department, Shanghai Jiao Tong University, 1058 Huanzhen Northroad, Shanghai, 200444, China.
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Research Center, Ren Ji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China.
- NHC Key Laboratory of Digestive Diseases, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
- Division of Gastroenterology and Hepatology, Baoshan Branch, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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9
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Yang Z, Wen J, Abdulkadir A, Cui Y, Erus G, Mamourian E, Melhem R, Srinivasan D, Govindarajan ST, Chen J, Habes M, Masters CL, Maruff P, Fripp J, Ferrucci L, Albert MS, Johnson SC, Morris JC, LaMontagne P, Marcus DS, Benzinger TLS, Wolk DA, Shen L, Bao J, Resnick SM, Shou H, Nasrallah IM, Davatzikos C. Gene-SGAN: discovering disease subtypes with imaging and genetic signatures via multi-view weakly-supervised deep clustering. Nat Commun 2024; 15:354. [PMID: 38191573 PMCID: PMC10774282 DOI: 10.1038/s41467-023-44271-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 12/06/2023] [Indexed: 01/10/2024] Open
Abstract
Disease heterogeneity has been a critical challenge for precision diagnosis and treatment, especially in neurologic and neuropsychiatric diseases. Many diseases can display multiple distinct brain phenotypes across individuals, potentially reflecting disease subtypes that can be captured using MRI and machine learning methods. However, biological interpretability and treatment relevance are limited if the derived subtypes are not associated with genetic drivers or susceptibility factors. Herein, we describe Gene-SGAN - a multi-view, weakly-supervised deep clustering method - which dissects disease heterogeneity by jointly considering phenotypic and genetic data, thereby conferring genetic correlations to the disease subtypes and associated endophenotypic signatures. We first validate the generalizability, interpretability, and robustness of Gene-SGAN in semi-synthetic experiments. We then demonstrate its application to real multi-site datasets from 28,858 individuals, deriving subtypes of Alzheimer's disease and brain endophenotypes associated with hypertension, from MRI and single nucleotide polymorphism data. Derived brain phenotypes displayed significant differences in neuroanatomical patterns, genetic determinants, biological and clinical biomarkers, indicating potentially distinct underlying neuropathologic processes, genetic drivers, and susceptibility factors. Overall, Gene-SGAN is broadly applicable to disease subtyping and endophenotype discovery, and is herein tested on disease-related, genetically-associated neuroimaging phenotypes.
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Affiliation(s)
- Zhijian Yang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Junhao Wen
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Laboratory of AI and Biomedical Science (LABS), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Ahmed Abdulkadir
- Laboratory for Research in Neuroimaging, Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Yuhan Cui
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guray Erus
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Mamourian
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Randa Melhem
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Dhivya Srinivasan
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sindhuja T Govindarajan
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiong Chen
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohamad Habes
- Biggs Alzheimer's Institute, University of Texas San Antonio Health Science Center, San Antonio, TX, USA
| | - Colin L Masters
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Paul Maruff
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Jurgen Fripp
- CSIRO Health and Biosecurity, Australian e-Health Research Centre CSIRO, Brisbane, QLD, Australia
| | - Luigi Ferrucci
- Translational Gerontology Branch, Longitudinal Studies Section, National Institute on Aging, National Institutes of Health, MedStar Harbor Hospital, 3001 S. Hanover Street, Baltimore, MD, USA
| | - Marilyn S Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sterling C Johnson
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - John C Morris
- Knight Alzheimer Disease Research Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Pamela LaMontagne
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel S Marcus
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tammie L S Benzinger
- Knight Alzheimer Disease Research Center, Washington University in St. Louis, St. Louis, MO, USA
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - David A Wolk
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingxuan Bao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, MD, USA
| | - Haochang Shou
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ilya M Nasrallah
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christos Davatzikos
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Singh S, Choudhury A, Hazelhurst S, Crowther NJ, Boua PR, Sorgho H, Agongo G, Nonterah EA, Micklesfield LK, Norris SA, Kisiangani I, Mohamed S, Gómez-Olivé FX, Tollman SM, Choma S, Brandenburg JT, Ramsay M. Genome-wide association study meta-analysis of blood pressure traits and hypertension in sub-Saharan African populations: an AWI-Gen study. Nat Commun 2023; 14:8376. [PMID: 38104120 PMCID: PMC10725455 DOI: 10.1038/s41467-023-44079-0] [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: 01/31/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
Most hypertension-related genome-wide association studies (GWASs) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure (BP)-related traits (systolic and diastolic BP, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N = 10,775), identifies two novel genome-wide significant signals (p < 5E-08): systolic BP near P2RY1 (rs77846204; intergenic variant, p = 4.95E-08) and pulse pressure near LINC01256 (rs80141533; intergenic variant, p = 1.76E-08). No genome-wide signals are detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p < 5E-06) are observed for all traits, with 29 SNPs associating with more than one trait and several replicating known associations. Polygenic risk scores (PRSs) developed from studies on different ancestries have limited transferability, with multi-ancestry PRS providing better prediction. This study provides insights into the genetics of BP variation in African populations.
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Affiliation(s)
- Surina Singh
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Nigel J Crowther
- Department of Chemical Pathology, National Health Laboratory Service, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Palwendé R Boua
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Sante, Ouagadougou, Burkina Faso
| | - Godfred Agongo
- Department of Biochemistry and Forensic Sciences, School of Chemical and Biochemical Sciences, C.K. Tedam University of Technology and Applied Sciences, Navrongo, Ghana
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- Julius Global Health, Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Lisa K Micklesfield
- SAMRC Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- SAMRC Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Health and Human Development, University of Southampton, Southampton, UK
| | | | - Shukri Mohamed
- African Population and Health Research Center, Nairobi, Kenya
| | - Francesc X Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephen M Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Solomon Choma
- Department of Medical Science, Public Health and Health Promotion, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
| | - J-T Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Strengthening Oncology Services, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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11
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Deng CH, Naithani S, Kumari S, Cobo-Simón I, Quezada-Rodríguez EH, Skrabisova M, Gladman N, Correll MJ, Sikiru AB, Afuwape OO, Marrano A, Rebollo I, Zhang W, Jung S. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database (Oxford) 2023; 2023:baad088. [PMID: 38079567 PMCID: PMC10712715 DOI: 10.1093/database/baad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.
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Affiliation(s)
- Cecilia H Deng
- Molecular and Digital Breeding, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
| | - Irene Cobo-Simón
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute of Forest Science (ICIFOR-INIA, CSIC), Madrid, Spain
| | - Elsa H Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria Skrabisova
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Nick Gladman
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - Melanie J Correll
- Agricultural and Biological Engineering Department, University of Florida, 1741 Museum Rd, Gainesville, FL 32611, USA
| | | | | | - Annarita Marrano
- Phoenix Bioinformatics, 39899 Balentine Drive, Suite 200, Newark, CA 94560, USA
| | | | - Wentao Zhang
- National Research Council Canada, 110 Gymnasium Pl, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sook Jung
- Department of Horticulture, Washington State University, 303c Plant Sciences Building, Pullman, WA 99164-6414, USA
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12
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Bakulski KM, Blostein F, London SJ. Linking Prenatal Environmental Exposures to Lifetime Health with Epigenome-Wide Association Studies: State-of-the-Science Review and Future Recommendations. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:126001. [PMID: 38048101 PMCID: PMC10695268 DOI: 10.1289/ehp12956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND The prenatal environment influences lifetime health; epigenetic mechanisms likely predominate. In 2016, the first international consortium paper on cigarette smoking during pregnancy and offspring DNA methylation identified extensive, reproducible exposure signals. This finding raised expectations for epigenome-wide association studies (EWAS) of other exposures. OBJECTIVE We review the current state-of-the-science for DNA methylation associations across prenatal exposures in humans and provide future recommendations. METHODS We reviewed 134 prenatal environmental EWAS of DNA methylation in newborns, focusing on 51 epidemiological studies with meta-analysis or replication testing. Exposures spanned cigarette smoking, alcohol consumption, air pollution, dietary factors, psychosocial stress, metals, other chemicals, and other exogenous factors. Of the reproducible DNA methylation signatures, we examined implementation as exposure biomarkers. RESULTS Only 19 (14%) of these prenatal EWAS were conducted in cohorts of 1,000 or more individuals, reflecting the still early stage of the field. To date, the largest perinatal EWAS sample size was 6,685 participants. For comparison, the most recent genome-wide association study for birth weight included more than 300,000 individuals. Replication, at some level, was successful with exposures to cigarette smoking, folate, dietary glycemic index, particulate matter with aerodynamic diameter < 10 μ m and < 2.5 μ m , nitrogen dioxide, mercury, cadmium, arsenic, electronic waste, PFAS, and DDT. Reproducible effects of a more limited set of prenatal exposures (smoking, folate) enabled robust methylation biomarker creation. DISCUSSION Current evidence demonstrates the scientific premise for reproducible DNA methylation exposure signatures. Better powered EWAS could identify signatures across many exposures and enable comprehensive biomarker development. Whether methylation biomarkers of exposures themselves cause health effects remains unclear. We expect that larger EWAS with enhanced coverage of epigenome and exposome, along with improved single-cell technologies and evolving methods for integrative multi-omics analyses and causal inference, will expand mechanistic understanding of causal links between environmental exposures, the epigenome, and health outcomes throughout the life course. https://doi.org/10.1289/EHP12956.
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Affiliation(s)
| | - Freida Blostein
- University of Michigan, Ann Arbor, Michigan, USA
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephanie J. London
- National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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13
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Sharafeldin N, Zhou L, Singh P, Crossman DK, Wang X, Hageman L, Landier W, Blanco JG, Burridge PW, Sapkota Y, Yasui Y, Armstrong GT, Robison LL, Hudson MM, Oeffinger K, Chow EJ, Armenian SH, Weisdorf DJ, Bhatia S. Gene-Level Analysis of Anthracycline-Induced Cardiomyopathy in Cancer Survivors: A Report From COG-ALTE03N1, BMTSS, and CCSS. JACC CardioOncol 2023; 5:807-818. [PMID: 38205005 PMCID: PMC10774788 DOI: 10.1016/j.jaccao.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 01/12/2024] Open
Abstract
Background Anthracyclines are highly effective in treating cancer, albeit with increased cardiomyopathy risk. Although risk is attributed to associations with single nucleotide polymorphisms (SNPs), multiple SNPs on a gene and their interactions remain unexamined. Objectives This study examined gene-level associations with cardiomyopathy among cancer survivors using whole-exome sequencing data. Methods For discovery, 278 childhood cancer survivors (129 cases; 149 matched control subjects) from the COG (Children's Oncology Group) study ALTE03N1 were included. Logic regression (machine learning) was used to identify gene-level SNP combinations for 7,212 genes and ordinal logistic regression to estimate gene-level associations with cardiomyopathy. Models were adjusted for primary cancer, age at cancer diagnosis, sex, race/ethnicity, cumulative anthracycline dose, chest radiation, cardiovascular risk factors, and 3 principal components. Statistical significance threshold of 6.93 × 10-6 accounted for multiple testing. Three independent cancer survivor populations (COG study, BMTSS [Blood or Marrow Transplant Survivor Study] and CCSS [Childhood Cancer Survivor Study]) were used to replicate gene-level associations and examine SNP-level associations from discovery genes using ordinal logistic, conditional logistic, and Cox regression models, respectively. Results Median age at cancer diagnosis for discovery cases and control subjects was 6 years and 8 years, respectively. Gene-level association for P2RX7 (OR: 0.10; 95% CI: 0.04-0.27; P = 2.19 × 10-6) was successfully replicated (HR: 0.65; 95% CI: 0.47-0.90; P = 0.009) in the CCSS cohort. Additional signals were identified on TNIK, LRRK2, MEFV, NOBOX, and FBN3. Individual SNPs across all discovery genes, except FBN3, were replicated. Conclusions In our study, SNP sets having 1 or no copies of P2RX7 variant alleles were associated with reduced risk of cardiomyopathy, presenting a potential therapeutic target to mitigate cardiac outcomes in cancer survivors.
