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Hsi RS, Zhang S, Triozzi JL, Hung AM, Xu Y, Bejan CA. Evaluation of Genetic Associations with Clinical Phenotypes of Kidney Stone Disease. EUR UROL SUPPL 2024; 67:38-44. [PMID: 39156495 PMCID: PMC11327546 DOI: 10.1016/j.euros.2024.07.109] [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] [Accepted: 07/10/2024] [Indexed: 08/20/2024] Open
Abstract
Background and objective Previous studies have reported a strong genetic contribution to kidney stone risk. This study aims to identify genetic associations of kidney stone disease within a large-scale electronic health record system. Methods We performed genome-wide association studies (GWASs) for nephrolithiasis from genotyped samples of 5571 cases and 83 692 controls. This analysis included a primary GWAS focused on nephrolithiasis and subsequent subgroup GWASs stratified by stone composition types. For significant risk variants, we performed association analyses with stone composition and first-time 24-h urine parameters. To assess disease severity, we investigated the associations with age at first stone diagnosis, age at first stone-related procedure, and time between first and second stone-related procedures. Key findings and limitations The primary GWAS analysis identified ten significant loci, all located on chromosome 16 within coding regions of the UMOD gene. The strongest signal was rs28544423 (odds ratio 1.17, 95% confidence interval 1.11-1.23, p = 2.7 × 10-9). In subgroup GWASs stratified by six kidney stone composition subtypes, 19 significant loci were identified including two loci in coding regions (brushite; NXPH1, rs79970906 and rs4725104). The UMOD single nucleotide polymorphism rs28544423 was associated with differences in 24-h excretion of urinary analytes, and the minor allele was positively associated with calcium oxalate dihydrate stone composition (p < 0.05). No associations were found between UMOD variants and disease severity. Limitations include an omitted variable bias and a misclassification bias. Conclusions and clinical implications We replicated germline variants associated with kidney stone disease risk at UMOD and reported novel variants associated with stone composition. Genetic variants of UMOD are associated with differences in 24-h urine parameters and stone composition, but not disease severity. Patient summary We identify genetic variants linked to kidney stone disease within an electronic health record (EHR) system. These findings suggest a role for the EHR to enable a precision-medicine approach for stone disease.
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Affiliation(s)
- Ryan S. Hsi
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Siwei Zhang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jefferson L. Triozzi
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adriana M. Hung
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- VA Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical informatics, Vanderbilt University, Nashville, TN, USA
| | - Cosmin A. Bejan
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
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Jiang L, Huang L, Dai C, Zheng R, Miyake M, Mori Y, Nakao SY, Morino K, Ymashiro K, Miao YB, Li Q, Ren W, Ye Z, Li H, Yang Z, Shi Y. Genome-Wide Association Analysis Identifies LILRB2 Gene for Pathological Myopia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308968. [PMID: 39207058 DOI: 10.1002/advs.202308968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 07/13/2024] [Indexed: 09/04/2024]
Abstract
Pathological myopia (PM) is one of the leading causes of blindness, especially in Asia. To identify the genetic risk factors of PM, a two-stage genome-wide association study (GWAS) and replication analysis in East Asian populations is conducted. The analysis identified LILRB2 in 19q13.42 as a new candidate locus for PM. The increased protein expression of LILRB2/Pirb (mouse orthologous protein) in PM patients and myopia mouse models is validated. It is further revealed that the increase in LILRB2/Pirb promoted fatty acid synthesis and lipid accumulation, leading to the destruction of choroidal function and the development of PM. This study revealed the association between LILRB2 and PM, uncovering the molecular mechanism of lipid metabolism disorders leading to the pathogenesis of PM due to LILRB2 upregulation.
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Affiliation(s)
- Lingxi Jiang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, 610072, China
| | - Lulin Huang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, 610072, China
| | - Chao Dai
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Rui Zheng
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Yuki Mori
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Shin-Ya Nakao
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Kazuya Morino
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Kenji Ymashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Japan
| | - Yang-Bao Miao
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Qi Li
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Weiming Ren
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Zimeng Ye
- School of Medicine, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Hongjing Li
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, 610072, China
| | - Zhenglin Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, 610072, China
- Jinfeng Laboratory, Chongqing, China, Chongqing, 400000, China
| | - Yi Shi
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, Sichuan, 610072, China
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Hara A, Sato T, Kress S, Suzuki K, Pham KO, Tajima A, Schikowski T, Nakamura H. Sex-specific associations between air pollutants and asthma prevalence in Japanese adults: a population-based study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-9. [PMID: 38741239 DOI: 10.1080/09603123.2024.2352597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
This study investigated the association between air pollutants and asthma prevalence in male and female Japanese adults. In this retrospective cross-sectional analysis, annual mean exposure levels of air pollutants, specifically nitrogen dioxide (NO2) and particulate matter with a median aerodynamic diameter ≤2.5 μm (PM2.5), were assessed at a local monitoring site. Multivariable logistic regression models, adjusted for genetic and/or lifestyle factors, were used to explore the association between air pollutants and asthma, with stratification by sex. A total of 1,497 participants aged ≥40 years were included. Their mean age was 65.9 ± 12.4 years, with 847 being women. Overall, 91 participants were diagnosed with asthma. In the multivariable model, ambient exposure levels of NO2 and PM2.5 were significantly associated with asthma in women but not in men. This study highlights sex as a significant determinant of the link between air pollutants and asthma exacerbation, particularly among female Japanese adults.
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Affiliation(s)
- Akinori Hara
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Sara Kress
- Working group: Environmental epidemiology of lung, brain and skin aging, IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Keita Suzuki
- Department of Public Health, Advanced Preventive Medical Sciences Research Center, Kanazawa University, Kanazawa, Japan
| | - Kim-Oanh Pham
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Tamara Schikowski
- Working group: Environmental epidemiology of lung, brain and skin aging, IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Hiroyuki Nakamura
- Department of Hygiene and Public Health, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
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Grinde KE, Browning BL, Reiner AP, Thornton TA, Browning SR. Adjusting for principal components can induce spurious associations in genome-wide association studies in admixed populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587682. [PMID: 38617337 PMCID: PMC11014513 DOI: 10.1101/2024.04.02.587682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/24/2024]
Abstract
Principal component analysis (PCA) is widely used to control for population structure in genome-wide association studies (GWAS). Top principal components (PCs) typically reflect population structure, but challenges arise in deciding how many PCs are needed and ensuring that PCs do not capture other artifacts such as regions with atypical linkage disequilibrium (LD). In response to the latter, many groups suggest performing LD pruning or excluding known high LD regions prior to PCA. However, these suggestions are not universally implemented and the implications for GWAS are not fully understood, especially in the context of admixed populations. In this paper, we investigate the impact of pre-processing and the number of PCs included in GWAS models in African American samples from the Women's Women's Health Initiative SNP Health Association Resource and two Trans-Omics for Precision Medicine Whole Genome Sequencing Project contributing studies (Jackson Heart Study and Genetic Epidemiology of Chronic Obstructive Pulmonary Disease Study). In all three samples, we find the first PC is highly correlated with genome-wide ancestry whereas later PCs often capture local genomic features. The pattern of which, and how many, genetic variants are highly correlated with individual PCs differs from what has been observed in prior studies focused on European populations and leads to distinct downstream consequences: adjusting for such PCs yields biased effect size estimates and elevated rates of spurious associations due to the phenomenon of collider bias. Excluding high LD regions identified in previous studies does not resolve these issues. LD pruning proves more effective, but the optimal choice of thresholds varies across datasets. Altogether, our work highlights unique issues that arise when using PCA to control for ancestral heterogeneity in admixed populations and demonstrates the importance of careful pre-processing and diagnostics to ensure that PCs capturing multiple local genomic features are not included in GWAS models.
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Affiliation(s)
- Kelsey E. Grinde
- Department of Mathematics, Statistics, and Computer Science, Macalester College, Saint Paul, Minnesota, 55105, USA
| | - Brian L. Browning
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, 98195, USA
| | - Alexander P. Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, 98195, USA
| | - Timothy A. Thornton
- Regeneron Genetics Center, Tarrytown, New York, 10591, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
| | - Sharon R. Browning
- Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA
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Artomov M, Loboda AA, Artyomov MN, Daly MJ. Public platform with 39,472 exome control samples enables association studies without genotype sharing. Nat Genet 2024; 56:327-335. [PMID: 38200129 PMCID: PMC10864173 DOI: 10.1038/s41588-023-01637-y] [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: 11/14/2018] [Accepted: 12/01/2023] [Indexed: 01/12/2024]
Abstract
Acquiring a sufficiently powered cohort of control samples matched to a case sample can be time-consuming or, in some cases, impossible. Accordingly, an ability to leverage genetic data from control samples that were already collected elsewhere could dramatically improve power in genetic association studies. Sharing of control samples can pose significant challenges, since most human genetic data are subject to strict sharing regulations. Here, using the properties of singular value decomposition and subsampling algorithm, we developed a method allowing selection of the best-matching controls in an external pool of samples compliant with personal data protection and eliminating the need for genotype sharing. We provide access to a library of 39,472 exome sequencing controls at http://dnascore.net enabling association studies for case cohorts lacking control subjects. Using this approach, control sets can be selected from this online library with a prespecified matching accuracy, ensuring well-calibrated association analysis for both rare and common variants.
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Affiliation(s)
- Mykyta Artomov
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
| | - Alexander A Loboda
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- ITMO University, St. Petersburg, Russia
- Almazov National Medical Research Center, St. Petersburg, Russia
| | - Maxim N Artyomov
- Department of Immunology and Pathology, Washington University in St. Louis, St. Louis, MO, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
- Institute for Molecular Medicine Finland, Helsinki, Finland.
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6
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Hsi RS, Zhang S, Triozzi JL, Hung AM, Xu Y, Bejan CA. Evaluation of genetic associations with clinical phenotypes of kidney stone disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.18.24301501. [PMID: 38343797 PMCID: PMC10854345 DOI: 10.1101/2024.01.18.24301501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Introduction and Objective We sought to replicate and discover genetic associations of kidney stone disease within a large-scale electronic health record (EHR) system. Methods We performed genome-wide association studies (GWASs) for nephrolithiasis from genotyped samples of 5,571 cases and 83,692 controls. Among the significant risk variants, we performed association analyses of stone composition and first-time 24-hour urine parameters. To assess disease severity, we investigated the associations of risk variants with age at first stone diagnosis, age at first procedure, and time from first to second procedure. Results The main GWAS analysis identified 10 significant loci, each located on chromosome 16 within coding regions of the UMOD gene, which codes for uromodulin, a urine protein with inhibitory activity for calcium crystallization. The strongest signal was from SNP 16:20359633-C-T (odds ratio [OR] 1.17, 95% CI 1.11-1.23), with the remaining significant SNPs having similar effect sizes. In subgroup GWASs by stone composition, 19 significant loci were identified, of which two loci were located in coding regions (brushite; NXPH1 , rs79970906 and rs4725104). The UMOD SNP 16:20359633-C-T was associated with differences in 24-hour excretion of urinary calcium, uric acid, phosphorus, sulfate; and the minor allele was positively associated with calcium oxalate dihydrate stone composition (p<0.05). No associations were found between UMOD variants and disease severity. Conclusions We replicated germline variants associated with kidney stone disease risk at UMOD and reported novel variants associated with stone composition. Genetic variants of UMOD are associated with differences in 24-hour urine parameters and stone composition, but not disease severity.
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Lima IS, da Silva TM, Weiss S, Homuth G, Lerch MM, Figueiredo CA, Alcantara-Neves NM, Barreto ML, Marques CR. Genome-wide association study of Helicobacter pylori serological status in Latin American children. Helicobacter 2023; 28:e13008. [PMID: 37497783 DOI: 10.1111/hel.13008] [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: 04/26/2023] [Revised: 06/07/2023] [Accepted: 07/10/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Few genome-wide association studies (GWAS) on Helicobacter pylori infection susceptibility have been conducted for admixed populations from developing countries. Here, we performed a GWAS to identify genetic factors associated with H. pylori serostatus in a cohort of admixed children from a large Latin American urban center. METHODS A cross-sectional study involving 1161 children from 4 to 11 years old living in poor areas of Salvador, in northeastern Brazil. Logistic regression analysis was performed to detect associations between single-nucleotide variants (SNVs) and H. pylori seropositivity, assuming an additive genetic model. Enrichment analyses were conducted using the MAGMA v1.10 software. RESULTS We found 22 SNVs to be suggestively associated (p < 10-5 ) with H. pylori seropositivity. The most suggestive SNV was the rs77955022 (p = 4.83e-07) located in an intronic region of EXOC3 at 5p15.33. The second most suggestively associated SNV was rs10914996 (p = 8.97e-07), located in an intergenic region at 1p34.3. Furthermore, we were able to replicate three SNVs (p < 0.05) in the Study of Health in Pomerania (SHIP) cohort: the rs2339212 and rs4795970, both located at 17q12 near TMEM132E, as well as the rs6595814, an intronic variant of FBN2 at 5q23.3. The enrichment analysis indicated the participation of genes and metabolic pathways related to the regulation of the digestive system and gastric acid secretion in the risk of seropositivity for H. pylori. CONCLUSIONS Additional studies are required to validate these association findings in larger population samples and to get insight into the underlying physiological mechanisms.
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Affiliation(s)
- Iasmin Souza Lima
- Multidisciplinary Institute in Health, Federal University of Bahia, Vitória da Conquista, Brazil
| | | | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Markus M Lerch
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | | | | | - Maurício Lima Barreto
- Center of Data and Knowledge Integration for Health, Instituto Gonçalo Muniz, Fundação Osvaldo Cruz, Salvador, Brazil
| | - Cintia Rodrigues Marques
- Multidisciplinary Institute in Health, Federal University of Bahia, Vitória da Conquista, Brazil
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Lin BD, Pries LK, van Os J, Luykx JJ, Rutten BPF, Guloksuz S. Adjusting for population stratification in polygenic risk score analyses: a guide for model specifications in the UK Biobank. J Hum Genet 2023; 68:653-656. [PMID: 37188914 DOI: 10.1038/s10038-023-01161-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/06/2023] [Accepted: 05/08/2023] [Indexed: 05/17/2023]
Abstract
The current study was conducted to provide a general guidance for model specifications in polygenic risk score (PRS) analyses of the UK Biobank, such as adjusting for covariates (i.e. age, sex, recruitment centers, and genetic batch) and the number of principal components (PCs) that need to be included. To cover behavioral, physical and mental health outcomes, we evaluated three continuous outcomes (BMI, smoking, drinking) and two binary outcomes (Major Depressive Disorder and educational attainment). We applied 3280 (656 per phenotype) different models including different sets of covariates. We evaluated these different model specifications by comparing regression parameters such as R2, coefficients, and P values, as well as ANOVA tests. Findings suggest that only up to three PCs appears to be sufficient for controlling population stratification for most outcomes, whereas including other covariates (particularly age and sex) appears to be more essential for model performance.
