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Liu X, Gao L, Peng Y, Fang Z, Wang J. PheSom: a term frequency-based method for measuring human phenotype similarity on the basis of MeSH vocabulary. Front Genet 2023; 14:1185790. [PMID: 37496714 PMCID: PMC10366691 DOI: 10.3389/fgene.2023.1185790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Background: Phenotype similarity calculation should be used to help improve drug repurposing. In this study, based on the MeSH terms describing the phenotypes deposited in OMIM, we proposed a method, namely, PheSom (Phenotype Similarity On MeSH), to measure the similarity between phenotypes. PheSom counted the number of overlapping MeSH terms between two phenotypes and then took the weight of every MeSH term within each phenotype into account according to the term frequency-inverse document frequency (FIDC). Phenotype-related genes were used for the evaluation of our method. Results: A 7,739 × 7,739 similarity score matrix was finally obtained and the number of phenotype pairs was dramatically decreased with the increase of similarity score. Besides, the overlapping rates of phenotype-related genes were remarkably increased with the increase of similarity score between phenotypes, which supports the reliability of our method. Conclusion: We anticipate our method can be applied to identifying novel therapeutic methods for complex diseases.
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Affiliation(s)
- Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Ling Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yonglin Peng
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhonghai Fang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Ju Wang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
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Aarsland D, Batzu L, Halliday GM, Geurtsen GJ, Ballard C, Ray Chaudhuri K, Weintraub D. Parkinson disease-associated cognitive impairment. Nat Rev Dis Primers 2021; 7:47. [PMID: 34210995 DOI: 10.1038/s41572-021-00280-3] [Citation(s) in RCA: 375] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 02/08/2023]
Abstract
Parkinson disease (PD) is the second most common neurodegenerative disorder, affecting >1% of the population ≥65 years of age and with a prevalence set to double by 2030. In addition to the defining motor symptoms of PD, multiple non-motor symptoms occur; among them, cognitive impairment is common and can potentially occur at any disease stage. Cognitive decline is usually slow and insidious, but rapid in some cases. Recently, the focus has been on the early cognitive changes, where executive and visuospatial impairments are typical and can be accompanied by memory impairment, increasing the risk for early progression to dementia. Other risk factors for early progression to dementia include visual hallucinations, older age and biomarker changes such as cortical atrophy, as well as Alzheimer-type changes on functional imaging and in cerebrospinal fluid, and slowing and frequency variation on EEG. However, the mechanisms underlying cognitive decline in PD remain largely unclear. Cortical involvement of Lewy body and Alzheimer-type pathologies are key features, but multiple mechanisms are likely involved. Cholinesterase inhibition is the only high-level evidence-based treatment available, but other pharmacological and non-pharmacological strategies are being tested. Challenges include the identification of disease-modifying therapies as well as finding biomarkers to better predict cognitive decline and identify patients at high risk for early and rapid cognitive impairment.
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Affiliation(s)
- Dag Aarsland
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK. .,Centre for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway.
| | - Lucia Batzu
- Parkinson's Foundation Centre of Excellence, King's College Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Glenda M Halliday
- Brain and Mind Centre and Faculty of Medicine and Health School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Gert J Geurtsen
- Amsterdam UMC, University of Amsterdam, Department of Medical Psychology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | | | - K Ray Chaudhuri
- Parkinson's Foundation Centre of Excellence, King's College Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Daniel Weintraub
- Departments of Psychiatry and Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Parkinson's Disease Research, Education and Clinical Center (PADRECC), Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA, USA
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Damena D, Denis A, Golassa L, Chimusa ER. Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects. BMC Med Genomics 2019; 12:120. [PMID: 31409341 PMCID: PMC6693204 DOI: 10.1186/s12920-019-0564-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 07/29/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND P. falciparum malaria has been recognized as one of the prominent evolutionary selective forces of human genome that led to the emergence of multiple host protective alleles. A comprehensive understanding of the genetic bases of severe malaria susceptibility and resistance can potentially pave ways to the development of new therapeutics and vaccines. Genome-wide association studies (GWASs) have recently been implemented in malaria endemic areas and identified a number of novel association genetic variants. However, there are several open questions around heritability, epistatic interactions, genetic correlations and associated molecular pathways among others. Here, we assess the progress and pitfalls of severe malaria susceptibility GWASs and discuss the biology of the novel variants. RESULTS We obtained all severe malaria susceptibility GWASs published thus far and accessed GWAS dataset of Gambian populations from European Phenome Genome Archive (EGA) through the MalariaGen consortium standard data access protocols. We noticed that, while some of the well-known variants including HbS and ABO blood group were replicated across endemic populations, only few novel variants were convincingly identified and their biological functions remain to be understood. We estimated SNP-heritability of severe malaria at 20.1% in Gambian populations and showed how advanced statistical genetic analytic methods can potentially be implemented in malaria susceptibility studies to provide useful functional insights. CONCLUSIONS The ultimate goal of malaria susceptibility study is to discover a novel causal biological pathway that provide protections against severe malaria; a fundamental step towards translational medicine such as development of vaccine and new therapeutics. Beyond singe locus analysis, the future direction of malaria susceptibility requires a paradigm shift from single -omics to multi-stage and multi-dimensional integrative functional studies that combines multiple data types from the human host, the parasite, the mosquitoes and the environment. The current biotechnological and statistical advances may eventually lead to the feasibility of systems biology studies and revolutionize malaria research.