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Affiliation(s)
- Noha Sharafeldin
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Liting Zhou
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Purnima Singh
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Xuexia Wang
- Department of Mathematics, University of North Texas, Denton, Texas, USA
| | - Lindsey Hageman
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Wendy Landier
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Javier G. Blanco
- The State University of New York at Buffalo, Buffalo, New York, USA
| | - Paul W. Burridge
- Department of Pharmacology, Northwestern University, Chicago, Illinois, USA
| | - Yadav Sapkota
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yutaka Yasui
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | | | | | | | - Eric J. Chow
- Seattle Children’s Hospital, University of Washington, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Saro H. Armenian
- Department of Population Sciences, City of Hope, Duarte, California, USA
| | - Daniel J. Weisdorf
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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14
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Park S, Jin HS. Association of IGF1R polymorphisms with kidney function-related traits. Genes Genomics 2023; 45:1509-1515. [PMID: 37477779 DOI: 10.1007/s13258-023-01430-5] [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: 08/29/2022] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Unimpaired kidney function is important for maintaining a healthy state of homeostasis in the body. A genome-wide association study (GWAS) conducted on kidney function-associated traits and novel loci of Japanese subjects found that insulin-like-growth factor 1 receptor (IGF1R) gene variants associated with replication were responsible for all three kinds of kidney functions and satisfied the Bonferroni significance level. OBJECTIVE This study aimed to investigate whether a comparable relationship exists in the Korean population. METHOD This study replicated three SNPs (rs28657002, rs10794486, and rs4966025) and conducted a linear regression analysis between 46 SNPs in the IGF1R gene and three kidney function-related traits, namely blood urea nitrogen (BUN), creatinine, and estimated glomerular filtration rate (eGFR) in Koreans. RESULTS The IGF1R gene was found to be replicated with a significant correlation in Koreans and was extended to the entire gene region to confirm its association with kidney-related functions. Three SNPs in IGF1R were replicated (rs28657002, BUN, P = 3.39 × 10-4; rs10794486, creatinine, P = 5.79 × 10-6; rs4966025, eGFR, P = 1.57 × 10-5) and five SNPs (rs28657002, rs10794486, rs4966025, rs12439557, and rs11247372) showed common significance among the three traits. Additionally, two significant SNPs (rs11857366 and rs28657002) showed the potential to affect IGF1R expression. CONCLUSIONS The results suggest that genetic polymorphisms in the IGF1R replicated previous studies and could affect kidney function. The results of this study will further enhance our understanding of how genetic differences in individuals affect kidney function-related traits.
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Affiliation(s)
- Sangjung Park
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, 20 Hoseo-Ro 79 Beon-Gil, Asan-Si, Chungcheongnam-Do, 31499, Republic of Korea
| | - Hyun-Seok Jin
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, 20 Hoseo-Ro 79 Beon-Gil, Asan-Si, Chungcheongnam-Do, 31499, Republic of Korea.
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15
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Shlykov MA, Giles EM, Kelly MP, Lin SJ, Pham VT, Saccone NL, Yanik EL. Evaluation of Genetic and Nongenetic Risk Factors for Degenerative Cervical Myelopathy. Spine (Phila Pa 1976) 2023; 48:1117-1126. [PMID: 37249397 PMCID: PMC10524420 DOI: 10.1097/brs.0000000000004735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/15/2023] [Indexed: 05/31/2023]
Abstract
STUDY DESIGN Cohort study. OBJECTIVE We aimed to evaluate the associations of genetic and nongenetic factors with degenerative cervical myelopathy (DCM). SUMMARY OF BACKGROUND DATA There is mounting evidence for an inherited predisposition for DCM, but uncertainty remains regarding specific genetic markers involved. Similarly, nongenetic factors are thought to play a role. MATERIALS AND METHODS Using diagnosis codes from hospital records linked to the UK Biobank cohort, patients with cervical spondylosis were identified followed by the identification of a subset with DCM. Nongenetic variables evaluated included age, sex, race, Townsend deprivation index, body mass index, occupational demands, osteoporosis, and smoking. Genome-wide association analyses were conducted using logistic regression adjusted for age, sex, population principal components, and follow-up. RESULTS A total of 851 DCM cases out of 2787 cervical spondylosis patients were identified. Several nongenetic factors were independently associated with DCM including age [odds ratio (OR)=1.11, 95% CI=1.01-1.21, P =0.024], male sex (OR=1.63, 95% CI=1.37-1.93, P <0.001), and relative socioeconomic deprivation (OR=1.03, 95% CI=1.00-1.06, P =0.030). Asian race was associated with lower DCM risk (OR=0.44, 95% CI=0.22-0.85, P =0.014). We did not identify genome-wide significant (≤5×10 -8 ) single-nucleotide polymorphisms (SNPs) associated with DCM. The strongest genome-wide signals were at SNP rs67256809 in the intergenic region of the genes LINC02582 and FBXO15 on chromosome 18 ( P =1.12×10 -7 ) and rs577081672 in the GTPBP1 gene on chromosome 22 ( P =2.9×10 -7 ). No SNPs reported in prior DCM studies were significant after adjusting for replication attempts. CONCLUSIONS Increasing age, male sex, and relative socioeconomic deprivation were identified as independent risk factors for DCM, whereas Asian race was inversely associated. SNPs of potential interest were identified in GTPBP1 and an intergenic region on chromosome 18, but these associations did not reach genome-wide significance. Identification of genetic and nongenetic DCM susceptibility markers may guide understanding of DCM disease processes, inform risk, guide prevention and potentially inform surgical outcomes. LEVEL OF EVIDENCE Prognostic level III.
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Affiliation(s)
| | | | | | - Shiow J Lin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | | | - Nancy L Saccone
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
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16
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Cullina S, Wojcik GL, Shemirani R, Klarin D, Gorman BR, Sorokin EP, Gignoux CR, Belbin GM, Pyarajan S, Asgari S, Tsao PS, Damrauer SM, Abul-Husn NS, Kenny EE. Admixture mapping of peripheral artery disease in a Dominican population reveals a putative risk locus on 2q35. Front Genet 2023; 14:1181167. [PMID: 37600667 PMCID: PMC10432698 DOI: 10.3389/fgene.2023.1181167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Peripheral artery disease (PAD) is a form of atherosclerotic cardiovascular disease, affecting ∼8 million Americans, and is known to have racial and ethnic disparities. PAD has been reported to have a significantly higher prevalence in African Americans (AAs) compared to non-Hispanic European Americans (EAs). Hispanic/Latinos (HLs) have been reported to have lower or similar rates of PAD compared to EAs, despite having a paradoxically high burden of PAD risk factors; however, recent work suggests prevalence may differ between sub-groups. Here, we examined a large cohort of diverse adults in the BioMe biobank in New York City. We observed the prevalence of PAD at 1.7% in EAs vs. 8.5% and 9.4% in AAs and HLs, respectively, and among HL sub-groups, the prevalence was found at 11.4% and 11.5% in Puerto Rican and Dominican populations, respectively. Follow-up analysis that adjusted for common risk factors demonstrated that Dominicans had the highest increased risk for PAD relative to EAs [OR = 3.15 (95% CI 2.33-4.25), p < 6.44 × 10-14]. To investigate whether genetic factors may explain this increased risk, we performed admixture mapping by testing the association between local ancestry and PAD in Dominican BioMe participants (N = 1,813) separately from European, African, and Native American (NAT) continental ancestry tracts. The top association with PAD was an NAT ancestry tract at chromosome 2q35 [OR = 1.96 (SE = 0.16), p < 2.75 × 10-05) with 22.6% vs. 12.9% PAD prevalence in heterozygous NAT tract carriers versus non-carriers, respectively. Fine-mapping at this locus implicated tag SNP rs78529201 located within a long intergenic non-coding RNA (lincRNA) LINC00607, a gene expression regulator of key genes related to thrombosis and extracellular remodeling of endothelial cells, suggesting a putative link of the 2q35 locus to PAD etiology. Efforts to reproduce the signal in other Hispanic cohorts were unsuccessful. In summary, we showed how leveraging health system data helped understand nuances of PAD risk across HL sub-groups and admixture mapping approaches elucidated a putative risk locus in a Dominican population.
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Affiliation(s)
- Sinead Cullina
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Genevieve L. Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Ruhollah Shemirani
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Derek Klarin
- VA Palo Alto Healthcare System, Palo Alto, CA, United States
- Division of Vascular Surgery, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Bryan R. Gorman
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, United States
- Booz Allen Hamilton, McLean, VA, United States
| | - Elena P. Sorokin
- Department of Genetics, Stanford University, Stanford, CA, United States
| | - Christopher R. Gignoux
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Colorado Center for Personalized Medicine, Aurora, CO, United States
| | - Gillian M. Belbin
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA, United States
- Department of Medicine, Brigham Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Samira Asgari
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Philip S. Tsao
- VA Palo Alto Healthcare System, Palo Alto, CA, United States
| | - Scott M. Damrauer
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, United States
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Noura S. Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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17
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Tanguay-Sabourin C, Fillingim M, Guglietti GV, Zare A, Parisien M, Norman J, Sweatman H, Da-Ano R, Heikkala E, Perez J, Karppinen J, Villeneuve S, Thompson SJ, Martel MO, Roy M, Diatchenko L, Vachon-Presseau E. A prognostic risk score for development and spread of chronic pain. Nat Med 2023; 29:1821-1831. [PMID: 37414898 PMCID: PMC10353938 DOI: 10.1038/s41591-023-02430-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 05/31/2023] [Indexed: 07/08/2023]
Abstract
Chronic pain is a complex condition influenced by a combination of biological, psychological and social factors. Using data from the UK Biobank (n = 493,211), we showed that pain spreads from proximal to distal sites and developed a biopsychosocial model that predicted the number of coexisting pain sites. This data-driven model was used to identify a risk score that classified various chronic pain conditions (area under the curve (AUC) 0.70-0.88) and pain-related medical conditions (AUC 0.67-0.86). In longitudinal analyses, the risk score predicted the development of widespread chronic pain, the spreading of chronic pain across body sites and high-impact pain about 9 years later (AUC 0.68-0.78). Key risk factors included sleeplessness, feeling 'fed-up', tiredness, stressful life events and a body mass index >30. A simplified version of this score, named the risk of pain spreading, obtained similar predictive performance based on six simple questions with binarized answers. The risk of pain spreading was then validated in the Northern Finland Birth Cohort (n = 5,525) and the PREVENT-AD cohort (n = 178), obtaining comparable predictive performance. Our findings show that chronic pain conditions can be predicted from a common set of biopsychosocial factors, which can aid in tailoring research protocols, optimizing patient randomization in clinical trials and improving pain management.
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Affiliation(s)
- Christophe Tanguay-Sabourin
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada.
- Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada.
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada.
| | - Matt Fillingim
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Gianluca V Guglietti
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Azin Zare
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Marc Parisien
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Jax Norman
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Hilary Sweatman
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Ronrick Da-Ano
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Eveliina Heikkala
- Research Unit of Population Health, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Jordi Perez
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Alan Edwards Pain Management Unit, McGill University Health Centre, Montreal, Quebec, Canada
| | - Jaro Karppinen
- Research Unit of Population Health, University of Oulu, Oulu, Finland
- Research Unit of Health Sciences and Technology, University of Oulu, Oulu, Finland
- Rehabilitation Services of Southern Karelia Social and Health Care District, Lappeenranta, Finland
| | - Sylvia Villeneuve
- Douglas Mental Health Institute Research Centre, McGill University, Montreal, Quebec, Canada
- McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Scott J Thompson
- Department of Anesthesiology, University of Minnesota, Minneapolis, MN, USA
| | - Marc O Martel
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Mathieu Roy
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Department of Psychology, McGill University, Montreal, Quebec, Canada
| | - Luda Diatchenko
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Etienne Vachon-Presseau
- Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada.
- Department of Anesthesia, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada.
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, Quebec, Canada.