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Affiliation(s)
- Bochao Danae Lin
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lotta-Katrin Pries
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Jim van Os
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Psychosis Studies, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Jurjen J Luykx
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- GGNet Mental Health, Warnsveld, The Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Sinan Guloksuz
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands.
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
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9
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Sahana G, Cai Z, Sanchez MP, Bouwman AC, Boichard D. Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle. J Dairy Sci 2023:S0022-0302(23)00357-0. [PMID: 37349208 DOI: 10.3168/jds.2022-22694] [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: 08/24/2022] [Accepted: 02/01/2023] [Indexed: 06/24/2023]
Abstract
Genotype data from dairy cattle selection programs have greatly facilitated GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models that go beyond additive effects, elucidate the genetic architecture of a trait, and finally, decipher the underlying biology of traits. The entire process, comprising data generation, quality control, statistical analyses, interpretation of association results, and linking results to biology should be designed and executed to minimize the generation of false-positive and false-negative associations and misleading links to biological processes. This review aims to provide general guidelines for data analysis that address data quality control, association tests, adjustment for population stratification, and significance evaluation to improve the reliability of conclusions. We also provide guidance on post-GWAS strategy and the interpretation of results. These guidelines are tailored to dairy cattle, which are characterized by long-range linkage disequilibrium, large half-sib families, and routinely collected phenotypes, requiring different approaches than those applied in human GWAS. We discuss common limitations and challenges that have been overlooked in the analysis and interpretation of GWAS to identify candidate sequence variants in dairy cattle.
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Affiliation(s)
- G Sahana
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark.
| | - Z Cai
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark
| | - M P Sanchez
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - A C Bouwman
- Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, the Netherlands
| | - D Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
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He Y, Zhang X, Zhang S, Zhang Y, Xie B, Huang M, Zhang J, Shen L, Long W, Liu Q. Prognostic RNA-editing signature predicts immune functions and therapy responses in gliomas. Front Genet 2023; 14:1120354. [PMID: 36845382 PMCID: PMC9945230 DOI: 10.3389/fgene.2023.1120354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Background: RNA-editing refers to post-transcriptional transcript alterations that lead to the formation of protein isoforms and the progression of various tumors. However, little is known about its roles in gliomas. Aim: The aim of this study is to identify prognosis-related RNA-editing sites (PREs) in glioma, and to explore their specific effects on glioma and potential mechanisms of action. Methods: Glioma genomic and clinical data were obtained from TCGA database and SYNAPSE platform. The PREs was identified with regression analyses and the corresponding prognostic model was evaluated with survival analysis and receiver operating characteristic curve. Functional enrichment of differentially expressed genes between risk groups was performed to explore action mechanisms. The CIBERSORT, ssGSEA, gene set variation analysis, and ESTIMATE algorithms were employed to assess the association between PREs risk score and variations of tumor microenvironment, immune cell infiltration, immune checkpoints, and immune responses. The maftools and pRRophetic packages were used to evaluate tumor mutation burden and predict drug sensitivity. Results: A total of thirty-five RNA-editing sites were identified as prognosis-related in glioma. Functional enrichment implied variation of immune-related pathways between groups. Notably, glioma samples with higher PREs risk score exhibited higher immune score, lower tumor purity, increased infiltration of macrophage and regulatory T cells, suppressed NK cell activation, elevated immune function score, upregulated immune checkpoint gene expression, and higher tumor mutation burden, all of which implied worse response to immune therapy. Finally, high-risk glioma samples are more sensitive to Z-LLNle-CHO and temozolomide, while the low-risk ones respond better to Lisitinib. Conclusion: We identified a PREs signature of thirty-five RNA editing sites and calculated their corresponding risk coefficients. Higher total signature risk score indicates worse prognosis and worse immune response and lower sensitivity to immune therapy. The novel PREs signature could help risk stratification, immunotherapy response prediction, individualized treatment strategy-making for glioma patients, and development of novel therapeutic approaches.
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Affiliation(s)
- Yi He
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Xingshu Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Sen Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zhang
- Department of Neurosurgery, People’s Hospital of Dengzhou, Dengzhou, Henan, China
| | - Bo Xie
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Meng Huang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China,Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China,Guangdong Cardiovascular Institute, Guangzhou, China
| | - Junjie Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lili Shen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenyong Long
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Wenyong Long, ; Qing Liu,
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China,*Correspondence: Wenyong Long, ; Qing Liu,
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11
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Li C, Chen Y, Chen Y, Ying Z, Hu Y, Kuang Y, Yang H, Song H, Zeng X. The Causal Association of Irritable Bowel Syndrome with Multiple Disease Outcomes: A Phenome-Wide Mendelian Randomization Study. J Clin Med 2023; 12:jcm12031106. [PMID: 36769754 PMCID: PMC9918111 DOI: 10.3390/jcm12031106] [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: 12/25/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND This study aimed to identify novel associations between irritable bowel syndrome (IBS) and a broad range of outcomes. METHODS In total, 346,352 white participants in the U.K. Biobank were randomly divided into two halves, in which a genome-wide association study (GWAS) of IBS and a polygenic risk score (PRS) analysis of IBS using GWAS summary statistics were conducted, respectively. A phenome-wide association study (PheWAS) based on the PRS of IBS was performed to identify disease outcomes associated with IBS. Then, the causalities of these associations were tested by both one-sample (individual-level data in U.K. Biobank) and two-sample (publicly available summary statistics) Mendelian randomization (MR). Sex-stratified PheWAS-MR analyses were performed in male and female, separately. RESULTS Our PheWAS identified five diseases associated with genetically predicted IBS. Conventional MR confirmed these causal associations between IBS and depression (OR: 1.07, 95%CI: 1.01-1.14, p = 0.02), diverticular diseases of the intestine (OR: 1.13, 95%CI: 1.08-1.19, p = 3.00 × 10-6), gastro-esophageal reflux disease (OR: 1.09, 95%CI: 1.05-1.13, p = 3.72 × 10-5), dyspepsia (OR: 1.21, 95%CI: 1.13-1.30, p = 9.28 × 10-8), and diaphragmatic hernia (OR: 1.10, 95%CI: 1.05-1.15, p = 2.75 × 10-5). The causality of these associations was observed in female only, but not men. CONCLUSIONS Increased risks of IBS is found to cause a series of disease outcomes. Our findings support further investigation on the clinical relevance of increased IBS risks with mental and digestive disorders.
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Affiliation(s)
- Chunyang Li
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Yilong Chen
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Yi Chen
- Department of Gastrointestinal Surgery, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
| | - Zhiye Ying
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Yao Hu
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Yalan Kuang
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Huazhen Yang
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Huan Song
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
| | - Xiaoxi Zeng
- Biomedical Big Data Center, West China Hospital, West China School of Medicine, Sichuan University, 37 Guo Xue Xiang, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, 17 Ren Min Nan Road 3rd Section, Chengdu 610041, China
- Correspondence: ; Tel.: +86-28-85422819
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12
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Efficient gene-environment interaction testing through bootstrap aggregating. Sci Rep 2023; 13:937. [PMID: 36650248 PMCID: PMC9845231 DOI: 10.1038/s41598-023-28172-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Gene-environment (GxE) interactions are an important and sophisticated component in the manifestation of complex phenotypes. Simple univariate tests lack statistical power due to the need for multiple testing adjustment and not incorporating potential interplay between several genetic loci. Approaches based on internally constructed genetic risk scores (GRS) require the partitioning of the available sample into training and testing data sets, thus, lowering the effective sample size for testing the GxE interaction itself. To overcome these issues, we propose a statistical test that employs bagging (bootstrap aggregating) in the GRS construction step and utilizes its out-of-bag prediction mechanism. This approach has the key advantage that the full available data set can be used for both constructing the GRS and testing the GxE interaction. To also incorporate interactions between genetic loci, we, furthermore, investigate if using random forests as the GRS construction method in GxE interaction testing further increases the statistical power. In a simulation study, we show that both novel procedures lead to a higher statistical power for detecting GxE interactions, while still controlling the type I error. The random-forests-based test outperforms a bagging-based test that uses the elastic net as its base learner in most scenarios. An application of the testing procedures to a real data set from a German cohort study suggests that there might be a GxE interaction involving exposure to air pollution regarding rheumatoid arthritis.
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13
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Kress S, Kilanowski A, Wigmann C, Zhao Q, Zhao T, Abramson MJ, Gappa M, Standl M, Unfried K, Schikowski T. Airway inflammation in adolescents and elderly women: Chronic air pollution exposure and polygenic susceptibility. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156655. [PMID: 35697214 DOI: 10.1016/j.scitotenv.2022.156655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIM The fractional exhaled nitric oxide (FeNO) concentration in the exhaled breath is a biomarker for eosinophilic airway inflammation. We explored the interplay between chronic air pollution exposure and polygenic susceptibility to airway inflammation at different critical age stages. METHODS Adolescents (15 yr) enrolled in the GINIplus/LISA birth cohorts (n = 2434) and 220 elderly women (75 yr on average) enrolled in the SALIA cohort with FeNO measurements available were investigated. Environmental main effects of the mean of ESCAPE land-use regression air pollutant concentrations within a time window of 15 years and main effects of the polygenic risk scores (PRS) using internal weights from elastic net regression of genome-wide derived single nucleotide polymorphisms were investigated. Furthermore, we examined gene-environment interaction (GxE) effects on natural log-transformed FeNO levels by adjusted linear regression models. RESULTS While we observed no significant environmental and polygenic main effects on airway inflammation in either age group, we found robust harmful effects of chronic nitrogen dioxide (NO2) exposure in the GxE models for elderly women (16.2 % increase in FeNO, p-value = 0.027). Stratified analyses found GxE effects between the PRS and chronic NO2 exposure in never-smoker elderly women and in adolescents without any inflammatory respiratory conditions. CONCLUSIONS FeNO measurement is a useful biomarker to detect higher risk of NO2-induced eosinophilic airway inflammation in the elderly. There was limited evidence for GxE effects on airway inflammation in adolescents or the elderly. Further GxE studies in subpopulations should be conducted to investigate the assumption that susceptibility to airway inflammation differs between age stages.
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Affiliation(s)
- Sara Kress
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, Düsseldorf 40225, Germany; Medical Research School Düsseldorf, Heinrich Heine University, Universitätsstraße 1, Düsseldorf 40225, Germany.
| | - Anna Kilanowski
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany; Institute for Medical Information Processing, Biometry, and Epidemiology; Pettenkofer School of Public Health, LMU Munich, Geschwister-Scholl-Platz 1, Munich 80539, Germany; Division of Metabolic and Nutritional Medicine, Dr. von Hauner Children's Hospital, University of Munich Medical Center, Lindwurmstr. 4, Munich 80337, Germany.
| | - Claudia Wigmann
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, Düsseldorf 40225, Germany.
| | - Qi Zhao
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, Düsseldorf 40225, Germany; Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan City 250012, Shandong Province, China; School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia.
| | - Tianyu Zhao
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.
| | - Michael J Abramson
- School of Public Health and Preventive Medicine, Monash University, 553 St Kilda Rd, Melbourne, VIC 3004, Australia.
| | - Monika Gappa
- Department of Paediatrics, Evangelisches Krankenhaus, Kirchfeldstraße 40, Düsseldorf 40217, Germany.
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Ingolstädter Landstr. 1, Neuherberg 85764, Germany; German Center for Lung Research (DZL), Aulweg 130, Gießen 35392, Germany.
| | - Klaus Unfried
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, Düsseldorf 40225, Germany.
| | - Tamara Schikowski
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, Düsseldorf 40225, Germany.
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14
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Kress S, Wigmann C, Zhao Q, Herder C, Abramson MJ, Schwender H, Schikowski T. Chronic air pollution-induced subclinical airway inflammation and polygenic susceptibility. Respir Res 2022; 23:265. [PMID: 36151579 PMCID: PMC9508765 DOI: 10.1186/s12931-022-02179-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022] Open
Abstract
Background Air pollutants can activate low-grade subclinical inflammation which further impairs respiratory health. We aimed to investigate the role of polygenic susceptibility to chronic air pollution-induced subclinical airway inflammation. Methods We used data from 296 women (69–79 years) enrolled in the population-based SALIA cohort (Study on the influence of Air pollution on Lung function, Inflammation and Aging). Biomarkers of airway inflammation were measured in induced-sputum samples at follow-up investigation in 2007–2010. Chronic air pollution exposures at residential addresses within 15 years prior to the biomarker assessments were used to estimate main environmental effects on subclinical airway inflammation. Furthermore, we calculated internally weighted polygenic risk scores based on genome-wide derived single nucleotide polymorphisms. Polygenic main and gene-environment interaction (GxE) effects were investigated by adjusted linear regression models. Results Higher exposures to nitrogen dioxide (NO2), nitrogen oxides (NOx), particulate matter with aerodynamic diameters of ≤ 2.5 μm, ≤ 10 μm, and 2.5–10 µm significantly increased the levels of leukotriene (LT)B4 by 19.7% (p-value = 0.005), 20.9% (p = 0.002), 22.1% (p = 0.004), 17.4% (p = 0.004), and 23.4% (p = 0.001), respectively. We found significant effects of NO2 (25.9%, p = 0.008) and NOx (25.9%, p-value = 0.004) on the total number of cells. No significant GxE effects were observed. The trends were mostly robust in sensitivity analyses. Conclusions While this study confirms that higher chronic exposures to air pollution increase the risk of subclinical airway inflammation in elderly women, we could not demonstrate a significant role of polygenic susceptibility on this pathway. Further studies are required to investigate the role of polygenic susceptibility. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02179-3.