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Affiliation(s)
- Delesa Damena
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7700 South Africa
| | - Awany Denis
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7700 South Africa
| | - Lemu Golassa
- Aklilu Lema Institute of Pathobiology, Addis Ababa University, PO box 1176, Addis Ababa, Ethiopia
| | - Emile R. Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7700 South Africa
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Smajlagić D, Kvarme Jacobsen K, Myrum C, Haavik J, Johansson S, Zayats T. Moderating effect of mode of delivery on the genetics of intelligence: Explorative genome-wide analyses in ALSPAC. Brain Behav 2018; 8:e01144. [PMID: 30378284 PMCID: PMC6305932 DOI: 10.1002/brb3.1144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/27/2018] [Accepted: 09/30/2018] [Indexed: 01/27/2023] Open
Abstract
INTRODUCTION Intelligence is a core construct of individual differences in cognitive abilities and a strong predictor of important life outcomes. Within recent years, rates of cesarean section have substantially increased globally, though little is known about its effect on neurodevelopmental trajectories. Thus, we aimed to investigate the influence of delivery by cesarean section on the genetics of intelligence in children. METHODS Participants were recruited through the Avon Longitudinal Study of Parents and Children (ALSPAC). Intelligence was measured by the Wechsler Intelligence Scale for Children (WISC). Genotyping was performed using the Illumina Human Hap 550 quad genome-wide SNP genotyping platform and was followed by imputation using MACH software. Genome-wide interaction analyses were conducted using linear regression. RESULTS A total of 2,421 children and 2,141,747 SNPs were subjected to the genome-wide interaction analyses. No variant reached genome-wide significance. The strongest interaction was observed at rs17800861 in the GRIN2A gene (β = -3.43, 95% CI = -4.74 to -2.12, p = 2.98E-07). This variant is predicted to be located within active chromatin compartments in the hippocampus and may influence binding of the NF-kappaB transcription factor. CONCLUSIONS Our results may indicate that mode of delivery might have a moderating effect on genetic disposition of intelligence in children. Studies of considerable sizes (>10,000) are likely required to more robustly detect variants governing such interaction. In summary, the presented findings prompt the need for further studies aimed at increasing our understanding of effects various modes of delivery may have on health outcomes in children.