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18
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Qiao J, Wu Y, Zhang S, Xu Y, Zhang J, Zeng P, Wang T. Evaluating significance of European-associated index SNPs in the East Asian population for 31 complex phenotypes. BMC Genomics 2023; 24:324. [PMID: 37312035 DOI: 10.1186/s12864-023-09425-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified many single-nucleotide polymorphisms (SNPs) associated with complex phenotypes in the European (EUR) population; however, the extent to which EUR-associated SNPs can be generalized to other populations such as East Asian (EAS) is not clear. RESULTS By leveraging summary statistics of 31 phenotypes in the EUR and EAS populations, we first evaluated the difference in heritability between the two populations and calculated the trans-ethnic genetic correlation. We observed the heritability estimates of some phenotypes varied substantially across populations and 53.3% of trans-ethnic genetic correlations were significantly smaller than one. Next, we examined whether EUR-associated SNPs of these phenotypes could be identified in EAS using the trans-ethnic false discovery rate method while accounting for winner's curse for SNP effect in EUR and difference of sample sizes in EAS. We found on average 54.5% of EUR-associated SNPs were also significant in EAS. Furthermore, we discovered non-significant SNPs had higher effect heterogeneity, and significant SNPs showed more consistent linkage disequilibrium and allele frequency patterns between the two populations. We also demonstrated non-significant SNPs were more likely to undergo natural selection. CONCLUSIONS Our study revealed the extent to which EUR-associated SNPs could be significant in the EAS population and offered deep insights into the similarity and diversity of genetic architectures underlying phenotypes in distinct ancestral groups.
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Affiliation(s)
- Jiahao Qiao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yuxuan Wu
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Shuo Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yue Xu
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Jinhui Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
| | - Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
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19
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Zhang J, Zhang S, Qiao J, Wang T, Zeng P. Similarity and diversity of genetic architecture for complex traits between East Asian and European populations. BMC Genomics 2023; 24:314. [PMID: 37308816 DOI: 10.1186/s12864-023-09434-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Genome-wide association studies have detected a large number of single-nucleotide polymorphisms (SNPs) associated with complex traits in diverse ancestral groups. However, the trans-ethnic similarity and diversity of genetic architecture is not well understood currently. RESULTS By leveraging summary statistics of 37 traits from East Asian (Nmax=254,373) or European (Nmax=693,529) populations, we first evaluated the trans-ethnic genetic correlation (ρg) and found substantial evidence of shared genetic overlap underlying these traits between the two populations, with [Formula: see text] ranging from 0.53 (se = 0.11) for adult-onset asthma to 0.98 (se = 0.17) for hemoglobin A1c. However, 88.9% of the genetic correlation estimates were significantly less than one, indicating potential heterogeneity in genetic effect across populations. We next identified common associated SNPs using the conjunction conditional false discovery rate method and observed 21.7% of trait-associated SNPs can be identified simultaneously in both populations. Among these shared associated SNPs, 20.8% showed heterogeneous influence on traits between the two ancestral populations. Moreover, we demonstrated that population-common associated SNPs often exhibited more consistent linkage disequilibrium and allele frequency pattern across ancestral groups compared to population-specific or null ones. We also revealed population-specific associated SNPs were much likely to undergo natural selection compared to population-common associated SNPs. CONCLUSIONS Our study provides an in-depth understanding of similarity and diversity regarding genetic architecture for complex traits across diverse populations, and can assist in trans-ethnic association analysis, genetic risk prediction, and causal variant fine mapping.
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Affiliation(s)
- Jinhui Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Shuo Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Jiahao Qiao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
- Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.
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20
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Efanova E, Bushueva O, Saranyuk R, Surovtseva A, Churnosov M, Solodilova M, Polonikov A. Polymorphisms of the GCLC Gene Are Novel Genetic Markers for Susceptibility to Psoriasis Associated with Alcohol Abuse and Cigarette Smoking. Life (Basel) 2023; 13:1316. [PMID: 37374099 DOI: 10.3390/life13061316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
The aim of this pilot study was to investigate whether single nucleotide polymorphisms (SNP) in the gene encoding the catalytic subunit of glutamate cysteine ligase (GCLC) are associated with the risk and clinical features of psoriasis. A total of 944 unrelated individuals, including 474 patients with a diagnosis of psoriasis and 470 healthy controls, were recruited for the study. Six common SNPs in the GCLC gene were genotyped using the MassArray-4 system. Polymorphisms rs648595 (OR = 0.56, 95% CI 0.35-0.90; Pperm = 0.017) and rs2397147 (OR = 0.54, 95% CI 0.30-0.98; Pperm = 0.05) were associated with susceptibility to psoriasis in males. In the male group, diplotype rs2397147-C/C × rs17883901-G/G was associated with a decreased risk of psoriasis (FDR-adjusted p = 0.014), whereas diplotype rs6933870-G/G × rs17883901-G/G (FDR-adjusted p = 0.045) showed an association with an increased disease risk in females. The joint effects of SNPs with tobacco smoking (rs648595 and rs17883901) and alcohol abuse (rs648595 and rs542914) on psoriasis risk were observed (Pperm ≤ 0.05). We also found multiple sex-independent associations between GCLC gene polymorphisms and various clinical features such as earlier disease onset, the psoriatic triad, and specific localizations of skin lesions. The present study is the first to show that polymorphisms of the GCLC gene are significantly associated with the risk of psoriasis and related to its clinical features.
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Affiliation(s)
- Ekaterina Efanova
- Medvenka Central District Hospital, 68 Sovetskaya Street, 307030 Kursk, Russia
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
| | - Olga Bushueva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
| | - Roman Saranyuk
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
- Center for Medical Examinations and Prevention, 2 Leninsky Komsomol Avenue, 305026 Kursk, Russia
| | - Anna Surovtseva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
| | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State University, 85 Pobedy Street, 308015 Belgorod, Russia
| | - Maria Solodilova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
| | - Alexey Polonikov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
- Laboratory of Statistical Genetics and Bioinformatics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
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21
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Cullina S, Wojcik GL, Shemirani R, Klarin D, Gorman BR, Sorokin EP, Gignoux CR, Belbin GM, Pyarajan S, Asgari S, Tsao PS, Damrauer SM, Abul-Husn NS, Kenny EE. Admixture Mapping of Peripheral Artery Disease in a Dominican Population Reveals a Novel Risk Locus on 2q35. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.27.23287788. [PMID: 37034679 PMCID: PMC10081406 DOI: 10.1101/2023.03.27.23287788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Peripheral artery disease (PAD) is a form of atherosclerotic cardiovascular disease, affecting ∼8 million Americans, and is known to have racial and ethnic disparities. PAD has been reported to have significantly higher prevalence in African Americans (AAs) compared to non-Hispanic European Americans (EAs). Hispanic/Latinos (HLs) have been reported to have lower or similar rates of PAD compared to EAs, despite having a paradoxically high burden of PAD risk factors, however recent work suggests prevalence may differ between sub-groups. Here we examined a large cohort of diverse adults in the Bio Me biobank in New York City (NYC). We observed the prevalence of PAD at 1.7% in EAs vs 8.5% and 9.4% in AAs and HLs, respectively; and among HL sub-groups, at 11.4% and 11.5% in Puerto Rican and Dominican populations, respectively. Follow-up analysis that adjusted for common risk factors demonstrated that Dominicans had the highest increased risk for PAD relative to EAs (OR=3.15 (95% CI 2.33-4.25), P <6.44×10 -14 ). To investigate whether genetic factors may explain this increased risk, we performed admixture mapping by testing the association between local ancestry (LA) and PAD in Dominican Bio Me participants (N=1,940) separately for European (EUR), African (AFR) and Native American (NAT) continental ancestry tracts. We identified a NAT ancestry tract at chromosome 2q35 that was significantly associated with PAD (OR=2.05 (95% CI 1.51-2.78), P <4.06×10 -6 ) with 22.5% vs 12.5% PAD prevalence in heterozygous NAT tract carriers versus non-carriers, respectively. Fine-mapping at this locus implicated tag SNP rs78529201 located within a long intergenic non-coding RNA (lincRNA) LINC00607 , a gene expression regulator of key genes related to thrombosis and extracellular remodeling of endothelial cells, suggesting a putative link of the 2q35 locus to PAD etiology. In summary, we showed how leveraging health systems data helped understand nuances of PAD risk across HL sub-groups and admixture mapping approaches elucidated a novel risk locus in a Dominican population.
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22
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Alonso N, Albagha OME, Azfer A, Larraz-Prieto B, Berg K, Riches PL, Ostanek B, Kocjan T, Marc J, Langdahl BL, Ralston SH. Genome-wide association study identifies genetic variants which predict the response of bone mineral density to teriparatide therapy. Ann Rheum Dis 2023:ard-2022-223618. [PMID: 36941031 DOI: 10.1136/ard-2022-223618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/15/2023] [Indexed: 03/23/2023]
Abstract
OBJECTIVES Teriparatide (TPTD) is an effective treatment for osteoporosis but the individual response to therapy is variable for reasons that are unclear. This study aimed to determine whether the response to TPTD might be influenced by genetic factors. METHODS We searched for predictors of the response of bone mineral density (BMD) to TPTD using a two-stage genome-wide association study in 437 patients with osteoporosis from three referral centres. Demographic and clinical data including the response of BMD to treatment at the lumbar spine and hip were extracted from the medical records of each participant. RESULTS Allelic variation at rs6430612 on chromosome 2, close to the CXCR4 gene was associated with the response of spine BMD to TPTD at a genome wide significant level (p=9.2×10-9 beta=-0.35 (-0.47 to -0.23)). The increase in BMD was almost twice as great in AA homozygotes at rs6430612 as compared with GG homozygotes with intermediate values in heterozygotes. The same variant was also associated with response of femoral neck and total hip BMD (p=0.007). An additional locus on chromosome 19 tagged by rs73056959 was associated with the response of femoral neck BMD to TPTD (p=3.5×10-9, beta=-1.61 (-2.14 to -1.07)). CONCLUSIONS Genetic factors influence the response to TPTD at the lumbar spine and hip with a magnitude of effect that is clinically relevant. Further studies are required to identify the causal genetic variants and underlying mechanisms as well as to explore how genetic testing for these variants might be implemented in clinical practice.
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Affiliation(s)
- Nerea Alonso
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Omar M E Albagha
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Asim Azfer
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Beatriz Larraz-Prieto
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kathryn Berg
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Philip L Riches
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Rheumatic Diseases Unit, Western General Hospital, Edinburgh, UK
| | - Barbara Ostanek
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaz Kocjan
- Department of Endocrinology, Diabetes and Metabolic Diseases, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Janja Marc
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Bente L Langdahl
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Stuart H Ralston
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Rheumatic Diseases Unit, Western General Hospital, Edinburgh, UK
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23
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Lal D, Brar T, Ramkumar SP, Li J, Kato A, Zhang L. Genetics and epigenetics of chronic rhinosinusitis. J Allergy Clin Immunol 2023; 151:848-868. [PMID: 36797169 DOI: 10.1016/j.jaci.2023.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 02/16/2023]
Abstract
Discerning the genetics and epigenetics of chronic rhinosinusitis (CRS) may optimize outcomes through early diagnostics, personalized and novel therapeutics, and early prognostication. CRS associated with cystic fibrosis and primary ciliary dyskinesia has well-characterized genetic mutations. Most CRS subjects, however, do not exhibit identifiable monogenic alterations. Clustering in related individuals is seen in CRS with nasal polyps. Spouses of subjects with CRS without nasal polyps also may be at increased risk of the same disease. These observations generate questions on genetic and environmental influences in CRS. Genome-wide association studies have identified variations and polymorphisms between CRS and control subjects in genes related to innate and adaptive immunity. Candidate gene and transcriptomics studies have investigated and identified genetic variations related to immunity, inflammation, epithelial barrier function, stress-response, antigen processing, T-cell regulation, and cytokines in CRS. Epigenetic studies have identified mechanisms through which environmental factors may affect these gene functions. However, causality is not determined for most variations. Inferences drawn from these data must be measured because most investigations report unreplicated results from small study populations. Large, replicated studies in tight cohorts across diverse populations remain a pressing need in studying CRS genetics.