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Affiliation(s)
- Sara Kress
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany.,Medical Research School Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Claudia Wigmann
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany
| | - Qi Zhao
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany.,Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China.,School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,German Center for Diabetes Research (DZD), Partner Düsseldorf, München-Neuherberg, Germany.,Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael J Abramson
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany
| | - Tamara Schikowski
- IUF - Leibniz Research Institute for Environmental Medicine, Auf'm Hennekamp 50, 40225, Düsseldorf, Germany.
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15
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Irigoien I, Cormand B, Soler-Artigas M, Sanchez-Mora C, Ramos-Quiroga JA, Arenas C. New Distance-Based approach for Genome-Wide Association Studies. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2938-2949. [PMID: 34181548 DOI: 10.1109/tcbb.2021.3092812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
With the rise of genome-wide association studies (GWAS), the analysis of typical GWAS data sets with thousands of single-nucleotide polymorphisms (SNPs) has become crucial in biomedicine research. Here, we propose a new method to identify SNPs related to disease in case-control studies. The method, based on genetic distances between individuals, takes into account the possible population substructure, and avoids the issues of multiple testing. The method provides two ordered lists of SNPs; one with SNPs which minor alleles can be considered risk alleles for the disease, and another one with SNPs which minor alleles can be considered as protective. These two lists provide a useful tool to help the researcher to decide where to focus attention in a first stage.
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16
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Kress S, Hara A, Wigmann C, Sato T, Suzuki K, Pham KO, Zhao Q, Areal A, Tajima A, Schwender H, Nakamura H, Schikowski T. The Role of Polygenic Susceptibility on Air Pollution-Associated Asthma between German and Japanese Elderly Women. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9869. [PMID: 36011501 PMCID: PMC9407879 DOI: 10.3390/ijerph19169869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Polygenic susceptibility likely influences individual responses to air pollutants and the risk of asthma. We compared the role of polygenic susceptibility on air pollution-associated asthma between German and Japanese women. We investigated women that were enrolled in the German SALIA cohort (n = 771, mean age = 73 years) and the Japanese Shika cohort (n = 847, mean age = 67 years) with known asthma status. Adjusted logistic regression models were used to assess the associations between (1) particulate matter with a median aerodynamic diameter ≤ 2.5μm (PM2.5) and nitrogen dioxide (NO2), (2) polygenic risk scores (PRS), and (3) gene-environment interactions (G × E) with asthma. We found an increased risk of asthma in Japanese women after exposure to low pollutant levels (PM2.5: median = 12.7µg/m3, p-value < 0.001, NO2: median = 8.5µg/m3, p-value < 0.001) and in German women protective polygenic effects (p-value = 0.008). While we found no significant G × E effects, the direction in both groups was that the PRS increased the effect of PM2.5 and decreased the effect of NO2 on asthma. Our study confirms that exposure to low air pollution levels increases the risk of asthma in Japanese women and indicates polygenic effects in German women; however, there was no evidence of G × E effects. Future genome-wide G × E studies should further explore the role of ethnic-specific polygenic susceptibility to asthma.
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Affiliation(s)
- Sara Kress
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany
- Medical Research School Düsseldorf, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Akinori Hara
- Department of Hygiene and Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Ishikawa, Japan
| | - Claudia Wigmann
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Ishikawa, Japan
| | - Keita Suzuki
- Department of Hygiene and Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Ishikawa, Japan
| | - Kim-Oanh Pham
- Department of Hygiene and Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Ishikawa, Japan
| | - Qi Zhao
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany
- Department of Epidemiology, School of Public Health, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan 250012, China
| | - Ashtyn Areal
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany
- Medical Research School Düsseldorf, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Ishikawa, Japan
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Hiroyuki Nakamura
- Department of Hygiene and Public Health, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Ishikawa, Japan
| | - Tamara Schikowski
- IUF—Leibniz Research Institute for Environmental Medicine, Auf’m Hennekamp 50, 40225 Düsseldorf, Germany
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17
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Practical forensic use of kinship determination using high-density SNP profiling based on a microarray platform, focusing on low-quantity DNA. Forensic Sci Int Genet 2022; 61:102752. [DOI: 10.1016/j.fsigen.2022.102752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/16/2022] [Accepted: 07/27/2022] [Indexed: 11/20/2022]
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18
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Sugasawa S, Noma H. Efficient testing and effect size estimation for set-based genetic association inference via semiparametric multilevel mixture modeling. Biom J 2022; 64:1142-1152. [PMID: 35543501 DOI: 10.1002/bimj.202100234] [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: 08/02/2021] [Revised: 01/25/2022] [Accepted: 04/03/2022] [Indexed: 11/10/2022]
Abstract
In genetic association studies, rare variants with extremely low allele frequencies play a crucial role in complex traits. Therefore, set-based testing methods that jointly assess the effects of groups of single nucleotide polymorphisms (SNPs) were developed to increase the powers of the association tests. However, these powers are still insufficient, and precise estimations of the effect sizes of individual SNPs are largely impossible. In this article, we provide an efficient set-based statistical inference framework that addresses both of these important issues simultaneously using an empirical Bayes method with semiparametric multilevel mixture modeling. We propose to utilize the hierarchical model that incorporates variations in set-specific effects and to apply the optimal discovery procedure (ODP) that achieves the largest overall power in multiple significance testing. In addition, we provide an optimal "set-based" estimator of the empirical distribution of effect sizes. The efficiency of the proposed methods is demonstrated through application to a genome-wide association study of coronary artery disease and through simulation studies. The results demonstrated numerous rare variants with large effect sizes for coronary artery disease, and the number of significant sets detected by the ODP was much greater than those identified by existing methods.
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Affiliation(s)
- Shonosuke Sugasawa
- Center for Spatial Information Science, The University of Tokyo, Chiba, Japan.,Research Center for Medical and Health Data Science, The Institute of Statistical Mathematics, Tokyo, Japan
| | - Hisashi Noma
- Research Center for Medical and Health Data Science, The Institute of Statistical Mathematics, Tokyo, Japan.,Department of Data Science, The Institute of Statistical Mathematics, Tokyo, Japan
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19
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Smajić S, Prada-Medina CA, Landoulsi Z, Ghelfi J, Delcambre S, Dietrich C, Jarazo J, Henck J, Balachandran S, Pachchek S, Morris CM, Antony P, Timmermann B, Sauer S, Pereira SL, Schwamborn JC, May P, Grünewald A, Spielmann M. Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state. Brain 2022; 145:964-978. [PMID: 34919646 PMCID: PMC9050543 DOI: 10.1093/brain/awab446] [Citation(s) in RCA: 169] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/21/2021] [Accepted: 11/18/2021] [Indexed: 11/29/2022] Open
Abstract
Idiopathic Parkinson's disease is characterized by a progressive loss of dopaminergic neurons, but the exact disease aetiology remains largely unknown. To date, Parkinson's disease research has mainly focused on nigral dopaminergic neurons, although recent studies suggest disease-related changes also in non-neuronal cells and in midbrain regions beyond the substantia nigra. While there is some evidence for glial involvement in Parkinson's disease, the molecular mechanisms remain poorly understood. The aim of this study was to characterize the contribution of all cell types of the midbrain to Parkinson's disease pathology by single-nuclei RNA sequencing and to assess the cell type-specific risk for Parkinson's disease using the latest genome-wide association study. We profiled >41 000 single-nuclei transcriptomes of post-mortem midbrain from six idiopathic Parkinson's disease patients and five age-/sex-matched controls. To validate our findings in a spatial context, we utilized immunolabelling of the same tissues. Moreover, we analysed Parkinson's disease-associated risk enrichment in genes with cell type-specific expression patterns. We discovered a neuronal cell cluster characterized by CADPS2 overexpression and low TH levels, which was exclusively present in idiopathic Parkinson's disease midbrains. Validation analyses in laser-microdissected neurons suggest that this cluster represents dysfunctional dopaminergic neurons. With regard to glial cells, we observed an increase in nigral microglia in Parkinson's disease patients. Moreover, nigral idiopathic Parkinson's disease microglia were more amoeboid, indicating an activated state. We also discovered a reduction in idiopathic Parkinson's disease oligodendrocyte numbers with the remaining cells being characterized by a stress-induced upregulation of S100B. Parkinson's disease risk variants were associated with glia- and neuron-specific gene expression patterns in idiopathic Parkinson's disease cases. Furthermore, astrocytes and microglia presented idiopathic Parkinson's disease-specific cell proliferation and dysregulation of genes related to unfolded protein response and cytokine signalling. While reactive patient astrocytes showed CD44 overexpression, idiopathic Parkinson's disease microglia revealed a pro-inflammatory trajectory characterized by elevated levels of IL1B, GPNMB and HSP90AA1. Taken together, we generated the first single-nuclei RNA sequencing dataset from the idiopathic Parkinson's disease midbrain, which highlights a disease-specific neuronal cell cluster as well as 'pan-glial' activation as a central mechanism in the pathology of the movement disorder. This finding warrants further research into inflammatory signalling and immunomodulatory treatments in Parkinson's disease.
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Affiliation(s)
- Semra Smajić
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | | | - Zied Landoulsi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Jenny Ghelfi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carola Dietrich
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Javier Jarazo
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- OrganoTherapeutics SARL-S, L-4362 Esch-sur-Alzette, Luxembourg
| | - Jana Henck
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | | | - Sinthuja Pachchek
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Christopher M. Morris
- Newcastle Brain Tissue Resource, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, NE1 7RU Newcastle upon Tyne, UK
| | - Paul Antony
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Sascha Sauer
- Max-Delbrück-Centrum für Molekulare Medizin, Genomics Group, D-13125 Berlin, Germany
| | - Sandro L. Pereira
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Jens C. Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- OrganoTherapeutics SARL-S, L-4362 Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- Institute of Neurogenetics, University of Lübeck, D-23562 Lübeck, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
- Institute of Human Genetics, Kiel University, D-42118 Kiel, Germany
- Institute of Human Genetics, University of Lübeck, D-23562 Lübeck, Germany
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20
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Collister JA, Liu X, Clifton L. Calculating Polygenic Risk Scores (PRS) in UK Biobank: A Practical Guide for Epidemiologists. Front Genet 2022; 13:818574. [PMID: 35251129 PMCID: PMC8894758 DOI: 10.3389/fgene.2022.818574] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/12/2022] [Indexed: 01/11/2023] Open
Abstract
A polygenic risk score estimates the genetic risk of an individual for some disease or trait, calculated by aggregating the effect of many common variants associated with the condition. With the increasing availability of genetic data in large cohort studies such as the UK Biobank, inclusion of this genetic risk as a covariate in statistical analyses is becoming more widespread. Previously this required specialist knowledge, but as tooling and data availability have improved it has become more feasible for statisticians and epidemiologists to calculate existing scores themselves for use in analyses. While tutorial resources exist for conducting genome-wide association studies and generating of new polygenic risk scores, fewer guides exist for the simple calculation and application of existing genetic scores. This guide outlines the key steps of this process: selection of suitable polygenic risk scores from the literature, extraction of relevant genetic variants and verification of their quality, calculation of the risk score and key considerations of its inclusion in statistical models, using the UK Biobank imputed data as a model data set. Many of the techniques in this guide will generalize to other datasets, however we also focus on some of the specific techniques required for using data in the formats UK Biobank have selected. This includes some of the challenges faced when working with large numbers of variants, where the computation time required by some tools is impractical. While we have focused on only a couple of tools, which may not be the best ones for every given aspect of the process, one barrier to working with genetic data is the sheer volume of tools available, and the difficulty for a novice to assess their viability. By discussing in depth a couple of tools that are adequate for the calculation even at large scale, we hope to make polygenic risk scores more accessible to a wider range of researchers.
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Affiliation(s)
- Jennifer A. Collister
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
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21
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Zanussi JT, Zhao J, Dorn CA, Liu G, Feng Q, Wei W, Mosley JD, Stein CM, Kawai VK. Identifying Potential Therapeutic Applications and Diagnostic Harms of Increased Bilirubin Concentrations: A Clinical and Genetic Approach. Clin Pharmacol Ther 2022; 111:435-443. [PMID: 34625956 PMCID: PMC8748314 DOI: 10.1002/cpt.2441] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/16/2021] [Indexed: 02/03/2023]
Abstract
Bilirubin has antioxidant and anti-inflammatory properties in vitro and in animal studies and protects against inflammatory, cardiovascular, and other diseases in observational studies; therefore, bilirubin has potential as a therapeutic agent. However, observational studies could be confounded by many factors. We used a genetic (n = 61,281) and clinical (n = 234,670) approach to define the association between bilirubin and 19 conditions with a putative protective signal in observational studies. We also tested if individuals with genetically higher bilirubin levels underwent more diagnostic tests. We used a common variant in UGT1A1 (rs6742078) associated with an 26% increase in bilirubin levels in the genetic studies. Carriers of the variant had higher bilirubin levels (P = 2.2 × 10-16 ) but there was no significant association with any of the 19 conditions. In a phenome-wide association study (pheWAS) to seek undiscovered genetic associations, the only significant finding was increased risk of "jaundice-not of newborn." Carriers of the variant allele were more likely to undergo an abdominal ultrasound (odds ratio = 1.04, [1.00-1.08], P = 0.03). In contrast, clinically measured bilirubin levels were significantly associated with 15 of the 19 conditions (P < 0.003) and with 431 clinical diagnoses in the pheWAS (P < 1 × 10-5 adjusted for sex, age, and follow-up). With additional adjustment for smoking and body mass index, 7 of 19 conditions and 260 pheWAS diagnoses remained significantly associated with bilirubin levels. In conclusion, bilirubin does not protect against inflammatory or other diseases using a genetic approach; the many putative beneficial associations reported clinically are likely due to confounding.