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Affiliation(s)
- Dinka Smajlagić
- Department of Clinical Science, KG Jebsen Center for Neuropsychiatric DisordersUniversity of BergenBergenNorway
- Center for Medical Genetics and Molecular MedicineHaukeland University HospitalBergenNorway
| | - Kaya Kvarme Jacobsen
- Department of Biomedicine, KG Jebsen Center for Neuropsychiatric DisordersUniversity of BergenBergenNorway
| | - Craig Myrum
- Department of Biomedicine, KG Jebsen Center for Neuropsychiatric DisordersUniversity of BergenBergenNorway
| | - Jan Haavik
- Department of Biomedicine, KG Jebsen Center for Neuropsychiatric DisordersUniversity of BergenBergenNorway
| | - Stefan Johansson
- Department of Clinical Science, KG Jebsen Center for Neuropsychiatric DisordersUniversity of BergenBergenNorway
- Center for Medical Genetics and Molecular MedicineHaukeland University HospitalBergenNorway
| | - Tetyana Zayats
- Department of Biomedicine, KG Jebsen Center for Neuropsychiatric DisordersUniversity of BergenBergenNorway
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Pharmacogenomics in type 2 diabetes: oral antidiabetic drugs. THE PHARMACOGENOMICS JOURNAL 2016; 16:399-410. [DOI: 10.1038/tpj.2016.54] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/08/2016] [Accepted: 05/11/2016] [Indexed: 02/06/2023]
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Martelle SE, Raffield LM, Palmer ND, Cox AJ, Freedman BI, Hugenschmidt CE, Williamson JD, Bowden DW. Dopamine pathway gene variants may modulate cognitive performance in the DHS - Mind Study. Brain Behav 2016; 6:e00446. [PMID: 27066308 PMCID: PMC4797918 DOI: 10.1002/brb3.446] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 01/04/2016] [Accepted: 01/11/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND There is an established association between type 2 diabetes and accelerated cognitive decline. The exact mechanism linking type 2 diabetes and reduced cognitive function is less clear. The monoamine system, which is extensively involved in cognition, can be altered by type 2 diabetes status. Thus, this study hypothesized that sequence variants in genes linked to dopamine metabolism and associated pathways are associated with cognitive function as assessed by the Digit Symbol Substitution Task, the Modified Mini-Mental State Examination, the Stroop Task, the Rey Auditory-Verbal Learning Task, and the Controlled Oral Word Association Task for Phonemic and Semantic Fluency in the Diabetes Heart Study, a type 2 diabetes-enriched familial cohort (n = 893). METHODS To determine the effects of candidate variants on cognitive performance, genetic association analyses were performed on the well-documented variable number tandem repeat located in the 3' untranslated region of the dopamine transporter, as well as on single-nucleotide polymorphisms covering genes in the dopaminergic pathway, the insulin signaling pathway, and the convergence of both. Next, polymorphisms in loci of interest with strong evidence for involvement in dopamine processing were extracted from genetic datasets available in a subset of the cohort (n = 572) derived from Affymetrix(®) Genome-Wide Human SNP Array 5.0 and 1000 Genomes imputation from this array. RESULTS The candidate gene analysis revealed one variant from the DOPA decarboxylase gene, rs10499695, to be associated with poorer performance on a subset of Rey Auditory-Verbal Learning Task measuring retroactive interference (P = 0.001, β = -0.45). Secondary analysis of genome-wide and imputed data uncovered another DOPA decarboxylase variant, rs62445903, also associated with retroactive interference (P = 7.21 × 10(-7), β = 0.3). These data suggest a role for dopaminergic genes, specifically a gene involved in regulation of dopamine synthesis, in cognitive performance in type 2 diabetes.
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Affiliation(s)
- Susan E Martelle
- Department of Physiology and Pharmacology Wake Forest School of Medicine Winston - Salem North Carolina; Center for Genomics and Personalized Medicine Research Wake Forest School of Medicine Winston - Salem North Carolina
| | - Laura M Raffield
- Center for Genomics and Personalized Medicine Research Wake Forest School of Medicine Winston - Salem North Carolina
| | - Nichole D Palmer
- Center for Genomics and Personalized Medicine Research Wake Forest School of Medicine Winston - Salem North Carolina
| | - Amanda J Cox
- Molecular Basis of Disease Griffith University Southport Brisbane Queensland Australia
| | - Barry I Freedman
- Department of Internal Medicine, Nephrology Wake Forest School of Medicine Winston - Salem North Carolina
| | - Christina E Hugenschmidt
- Department of Internal Medicine, Gerontology and Geriatric Medicine Wake Forest School of Medicine Winston - Salem North Carolina
| | - Jeff D Williamson
- Department of Internal Medicine, Gerontology and Geriatric Medicine Wake Forest School of Medicine Winston - Salem North Carolina
| | - Don W Bowden
- Center for Genomics and Personalized Medicine Research Wake Forest School of Medicine Winston - Salem North Carolina
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