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Affiliation(s)
- Devyani Lal
- Department of Otolaryngology Head and Neck Surgery, Mayo Clinic in Arizona, Phoenix, Ariz.
| | - Tripti Brar
- Department of Otolaryngology Head and Neck Surgery, Mayo Clinic in Arizona, Phoenix, Ariz
| | - Shreya Pusapadi Ramkumar
- Department of Otolaryngology Head and Neck Surgery, Mayo Clinic in Arizona, Phoenix, Ariz; Saint Louis University School of Medicine, St Louis, Mo
| | - Jingyun Li
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Tongren Hospital, Capital Medical University, Beijing, China; Department of Allergy, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China; Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Atsushi Kato
- Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Luo Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Tongren Hospital, Capital Medical University, Beijing, China; Department of Allergy, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Laboratory of Allergic Diseases and Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China; Research Unit of Diagnosis and Treatment of Chronic Nasal Diseases, Chinese Academy of Medical Sciences, Beijing, China
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24
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Singh S, Choudhury A, Hazelhurst S, Crowther N, Boua P, Sorgho H, Agongo G, Nonterah E, Micklesfield L, Norris S, Kisiangani I, Mohamed S, Gomez-Olive F, Tollman S, Choma S, Brandenburg JT, Ramsay M. Genome-wide Association Study Meta-analysis of Blood Pressure Traits and Hypertension in Sub-Saharan African Populations: An AWI-Gen Study. RESEARCH SQUARE 2023:rs.3.rs-2532794. [PMID: 36824767 PMCID: PMC9949264 DOI: 10.21203/rs.3.rs-2532794/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Most hypertension-related genome-wide association studies (GWAS) focus on non-African populations, despite hypertension (a major risk factor for cardiovascular disease) being highly prevalent in Africa. The AWI-Gen study GWAS meta-analysis for blood pressure-related traits (systolic and diastolic blood pressure, pulse pressure, mean-arterial pressure and hypertension) from three sub-Saharan African geographic regions (N=10,775), identified two genome-wide significant signals (p<5E-08): systolic blood pressure near P2RY1 (rs77846204; intergenic variant, p=4.25E-08) and pulse pressure near Linc01256 (rs80141533; intergenic variant, p=4.25E-08). No genome-wide signals were detected for the AWI-Gen GWAS meta-analysis with previous African-ancestry GWASs (UK Biobank (African), Uganda Genome Resource). Suggestive signals (p<5E-06) were observed for all traits, with 29 displaying pleiotropic effects and several replicating known associations. Polygenic risk scores developed from studies on different ancestries had limited transferability, with multi-ancestry models providing better prediction. This study provides insights into the genetics and physiology of blood pressure variation in African populations.
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Affiliation(s)
- Surina Singh
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences & School of Electrical & Information Engineering, University of the Witwatersrand
| | - Nigel Crowther
- 11Department of Chemical Pathology, National Health Laboratory Service
| | - Palwende Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé
| | | | | | | | - Shane Norris
- SAMRC Developmental Pathways For Health Research Unit, Department of Paediatrics & Child Health, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Francesc Gomez-Olive
- 8MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand
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25
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Meijer M, Franke B, Sandi C, Klein M. Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis. Neurosci Biobehav Rev 2023; 145:104997. [PMID: 36566803 DOI: 10.1016/j.neubiorev.2022.104997] [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: 08/08/2022] [Revised: 11/24/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide association studies (EWAS) for externalizing behaviours have been limited in sample size, and, therefore, candidate genes and biomarkers with robust evidence are still lacking. We 1) performed a systematic literature review of EWAS of attention-deficit/hyperactivity disorder (ADHD)- and aggression-related behaviours conducted in peripheral tissue and cord blood and 2) combined the most strongly associated DNAm sites observed in individual studies (p < 10-3) to identify candidate genes and biological systems for ADHD and aggressive behaviours. We observed enrichment for neuronal processes and neuronal cell marker genes for ADHD. Astrocyte and granulocytes cell markers among genes annotated to DNAm sites were relevant for both ADHD and aggression-related behaviours. Only 1 % of the most significant epigenetic findings for ADHD/ADHD symptoms were likely to be directly explained by genetic factors involved in ADHD. Finally, we discuss how the field would greatly benefit from larger sample sizes and harmonization of assessment instruments.
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Affiliation(s)
- Mandy Meijer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carmen Sandi
- Laboratory of Behavioural Genetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marieke Klein
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92093, USA.
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26
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David FS, Stein F, Andlauer TFM, Streit F, Witt SH, Herms S, Hoffmann P, Heilmann-Heimbach S, Opel N, Repple J, Jansen A, Nenadić I, Papiol S, Heilbronner U, Kalman JL, Schaupp SK, Senner F, Schulte EC, Falkai PG, Schulze TG, Dannlowski U, Kircher T, Rietschel M, Nöthen MM, Krug A, Forstner AJ. Genetic contributions to transdiagnostic symptom dimensions in patients with major depressive disorder, bipolar disorder, and schizophrenia spectrum disorders. Schizophr Res 2023; 252:161-171. [PMID: 36652833 DOI: 10.1016/j.schres.2023.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/22/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023]
Abstract
Major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia spectrum disorders (SZ) exhibit considerable phenotypic and genetic overlap. However, the contribution of genetic factors to their shared psychopathological symptom dimensions remains unclear. The present exploratory study investigated genetic contributions to the symptom dimensions "Depression", "Negative syndrome", "Positive formal thought disorder", "Paranoid-hallucinatory syndrome", and "Increased appetite" in a transdiagnostic subset of the German FOR2107 cohort (n = 1042 patients with MDD, BD, or SZ). As replication cohort, a subset of the German/Austrian PsyCourse study (n = 816 patients with MDD, BD, or SZ) was employed. First, the relationship between symptom dimensions and common variants associated with MDD, BD, and SZ was investigated via polygenic risk score (PRS) association analyses, with disorder-specific PRS as predictors and symptom dimensions as outcomes. In the FOR2107 study sample, PRS for BD and SZ were positively associated with "Positive formal thought disorder", the PRS for SZ was positively associated with "Paranoid-hallucinatory syndrome", and the PRS for BD was negatively associated with "Depression". The effects of PRS for SZ were replicated in PsyCourse. No significant associations were observed for the MDD PRS. Second, genome-wide association studies (GWAS) were performed for the five symptom dimensions. No genome-wide significant associations and no replicable suggestive associations (p < 1e-6 in the GWAS) were identified. In summary, our results suggest that, similar to diagnostic categories, transdiagnostic psychiatric symptom dimensions are attributable to polygenic contributions with small effect sizes. Further studies in larger thoroughly phenotyped psychiatric cohorts are required to elucidate the genetic factors that shape psychopathological symptom dimensions.
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Affiliation(s)
- Friederike S David
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frederike Stein
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany; Center for Mind, Brain and Behavior, University of Marburg, Marburg, Germany
| | - Till F M Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany; Center for Innovative Psychiatry and Psychotherapy Research, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Nils Opel
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Jonathan Repple
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Andreas Jansen
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany; Center for Mind, Brain and Behavior, University of Marburg, Marburg, Germany; Core-Facility Brainimaging, Faculty of Medicine, University of Marburg, Marburg, Germany
| | - Igor Nenadić
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany; Center for Mind, Brain and Behavior, University of Marburg, Marburg, Germany
| | - Sergi Papiol
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany; Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Urs Heilbronner
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Janos L Kalman
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany; Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Sabrina K Schaupp
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Fanny Senner
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany; Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Eva C Schulte
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany; Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Peter G Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany; Department of Psychiatry & Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Udo Dannlowski
- Institute for Translational Psychiatry, University of Münster, Münster, Germany
| | - Tilo Kircher
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany; Center for Mind, Brain and Behavior, University of Marburg, Marburg, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Axel Krug
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany; Department of Psychiatry und Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany; Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany; Centre for Human Genetics, University of Marburg, Marburg, Germany.
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27
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Woodward AA, Urbanowicz RJ, Naj AC, Moore JH. Genetic heterogeneity: Challenges, impacts, and methods through an associative lens. Genet Epidemiol 2022; 46:555-571. [PMID: 35924480 PMCID: PMC9669229 DOI: 10.1002/gepi.22497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023]
Abstract
Genetic heterogeneity describes the occurrence of the same or similar phenotypes through different genetic mechanisms in different individuals. Robustly characterizing and accounting for genetic heterogeneity is crucial to pursuing the goals of precision medicine, for discovering novel disease biomarkers, and for identifying targets for treatments. Failure to account for genetic heterogeneity may lead to missed associations and incorrect inferences. Thus, it is critical to review the impact of genetic heterogeneity on the design and analysis of population level genetic studies, aspects that are often overlooked in the literature. In this review, we first contextualize our approach to genetic heterogeneity by proposing a high-level categorization of heterogeneity into "feature," "outcome," and "associative" heterogeneity, drawing on perspectives from epidemiology and machine learning to illustrate distinctions between them. We highlight the unique nature of genetic heterogeneity as a heterogeneous pattern of association that warrants specific methodological considerations. We then focus on the challenges that preclude effective detection and characterization of genetic heterogeneity across a variety of epidemiological contexts. Finally, we discuss systems heterogeneity as an integrated approach to using genetic and other high-dimensional multi-omic data in complex disease research.
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Affiliation(s)
- Alexa A. Woodward
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Ryan J. Urbanowicz
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jason H. Moore
- Department of Computational BiomedicineCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
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28
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Bojarczuk A, Boulygina EA, Dzitkowska-Zabielska M, Łubkowska B, Leońska-Duniec A, Egorova ES, Semenova EA, Andryushchenko LB, Larin AK, Generozov EV, Cięszczyk P, Ahmetov II. Genome-Wide Association Study of Exercise-Induced Fat Loss Efficiency. Genes (Basel) 2022; 13:1975. [PMID: 36360211 PMCID: PMC9690053 DOI: 10.3390/genes13111975] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 04/21/2024] Open
Abstract
There is a wide range of individual variability in the change of body weight in response to exercise, and this variability partly depends on genetic factors. The study aimed to determine DNA polymorphisms associated with fat loss efficiency in untrained women with normal weight in response to a 12-week aerobic training program using the GWAS approach, followed by a cross-sectional study in athletes. The study involved 126 untrained young Polish women (age 21.4 ± 1.7 years; body mass index (BMI): 21.7 (2.4) kg/m2) and 550 Russian athletes (229 women, age 23.0 ± 4.1; 321 men, age 23.9 ± 4.7). We identified one genome-wide significant polymorphism (rs116143768) located in the ACSL1 gene (acyl-CoA synthetase long-chain family member 1, implicated in fatty acid oxidation), with a rare T allele associated with higher fat loss efficiency in Polish women (fat mass decrease: CC genotype (n = 122) -3.8%; CT genotype (n = 4) -31.4%; p = 1.18 × 10-9). Furthermore, male athletes with the T allele (n = 7) had significantly lower BMI (22.1 (3.1) vs. 25.3 (4.2) kg/m2, p = 0.046) than subjects with the CC genotype (n = 314). In conclusion, we have shown that the rs116143768 T allele of the ACSL1 gene is associated with higher fat loss efficiency in response to aerobic training in untrained women and lower BMI in physically active men.
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Affiliation(s)
- Aleksandra Bojarczuk
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | | | | | - Beata Łubkowska
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | - Agata Leońska-Duniec
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | - Emiliya S. Egorova
- Laboratory of Genetics of Aging and Longevity, Kazan State Medical University, 420012 Kazan, Russia
| | - Ekaterina A. Semenova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Research Institute of Physical Culture and Sport, Volga Region State University of Physical Culture, Sport and Tourism, 420138 Kazan, Russia
| | - Liliya B. Andryushchenko
- Department of Physical Education, Plekhanov Russian University of Economics, 115093 Moscow, Russia
| | - Andrey K. Larin
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Edward V. Generozov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Pawel Cięszczyk
- Faculty of Physical Culture, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | - Ildus I. Ahmetov
- Laboratory of Genetics of Aging and Longevity, Kazan State Medical University, 420012 Kazan, Russia
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Department of Physical Education, Plekhanov Russian University of Economics, 115093 Moscow, Russia
- Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool L3 5AF, UK
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29
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Qiao J, Shao Z, Wu Y, Zeng P, Wang T. Detecting associated genes for complex traits shared across East Asian and European populations under the framework of composite null hypothesis testing. Lab Invest 2022; 20:424. [PMID: 36138484 PMCID: PMC9503281 DOI: 10.1186/s12967-022-03637-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/12/2022] [Indexed: 11/21/2022]
Abstract
Background Detecting trans-ethnic common associated genetic loci can offer important insights into shared genetic components underlying complex diseases/traits across diverse continental populations. However, effective statistical methods for such a goal are currently lacking. Methods By leveraging summary statistics available from global-scale genome-wide association studies, we herein proposed a novel genetic overlap detection method called CONTO (COmposite Null hypothesis test for Trans-ethnic genetic Overlap) from the perspective of high-dimensional composite null hypothesis testing. Unlike previous studies which generally analyzed individual genetic variants, CONTO is a gene-centric method which focuses on a set of genetic variants located within a gene simultaneously and assesses their joint significance with the trait of interest. By borrowing the similar principle of joint significance test (JST), CONTO takes the maximum P value of multiple associations as the significance measurement. Results Compared to JST which is often overly conservative, CONTO is improved in two aspects, including the construction of three-component mixture null distribution and the adjustment of trans-ethnic genetic correlation. Consequently, CONTO corrects the conservativeness of JST with well-calibrated P values and is much more powerful validated by extensive simulation studies. We applied CONTO to discover common associated genes for 31 complex diseases/traits between the East Asian and European populations, and identified many shared trait-associated genes that had otherwise been missed by JST. We further revealed that population-common genes were generally more evolutionarily conserved than population-specific or null ones. Conclusion Overall, CONTO represents a powerful method for detecting common associated genes across diverse ancestral groups; our results provide important implications on the transferability of GWAS discoveries in one population to others. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03637-8.