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Affiliation(s)
- Jacy T. Zanussi
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Juan Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Chad A. Dorn
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ge Liu
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - QiPing Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - WeiQi Wei
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jonathan D. Mosley
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - C. Michael Stein
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Vivian K. Kawai
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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22
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Suitability of GWAS as a Tool to Discover SNPs Associated with Tick Resistance in Cattle: A Review. Pathogens 2021; 10:pathogens10121604. [PMID: 34959558 PMCID: PMC8707706 DOI: 10.3390/pathogens10121604] [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: 10/18/2021] [Revised: 11/22/2021] [Accepted: 12/01/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the biological mechanisms underlying tick resistance in cattle holds the potential to facilitate genetic improvement through selective breeding. Genome wide association studies (GWAS) are popular in research on unraveling genetic determinants underlying complex traits such as tick resistance. To date, various studies have been published on single nucleotide polymorphisms (SNPs) associated with tick resistance in cattle. The discovery of SNPs related to tick resistance has led to the mapping of associated candidate genes. Despite the success of these studies, information on genetic determinants associated with tick resistance in cattle is still limited. This warrants the need for more studies to be conducted. In Africa, the cost of genotyping is still relatively expensive; thus, conducting GWAS is a challenge, as the minimum number of animals recommended cannot be genotyped. These population size and genotype cost challenges may be overcome through the establishment of collaborations. Thus, the current review discusses GWAS as a tool to uncover SNPs associated with tick resistance, by focusing on the study design, association analysis, factors influencing the success of GWAS, and the progress on cattle tick resistance studies.
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23
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Das S, Saket B, Kwon BC, Endert A. Geono-Cluster: Interactive Visual Cluster Analysis for Biologists. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2021; 27:4401-4412. [PMID: 32746262 DOI: 10.1109/tvcg.2020.3002166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biologists often perform clustering analysis to derive meaningful patterns, relationships, and structures from data instances and attributes. Though clustering plays a pivotal role in biologists' data exploration, it takes non-trivial efforts for biologists to find the best grouping in their data using existing tools. Visual cluster analysis is currently performed either programmatically or through menus and dialogues in many tools, which require parameter adjustments over several steps of trial-and-error. In this article, we introduce Geono-Cluster, a novel visual analysis tool designed to support cluster analysis for biologists who do not have formal data science training. Geono-Cluster enables biologists to apply their domain expertise into clustering results by visually demonstrating how their expected clustering outputs should look like with a small sample of data instances. The system then predicts users' intentions and generates potential clustering results. Our study follows the design study protocol to derive biologists' tasks and requirements, design the system, and evaluate the system with experts on their own dataset. Results of our study with six biologists provide initial evidence that Geono-Cluster enables biologists to create, refine, and evaluate clustering results to effectively analyze their data and gain data-driven insights. At the end, we discuss lessons learned and implications of our study.
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24
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de Vries JH, Kling D, Vidaki A, Arp P, Kalamara V, Verbiest MMPJ, Piniewska-Róg D, Parsons TJ, Uitterlinden AG, Kayser M. Impact of SNP microarray analysis of compromised DNA on kinship classification success in the context of investigative genetic genealogy. Forensic Sci Int Genet 2021; 56:102625. [PMID: 34753062 DOI: 10.1016/j.fsigen.2021.102625] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/04/2022]
Abstract
Single nucleotide polymorphism (SNP) data generated with microarray technologies have been used to solve murder cases via investigative leads obtained from identifying relatives of the unknown perpetrator included in accessible genomic databases, an approach referred to as investigative genetic genealogy (IGG). However, SNP microarrays were developed for relatively high input DNA quantity and quality, while DNA typically obtainable from crime scene stains is of low DNA quantity and quality, and SNP microarray data obtained from compromised DNA are largely missing. By applying the Illumina Global Screening Array (GSA) to 264 DNA samples with systematically altered quantity and quality, we empirically tested the impact of SNP microarray analysis of compromised DNA on kinship classification success, as relevant in IGG. Reference data from manufacturer-recommended input DNA quality and quantity were used to estimate genotype accuracy in the compromised DNA samples and for simulating data of different degree relatives. Although stepwise decrease of input DNA amount from 200 ng to 6.25 pg led to decreased SNP call rates and increased genotyping errors, kinship classification success did not decrease down to 250 pg for siblings and 1st cousins, 1 ng for 2nd cousins, while at 25 pg and below kinship classification success was zero. Stepwise decrease of input DNA quality via increased DNA fragmentation resulted in the decrease of genotyping accuracy as well as kinship classification success, which went down to zero at the average DNA fragment size of 150 base pairs. Combining decreased DNA quantity and quality in mock casework and skeletal samples further highlighted possibilities and limitations. Overall, GSA analysis achieved maximal kinship classification success from 800 to 200 times lower input DNA quantities than manufacturer-recommended, although DNA quality plays a key role too, while compromised DNA produced false negative kinship classifications rather than false positive ones.
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Affiliation(s)
- Jard H de Vries
- Erasmus MC, University Medical Center Rotterdam, Department of Internal Medicine, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Daniel Kling
- Department of Forensic Genetics and Toxicology, National Board of Forensic Medicine, Artillerigatan 12, 587 58 Linköping, Sweden
| | - Athina Vidaki
- Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Pascal Arp
- Erasmus MC, University Medical Center Rotterdam, Department of Internal Medicine, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Vivian Kalamara
- Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Michael M P J Verbiest
- Erasmus MC, University Medical Center Rotterdam, Department of Internal Medicine, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Danuta Piniewska-Róg
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; Department of Forensic Medicine, Jagiellonian University Medical College, 31-531 Krakow, Poland
| | - Thomas J Parsons
- International Commission on Missing Persons, Koninginnegracht 12a, 2514 AA Den Haag, the Netherlands
| | - André G Uitterlinden
- Erasmus MC, University Medical Center Rotterdam, Department of Internal Medicine, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands; Erasmus MC, University Medical Center Rotterdam, Department of Epidemiology, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Manfred Kayser
- Erasmus MC, University Medical Center Rotterdam, Department of Genetic Identification, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands.
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25
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Canales FJ, Montilla-Bascón G, Bekele WA, Howarth CJ, Langdon T, Rispail N, Tinker NA, Prats E. Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2063-2077. [PMID: 33770189 DOI: 10.5061/dryad.0gb5mkm0g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 05/19/2023]
Abstract
Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.
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Affiliation(s)
- F J Canales
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - G Montilla-Bascón
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - W A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - C J Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth Univ, Aberystwyth, UK
| | - T Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth Univ, Aberystwyth, UK
| | - N Rispail
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - N A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - E Prats
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain.
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26
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Canales FJ, Montilla-Bascón G, Bekele WA, Howarth CJ, Langdon T, Rispail N, Tinker NA, Prats E. Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2063-2077. [PMID: 33770189 PMCID: PMC8263550 DOI: 10.1007/s00122-021-03805-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/24/2021] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.
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Affiliation(s)
- F J Canales
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - G Montilla-Bascón
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - W A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - C J Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth Univ, Aberystwyth, UK
| | - T Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth Univ, Aberystwyth, UK
| | - N Rispail
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain
| | - N A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - E Prats
- Institute for Sustainable Agriculture, CSIC, Avenida Menéndez Pidal, 14004, Córdoba, Spain.
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27
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Read RW, Schlauch KA, Lombardi VC, Cirulli ET, Washington NL, Lu JT, Grzymski JJ. Genome-Wide Identification of Rare and Common Variants Driving Triglyceride Levels in a Nevada Population. Front Genet 2021; 12:639418. [PMID: 33763119 PMCID: PMC7982958 DOI: 10.3389/fgene.2021.639418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/12/2021] [Indexed: 01/08/2023] Open
Abstract
Clinical conditions correlated with elevated triglyceride levels are well-known: coronary heart disease, hypertension, and diabetes. Underlying genetic and phenotypic mechanisms are not fully understood, partially due to lack of coordinated genotypic-phenotypic data. Here we use a subset of the Healthy Nevada Project, a population of 9,183 sequenced participants with longitudinal electronic health records to examine consequences of altered triglyceride levels. Specifically, Healthy Nevada Project participants sequenced by the Helix Exome+ platform were cross-referenced to their electronic medical records to identify: (1) rare and common single-variant genome-wide associations; (2) gene-based associations using a Sequence Kernel Association Test; (3) phenome-wide associations with triglyceride levels; and (4) pleiotropic variants linked to triglyceride levels. The study identified 549 significant single-variant associations (p < 8.75 × 10-9), many in chromosome 11's triglyceride hotspot: ZPR1, BUD13, APOC3, APOA5. A well-known protective loss-of-function variant in APOC3 (R19X) was associated with a 51% decrease in triglyceride levels in the cohort. Sixteen gene-based triglyceride associations were identified; six of these genes surprisingly did not include a single variant with significant associations. Results at the variant and gene level were validated with the UK Biobank. The combination of a single-variant genome-wide association, a gene-based association method, and phenome wide-association studies identified rare and common variants, genes, and phenotypes associated with elevated triglyceride levels, some of which may have been overlooked with standard approaches.
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Affiliation(s)
- Robert W. Read
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
| | - Karen A. Schlauch
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
| | - Vincent C. Lombardi
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, Reno, NV, United States
| | | | | | - James T. Lu
- Helix Opco, LLC., San Mateo, CA, United States
| | - Joseph J. Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, NV, United States
- Renown Health, Reno, NV, United States
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28
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Martin AM, Cassirer EF, Waits LP, Plowright RK, Cross PC, Andrews KR. Genomic association with pathogen carriage in bighorn sheep ( Ovis canadensis). Ecol Evol 2021; 11:2488-2502. [PMID: 33767816 PMCID: PMC7981200 DOI: 10.1002/ece3.7159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/03/2022] Open
Abstract
Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population-level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well-studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family-based genome-wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome-wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP-based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.
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Affiliation(s)
- Alynn M. Martin
- United States Geological SurveyNorthern Rocky Mountain Science CenterBozemanMTUSA
| | | | | | - Raina K. Plowright
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Paul C. Cross
- United States Geological SurveyNorthern Rocky Mountain Science CenterBozemanMTUSA
| | - Kimberly R. Andrews
- Institute for Bioinformatics and Evolutionary Studies (IBEST)University of IdahoMoscowIDUSA
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29
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Jalil Sarghale A, Moradi Shahrebabak M, Moradi Shahrebabak H, Nejati Javaremi A, Saatchi M, Khansefid M, Miar Y. Genome-wide association studies for methane emission and ruminal volatile fatty acids using Holstein cattle sequence data. BMC Genet 2020; 21:129. [PMID: 33228565 PMCID: PMC7684878 DOI: 10.1186/s12863-020-00953-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 11/12/2020] [Indexed: 01/02/2023] Open
Abstract
Background Methane emission by ruminants has contributed considerably to the global warming and understanding the genomic architecture of methane production may help livestock producers to reduce the methane emission from the livestock production system. The goal of our study was to identify genomic regions affecting the predicted methane emission (PME) from volatile fatty acids (VFAs) indicators and VFA traits using imputed whole-genome sequence data in Iranian Holstein cattle. Results Based on the significant-association threshold (p < 5 × 10− 8), 33 single nucleotide polymorphisms (SNPs) were detected for PME per kg milk (n = 2), PME per kg fat (n = 14), and valeric acid (n = 17). Besides, 69 genes were identified for valeric acid (n = 18), PME per kg milk (n = 4) and PME per kg fat (n = 47) that were located within 1 Mb of significant SNPs. Based on the gene ontology (GO) term analysis, six promising candidate genes were significantly clustered in organelle organization (GO:0004984, p = 3.9 × 10− 2) for valeric acid, and 17 candidate genes significantly clustered in olfactory receptors activity (GO:0004984, p = 4 × 10− 10) for PME traits. Annotation results revealed 31 quantitative trait loci (QTLs) for milk yield and its components, body weight, and residual feed intake within 1 Mb of significant SNPs. Conclusions Our results identified 33 SNPs associated with PME and valeric acid traits, as well as 17 olfactory receptors activity genes for PME traits related to feed intake and preference. Identified SNPs were close to 31 QTLs for milk yield and its components, body weight, and residual feed intake traits. In addition, these traits had high correlations with PME trait. Overall, our findings suggest that marker-assisted and genomic selection could be used to improve the difficult and expensive-to-measure phenotypes such as PME. Moreover, prediction of methane emission by VFA indicators could be useful for increasing the size of reference population required in genome-wide association studies and genomic selection.
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Affiliation(s)
- Ali Jalil Sarghale
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran.,Department of Animal Science and Aquaculture, Dalhousie University, Truro, B2N 5E3, Canada
| | - Mohammad Moradi Shahrebabak
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran.
| | - Hossein Moradi Shahrebabak
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Ardeshir Nejati Javaremi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Mahdi Saatchi
- Department of Animal Science, Iowa State University, 806 Stange Road, Ames, IA, 50011, USA.,American Simmental Association, Bozeman, MT, 59715, USA
| | - Majid Khansefid
- Agriculture Victoria, AgriBio Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, B2N 5E3, Canada.