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Affiliation(s)
- Jiahao Qiao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Zhonghe Shao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yuxuan Wu
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China. .,Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China. .,Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China. .,Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China. .,Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
| | - Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
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30
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Chen BH. Minimum standards for evaluating machine-learned models of high-dimensional data. FRONTIERS IN AGING 2022; 3:901841. [PMID: 36176975 PMCID: PMC9513121 DOI: 10.3389/fragi.2022.901841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022]
Abstract
The maturation of machine learning and technologies that generate high dimensional data have led to the growth in the number of predictive models, such as the “epigenetic clock”. While powerful, machine learning algorithms run a high risk of overfitting, particularly when training data is limited, as is often the case with high-dimensional data (“large p, small n”). Making independent validation a requirement of “algorithmic biomarker” development would bring greater clarity to the field by more efficiently identifying prediction or classification models to prioritize for further validation and characterization. Reproducibility has been a mainstay in science, but only recently received attention in defining its various aspects and how to apply these principles to machine learning models. The goal of this paper is merely to serve as a call-to-arms for greater rigor and attention paid to newly developed models for prediction or classification.
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Affiliation(s)
- Brian H. Chen
- FOXO Technologies Inc, Minneapolis, MN, United States
- The Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, United States
- *Correspondence: Brian H. Chen,
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31
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Schormair B, Zhao C, Salminen AV, Oexle K, Winkelmann J. Reassessment of candidate gene studies for idiopathic restless legs syndrome in a large genome-wide association study dataset of European ancestry. Sleep 2022; 45:6576194. [PMID: 35486972 PMCID: PMC9366638 DOI: 10.1093/sleep/zsac098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/06/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Study Objectives
Several candidate gene studies have been published for idiopathic restless legs syndrome (RLS) in populations of European ancestry, but the reported associations have not been confirmed in independent samples. Our aim was to reassess these findings in a large case–control dataset in order to evaluate their validity.
Methods
We screened PubMed for RLS candidate gene studies. We used the genome-wide association study (GWAS) dataset of the International EU-RLS-GENE Consortium as our replication sample, which provided genome-wide single-variant association data based on at most 17 220 individuals of European ancestry. We performed additional gene-based tests using the software MAGMA and assessed the power of our study using the genpwr R package.
Results
We identified 14 studies conducted in European samples which assessed 45 variants in 27 genes of which 5 variants had been reported as significantly associated. None of these individual variants were replicated in our GWAS-based reassessment (nominal p > 0.05) and gene-based tests for the respective five genes ADH1B, GABRR3, HMOX1, MAOA, and VDR, were also nonsignificant (nominal p > 0.05). Our replication dataset was well powered to detect the reported effects, even when adjusting for effect size overestimation due to winner’s curse. Power estimates were close to 100% for all variants.
Conclusion
In summary, none of the significant single-variant associations from candidate gene studies were confirmed in our GWAS dataset. Therefore, these associations were likely false positive. Our observations emphasize the need for large sample sizes and stringent significance thresholds in future association studies for RLS.
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Affiliation(s)
- Barbara Schormair
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH) , Neuherberg , Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich , Munich , Germany
| | - Chen Zhao
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH) , Neuherberg , Germany
| | - Aaro V Salminen
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH) , Neuherberg , Germany
| | - Konrad Oexle
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH) , Neuherberg , Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich , Munich , Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH) , Neuherberg , Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich , Munich , Germany
- Chair of Neurogenetics, School of Medicine, Technical University of Munich , Munich , Germany
- Munich Cluster for Systems Neurology (SyNergy) , Munich , Germany
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32
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Tao J, Helali AE, Ho JC, Lam WWT, Pang H. An Evaluation of Gene-Diet Interaction Statistical Methods and Discovery of rs7175421-Whole Grain Interaction in Lung Cancer. Nutr Cancer 2022; 75:219-227. [PMID: 35930377 DOI: 10.1080/01635581.2022.2104878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dietary factors show different effects on genetically diverse populations. Scientific research uses gene-environment interaction models to study the effects of dietary factors on genetically diverse populations for lung cancer risk. However, previous study designs have not investigated the degree of type I error inflation and, in some instances, have not corrected for multiple testing. Using a motivating investigation of diet-gene interaction and lung cancer risk, we propose a training and testing strategy and perform real-world simulations to select the appropriate statistical methods to reduce false-positive discoveries. The simulation results show that the unconstrained maximum likelihood (UML) method controls the type I error better than the constrained maximum likelihood (CML). The empirical Bayesian (EB) method can compete with the UML method in achieving statistical power and controlling type I error. We observed a significant interaction between SNP rs7175421 with dietary whole grain in lung cancer prevention, with an effect size (standard error) of -0.312 (0.112) for EB estimate. SNP rs7175421 may interact with dietary whole grains in modulating lung cancer risk. Evaluating statistical methods for gene-diet interaction analysis can help balance the statistical power and type I error.
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Affiliation(s)
- Jun Tao
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Aya El Helali
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - James C Ho
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Wendy W T Lam
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China.,Jockey Club Institute of Cancer Care, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Herbert Pang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China.,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
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33
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Mohit, Sharma I, Sharma V, Kumar S, Rastogi G, Dutt P, Shrivastava A, Rai N, Chand P. Empirical assessment of allele frequencies of genome wide association study variants associated with obstructive sleep apnea. Am J Transl Res 2022; 14:3464-3471. [PMID: 35702131 PMCID: PMC9185076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/26/2022] [Indexed: 08/30/2024]
Abstract
OBJECTIVE Obstructive Sleep Apnea (OSA) is a heterogeneous disorder with a complex interplay of genetic and environmental factors. Over the years, with advancement in genotyping and sequencing techniques, various loci have shown an association with OSA. It is pertinent to understand the status of these associated variants in different ethnic groups. The aim of the study was to assess the genetic affinity among different population groups by evaluating the risk allele frequencies of variants associated with OSA. METHOD The variants associated with OSA were obtained from the GWAS catalog with a significant p value of <5 × 10-7; 95 variants were obtained (www.ebi.ac.uk/gwas). Further, the variants were narrowed down on the basis of risk allele frequencies (>5%). The fst was calculated to assess the genetic affinity between super population groups and among the sub-population groups present in the 1000 genome project. RESULT The fst values observed indicated all super populations were genetically related (SAS, AMR, EAS and EUR) except in the African (AFR) population group. Further, the closely related super population i.e., SAS, AMR, EAS and EUR when bifurcated on the basis of sub-population groups shows population stratification and SAS population groups form separate clusters on the MDS plot. CONCLUSION The study highlights genetic heterogeneity among different population groups that gets diluted and results are biased when the samples are pooled irrespective of their endogamous groups. Our results provide insight to researchers to target specific endogamous groups for future studies on OSA.
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Affiliation(s)
- Mohit
- Department of Prosthodontics, King George’s Medical UniversityLucknow 226003, Uttar Pradesh, India
- Center for Advance Research, Faculty of Medicine, King George’s Medical UniversityLucknow 226003, Uttar Pradesh, India
| | - Indu Sharma
- Ancient DNA Laboratory, Birbal Sahni Institute of PalaeosciencesLucknow, Uttar Pradesh, India
| | - Varun Sharma
- Ancient DNA Laboratory, Birbal Sahni Institute of PalaeosciencesLucknow, Uttar Pradesh, India
| | - Sachin Kumar
- Ancient DNA Laboratory, Birbal Sahni Institute of PalaeosciencesLucknow, Uttar Pradesh, India
| | - Garima Rastogi
- NMC Genetics India Pvt Ltd.Gurugram 122002, Haryana, India
| | - Pranjali Dutt
- Department of Prosthodontics, King George’s Medical UniversityLucknow 226003, Uttar Pradesh, India
| | - Ashutosh Shrivastava
- Center for Advance Research, Faculty of Medicine, King George’s Medical UniversityLucknow 226003, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Laboratory, Birbal Sahni Institute of PalaeosciencesLucknow, Uttar Pradesh, India
| | - Pooran Chand
- Department of Prosthodontics, King George’s Medical UniversityLucknow 226003, Uttar Pradesh, India
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34
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Prokopenko D, Morgan SL, Lange C, Hide W, Bertram L, Tanzi RE. Reply to Neupane et al.: Replication study of AD-associated rare variants. Alzheimers Dement 2022; 18:863-864. [PMID: 35142036 PMCID: PMC9302627 DOI: 10.1002/alz.12584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Dmitry Prokopenko
- Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Sarah L Morgan
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, US.,Blizard Institute, Queen Mary University of London, London, UK
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, US
| | - Winston Hide
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, US.,Department of Neuroscience, Sheffield Institute for Translational Neurosciences, University of Sheffield, Sheffield, UK
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Germany.,Department of Psychology, University of Oslo, Oslo, Norway
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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35
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Cao X, Wang X, Zhang S, Sha Q. Gene-based association tests using GWAS summary statistics and incorporating eQTL. Sci Rep 2022; 12:3553. [PMID: 35241742 PMCID: PMC8894384 DOI: 10.1038/s41598-022-07465-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 02/11/2022] [Indexed: 01/29/2023] Open
Abstract
Although genome-wide association studies (GWAS) have been successfully applied to a variety of complex diseases and identified many genetic variants underlying complex diseases via single marker tests, there is still a considerable heritability of complex diseases that could not be explained by GWAS. One alternative approach to overcome the missing heritability caused by genetic heterogeneity is gene-based analysis, which considers the aggregate effects of multiple genetic variants in a single test. Another alternative approach is transcriptome-wide association study (TWAS). TWAS aggregates genomic information into functionally relevant units that map to genes and their expression. TWAS is not only powerful, but can also increase the interpretability in biological mechanisms of identified trait associated genes. In this study, we propose a powerful and computationally efficient gene-based association test, called Overall. Using extended Simes procedure, Overall aggregates information from three types of traditional gene-based association tests and also incorporates expression quantitative trait locus (eQTL) information into a gene-based association test using GWAS summary statistics. We show that after a small number of replications to estimate the correlation among the integrated gene-based tests, the p values of Overall can be calculated analytically. Simulation studies show that Overall can control type I error rates very well and has higher power than the tests that we compared with. We also apply Overall to two schizophrenia GWAS summary datasets and two lipids GWAS summary datasets. The results show that this newly developed method can identify more significant genes than other methods we compared with.
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Affiliation(s)
- Xuewei Cao
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Xuexia Wang
- Department of Mathematics, University of North Texas, Denton, TX, USA
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, MI, 49931, USA.
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36
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Temprosa M, Moore SC, Zanetti KA, Appel N, Ruggieri D, Mazzilli KM, Chen KL, Kelly RS, Lasky-Su JA, Loftfield E, McClain K, Park B, Trijsburg L, Zeleznik OA, Mathé EA. COMETS Analytics: An Online Tool for Analyzing and Meta-Analyzing Metabolomics Data in Large Research Consortia. Am J Epidemiol 2022; 191:147-158. [PMID: 33889934 PMCID: PMC8897993 DOI: 10.1093/aje/kwab120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Consortium-based research is crucial for producing reliable, high-quality findings, but existing tools for consortium studies have important drawbacks with respect to data protection, ease of deployment, and analytical rigor. To address these concerns, we developed COnsortium of METabolomics Studies (COMETS) Analytics to support and streamline consortium-based analyses of metabolomics and other -omics data. The application requires no specialized expertise and can be run locally to guarantee data protection or through a Web-based server for convenience and speed. Unlike other Web-based tools, COMETS Analytics enables standardized analyses to be run across all cohorts, using an algorithmic, reproducible approach to diagnose, document, and fix model issues. This eliminates the time-consuming and potentially error-prone step of manually customizing models by cohort, helping to accelerate consortium-based projects and enhancing analytical reproducibility. We demonstrated that the application scales well by performing 2 data analyses in 45 cohort studies that together comprised measurements of 4,647 metabolites in up to 134,742 participants. COMETS Analytics performed well in this test, as judged by the minimal errors that analysts had in preparing data inputs and the successful execution of all models attempted. As metabolomics gathers momentum among biomedical and epidemiologic researchers, COMETS Analytics may be a useful tool for facilitating large-scale consortium-based research.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ewy A Mathé
- Correspondence to Dr. Ewy Mathé, Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850 (e-mail: )
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Zazuli Z, de Jong C, Xu W, Vijverberg SJH, Masereeuw R, Patel D, Mirshams M, Khan K, Cheng D, Ordonez-Perez B, Huang S, Spreafico A, Hansen AR, Goldstein DP, de Almeida JR, Bratman SV, Hope A, Knox JJ, Wong RKS, Darling GE, Kitchlu A, van Haarlem SWA, van der Meer F, van Lindert ASR, ten Heuvel A, Brouwer J, Ross CJD, Carleton BC, Egberts TCG, Herder GJM, Deneer VHM, Maitland-van der Zee AH, Liu G. Association between Genetic Variants and Cisplatin-Induced Nephrotoxicity: A Genome-Wide Approach and Validation Study. J Pers Med 2021; 11:jpm11111233. [PMID: 34834585 PMCID: PMC8623115 DOI: 10.3390/jpm11111233] [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: 10/19/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/16/2022] Open
Abstract
This study aims to evaluate genetic risk factors for cisplatin-induced nephrotoxicity by investigating not previously studied genetic risk variants and further examining previously reported genetic associations. A genome-wide study (GWAS) was conducted in genetically estimated Europeans in a discovery cohort of cisplatin-treated adults from Toronto, Canada, followed by a candidate gene approach in a validation cohort from the Netherlands. In addition, previously reported genetic associations were further examined in both the discovery and validation cohorts. The outcome, nephrotoxicity, was assessed in two ways: (i) decreased estimated glomerular filtration rate (eGFR), calculated using the Chronic Kidney Disease Epidemiology Collaboration formula (CKD-EPI) and (ii) increased serum creatinine according to the Common Terminology Criteria for Adverse Events v4.03 for acute kidney injury (AKI-CTCAE). Four different Illumina arrays were used for genotyping. Standard quality control was applied for pre- and post-genotype imputation data. In the discovery cohort (n = 608), five single-nucleotide polymorphisms (SNPs) reached genome-wide significance. The A allele in rs4388268 (minor allele frequency = 0.23), an intronic variant of the BACH2 gene, was consistently associated with increased risk of cisplatin-induced nephrotoxicity in both definitions, meeting genome-wide significance (β = −8.4, 95% CI −11.4–−5.4, p = 3.9 × 10−8) for decreased eGFR and reaching suggestive association (OR = 3.9, 95% CI 2.3–6.7, p = 7.4 × 10−7) by AKI-CTCAE. In the validation cohort of 149 patients, this variant was identified with the same direction of effect (eGFR: β = −1.5, 95% CI −5.3–2.4, AKI-CTCAE: OR = 1.7, 95% CI 0.8–3.5). Findings of our previously published candidate gene study could not be confirmed after correction for multiple testing. Genetic predisposition of BACH2 (rs4388268) might be important in the development of cisplatin-induced nephrotoxicity, indicating opportunities for mechanistic understanding, tailored therapy and preventive strategies.
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Affiliation(s)
- Zulfan Zazuli
- Department of Respiratory Medicine, Academic Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands or (Z.Z.); (S.J.H.V.)
- Department of Pharmacology-Clinical Pharmacy, School of Pharmacy, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Corine de Jong
- Department of Clinical Pharmacy, St. Antonius Hospital, 3430 EM Nieuwegein, The Netherlands;
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; (T.C.G.E.); (V.H.M.D.)
| | - Wei Xu
- Department of Biostatistics, Dalla Lana School of Public Health, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada;
| | - Susanne J. H. Vijverberg
- Department of Respiratory Medicine, Academic Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands or (Z.Z.); (S.J.H.V.)
| | - Rosalinde Masereeuw
- Division of Pharmacology, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands;
| | - Devalben Patel
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Maryam Mirshams
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Khaleeq Khan
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Dangxiao Cheng
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Bayardo Ordonez-Perez
- Department of Laboratory Medicine and Pathology, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada;
| | - Shaohui Huang
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (S.H.); (S.V.B.); (A.H.); (R.K.S.W.)
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.G.); (J.R.d.A.)
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Aaron R. Hansen
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - David P. Goldstein
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.G.); (J.R.d.A.)
| | - John R. de Almeida
- Department of Otolaryngology–Head and Neck Surgery, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.G.); (J.R.d.A.)
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (S.H.); (S.V.B.); (A.H.); (R.K.S.W.)
| | - Andrew Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (S.H.); (S.V.B.); (A.H.); (R.K.S.W.)
| | - Jennifer J. Knox
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
| | - Rebecca K. S. Wong
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (S.H.); (S.V.B.); (A.H.); (R.K.S.W.)
| | - Gail E. Darling
- Department of Thoracic Surgery, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada;
| | - Abhijat Kitchlu
- Department of Medicine, Nephrology, University Health Network, University of Toronto, Toronto, ON M5G 2M9, Canada;
| | | | - Femke van der Meer
- Department of Pulmonology, Diakonessenhuis, 3582 KE Utrecht, The Netherlands;
| | - Anne S. R. van Lindert
- Department of Pulmonology, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands;
| | - Alexandra ten Heuvel
- Department of Pulmonology, Groene Hart Hospital, 2803 HH Gouda, The Netherlands;
| | - Jan Brouwer
- Department of Pulmonology, Rivierenland Hospital, 4002 WP Tiel, The Netherlands;
| | - Colin J. D. Ross
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; (C.J.D.R.); (B.C.C.)
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Bruce C. Carleton
- British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada; (C.J.D.R.); (B.C.C.)
- Division of Translational Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, BC V1Y 1T3, Canada
- Pharmaceutical Outcomes Program, British Columbia Children’s Hospital, Vancouver, BC V5Z 4H4, Canada
| | - Toine C. G. Egberts
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; (T.C.G.E.); (V.H.M.D.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Gerarda J. M. Herder
- Meander Medical Center, Department of Pulmonology, 3813 TZ Amersfoort, The Netherlands;
| | - Vera H. M. Deneer
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands; (T.C.G.E.); (V.H.M.D.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Anke H. Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands or (Z.Z.); (S.J.H.V.)
- Correspondence: (A.H.M.-v.d.Z.); (G.L.); Tel.: +31-(0)20-566-8137 (A.H.M.-v.d.Z.); +416-946-4501 (ext. 3428) (G.L.)
| | - Geoffrey Liu
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; (D.P.); (M.M.); (K.K.); (D.C.); (A.S.); (A.R.H.); (J.J.K.)
- Departments of Medical Biophysics, Pharmacology and Toxicology, and Epidemiology, Dalla Lana School of Public Health and University of Toronto, Toronto, ON M5T 3M7, Canada
- Correspondence: (A.H.M.-v.d.Z.); (G.L.); Tel.: +31-(0)20-566-8137 (A.H.M.-v.d.Z.); +416-946-4501 (ext. 3428) (G.L.)
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Generalizability of GWA-Identified Genetic Risk Variants for Metabolic Traits to Populations from the Arabian Peninsula. Genes (Basel) 2021; 12:genes12101637. [PMID: 34681031 PMCID: PMC8535608 DOI: 10.3390/genes12101637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/25/2022] Open
Abstract
The Arabian Peninsula, located at the nexus of Africa, Europe, and Asia, was implicated in early human migration. The Arab population is characterized by consanguinity and endogamy leading to inbreeding. Global genome-wide association (GWA) studies on metabolic traits under-represent the Arab population. Replicability of GWA-identified association signals in the Arab population has not been satisfactorily explored. It is important to assess how well GWA-identified findings generalize if their clinical interpretations are to benefit the target population. Our recent study from Kuwait, which performed genome-wide imputation and meta-analysis, observed 304 (from 151 genes) of the 4746 GWA-identified metabolic risk variants replicable in the Arab population. A recent large GWA study from Qatar found replication of 30 GWA-identified lipid risk variants. These complementing studies from the Peninsula increase the confidence in generalizing metabolic risk loci to the Arab population. However, both the studies reported a low extent of transferability. In this review, we examine the observed low transferability in the context of differences in environment, genetic correlations (allele frequencies, linkage disequilibrium, effect sizes, and heritability), and phenotype variance. We emphasize the need for large-scale GWA studies on deeply phenotyped cohorts of at least 20,000 Arab individuals. The review further presents GWA-identified metabolic risk variants generalizable to the Arab population.
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Orlova EA, Ogarkov OB, Khromova PA, Sinkov VV, Khasnatinov MA, Zhdanova SN, Rychkova LV, Kolesnikova LI. SNP rs657152 Is Not Associated with the Level of Viral Load in COVID-19 or the Probability of Disease in the Population of Caucasians in Eastern Siberia. RUSS J GENET+ 2021; 57:982-984. [PMID: 34483600 PMCID: PMC8404754 DOI: 10.1134/s1022795421080093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/25/2022]
Abstract
Cross-replicating associations with rs657152 at the 9q34.2c locus and rs11385942 at the 3p21.31 locus found in patients with severe COVID-19 in the Caucasian population require the study of the discovered phenomenon in various populations, including as an independent biological marker. Primers and TaqMan probes for PCR discrimination of the A and C alleles in single nucleotide polymorphism (SNP) rs657152 have been developed. The polymorphism of the rs657152 A/C locus was determined in 129 patients with COVID-19 and in a control group of 466 healthy individuals. There were no significant differences in the frequency of distribution of the A and C alleles, 0.47/0.53 and 0.45/0.55, between patients and healthy subjects, respectively. Also, no differences were found in the distribution of alleles in patients with a high viral load in the smear (Ct in the range of 16-25) in comparison with an average and low viral load (Ct in the range of 26-40).
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Affiliation(s)
- E. A. Orlova
- Scientific Center for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - O. B. Ogarkov
- Scientific Center for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - P. A. Khromova
- Scientific Center for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - V. V. Sinkov
- Scientific Center for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - M. A. Khasnatinov
- Scientific Center for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - S. N. Zhdanova
- Scientific Center for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - L. V. Rychkova
- Scientific Center for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - L. I. Kolesnikova
- Scientific Center for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
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Azarova I, Klyosova E, Polonikov A. The Link between Type 2 Diabetes Mellitus and the Polymorphisms of Glutathione-Metabolizing Genes Suggests a New Hypothesis Explaining Disease Initiation and Progression. Life (Basel) 2021; 11:life11090886. [PMID: 34575035 PMCID: PMC8466482 DOI: 10.3390/life11090886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 01/11/2023] Open
Abstract
The present study investigated whether type 2 diabetes (T2D) is associated with polymorphisms of genes encoding glutathione-metabolizing enzymes such as glutathione synthetase (GSS) and gamma-glutamyl transferase 7 (GGT7). A total of 3198 unrelated Russian subjects including 1572 T2D patients and 1626 healthy subjects were enrolled. Single nucleotide polymorphisms (SNPs) of the GSS and GGT7 genes were genotyped using the MassArray-4 system. We found that the GSS and GGT7 gene polymorphisms alone and in combinations are associated with T2D risk regardless of sex, age, and body mass index, as well as correlated with plasma glutathione, hydrogen peroxide, and fasting blood glucose levels. Polymorphisms of GSS (rs13041792) and GGT7 (rs6119534 and rs11546155) genes were associated with the tissue-specific expression of genes involved in unfolded protein response and the regulation of proteostasis. Transcriptome-wide association analysis has shown that the pancreatic expression of some of these genes such as EDEM2, MYH7B, MAP1LC3A, and CPNE1 is linked to the genetic risk of T2D. A comprehensive analysis of the data allowed proposing a new hypothesis for the etiology of type 2 diabetes that endogenous glutathione deficiency might be a key condition responsible for the impaired folding of proinsulin which triggered an unfolded protein response, ultimately leading to beta-cell apoptosis and disease development.