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30
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Ovejero‐Benito MC, Muñoz‐Aceituno E, Sabador D, Almoguera B, Prieto‐Pérez R, Hakonarson H, Coto‐Segura P, Carretero G, Reolid A, Llamas‐Velasco M, Abad‐Santos F, Daudén E. Genome‐wide association analysis of psoriasis patients treated with anti‐TNF drugs. Exp Dermatol 2020; 29:1225-1232. [DOI: 10.1111/exd.14215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/01/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023]
Affiliation(s)
- María C. Ovejero‐Benito
- Clinical Pharmacology Department Hospital Universitario de la Princesa Instituto Teófilo Hernando Universidad Autónoma de Madrid (UAM) Instituto de Investigación Sanitaria la Princesa (IIS‐IP) Madrid Spain
| | - Ester Muñoz‐Aceituno
- Dermatology Department Hospital Universitario de la Princesa Instituto de Investigación Sanitaria La Princesa (IIS‐IP) Madrid Spain
| | - David Sabador
- Clinical Pharmacology Department Hospital Universitario de la Princesa Instituto Teófilo Hernando Universidad Autónoma de Madrid (UAM) Instituto de Investigación Sanitaria la Princesa (IIS‐IP) Madrid Spain
| | - Berta Almoguera
- Hospital Universitario Fundación Jiménez Díaz (HUFJD). CIBERER Madrid Spain
- Center for Applied Genomics The Children's Hospital of Philadelphia Philadelphia PA USA
| | - Rocío Prieto‐Pérez
- Clinical Pharmacology Department Hospital Universitario de la Princesa Instituto Teófilo Hernando Universidad Autónoma de Madrid (UAM) Instituto de Investigación Sanitaria la Princesa (IIS‐IP) Madrid Spain
| | - Hakon Hakonarson
- Center for Applied Genomics The Children's Hospital of Philadelphia Philadelphia PA USA
- Department of Pediatrics The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA
| | | | - Gregorio Carretero
- Dermatology Department Hospital Universitario de Gran Canaria Dr. Negrín Las Palmas de Gran Canaria Spain
| | - Alejandra Reolid
- Dermatology Department Hospital Universitario de la Princesa Instituto de Investigación Sanitaria La Princesa (IIS‐IP) Madrid Spain
| | - Mar Llamas‐Velasco
- Dermatology Department Hospital Universitario de la Princesa Instituto de Investigación Sanitaria La Princesa (IIS‐IP) Madrid Spain
| | - Francisco Abad‐Santos
- Clinical Pharmacology Department Hospital Universitario de la Princesa Instituto Teófilo Hernando Universidad Autónoma de Madrid (UAM) Instituto de Investigación Sanitaria la Princesa (IIS‐IP) Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) Instituto de Salud Carlos III Madrid Spain
| | - Esteban Daudén
- Dermatology Department Hospital Universitario de la Princesa Instituto de Investigación Sanitaria La Princesa (IIS‐IP) Madrid Spain
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31
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Chen Y, Peloso GM, Liu CT, DeStefano AL, Dupuis J. Evaluation of population stratification adjustment using genome-wide or exonic variants. Genet Epidemiol 2020; 44:702-716. [PMID: 32608112 PMCID: PMC7722041 DOI: 10.1002/gepi.22332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/13/2020] [Accepted: 06/18/2020] [Indexed: 11/11/2022]
Abstract
Population stratification may cause an inflated type-I error and spurious association when assessing the association between genetic variations with an outcome. Many genetic association studies are now using exonic variants, which captures only 1% of the genome, however, population stratification adjustments have not been evaluated in the context of exonic variants. We compare the performance of two established approaches: principal components analysis (PCA) and mixed-effects models and assess the utility of genome-wide (GW) and exonic variants, by simulation and using a data set from the Framingham Heart Study. Our results illustrate that although the PCs and genetic relationship matrices computed by GW and exonic markers are different, the type-I error rate of association tests for common variants with additive effect appear to be properly controlled in the presence of population stratification. In addition, by considering single nucleotide variants (SNVs) that have different levels of confounding by population stratification, we also compare the power across multiple association approaches to account for population stratification such as PC-based corrections and mixed-effects models. We find that while these two methods achieve a similar power for SNVs that have a low or medium level of confounding by population stratification, mixed-effects model can reach a higher power for SNVs highly confounded by population stratification.
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Affiliation(s)
- Yuning Chen
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Anita L DeStefano
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
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32
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í Kongsstovu S, Dahl HA, Gislason H, Homrum E, Jacobsen JA, Flicek P, Mikalsen S. Identification of male heterogametic sex-determining regions on the Atlantic herring Clupea harengus genome. JOURNAL OF FISH BIOLOGY 2020; 97:190-201. [PMID: 32293027 PMCID: PMC7115899 DOI: 10.1111/jfb.14349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
The sex determination system of Atlantic herring Clupea harengus L., a commercially important fish, was investigated. Low coverage whole-genome sequencing of 48 females and 55 males and a genome-wide association study revealed two regions on chromosomes 8 and 21 associated with sex. The genotyping data of the single nucleotide polymorphisms associated with sex showed that 99.4% of the available female genotypes were homozygous, whereas 68.6% of the available male genotypes were heterozygous. This is close to the theoretical expectation of homo/heterozygous distribution at low sequencing coverage when the males are factually heterozygous. This suggested a male heterogametic sex determination system in C. harengus, consistent with other species within the Clupeiformes group. There were 76 protein coding genes on the sex regions but none of these genes were previously reported master sex regulation genes, or obviously related to sex determination. However, many of these genes are expressed in testis or ovary in other species, but the exact genes controlling sex determination in C. harengus could not be identified.
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Affiliation(s)
- Sunnvør í Kongsstovu
- Amplexa Genetics A/STórshavnFaroe Islands
- Faculty of Science and TechnologyUniversity of the Faroe IslandsTórshavnFaroe Islands
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteCambridgeUK
| | | | - Hannes Gislason
- Faculty of Science and TechnologyUniversity of the Faroe IslandsTórshavnFaroe Islands
| | - Eydna Homrum
- Faroe Marine Research InstituteTórshavnFaroe Islands
| | | | - Paul Flicek
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteCambridgeUK
| | - Svein‐Ole Mikalsen
- Faculty of Science and TechnologyUniversity of the Faroe IslandsTórshavnFaroe Islands
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33
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Harlemon M, Ajayi O, Kachambwa P, Kim MS, Simonti CN, Quiver MH, Petersen DC, Mittal A, Fernandez PW, Hsing AW, Baichoo S, Agalliu I, Jalloh M, Gueye SM, Snyper NYF, Adusei B, Mensah JE, Abrahams AOD, Adebiyi AO, Orunmuyi AT, Aisuodionoe-Shadrach OI, Nwegbu MM, Joffe M, Chen WC, Irusen H, Neugut AI, Quintana Y, Seutloali M, Fadipe MB, Warren C, Woehrmann MH, Zhang P, Ongaco CM, Mawhinney M, McBride J, Andrews CV, Adams M, Pugh E, Rebbeck TR, Petersen LN, Lachance J. A Custom Genotyping Array Reveals Population-Level Heterogeneity for the Genetic Risks of Prostate Cancer and Other Cancers in Africa. Cancer Res 2020; 80:2956-2966. [PMID: 32393663 PMCID: PMC7335354 DOI: 10.1158/0008-5472.can-19-2165] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/03/2019] [Accepted: 05/06/2020] [Indexed: 12/25/2022]
Abstract
Although prostate cancer is the leading cause of cancer mortality for African men, the vast majority of known disease associations have been detected in European study cohorts. Furthermore, most genome-wide association studies have used genotyping arrays that are hindered by SNP ascertainment bias. To overcome these disparities in genomic medicine, the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network has developed a genotyping array that is optimized for African populations. The MADCaP Array contains more than 1.5 million markers and an imputation backbone that successfully tags over 94% of common genetic variants in African populations. This array also has a high density of markers in genomic regions associated with cancer susceptibility, including 8q24. We assessed the effectiveness of the MADCaP Array by genotyping 399 prostate cancer cases and 403 controls from seven urban study sites in sub-Saharan Africa. Samples from Ghana and Nigeria clustered together, whereas samples from Senegal and South Africa yielded distinct ancestry clusters. Using the MADCaP array, we identified cancer-associated loci that have large allele frequency differences across African populations. Polygenic risk scores for prostate cancer were higher in Nigeria than in Senegal. In summary, individual and population-level differences in prostate cancer risk were revealed using a novel genotyping array. SIGNIFICANCE: This study presents an Africa-specific genotyping array, which enables investigators to identify novel disease associations and to fine-map genetic loci that are associated with prostate and other cancers.
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Affiliation(s)
- Maxine Harlemon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
- Clark Atlanta University, Atlanta, Georgia
| | - Olabode Ajayi
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | - Michelle S Kim
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Corinne N Simonti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Melanie H Quiver
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | | | | | - Pedro W Fernandez
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Ilir Agalliu
- Albert Einstein College of Medicine, Bronx, New York
| | - Mohamed Jalloh
- Hôpital Général de Grand Yoff, Institut de Formation et de Recherche en Urologie et Santé Familiale, Dakar, Senegal
| | - Serigne M Gueye
- Hôpital Général de Grand Yoff, Institut de Formation et de Recherche en Urologie et Santé Familiale, Dakar, Senegal
| | | | | | - James E Mensah
- Korle-Bu Teaching Hospital and University of Ghana, Accra, Ghana
| | | | | | | | | | - Maxwell M Nwegbu
- College of Health Sciences, University of Abuja and University of Abuja Teaching Hospital, Abuja, Nigeria
| | - Maureen Joffe
- Non-Communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd, Johannesburg, South Africa
- MRC Developmental Pathways to Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Wenlong C Chen
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
| | - Hayley Irusen
- Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Alfred I Neugut
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Yuri Quintana
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | | | - Mayowa B Fadipe
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | | | - Peng Zhang
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Chrissie M Ongaco
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Michelle Mawhinney
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Jo McBride
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | | | - Marcia Adams
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Johns Hopkins University, Baltimore, Maryland
| | - Timothy R Rebbeck
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.
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34
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Rajan R, Divya KP, Kandadai RM, Yadav R, Satagopam VP, Madhusoodanan UK, Agarwal P, Kumar N, Ferreira T, Kumar H, Sreeram Prasad AV, Shetty K, Mehta S, Desai S, Kumar S, Prashanth LK, Bhatt M, Wadia P, Ramalingam S, Wali GM, Pandey S, Bartusch F, Hannussek M, Krüger J, Kumar-Sreelatha A, Grover S, Lichtner P, Sturm M, Roeper J, Busskamp V, Chandak GR, Schwamborn J, Seth P, Gasser T, Riess O, Goyal V, Pal PK, Borgohain R, Krüger R, Kishore A, Sharma M. Genetic Architecture of Parkinson's Disease in the Indian Population: Harnessing Genetic Diversity to Address Critical Gaps in Parkinson's Disease Research. Front Neurol 2020; 11:524. [PMID: 32655481 PMCID: PMC7323575 DOI: 10.3389/fneur.2020.00524] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/13/2020] [Indexed: 12/21/2022] Open
Abstract
Over the past two decades, our understanding of Parkinson's disease (PD) has been gleaned from the discoveries made in familial and/or sporadic forms of PD in the Caucasian population. The transferability and the clinical utility of genetic discoveries to other ethnically diverse populations are unknown. The Indian population has been under-represented in PD research. The Genetic Architecture of PD in India (GAP-India) project aims to develop one of the largest clinical/genomic bio-bank for PD in India. Specifically, GAP-India project aims to: (1) develop a pan-Indian deeply phenotyped clinical repository of Indian PD patients; (2) perform whole-genome sequencing in 500 PD samples to catalog Indian genetic variability and to develop an Indian PD map for the scientific community; (3) perform a genome-wide association study to identify novel loci for PD and (4) develop a user-friendly web-portal to disseminate results for the scientific community. Our "hub-spoke" model follows an integrative approach to develop a pan-Indian outreach to develop a comprehensive cohort for PD research in India. The alignment of standard operating procedures for recruiting patients and collecting biospecimens with international standards ensures harmonization of data/bio-specimen collection at the beginning and also ensures stringent quality control parameters for sample processing. Data sharing and protection policies follow the guidelines established by local and national authorities.We are currently in the recruitment phase targeting recruitment of 10,200 PD patients and 10,200 healthy volunteers by the end of 2020. GAP-India project after its completion will fill a critical gap that exists in PD research and will contribute a comprehensive genetic catalog of the Indian PD population to identify novel targets for PD.
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Affiliation(s)
- Roopa Rajan
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India
| | - K P Divya
- Sree Chitra Tirunal Institute for Medical Sciences, Trivandrum, India
| | | | - Ravi Yadav
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Venkata P Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg.,ELIXIR-Luxembourg Node, Belvaux, Luxembourg
| | - U K Madhusoodanan
- Sree Chitra Tirunal Institute for Medical Sciences, Trivandrum, India
| | - Pankaj Agarwal
- Movement Disorders Clinic, Global Hospitals, Mumbai, India
| | - Niraj Kumar
- All India Institute of Medical Sciences, Rishikesh, India
| | | | | | | | - Kuldeep Shetty
- Narayana Hrudayalaya Multispeciality Hospital, Bangalore, India
| | - Sahil Mehta
- Department of Neurology, PGIMER, Chandigarh, India
| | - Soaham Desai
- Shree Krishna Hospital and Pramukhswami Medical College, Karamsad, India
| | - Suresh Kumar
- Department of Neurology, Vijaya Health Centre, Chennai, India
| | - L K Prashanth
- Center for Parkinson's Disease and Movement Disorders, Vikram Hospital, Bangalore, India
| | - Mohit Bhatt
- Kokilaben Dhirubhai Ambani Hospital, Mumbai, India
| | | | - Sudha Ramalingam
- Department of Community Medicine, PSG Institute of Medical Sciences and Research, Coimbatore, India
| | - G M Wali
- Neurospecialities Centre, Belgaum, India
| | - Sanjay Pandey
- Department of Neurology, G. B. Pant Institute of Medical Education and Research, New Delhi, India
| | - Felix Bartusch
- Zentrum für Datenverarbeitung (ZDV), University of Tubingen, Tübingen, Germany
| | | | - Jens Krüger
- Zentrum für Datenverarbeitung (ZDV), University of Tubingen, Tübingen, Germany
| | - Ashwin Kumar-Sreelatha
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tubingen, Tübingen, Germany
| | - Sandeep Grover
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tubingen, Tübingen, Germany
| | - Peter Lichtner
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Human Genetics, Neuherberg, Germany
| | - Marc Sturm
- Institute for Medical Genetics and Applied Genomics, University of Tubingen, Tübingen, Germany
| | - Jochen Roeper
- Institute of Neurophysiology, Goethe University Frankfurt, Frankfurt, Germany
| | - Volker Busskamp
- Department of Ophthalmology, Universitäts-Augenklinik Bonn, University of Bonn, Bonn, Germany
| | | | - Jens Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg
| | - Pankaj Seth
- National Brain Research Centre, Gurugram, India
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute for Medical Genetics and Applied Genomics, University of Tubingen, Tübingen, Germany
| | - Vinay Goyal
- Department of Neurology, All India Institute of Medical Sciences, New Delhi, India.,Medanta the Medicity, Gurgaon, India
| | - Pramod Kumar Pal
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Rupam Borgohain
- Department of Neurology, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg, Luxembourg.,Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Asha Kishore
- Sree Chitra Tirunal Institute for Medical Sciences, Trivandrum, India
| | - Manu Sharma
- Department of Neurology, G. B. Pant Institute of Medical Education and Research, New Delhi, India
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35
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Yan Z, Martin SH, Gotzek D, Arsenault SV, Duchen P, Helleu Q, Riba-Grognuz O, Hunt BG, Salamin N, Shoemaker D, Ross KG, Keller L. Evolution of a supergene that regulates a trans-species social polymorphism. Nat Ecol Evol 2020; 4:240-249. [PMID: 31959939 DOI: 10.1038/s41559-019-1081-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/04/2019] [Indexed: 11/09/2022]
Abstract
Supergenes are clusters of linked genetic loci that jointly affect the expression of complex phenotypes, such as social organization. Little is known about the origin and evolution of these intriguing genomic elements. Here we analyse whole-genome sequences of males from native populations of six fire ant species and show that variation in social organization is under the control of a novel supergene haplotype (termed Sb), which evolved by sequential incorporation of three inversions spanning half of a 'social chromosome'. Two of the inversions interrupt protein-coding genes, resulting in the increased expression of one gene and modest truncation in the primary protein structure of another. All six socially polymorphic species studied harbour the same three inversions, with the single origin of the supergene in their common ancestor inferred by phylogenomic analyses to have occurred half a million years ago. The persistence of Sb along with the ancestral SB haplotype through multiple speciation events provides a striking example of a functionally important trans-species social polymorphism presumably maintained by balancing selection. We found that while recombination between the Sb and SB haplotypes is severely restricted in all species, a low level of gene flux between the haplotypes has occurred following the appearance of the inversions, potentially mitigating the evolutionary degeneration expected at genomic regions that cannot freely recombine. These results provide a detailed picture of the structural genomic innovations involved in the formation of a supergene controlling a complex social phenotype.
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Affiliation(s)
- Zheng Yan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Simon H Martin
- Institute of Evolutionary Biology, the University of Edinburgh, Edinburgh, UK
| | - Dietrich Gotzek
- Department of Entomology and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Pablo Duchen
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Quentin Helleu
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Oksana Riba-Grognuz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - DeWayne Shoemaker
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Kenneth G Ross
- Department of Entomology, University of Georgia, Athens, GA, USA.
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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36
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WHEELER NICHOLASR, BENCHEK PENELOPE, KUNKLE BRIANW, HAMILTON-NELSON KARAL, WARFE MIKE, FONDRAN JEREMYR, HAINES JONATHANL, BUSH WILLIAMS. Hadoop and PySpark for reproducibility and scalability of genomic sequencing studies. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020; 25:523-534. [PMID: 31797624 PMCID: PMC6956992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Modern genomic studies are rapidly growing in scale, and the analytical approaches used to analyze genomic data are increasing in complexity. Genomic data management poses logistic and computational challenges, and analyses are increasingly reliant on genomic annotation resources that create their own data management and versioning issues. As a result, genomic datasets are increasingly handled in ways that limit the rigor and reproducibility of many analyses. In this work, we examine the use of the Spark infrastructure for the management, access, and analysis of genomic data in comparison to traditional genomic workflows on typical cluster environments. We validate the framework by reproducing previously published results from the Alzheimer's Disease Sequencing Project. Using the framework and analyses designed using Jupyter notebooks, Spark provides improved workflows, reduces user-driven data partitioning, and enhances the portability and reproducibility of distributed analyses required for large-scale genomic studies.
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Affiliation(s)
- NICHOLAS R. WHEELER
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road Cleveland OH 44106, USA
| | - PENELOPE BENCHEK
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road Cleveland OH 44106, USA
| | - BRIAN W. KUNKLE
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - KARA L. HAMILTON-NELSON
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, 1501 NW 10th Ave, Miami, FL 33136, USA
| | - MIKE WARFE
- Cleveland Institute for Computational Biology, Center for Advanced Research Computing, University Technology, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road Cleveland OH 44106, USA
| | - JEREMY R. FONDRAN
- Cleveland Institute for Computational Biology, Center for Advanced Research Computing, University Technology, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road Cleveland OH 44106, USA
| | - JONATHAN L. HAINES
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road Cleveland OH 44106, USA
| | - WILLIAM S. BUSH
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road Cleveland OH 44106, USA
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Gloaguen E, Dizier MH, Boissel M, Rocheleau G, Canouil M, Froguel P, Tichet J, Roussel R, Julier C, Balkau B, Mathieu F. General regression model: A "model-free" association test for quantitative traits allowing to test for the underlying genetic model. Ann Hum Genet 2019; 84:280-290. [PMID: 31834638 DOI: 10.1111/ahg.12372] [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: 07/20/2018] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 11/26/2022]
Abstract
Most genome-wide association studies used genetic-model-based tests assuming an additive mode of inheritance, leading to underpowered association tests in case of departure from additivity. The general regression model (GRM) association test proposed by Fisher and Wilson in 1980 makes no assumption on the genetic model. Interestingly, it also allows formal testing of the underlying genetic model. We conducted a simulation study of quantitative traits to compare the power of the GRM test to the classical linear regression tests, the maximum of the three statistics (MAX), and the allele-based (allelic) tests. Simulations were performed on two samples sizes, using a large panel of genetic models, varying genetic models, minor allele frequencies, and the percentage of explained variance. In case of departure from additivity, the GRM was more powerful than the additive regression tests (power gain reaching 80%) and had similar power when the true model is additive. GRM was also as or more powerful than the MAX or allelic tests. The true simulated model was mostly retained by the GRM test. Application of GRM to HbA1c illustrates its gain in power. To conclude, GRM increases power to detect association for quantitative traits, allows determining the genetic model and is easily applicable.
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Affiliation(s)
- Emilie Gloaguen
- Inserm UMRS-958, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Marie-Hélène Dizier
- Inserm UMR-946, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Mathilde Boissel
- Université de Lille, UMR 8199 - EGID, Lille, France.,CNRS, Paris, France.,Institut Pasteur de Lille, Lille, France
| | - Ghislain Rocheleau
- Université de Lille, UMR 8199 - EGID, Lille, France.,CNRS, Paris, France.,Institut Pasteur de Lille, Lille, France
| | - Mickaël Canouil
- Université de Lille, UMR 8199 - EGID, Lille, France.,CNRS, Paris, France.,Institut Pasteur de Lille, Lille, France
| | - Philippe Froguel
- Université de Lille, UMR 8199 - EGID, Lille, France.,CNRS, Paris, France.,Institut Pasteur de Lille, Lille, France.,Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
| | | | - Ronan Roussel
- Inserm U1138, Centre de Recherche des Cordeliers, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Diabetology, Endocrinology and Nutrition Department, DHU FIRE, Hôpital Bichat, AP-HP, Paris, France
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- Inserm UMRS-958, Paris, France
| | - Cécile Julier
- Inserm UMRS-958, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Flavie Mathieu
- Mission Associations Recherche & Société - Inserm Siège, DISC, Paris, France.,Paris Diderot, Sorbonne Paris Cité, Paris, France
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38
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Yin L, Chau CKL, Sham PC, So HC. Integrating Clinical Data and Imputed Transcriptome from GWAS to Uncover Complex Disease Subtypes: Applications in Psychiatry and Cardiology. Am J Hum Genet 2019; 105:1193-1212. [PMID: 31785786 PMCID: PMC6904812 DOI: 10.1016/j.ajhg.2019.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/22/2019] [Indexed: 12/19/2022] Open
Abstract
Classifying subjects into clinically and biologically homogeneous subgroups will facilitate the understanding of disease pathophysiology and development of targeted prevention and intervention strategies. Traditionally, disease subtyping is based on clinical characteristics alone, but subtypes identified by such an approach may not conform exactly to the underlying biological mechanisms. Very few studies have integrated genomic profiles (e.g., those from GWASs) with clinical symptoms for disease subtyping. Here we proposed an analytic framework capable of finding complex diseases subgroups by leveraging both GWAS-predicted gene expression levels and clinical data by a multi-view bicluster analysis. This approach connects SNPs to genes via their effects on expression, so the analysis is more biologically relevant and interpretable than a pure SNP-based analysis. Transcriptome of different tissues can also be readily modeled. We also proposed various evaluation metrics for assessing clustering performance. Our framework was able to subtype schizophrenia subjects into diverse subgroups with different prognosis and treatment response. We also applied the framework to the Northern Finland Birth Cohort (NFBC) 1966 dataset and identified high and low cardiometabolic risk subgroups in a gender-stratified analysis. The prediction strength by cross-validation was generally greater than 80%, suggesting good stability of the clustering model. Our results suggest a more data-driven and biologically informed approach to defining metabolic syndrome and subtyping psychiatric disorders. Moreover, we found that the genes "blindly" selected by the algorithm are significantly enriched for known susceptibility genes discovered in GWASs of schizophrenia or cardiovascular diseases. The proposed framework opens up an approach to subject stratification.
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Affiliation(s)
- Liangying Yin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Carlos K L Chau
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, University of Hong Kong, Hong Kong SAR, China; State Key Laboratory for Cognitive and Brain Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Hon-Cheong So
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Zoology Institute of Zoology and The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Hong Kong SAR, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China.
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39
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Patron J, Serra-Cayuela A, Han B, Li C, Wishart DS. Assessing the performance of genome-wide association studies for predicting disease risk. PLoS One 2019; 14:e0220215. [PMID: 31805043 PMCID: PMC6894795 DOI: 10.1371/journal.pone.0220215] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 11/01/2019] [Indexed: 12/24/2022] Open
Abstract
To date more than 3700 genome-wide association studies (GWAS) have been published that look at the genetic contributions of single nucleotide polymorphisms (SNPs) to human conditions or human phenotypes. Through these studies many highly significant SNPs have been identified for hundreds of diseases or medical conditions. However, the extent to which GWAS-identified SNPs or combinations of SNP biomarkers can predict disease risk is not well known. One of the most commonly used approaches to assess the performance of predictive biomarkers is to determine the area under the receiver-operator characteristic curve (AUROC). We have developed an R package called G-WIZ to generate ROC curves and calculate the AUROC using summary-level GWAS data. We first tested the performance of G-WIZ by using AUROC values derived from patient-level SNP data, as well as literature-reported AUROC values. We found that G-WIZ predicts the AUROC with <3% error. Next, we used the summary level GWAS data from GWAS Central to determine the ROC curves and AUROC values for 569 different GWA studies spanning 219 different conditions. Using these data we found a small number of GWA studies with SNP-derived risk predictors that have very high AUROCs (>0.75). On the other hand, the average GWA study produces a multi-SNP risk predictor with an AUROC of 0.55. Detailed AUROC comparisons indicate that most SNP-derived risk predictions are not as good as clinically based disease risk predictors. All our calculations (ROC curves, AUROCs, explained heritability) are in a publicly accessible database called GWAS-ROCS (http://gwasrocs.ca). The G-WIZ code is freely available for download at https://github.com/jonaspatronjp/GWIZ-Rscript/.
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Affiliation(s)
- Jonas Patron
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | | | - Beomsoo Han
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Carin Li
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - David Scott Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
- Department of Computing Science, University of Alberta, Edmonton, Canada
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40
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Zlobin A, Volkova N, Borodin P, Aksenovich T, Tsepilov Y. Recent advances in understanding genetic variants associated with growth, carcass and meat productivity traits in sheep ( Ovis aries): an update. Arch Anim Breed 2019; 62:579-583. [PMID: 31893215 PMCID: PMC6904904 DOI: 10.5194/aab-62-579-2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 09/17/2019] [Indexed: 12/17/2022] Open
Abstract
Identification of quantitative trait loci (QTLs) and candidate genes that affect growth intensity is a prerequisite for the marker-assisted selection of economically important traits. The number of QTL studies on sheep is relatively small in comparison to those on cattle and pigs. The current QTL sheep database - Sheep QTLdb - contains information on 1658 QTLs for 225 different traits. A few genes and markers associated with growth, carcass and meat productivity traits have been reported. The information about QTLs from the Sheep QTLdb cannot be directly used in marker-assisted selection due to the lack of essential information such as effective and reference alleles, the effect direction etc., and it requires manual curation and validation. In this study we performed a comprehensive search for QTLs focusing on single nucleotide polymorphisms (SNPs) associated with growth and meat traits in sheep. The database contains information about 156 SNP-trait associations (123 unique SNPs) and a list of 165 associated genes. The updated information is freely available at https://github.com/Defrag1236/Ovines_2018 (last access: 18 September 2019). This information can be useful for further association studies and preliminary estimation of genetic variability for economically important traits in different breeds.