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Affiliation(s)
- Iuliia Azarova
- Department of Biological Chemistry, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia;
- Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., 305041 Kursk, Russia;
| | - Elena Klyosova
- Laboratory of Biochemical Genetics and Metabolomics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., 305041 Kursk, Russia;
| | - Alexey Polonikov
- Laboratory of Statistical Genetics and Bioinformatics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya St., 305041 Kursk, Russia
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
- Correspondence: ; Tel.: +7-471-258-8147
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Preregistration and Registered Reports: A Key Pathway to Enhancing Robustness and Replicability in Mental Health Research. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2021; 1:80-82. [DOI: 10.1016/j.bpsgos.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
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Mieth B, Rozier A, Rodriguez JA, Höhne MMC, Görnitz N, Müller KR. DeepCOMBI: explainable artificial intelligence for the analysis and discovery in genome-wide association studies. NAR Genom Bioinform 2021; 3:lqab065. [PMID: 34296082 PMCID: PMC8291080 DOI: 10.1093/nargab/lqab065] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 02/06/2023] Open
Abstract
Deep learning has revolutionized data science in many fields by greatly improving prediction performances in comparison to conventional approaches. Recently, explainable artificial intelligence has emerged as an area of research that goes beyond pure prediction improvement by extracting knowledge from deep learning methodologies through the interpretation of their results. We investigate such explanations to explore the genetic architectures of phenotypes in genome-wide association studies. Instead of testing each position in the genome individually, the novel three-step algorithm, called DeepCOMBI, first trains a neural network for the classification of subjects into their respective phenotypes. Second, it explains the classifiers’ decisions by applying layer-wise relevance propagation as one example from the pool of explanation techniques. The resulting importance scores are eventually used to determine a subset of the most relevant locations for multiple hypothesis testing in the third step. The performance of DeepCOMBI in terms of power and precision is investigated on generated datasets and a 2007 study. Verification of the latter is achieved by validating all findings with independent studies published up until 2020. DeepCOMBI is shown to outperform ordinary raw P-value thresholding and other baseline methods. Two novel disease associations (rs10889923 for hypertension, rs4769283 for type 1 diabetes) were identified.
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Affiliation(s)
- Bettina Mieth
- Machine Learning Group, Technische Universität Berlin, Berlin 10587, Germany
| | - Alexandre Rozier
- Machine Learning Group, Technische Universität Berlin, Berlin 10587, Germany
| | - Juan Antonio Rodriguez
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Marina M C Höhne
- Machine Learning Group, Technische Universität Berlin, Berlin 10587, Germany
| | | | - Klaus-Robert Müller
- Machine Learning Group, Technische Universität Berlin, Berlin 10587, Germany
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Ortega-Loubon C, Martínez-Paz P, García-Morán E, Tamayo-Velasco Á, López-Hernández FJ, Jorge-Monjas P, Tamayo E. Genetic Susceptibility to Acute Kidney Injury. J Clin Med 2021; 10:jcm10143039. [PMID: 34300206 PMCID: PMC8307812 DOI: 10.3390/jcm10143039] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/14/2022] Open
Abstract
Acute kidney injury (AKI) is a widely held concern related to a substantial burden of morbidity, mortality and expenditure in the healthcare system. AKI is not a simple illness but a complex conglomeration of syndromes that often occurs as part of other syndromes in its wide clinical spectrum of the disease. Genetic factors have been suggested as potentially responsible for its susceptibility and severity. As there is no current cure nor an effective treatment other than generally accepted supportive measures and renal replacement therapy, updated knowledge of the genetic implications may serve as a strategic tactic to counteract its dire consequences. Further understanding of the genetics that predispose AKI may shed light on novel approaches for the prevention and treatment of this condition. This review attempts to address the role of key genes in the appearance and development of AKI, providing not only a comprehensive update of the intertwined process involved but also identifying specific markers that could serve as precise targets for further AKI therapies.
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Affiliation(s)
- Christian Ortega-Loubon
- BioCritic. Group for Biomedical Research in Critical Care Medicine, University of Valladolid, 47003 Valladolid, Spain; (C.O.-L.); (E.G.-M.); (Á.T.-V.); (F.J.L.-H.); (E.T.)
- Department of Cardiovascular Surgery, Hospital Clinic of Barcelona, 08036 Barcelona, Spain
| | - Pedro Martínez-Paz
- BioCritic. Group for Biomedical Research in Critical Care Medicine, University of Valladolid, 47003 Valladolid, Spain; (C.O.-L.); (E.G.-M.); (Á.T.-V.); (F.J.L.-H.); (E.T.)
- Department of Surgery, Faculty of Medicine, University of Valladolid, 47003 Valladolid, Spain
- Correspondence: (P.M.-P.); (P.J.-M.); Tel.: +34-9834200000 (P.M.-P.); +34-687978535 (P.J.-M)
| | - Emilio García-Morán
- BioCritic. Group for Biomedical Research in Critical Care Medicine, University of Valladolid, 47003 Valladolid, Spain; (C.O.-L.); (E.G.-M.); (Á.T.-V.); (F.J.L.-H.); (E.T.)
- Department of Cardiology, Clinical University Hospital of Valladolid, 47003 Valladolid, Spain
| | - Álvaro Tamayo-Velasco
- BioCritic. Group for Biomedical Research in Critical Care Medicine, University of Valladolid, 47003 Valladolid, Spain; (C.O.-L.); (E.G.-M.); (Á.T.-V.); (F.J.L.-H.); (E.T.)
- Department of Hematology and Hemotherapy, Clinical University Hospital of Valladolid, 47003 Valladolid, Spain
| | - Francisco J. López-Hernández
- BioCritic. Group for Biomedical Research in Critical Care Medicine, University of Valladolid, 47003 Valladolid, Spain; (C.O.-L.); (E.G.-M.); (Á.T.-V.); (F.J.L.-H.); (E.T.)
- Institute of Biomedical Research of Salamnca (IBSAL), University Hospital of Salamanca, 37007 Salamanca, Spain
- Group of Translational Research on Renal and Cardiovascular Diseases (TRECARD), Departmental Building Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Pablo Jorge-Monjas
- BioCritic. Group for Biomedical Research in Critical Care Medicine, University of Valladolid, 47003 Valladolid, Spain; (C.O.-L.); (E.G.-M.); (Á.T.-V.); (F.J.L.-H.); (E.T.)
- Department of Anesthesiology and Critical Care, Clinical University Hospital of Valladolid, Ramón y Cajal Ave, 47003 Valladolid, Spain
- Correspondence: (P.M.-P.); (P.J.-M.); Tel.: +34-9834200000 (P.M.-P.); +34-687978535 (P.J.-M)
| | - Eduardo Tamayo
- BioCritic. Group for Biomedical Research in Critical Care Medicine, University of Valladolid, 47003 Valladolid, Spain; (C.O.-L.); (E.G.-M.); (Á.T.-V.); (F.J.L.-H.); (E.T.)
- Department of Anesthesiology and Critical Care, Clinical University Hospital of Valladolid, Ramón y Cajal Ave, 47003 Valladolid, Spain
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Grinberg NF, Wallace C. Multi-tissue transcriptome-wide association studies. Genet Epidemiol 2021; 45:324-337. [PMID: 33369784 PMCID: PMC8048510 DOI: 10.1002/gepi.22374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/04/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022]
Abstract
A transcriptome-wide association study (TWAS) attempts to identify disease associated genes by imputing gene expression into a genome-wide association study (GWAS) using an expression quantitative trait loci (eQTL) data set and then testing for associations with a trait of interest. Regulatory processes may be shared across related tissues and one natural extension of TWAS is harnessing cross-tissue correlation in gene expression to improve prediction accuracy. Here, we studied multi-tissue extensions of lasso regression and random forests (RF), joint lasso and RF-MTL (multi-task learning RF), respectively. We found that, on our chosen eQTL data set, multi-tissue methods were generally more accurate than their single-tissue counterparts, with RF-MTL performing the best. Simulations showed that these benefits generally translated into more associated genes identified, although highlighted that joint lasso had a tendency to erroneously identify genes in one tissue if there existed an eQTL signal for that gene in another. Applying the four methods to a type 1 diabetes GWAS, we found that multi-tissue methods found more unique associated genes for most of the tissues considered. We conclude that multi-tissue methods are competitive and, for some cell types, superior to single-tissue approaches and hold much promise for TWAS studies.
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Affiliation(s)
- Nastasiya F. Grinberg
- Department of Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge Institute of Therapeutic Immunology and Infectious DiseaseUniversity of CambridgeCambridgeUK
| | - Chris Wallace
- Department of Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge Institute of Therapeutic Immunology and Infectious DiseaseUniversity of CambridgeCambridgeUK
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
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45
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Shadrina AS, Zlobin AS, Zaytseva OO, Klarić L, Sharapov SZ, D Pakhomov E, Perola M, Esko T, Hayward C, Wilson JF, Lauc G, Aulchenko YS, Tsepilov YA. Multivariate genome-wide analysis of immunoglobulin G N-glycosylation identifies new loci pleiotropic with immune function. Hum Mol Genet 2021; 30:1259-1270. [PMID: 33710309 DOI: 10.1093/hmg/ddab072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
The N-glycosylation of immunoglobulin G (IgG) affects its structure and function. It has been demonstrated that IgG N-glycosylation patterns are inherited as complex quantitative traits. Genome-wide association studies identified loci harboring genes encoding enzymes directly involved in protein glycosylation as well as loci likely to be involved in regulation of glycosylation biochemical pathways. Many of these loci could be linked to immune functions and risk of inflammatory and autoimmune diseases. The aim of the present study was to discover and replicate new loci associated with IgG N-glycosylation and to investigate possible pleiotropic effects of these loci onto immune function and the risk of inflammatory and autoimmune diseases. We conducted a multivariate genome-wide association analysis of 23 IgG N-glycosylation traits measured in 8090 individuals of European ancestry. The discovery stage was followed up by replication in 3147 people and in silico functional analysis. Our study increased the total number of replicated loci from 22 to 29. For the discovered loci, we suggest a number of genes potentially involved in the control of IgG N-glycosylation. Among the new loci, two (near RNF168 and TNFRSF13B) were previously implicated in rare immune deficiencies and were associated with levels of circulating immunoglobulins. For one new locus (near AP5B1/OVOL1), we demonstrated a potential pleiotropic effect on the risk of asthma. Our findings underline an important link between IgG N-glycosylation and immune function and provide new clues to understanding their interplay.
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Affiliation(s)
- Alexandra S Shadrina
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Alexander S Zlobin
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Olga O Zaytseva
- Genos Glycoscience Research Laboratory, Zagreb 10000, Croatia
| | - Lucija Klarić
- Genos Glycoscience Research Laboratory, Zagreb 10000, Croatia.,MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sodbo Z Sharapov
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Eugene D Pakhomov
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Marcus Perola
- Genomics and Biomarkers Unit, Department of Health, National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - James F Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.,Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb 10000, Croatia
| | - Yurii S Aulchenko
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia.,PolyOmica, 's-Hertogenbosch 5237 PA, The Netherlands
| | - Yakov A Tsepilov
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia.,Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University, Novosibirsk 630090, Russia
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46
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Sharapov SZ, Shadrina AS, Tsepilov YA, Elgaeva EE, Tiys ES, Feoktistova SG, Zaytseva OO, Vuckovic F, Cuadrat R, Jäger S, Wittenbecher C, Karssen LC, Timofeeva M, Tillin T, Trbojević-Akmačić I, Štambuk T, Rudman N, Krištić J, Šimunović J, Momčilović A, Vilaj M, Jurić J, Slana A, Gudelj I, Klarić T, Puljak L, Skelin A, Kadić AJ, Van Zundert J, Chaturvedi N, Campbell H, Dunlop M, Farrington SM, Doherty M, Dagostino C, Gieger C, Allegri M, Williams F, Schulze MB, Lauc G, Aulchenko YS. Replication of 15 loci involved in human plasma protein N-glycosylation in 4802 samples from four cohorts. Glycobiology 2021; 31:82-88. [PMID: 32521004 PMCID: PMC7874387 DOI: 10.1093/glycob/cwaa053] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/27/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
Human protein glycosylation is a complex process, and its in vivo regulation is poorly understood. Changes in glycosylation patterns are associated with many human diseases and conditions. Understanding the biological determinants of protein glycome provides a basis for future diagnostic and therapeutic applications. Genome-wide association studies (GWAS) allow to study biology via a hypothesis-free search of loci and genetic variants associated with a trait of interest. Sixteen loci were identified by three previous GWAS of human plasma proteome N-glycosylation. However, the possibility that some of these loci are false positives needs to be eliminated by replication studies, which have been limited so far. Here, we use the largest set of samples so far (4802 individuals) to replicate the previously identified loci. For all but one locus, the expected replication power exceeded 95%. Of the 16 loci reported previously, 15 were replicated in our study. For the remaining locus (near the KREMEN1 gene), the replication power was low, and hence, replication results were inconclusive. The very high replication rate highlights the general robustness of the GWAS findings as well as the high standards adopted by the community that studies genetic regulation of protein glycosylation. The 15 replicated loci present a good target for further functional studies. Among these, eight loci contain genes encoding glycosyltransferases: MGAT5, B3GAT1, FUT8, FUT6, ST6GAL1, B4GALT1, ST3GAL4 and MGAT3. The remaining seven loci offer starting points for further functional follow-up investigation into molecules and mechanisms that regulate human protein N-glycosylation in vivo.