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Affiliation(s)
- Alexander S. Zlobin
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
| | - Natalia A. Volkova
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
| | - Pavel M. Borodin
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Tatiana I. Aksenovich
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
| | - Yakov A. Tsepilov
- Institute of Cytology and Genetics, Siberian Branch of the Russian
Academy of Sciences, Novosibirsk, Russia
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy,
Moscow Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
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41
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Fitzgerald KC, Kim K, Smith MD, Aston SA, Fioravante N, Rothman AM, Krieger S, Cofield SS, Kimbrough DJ, Bhargava P, Saidha S, Whartenby KA, Green AJ, Mowry EM, Cutter GR, Lublin FD, Baranzini SE, De Jager PL, Calabresi PA. Early complement genes are associated with visual system degeneration in multiple sclerosis. Brain 2019; 142:2722-2736. [PMID: 31289819 PMCID: PMC6776113 DOI: 10.1093/brain/awz188] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/17/2019] [Accepted: 04/28/2019] [Indexed: 11/12/2022] Open
Abstract
Multiple sclerosis is a heterogeneous disease with an unpredictable course and a wide range of severity; some individuals rapidly progress to a disabled state whereas others experience only mild symptoms. Though genetic studies have identified variants that are associated with an increased risk of developing multiple sclerosis, no variants have been consistently associated with multiple sclerosis severity. In part, the lack of findings is related to inherent limitations of clinical rating scales; these scales are insensitive to early degenerative changes that underlie disease progression. Optical coherence tomography imaging of the retina and low-contrast letter acuity correlate with and predict clinical and imaging-based outcomes in multiple sclerosis. Therefore, they may serve as sensitive phenotypes to discover genetic predictors of disease course. We conducted a set of genome-wide association studies of longitudinal structural and functional visual pathway phenotypes in multiple sclerosis. First, we assessed genetic predictors of ganglion cell/inner plexiform layer atrophy in a discovery cohort of 374 patients with multiple sclerosis using mixed-effects models adjusting for age, sex, disease duration, optic neuritis and genetic ancestry and using a combination of single-variant and network-based analyses. For candidate variants identified in discovery, we conducted a similar set of analyses of ganglion cell/inner plexiform layer thinning in a replication cohort (n = 376). Second, we assessed genetic predictors of sustained loss of 5-letters in low-contrast letter acuity in discovery (n = 582) using multivariable-adjusted Cox proportional hazards models. We then evaluated candidate variants/pathways in a replication cohort. (n = 253). Results of both studies revealed novel subnetworks highly enriched for connected genes in early complement activation linked to measures of disease severity. Within these networks, C3 was the gene most strongly associated with ganglion cell/inner plexiform layer atrophy (P = 0.004) and C1QA and CR1 were top results in analysis of sustained low-contrast letter acuity loss. Namely, variant rs158772, linked to C1QA, and rs61822967, linked to CR1, were associated with 71% and 40% increases in risk of sustained LCLA loss, respectively, in meta-analysis pooling discovery and replication cohorts (rs158772: hazard ratio: 1.71; 95% confidence interval 1.30-2.25; P = 1.3 × 10-4; rs61822967: hazard ratio: 1.40; 95% confidence interval: 1.16-1.68; P = 4.1 × 10-4). In conclusion, early complement pathway gene variants were consistently associated with structural and functional measures of multiple sclerosis severity. These results from unbiased analyses are strongly supported by several prior reports that mechanistically implicated early complement factors in neurodegeneration.
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Affiliation(s)
| | - Kicheol Kim
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew D Smith
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sean A Aston
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nicholas Fioravante
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Alissa M Rothman
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephen Krieger
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey S Cofield
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Pavan Bhargava
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shiv Saidha
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Katharine A Whartenby
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ari J Green
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | - Ellen M Mowry
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gary R Cutter
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Fred D Lublin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sergio E Baranzini
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Peter A Calabresi
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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42
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Jabbari E, Woodside J, Tan MMX, Pavese N, Bandmann O, Ghosh BCP, Massey LA, Capps E, Warner TT, Lees AJ, Revesz T, Holton JL, Williams NM, Grosset DG, Morris HR. The genetic and clinico-pathological profile of early-onset progressive supranuclear palsy. Mov Disord 2019; 34:1307-1314. [PMID: 31299107 PMCID: PMC6790973 DOI: 10.1002/mds.27786] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Studies on early-onset presentations of progressive supranuclear palsy (PSP) have been limited to those where a rare monogenic cause has been identified. Here, we have defined early-onset PSP (EOPSP) and investigated its genetic and clinico-pathological profile in comparison with late-onset PSP (LOPSP) and Parkinson's disease (PD). METHODS We included subjects from the Queen Square Brain Bank, PROSPECT-UK study, and Tracking Parkinson's study. Group comparisons of data were made using Welch's t-test and Kruskal-Wallis analysis of variance. EOPSP was defined as the youngest decile of motor age at onset (≤55 years) in the Queen Square Brain Bank PSP case series. RESULTS We identified 33 EOPSP, 328 LOPSP, and 2000 PD subjects. The early clinical features of EOPSP usually involve limb parkinsonism and gait freezing, with 50% of cases initially misdiagnosed as having PD. We found that an initial clinical diagnosis of EOPSP had lower diagnostic sensitivity (33%) and positive predictive value (38%) in comparison with LOPSP (80% and 76%) using a postmortem diagnosis of PSP as the gold standard. 3/33 (9%) of the EOPSP group had an underlying monogenic cause. Using a PSP genetic risk score (GRS), we showed that the genetic risk burden in the EOPSP (mean z-score, 0.59) and LOPSP (mean z-score, 0.48) groups was significantly higher (P < 0.05) when compared with the PD group (mean z-score, -0.08). CONCLUSIONS The initial clinical profile of EOPSP is often PD-like. At the group level, a PSP GRS was able to differentiate EOPSP from PD, and this may be helpful in future diagnostic algorithms. © 2019 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Edwin Jabbari
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom.,Movement Disorders Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - John Woodside
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom.,Movement Disorders Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Manuela M X Tan
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom.,Movement Disorders Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Nicola Pavese
- Division of Neuroscience, Newcastle University, Newcastle, United Kingdom
| | - Oliver Bandmann
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Boyd C P Ghosh
- Wessex Neurological Centre, University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Luke A Massey
- Department of Neurology, Poole Hospital NHS Foundation Trust, Poole, United Kingdom
| | - Erica Capps
- Care of the Elderly Department, Shrewsbury and Telford Hospital NHS Trust, Shrewsbury, United Kingdom
| | - Tom T Warner
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, United Kingdom.,Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Andrew J Lees
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, United Kingdom.,Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Tamas Revesz
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, United Kingdom.,Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Janice L Holton
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, United Kingdom.,Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Nigel M Williams
- Institute of Psychological Medicine and Clinical Neurosciences, Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Donald G Grosset
- Department of Neurology, Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom.,Movement Disorders Centre, UCL Queen Square Institute of Neurology, London, United Kingdom
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43
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Nel M, Mulder N, Europa TA, Heckmann JM. Using Whole Genome Sequencing in an African Subphenotype of Myasthenia Gravis to Generate a Pathogenetic Hypothesis. Front Genet 2019; 10:136. [PMID: 30881381 PMCID: PMC6406016 DOI: 10.3389/fgene.2019.00136] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/11/2019] [Indexed: 12/25/2022] Open
Abstract
Myasthenia gravis (MG) is a rare, treatable antibody-mediated disease which is characterized by muscle weakness. The pathogenic antibodies are most frequently directed at the acetylcholine receptors (AChRs) at the skeletal muscle endplate. An ophthalmoplegic subphenotype of MG (OP-MG), which is characterized by treatment resistant weakness of the extraocular muscles (EOMs), occurs in a proportion of myasthenics with juvenile symptom onset and African genetic ancestry. Since the pathogenetic mechanism(s) underlying OP-MG is unknown, the aim of this study was to use a hypothesis-generating genome-wide analysis to identify candidate OP-MG susceptibility genes and pathways. Whole genome sequencing (WGS) was performed on 25 AChR-antibody positive myasthenic individuals of African genetic ancestry sampled from the phenotypic extremes: 15 with OP-MG and 10 individuals with control MG (EOM treatment-responsive). Variants were called according to the Genome Analysis Toolkit (GATK) best practice guidelines using the hg38 reference genome. In addition to single variant association analysis, variants were mapped to genes (±200 kb) using VEGAS2 to calculate gene-based test statistics and HLA allele group assignment was inferred through "best-match" alignment of reads against the IMGT/HLA database. While there were no single variant associations that reached genome-wide significance in this exploratory sample, several genes with significant gene-based test statistics and known to be expressed in skeletal muscle had biological functions which converge on muscle atrophy signaling and myosin II function. The closely linked HLA-DPA1 and HLA-DPB1 genes were associated with OP-MG subjects (gene-based p < 0.05) and the frequency of a functional A > G SNP (rs9277534) in the HLA-DPB1 3'UTR, which increases HLA-DPB1 expression, differed between the two groups (G-allele 0.30 in OP-MG vs. 0.60 in control MG; p = 0.04). Furthermore, we show that rs9277534 is an HLA-DBP1 expression quantitative trait locus in patient-derived myocytes (p < 1 × 10-3). The application of a SNP to gene to pathway approach to this exploratory WGS dataset of African myasthenic individuals, and comparing dichotomous subphenotypes, resulted in the identification of candidate genes and pathways that may contribute to OP-MG susceptibility. Overall, the hypotheses generated by this work remain to be verified by interrogating candidate gene and pathway expression in patient-derived extraocular muscle.
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Affiliation(s)
- Melissa Nel
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicola Mulder
- Computational Biology Division, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Tarin A Europa
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Jeannine M Heckmann
- Neurology Research Group, Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
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44
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Hernandez-Pacheco N, Farzan N, Francis B, Karimi L, Repnik K, Vijverberg SJ, Soares P, Schieck M, Gorenjak M, Forno E, Eng C, Oh SS, Pérez-Méndez L, Berce V, Tavendale R, Samedy LA, Hunstman S, Hu D, Meade K, Farber HJ, Avila PC, Serebrisky D, Thyne SM, Brigino-Buenaventura E, Rodriguez-Cintron W, Sen S, Kumar R, Lenoir M, Rodriguez-Santana JR, Celedón JC, Mukhopadhyay S, Potočnik U, Pirmohamed M, Verhamme KM, Kabesch M, Palmer CNA, Hawcutt DB, Flores C, Maitland-van der Zee AH, Burchard EG, Pino-Yanes M. Genome-wide association study of inhaled corticosteroid response in admixed children with asthma. Clin Exp Allergy 2019; 49:789-798. [PMID: 30697902 DOI: 10.1111/cea.13354] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/30/2018] [Accepted: 12/29/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Inhaled corticosteroids (ICS) are the most widely prescribed and effective medication to control asthma symptoms and exacerbations. However, many children still have asthma exacerbations despite treatment, particularly in admixed populations, such as Puerto Ricans and African Americans. A few genome-wide association studies (GWAS) have been performed in European and Asian populations, and they have demonstrated the importance of the genetic component in ICS response. OBJECTIVE We aimed to identify genetic variants associated with asthma exacerbations in admixed children treated with ICS and to validate previous GWAS findings. METHODS A meta-analysis of two GWAS of asthma exacerbations was performed in 1347 admixed children treated with ICS (Hispanics/Latinos and African Americans), analysing 8.7 million genetic variants. Those with P ≤ 5 × 10-6 were followed up for replication in 1697 asthmatic patients from six European studies. Associations of ICS response described in published GWAS were followed up for replication in the admixed populations. RESULTS A total of 15 independent variants were suggestively associated with asthma exacerbations in admixed populations (P ≤ 5 × 10-6 ). One of them, located in the intergenic region of APOBEC3B and APOBEC3C, showed evidence of replication in Europeans (rs5995653, P = 7.52 × 10-3 ) and was also associated with change in lung function after treatment with ICS (P = 4.91 × 10-3 ). Additionally, the reported association of the L3MBTL4-ARHGAP28 genomic region was confirmed in admixed populations, although a different variant was identified. CONCLUSIONS AND CLINICAL RELEVANCE This study revealed the novel association of APOBEC3B and APOBEC3C with asthma exacerbations in children treated with ICS and replicated previously identified genomic regions. This contributes to the current knowledge about the multiple genetic markers determining responsiveness to ICS which could lead in the future the clinical identification of those asthma patients who are not able to respond to such treatment.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Ben Francis
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Leila Karimi
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Patricia Soares
- Academic Department of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Maximilian Schieck
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany.,Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh of the University of Pittsburgh, Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, California
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, California
| | - Lina Pérez-Méndez
- Department of Clinic Epidemiology and Biostatistics, Research Unit, Hospital Universitario N.S. de Candelaria, Gerencia de Atención Primaria, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia
| | - Roger Tavendale
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Lesly-Anne Samedy
- Department of Medicine, University of California, San Francisco, California.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Scott Hunstman
- Department of Medicine, University of California, San Francisco, California
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, California
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, California
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Pedro C Avila
- Department of Medicine, Northwestern University, Chicago, Illinois.,Allergy & ENT Associates, The Woodland, Texas
| | | | - Shannon M Thyne
- Department of Pediatrics, University of California, San Francisco, California
| | | | | | - Saunak Sen
- University of Tennessee Health Science Center, Memphis, Tennessee
| | - Rajesh Kumar
- Feinberg School of Medicine's Division of Allergy and Immunology, Northwestern University, Chicago, Illinois.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | | | | | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh of the University of Pittsburgh, Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK.,Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Colin N A Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Daniel B Hawcutt
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK.,Alder Hey Children's Hospital, Liverpool, UK
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, Netherlands.,Department of Pediatric Respiratory Medicine and Allergy, Emma's Children Hospital, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, California.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Nazarian A, Yashin AI, Kulminski AM. Genome-wide analysis of genetic predisposition to Alzheimer's disease and related sex disparities. ALZHEIMERS RESEARCH & THERAPY 2019; 11:5. [PMID: 30636644 PMCID: PMC6330399 DOI: 10.1186/s13195-018-0458-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 12/06/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common cause of dementia in the elderly and the sixth leading cause of death in the United States. AD is mainly considered a complex disorder with polygenic inheritance. Despite discovering many susceptibility loci, a major proportion of AD genetic variance remains to be explained. METHODS We investigated the genetic architecture of AD in four publicly available independent datasets through genome-wide association, transcriptome-wide association, and gene-based and pathway-based analyses. To explore differences in the genetic basis of AD between males and females, analyses were performed on three samples in each dataset: males and females combined, only males, or only females. RESULTS Our genome-wide association analyses corroborated the associations of several previously detected AD loci and revealed novel significant associations of 35 single-nucleotide polymorphisms (SNPs) outside the chromosome 19q13 region at the suggestive significance level of p < 5E-06. These SNPs were mapped to 21 genes in 19 chromosomal regions. Of these, 17 genes were not associated with AD at genome-wide or suggestive levels of associations by previous genome-wide association studies. Also, the chromosomal regions corresponding to 8 genes did not contain any previously detected AD-associated SNPs with p < 5E-06. Our transcriptome-wide association and gene-based analyses revealed that 26 genes located in 20 chromosomal regions outside chromosome 19q13 had evidence of potential associations with AD at a false discovery rate of 0.05. Of these, 13 genes/regions did not contain any previously AD-associated SNPs at genome-wide or suggestive levels of associations. Most of the newly detected AD-associated SNPs and genes were sex specific, indicating sex disparities in the genetic basis of AD. Also, 7 of 26 pathways that showed evidence of associations with AD in our pathway-bases analyses were significant only in females. CONCLUSIONS Our findings, particularly the newly discovered sex-specific genetic contributors, provide novel insight into the genetic architecture of AD and can advance our understanding of its pathogenesis.