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Affiliation(s)
- Sodbo Zh Sharapov
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva, 10, Novosibirsk, 630090, Russia
| | - Alexandra S Shadrina
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva, 10, Novosibirsk, 630090, Russia
| | - Yakov A Tsepilov
- Laboratory of Theoretical and Applied Functional Genomics, Novosibirsk State University, Pirogova 1, Novosibirsk, 630090, Russia
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva, 10, Novosibirsk, 630090, Russia
| | - Elizaveta E Elgaeva
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva, 10, Novosibirsk, 630090, Russia
| | - Evgeny S Tiys
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva, 10, Novosibirsk, 630090, Russia
| | - Sofya G Feoktistova
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva, 10, Novosibirsk, 630090, Russia
| | - Olga O Zaytseva
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Frano Vuckovic
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Rafael Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam- Rehbruecke, 14558 Nuthetal, Germany
| | - Susanne Jäger
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam- Rehbruecke, 14558 Nuthetal, Germany
- German Center for Diabetes Research (DZD), ngolstädter Landstraβe 1, Neuherberg, 85764, Germany
| | - Clemens Wittenbecher
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam- Rehbruecke, 14558 Nuthetal, Germany
- German Center for Diabetes Research (DZD), ngolstädter Landstraβe 1, Neuherberg, 85764, Germany
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Maria Timofeeva
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh EH4 2XU, UK
- D-IAS, Danish Institute for Advanced Study, Department of Public Health, University of Southern Denmark, , J.B. Winsløws Vej 9, DK-5000 Odense C, Denmark
| | - Therese Tillin
- MRC Unit for Lifelong Health & Ageing University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Tamara Štambuk
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Najda Rudman
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, 10000, Croatia
| | - Jasminka Krištić
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Jelena Šimunović
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Ana Momčilović
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Marija Vilaj
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Julija Jurić
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Anita Slana
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Ivan Gudelj
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Thomas Klarić
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Livia Puljak
- Catholic University of Croatia, Ilica, 242 Zagreb, 10000, Croatia
| | - Andrea Skelin
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
- St. Catherine Specialty Hospital, 10000 Zagreb & 49210, Zabok, Croatia
| | - Antonia Jeličić Kadić
- University Hospital Center Split, Department of Pediatrics, Spinčićeva ul. 1, Split, 21000, Croatia
| | - Jan Van Zundert
- Department of Anesthesiology and Multidisciplinary Paincentre, ZOL, Genk/Lanaken, Belgium
- Department of Anesthesiology and Pain Medicine, Maastricht University Medical Centre, P. Debyelaan 25, Maastricht, 6229 HX, The Netherlands
| | - Nishi Chaturvedi
- MRC Unit for Lifelong Health & Ageing University College London, Gower Street, London, WC1E 6BT, UK
| | - Harry Campbell
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Susan M Farrington
- Colon Cancer Genetics Group, Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics & Molecular Medicine, Western General Hospital, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Margaret Doherty
- Institute of Technology Sligo, Department of Life Sciences, Ash Ln, Bellanode, Sligo, F91 YW50, Ireland
- National Institute for Bioprocessing Research & Training, 24 Foster’s Ave, Belfield, Blackrock, Co.,Dublin, A94 X099, Ireland
| | - Concetta Dagostino
- Department of Medicine and Surgery, University of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Christian Gieger
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Centre Munich, German Research Center for Environmental Health, Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Massimo Allegri
- Pain Therapy Department Policlinico Monza Hospital, 20090 Monza, Italy
| | - Frances Williams
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King’s College London, St Thomas’ Campus, Lambeth Palace Road, London SE1 7EH, UK
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam- Rehbruecke, 14558 Nuthetal, Germany
- German Center for Diabetes Research (DZD), ngolstädter Landstraβe 1, Neuherberg, 85764, Germany
- Institute of Nutrition Science, University of Potsdam, 14558 Nuthetal, Germany
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Yurii S Aulchenko
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva, 10, Novosibirsk, 630090, Russia
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47
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Wu L, Li Z, Zhou J, Ma B, Yu F, Zheng X, Hu X, Ma Z, Su X. An association analysis for genetic factors for dental caries susceptibility in a cohort of Chinese children. Oral Dis 2020; 28:480-494. [DOI: 10.1111/odi.13758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/17/2020] [Accepted: 12/14/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Lingli Wu
- Department of Dentistry Key Laboratory of Oral Diseases of Gansu Province Key Laboratory of Stomatology of State Ethnic Affairs Commission Northwest Minzu University Lanzhou China
| | - Zhiqiang Li
- Department of Dentistry Key Laboratory of Oral Diseases of Gansu Province Key Laboratory of Stomatology of State Ethnic Affairs Commission Northwest Minzu University Lanzhou China
| | - Jianye Zhou
- Department of Dentistry Key Laboratory of Oral Diseases of Gansu Province Key Laboratory of Stomatology of State Ethnic Affairs Commission Northwest Minzu University Lanzhou China
| | - Bin Ma
- Department of Dentistry Key Laboratory of Oral Diseases of Gansu Province Key Laboratory of Stomatology of State Ethnic Affairs Commission Northwest Minzu University Lanzhou China
| | - Fei Yu
- Department of Dentistry Lanzhou University Lanzhou, Gansu Province China
| | - Xin Zheng
- Department of Dentistry Key Laboratory of Oral Diseases of Gansu Province Key Laboratory of Stomatology of State Ethnic Affairs Commission Northwest Minzu University Lanzhou China
| | - Xiaopan Hu
- Department of Dentistry Key Laboratory of Oral Diseases of Gansu Province Key Laboratory of Stomatology of State Ethnic Affairs Commission Northwest Minzu University Lanzhou China
| | - Zhongming Ma
- Department of Dentistry Key Laboratory of Oral Diseases of Gansu Province Key Laboratory of Stomatology of State Ethnic Affairs Commission Northwest Minzu University Lanzhou China
| | - Xuelian Su
- Department of Dentistry Key Laboratory of Oral Diseases of Gansu Province Key Laboratory of Stomatology of State Ethnic Affairs Commission Northwest Minzu University Lanzhou China
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48
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Moradifard S, Hoseinbeyki M, Emam MM, Parchiniparchin F, Ebrahimi-Rad M. Association of the Sp1 binding site and -1997 promoter variations in COL1A1 with osteoporosis risk: The application of meta-analysis and bioinformatics approaches offers a new perspective for future research. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2020; 786:108339. [PMID: 33339581 DOI: 10.1016/j.mrrev.2020.108339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 08/11/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022]
Abstract
As a complex disease, osteoporosis is influenced by several genetic markers. Many studies have examined the link between the Sp1 binding site +1245 G > T (rs1800012) and -1997 G > T (rs1107946) variations in the COL1A1 gene with osteoporosis risk. However, the findings of these studies have been contradictory; therefore, we performed a meta-analysis to aggregate additional information and obtain increased statistical power to more efficiently estimate this correlation. A meta-analysis was conducted with studies published between 1991-2020 that were identified by a systematic electronic search of the Scopus and Clarivate Analytics databases. Studies with bone mineral density (BMD) data and complete genotypes of the single-nucleotide variations (SNVs) for the overall and postmenopausal female population were included in this meta-analysis and analyzed using the R metaphor package. A relationship between rs1800012 and significantly decreased BMD values at the lumbar spine and femoral neck was found in individuals carrying the "ss" versus the "SS" genotype in the overall population according to a random effects model (p < 0.0001). Similar results were also found in the postmenopausal female population (p = 0.003 and 0.0002, respectively). Such findings might be an indication of increased osteoporosis risk in both studied groups in individuals with the "ss" genotype. Although no association was identified between the -1997 G > T and low BMD in the overall population, those individuals with the "GT" genotype showed a higher level of BMD than those with "GG" in the subgroup analysis (p = 0.007). To determine which transcription factor (TF) might bind to the -1997 G > T in COL1A1, 45 TFs were identified based on bioinformatics predictions. According to the GSE35958 microarray dataset, 16 of 45 TFs showed differential expression profiles in osteoporotic human mesenchymal stem cells relative to normal samples from elderly donors. By identifying candidate TFs for the -1997 G > T site, our study offers a new perspective for future research.
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Affiliation(s)
| | | | - Mohammad Mehdi Emam
- Rheumatology Ward, Loghman Hospital, Shahid Beheshti Medical University (SBMU), Tehran, Iran
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49
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Darst BF. Findings from a Genetic Sequencing Investigation of Men with Familial and Aggressive Prostate Cancer. Eur Urol 2020; 79:362-363. [PMID: 32994065 DOI: 10.1016/j.eururo.2020.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/03/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Burcu F Darst
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
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50
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Hebbar P, Abubaker JA, Abu-Farha M, Alsmadi O, Elkum N, Alkayal F, John SE, Channanath A, Iqbal R, Pitkaniemi J, Tuomilehto J, Sladek R, Al-Mulla F, Thanaraj TA. Genome-wide landscape establishes novel association signals for metabolic traits in the Arab population. Hum Genet 2020; 140:505-528. [PMID: 32902719 PMCID: PMC7889551 DOI: 10.1007/s00439-020-02222-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
While the Arabian population has a high prevalence of metabolic disorders, it has not been included in global studies that identify genetic risk loci for metabolic traits. Determining the transferability of such largely Euro-centric established risk loci is essential to transfer the research tools/resources, and drug targets generated by global studies to a broad range of ethnic populations. Further, consideration of populations such as Arabs, that are characterized by consanguinity and a high level of inbreeding, can lead to identification of novel risk loci. We imputed published GWAS data from two Kuwaiti Arab cohorts (n = 1434 and 1298) to the 1000 Genomes Project haplotypes and performed meta-analysis for associations with 13 metabolic traits. We compared the observed association signals with those established for metabolic traits. Our study highlighted 70 variants from 9 different genes, some of which have established links to metabolic disorders. By relaxing the genome-wide significance threshold, we identified ‘novel’ risk variants from 11 genes for metabolic traits. Many novel risk variant association signals were observed at or borderline to genome-wide significance. Furthermore, 349 previously established variants from 187 genes were validated in our study. Pleiotropic effect of risk variants on multiple metabolic traits were observed. Fine-mapping illuminated rs7838666/CSMD1 rs1864163/CETP and rs112861901/[INTS10,LPL] as candidate causal variants influencing fasting plasma glucose and high-density lipoprotein levels. Computational functional analysis identified a variety of gene regulatory signals around several variants. This study enlarges the population ancestry diversity of available GWAS and elucidates new variants in an ethnic group burdened with metabolic disorders.
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Affiliation(s)
- Prashantha Hebbar
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait.,Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | | | - Naser Elkum
- Sidra Medical and Research Center, Doha, Qatar
| | - Fadi Alkayal
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait
| | - Sumi Elsa John
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait
| | | | - Rasheeba Iqbal
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait
| | - Janne Pitkaniemi
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jaakko Tuomilehto
- Department of Public Health, University of Helsinki, Helsinki, Finland.,Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Robert Sladek
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Fahd Al-Mulla
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait.
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