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Affiliation(s)
- Alireza Nazarian
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA.
| | - Anatoliy I Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Erwin Mill Building, 2024 W. Main St., Durham, NC, 27705, USA.
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Lin HA, Chen SY, Chang FY, Tung CW, Chen YC, Shen WC, Chen RS, Wu CW, Chung CL. Genome-wide association study of rice genes and loci conferring resistance to Magnaporthe oryzae isolates from Taiwan. BOTANICAL STUDIES 2018; 59:32. [PMID: 30578469 PMCID: PMC6303224 DOI: 10.1186/s40529-018-0248-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 12/12/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Rice blast, caused by Magnaporthe oryzae, is an important rice disease occurring in all rice-growing areas. To manage blast disease effectively and in an environmentally friendly way, it is important to continually discover diverse resistant resources for breeding. In this study, genome-wide association study (GWAS) was used to map genes/loci resistant to rice blast in the open-access rice diversity panel 1 (RDP1), previously genotyped with a 44K single-nucleotide polymorphism array. Two geographically and genetically different M. oryzae isolates from Taiwan, D41-2 and 12YL-DL3-2, were used to challenge RDP1. Infected leaves were visually rated for lesion type (LT) and evaluated for proportion of diseased leaf area (%DLA) by image analysis software. RESULTS A total of 32 quantitative trait loci (QTLs) were identified, including 6 from LT, 30 from DLA, and 4 from both LT and DLA. In all, 22 regions co-localized with previously reported resistance (R) genes and/or QTLs, including two cloned R genes, Pita and Ptr; 19 mapped R loci, and 20 QTLs. We identified 100 candidate genes encoding leucine-rich repeat-containing proteins, transcription factors, ubiquitination-related proteins, and peroxidases, among others, in the QTL intervals. Putative resistance and susceptibility haplotypes of the 32 QTL regions for each tested rice accessions were also determined. CONCLUSIONS By using Taiwanese M. oryzae isolates and image-based phenotyping for detailed GWAS, this study offers insights into the genetics underlying the natural variation of blast resistance in RDP1. The results can help facilitate the selection of desirable donors for gene/QTL validation and blast resistance breeding.
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Affiliation(s)
- Heng-An Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Szu-Yu Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Fang-Yu Chang
- Kaohsiung District Agricultural Research and Extension Station, No. 2-6, Dehe Rd., Pingtung County, 90846 Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Yi-Chia Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Wei-Chiang Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Ruey-Shyang Chen
- Department of Biochemical Science and Technology, National Chiayi University, No. 300, Syuefu Rd., Chiayi City, 60004 Taiwan
| | - Chih-Wen Wu
- Kaohsiung District Agricultural Research and Extension Station, No. 2-6, Dehe Rd., Pingtung County, 90846 Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
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Jabbari E, Woodside J, Tan MMX, Shoai M, Pittman A, Ferrari R, Mok KY, Zhang D, Reynolds RH, de Silva R, Grimm MJ, Respondek G, Müller U, Al-Sarraj S, Gentleman SM, Lees AJ, Warner TT, Hardy J, Revesz T, Höglinger GU, Holton JL, Ryten M, Morris HR. Variation at the TRIM11 locus modifies progressive supranuclear palsy phenotype. Ann Neurol 2018; 84:485-496. [PMID: 30066433 PMCID: PMC6221133 DOI: 10.1002/ana.25308] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 12/27/2022]
Abstract
Objective The basis for clinical variation related to underlying progressive supranuclear palsy (PSP) pathology is unknown. We performed a genome‐wide association study (GWAS) to identify genetic determinants of PSP phenotype. Methods Two independent pathological and clinically diagnosed PSP cohorts were genotyped and phenotyped to create Richardson syndrome (RS) and non‐RS groups. We carried out separate logistic regression GWASs to compare RS and non‐RS groups and then combined datasets to carry out a whole cohort analysis (RS = 367, non‐RS = 130). We validated our findings in a third cohort by referring to data from 100 deeply phenotyped cases from a recent GWAS. We assessed the expression/coexpression patterns of our identified genes and used our data to carry out gene‐based association testing. Results Our lead single nucleotide polymorphism (SNP), rs564309, showed an association signal in both cohorts, reaching genome‐wide significance in our whole cohort analysis (odds ratio = 5.5, 95% confidence interval = 3.2–10.0, p = 1.7 × 10−9). rs564309 is an intronic variant of the tripartite motif‐containing protein 11 (TRIM11) gene, a component of the ubiquitin proteasome system (UPS). In our third cohort, minor allele frequencies of surrogate SNPs in high linkage disequilibrium with rs564309 replicated our findings. Gene‐based association testing confirmed an association signal at TRIM11. We found that TRIM11 is predominantly expressed neuronally, in the cerebellum and basal ganglia. Interpretation Our study suggests that the TRIM11 locus is a genetic modifier of PSP phenotype and potentially adds further evidence for the UPS having a key role in tau pathology, therefore representing a target for disease‐modifying therapies. Ann Neurol 2018;84:485–496
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Affiliation(s)
- Edwin Jabbari
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, United Kingdom
| | - John Woodside
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, United Kingdom
| | - Manuela M X Tan
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, United Kingdom
| | - Maryam Shoai
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom
| | - Alan Pittman
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom
| | - Raffaele Ferrari
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom
| | - Kin Y Mok
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom
| | - David Zhang
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom
| | - Regina H Reynolds
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom
| | - Rohan de Silva
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom.,Reta Lila Weston Institute, UCL Institute of Neurology, London, United Kingdom
| | - Max-Joseph Grimm
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE); Department of Neurology, Technical University of Munich; Munich Cluster for Systems Neurology SyNergy, Munich, Germany
| | - Gesine Respondek
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE); Department of Neurology, Technical University of Munich; Munich Cluster for Systems Neurology SyNergy, Munich, Germany
| | - Ulrich Müller
- Institute for Human Genetics, Justus Liebig University, Giessen, Germany
| | - Safa Al-Sarraj
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Stephen M Gentleman
- Multiple Sclerosis and Parkinson's UK Brain Bank, Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Andrew J Lees
- Reta Lila Weston Institute, UCL Institute of Neurology, London, United Kingdom.,Queen Square Brain Bank for Neurological Disorders, UCL Institute of Neurology, London, United Kingdom
| | - Thomas T Warner
- Reta Lila Weston Institute, UCL Institute of Neurology, London, United Kingdom.,Queen Square Brain Bank for Neurological Disorders, UCL Institute of Neurology, London, United Kingdom
| | - John Hardy
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom
| | - Tamas Revesz
- Reta Lila Weston Institute, UCL Institute of Neurology, London, United Kingdom.,Queen Square Brain Bank for Neurological Disorders, UCL Institute of Neurology, London, United Kingdom
| | - Günter U Höglinger
- Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE); Department of Neurology, Technical University of Munich; Munich Cluster for Systems Neurology SyNergy, Munich, Germany
| | - Janice L Holton
- Reta Lila Weston Institute, UCL Institute of Neurology, London, United Kingdom.,Queen Square Brain Bank for Neurological Disorders, UCL Institute of Neurology, London, United Kingdom
| | - Mina Ryten
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, United Kingdom
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, United Kingdom
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Marees AT, de Kluiver H, Stringer S, Vorspan F, Curis E, Marie‐Claire C, Derks EM. A tutorial on conducting genome-wide association studies: Quality control and statistical analysis. Int J Methods Psychiatr Res 2018; 27:e1608. [PMID: 29484742 PMCID: PMC6001694 DOI: 10.1002/mpr.1608] [Citation(s) in RCA: 355] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 12/11/2017] [Accepted: 12/20/2017] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Genome-wide association studies (GWAS) have become increasingly popular to identify associations between single nucleotide polymorphisms (SNPs) and phenotypic traits. The GWAS method is commonly applied within the social sciences. However, statistical analyses will need to be carefully conducted and the use of dedicated genetics software will be required. This tutorial aims to provide a guideline for conducting genetic analyses. METHODS We discuss and explain key concepts and illustrate how to conduct GWAS using example scripts provided through GitHub (https://github.com/MareesAT/GWA_tutorial/). In addition to the illustration of standard GWAS, we will also show how to apply polygenic risk score (PRS) analysis. PRS does not aim to identify individual SNPs but aggregates information from SNPs across the genome in order to provide individual-level scores of genetic risk. RESULTS The simulated data and scripts that will be illustrated in the current tutorial provide hands-on practice with genetic analyses. The scripts are based on PLINK, PRSice, and R, which are commonly used, freely available software tools that are accessible for novice users. CONCLUSIONS By providing theoretical background and hands-on experience, we aim to make GWAS more accessible to researchers without formal training in the field.
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Affiliation(s)
- Andries T. Marees
- Department of PsychiatryAmsterdam Medical CenterAmsterdamThe Netherlands
- Inserm, UMR‐S 1144ParisFrance
- Université Paris DescartesUMR‐S 1144ParisFrance
- Université Paris DiderotSorbonne Paris Cité, UMR‐S 1144ParisFrance
- QIMR BerghoferTranslational Neurogenomics GroupBrisbaneAustralia
| | - Hilde de Kluiver
- GGZ inGeest and Department of Psychiatry, Amsterdam Public Health research instituteVU University Medical CenterAmsterdamThe Netherlands
| | - Sven Stringer
- Department of Complex Trait GeneticsVU UniversityAmsterdamThe Netherlands
| | - Florence Vorspan
- Department of PsychiatryAmsterdam Medical CenterAmsterdamThe Netherlands
- Inserm, UMR‐S 1144ParisFrance
- Université Paris DescartesUMR‐S 1144ParisFrance
- Université Paris DiderotSorbonne Paris Cité, UMR‐S 1144ParisFrance
- Service de Médecine AddictologiqueAPHP, Hôpital Fernand WidalParisFrance
- Faculté de MédecineUniversité Paris DiderotParisFrance
| | - Emmanuel Curis
- Université Paris DescartesUMR‐S 1144ParisFrance
- Laboratoire de biomathématiques, faculté de pharmacie de ParisUniversité Paris DescartesParisFrance
- Service de biostatistiques et informatique médicalesHôpital Saint‐Louis, APHPParisFrance
| | - Cynthia Marie‐Claire
- Inserm, UMR‐S 1144ParisFrance
- Université Paris DescartesUMR‐S 1144ParisFrance
- Université Paris DiderotSorbonne Paris Cité, UMR‐S 1144ParisFrance
| | - Eske M. Derks
- Department of PsychiatryAmsterdam Medical CenterAmsterdamThe Netherlands
- QIMR BerghoferTranslational Neurogenomics GroupBrisbaneAustralia
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Validating a breast cancer score in Spanish women. The MCC-Spain study. Sci Rep 2018; 8:3036. [PMID: 29445177 PMCID: PMC5813036 DOI: 10.1038/s41598-018-20832-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/23/2018] [Indexed: 12/31/2022] Open
Abstract
A breast-risk score, published in 2016, was developed in white-American women using 92 genetic variants (GRS92), modifiable and non-modifiable risk factors. With the aim of validating the score in the Spanish population, 1,732 breast cancer cases and 1,910 controls were studied. The GRS92, modifiable and non-modifiable risk factor scores were estimated via logistic regression. SNPs without available genotyping were simulated as in the aforementioned 2016 study. The full model score was obtained by combining GRS92, modifiable and non-modifiable risk factor scores. Score performances were tested via the area under the ROC curve (AUROC), net reclassification index (NRI) and integrated discrimination improvement (IDI). Compared with non-modifiable and modifiable factor scores, GRS92 had higher discrimination power (AUROC: 0.6195, 0.5885 and 0.5214, respectively). Adding the non-modifiable factor score to GRS92 improved patient classification by 23.6% (NRI = 0.236), while the modifiable factor score only improved it by 7.2%. The full model AUROC reached 0.6244. A simulation study showed the ability of the full model for identifying women at high risk for breast cancer. In conclusion, a model combining genetic and risk factors can be used for stratifying women by their breast cancer risk, which can be applied to individualizing genetic counseling and screening recommendations.
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50
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Rispail N, Montilla-Bascón G, Sánchez-Martín J, Flores F, Howarth C, Langdon T, Rubiales D, Prats E. Multi-Environmental Trials Reveal Genetic Plasticity of Oat Agronomic Traits Associated With Climate Variable Changes. FRONTIERS IN PLANT SCIENCE 2018; 9:1358. [PMID: 30283476 PMCID: PMC6156136 DOI: 10.3389/fpls.2018.01358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/28/2018] [Indexed: 05/06/2023]
Abstract
Although oat cultivation around the Mediterranean basin is steadily increasing, its yield in these regions lags far behind those of Northern Europe. This results mainly from the poor adaptation of current oat cultivars to Mediterranean environments. Local landraces may act as reservoirs of favorable traits that could contribute to increase oat resilience in this region. To aid selection of suitable agro-climate adapted genotypes we integrated genome-wide association approaches with analysis of field assessed phenotypes of genetic variants and of the weight of associated markers across different environmental variables. Association models accounting for oat population structure were applied on either arithmetic means or best linear unbiased prediction (BLUPs) to ensure robust identification of associations with the agronomic traits evaluated. The meta-analysis of the six joint environments (mega-environment) identified several markers associated with several agronomic traits and crown rust severity. Five of these associated markers were located within expressed genes. These associations were only mildly influenced by climatic variables indicating that these markers are good candidates to improve the genetic potential of oat under Mediterranean conditions. The models also highlighted several marker-trait associations, strongly affected by particular climatic variables including high rain pre- or post-heading dates and high temperatures, revealing strong potential for oat adaptation to specific agro-climatic conditions. These results will contribute to increase oat resilience for particular climatic conditions and facilitate breeding for plant adaptation to a wider range of climatic conditions in the current scenario of climate change.
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Affiliation(s)
| | | | | | - Fernando Flores
- ETSI La Rábida, University of Huelva, Palos de la Frontera, Spain
| | - Catherine Howarth
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, United Kingdom
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | - Elena Prats
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
- *Correspondence: Elena Prats,
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