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Mitchell KJ. Variability in Neural Circuit Formation. Cold Spring Harb Perspect Biol 2024; 16:a041504. [PMID: 38253418 PMCID: PMC10910361 DOI: 10.1101/cshperspect.a041504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The study of neural development is usually concerned with the question of how nervous systems get put together. Variation in these processes is usually of interest as a means of revealing these normative mechanisms. However, variation itself can be an object of study and is of interest from multiple angles. First, the nature of variation in both the processes and the outcomes of neural development is relevant to our understanding of how these processes and outcomes are encoded in the genome. Second, variation in the wiring of the brain in humans may underlie variation in all kinds of psychological and behavioral traits, as well as neurodevelopmental disorders. And third, genetic variation that affects circuit development provides the raw material for evolutionary change. Here, I examine these different aspects of variation in circuit development and consider what they may tell us about these larger questions.
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Affiliation(s)
- Kevin J Mitchell
- Smurfit Institute of Genetics and Institute of Neuroscience, Trinity College Dublin, Dublin D02 PN40, Ireland
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Zhou XY, Liu RK, Zeng CP. Exploring the novel SNPs in neuroticism and birth weight based on GWAS datasets. BMC Med Genomics 2023; 16:167. [PMID: 37454083 PMCID: PMC10349512 DOI: 10.1186/s12920-023-01591-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: 09/08/2022] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVES Epidemiological studies have confirmed that low birth weight (BW) is related to neuroticism and they may have a common genetic mechanism based on phenotypic correlation research. We conducted our study on a European population with 159,208 neuroticism and 289,142 birth weight samples. In this study, we aimed to identify new neuroticism single nucleotide polymorphisms (SNPs) and pleiotropic SNPs associated with neuroticism and BW and to provide more theoretical basis for the pathogenesis of the disease. METHODS We estimated the pleiotropic enrichment between neuroticism and BW in two independent Genome-wide association studies (GWAS) when the statistical thresholds were Conditional False Discovery Rate (cFDR) < 0.01 and Conjunctional Conditional False Discovery Rate (ccFDR) < 0.05. We performed gene annotation and gene functional analysis on the selected significant SNPs to determine the biological role of gene function and pathogenesis. Two-sample Mendelian Randomization (TSMR) analysis was performed to explore the causal relationship between the neuroticism and BW. RESULTS The conditional quantile-quantile plots (Q-Q plot) indicated that neuroticism and BW have strong genetic pleiotropy enrichment trends. With the threshold of cFDR < 0.001, we identified 126 SNPs related to neuroticism and 172 SNPs related to BW. With the threshold of ccFDR < 0.05, we identified 62 SNPs related to both neuroticism and BW. Among these SNPs, rs8039305 and rs35755513 have eQTL (expressed quantitative trait loci) and meQTL (methylation quantitative trait loci) effects simultaneously. Through GO enrichment analysis we also found that the two pathways of positive regulation of "mesenchymal cell proliferation" and "DNA-binding transcription factor activity" were significantly enriched in neuroticism and BW. Mendelian randomization analysis results indicate that there is no obvious causal relationship between neuroticism and birth weight. CONCLUSION We found 126 SNPs related to neuroticism, 172 SNPs related to BW and 62 SNPs associated with both neuroticism and BW, which provided a theoretical basis for their genetic mechanism and novel potential targets for treatment/intervention development.
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Affiliation(s)
- Xiao-Ying Zhou
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510330, China
- Department of Endocrinology and Metabolism, SSL Central Hospital of Dongguan City, No.1, Xianglong Road, Dongguan, 523326, China
| | - Rui-Ke Liu
- Department of Endocrinology and Metabolism, SSL Central Hospital of Dongguan City, No.1, Xianglong Road, Dongguan, 523326, China.
| | - Chun-Ping Zeng
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510330, China.
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Efanova E, Bushueva O, Saranyuk R, Surovtseva A, Churnosov M, Solodilova M, Polonikov A. Polymorphisms of the GCLC Gene Are Novel Genetic Markers for Susceptibility to Psoriasis Associated with Alcohol Abuse and Cigarette Smoking. Life (Basel) 2023; 13:1316. [PMID: 37374099 DOI: 10.3390/life13061316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
The aim of this pilot study was to investigate whether single nucleotide polymorphisms (SNP) in the gene encoding the catalytic subunit of glutamate cysteine ligase (GCLC) are associated with the risk and clinical features of psoriasis. A total of 944 unrelated individuals, including 474 patients with a diagnosis of psoriasis and 470 healthy controls, were recruited for the study. Six common SNPs in the GCLC gene were genotyped using the MassArray-4 system. Polymorphisms rs648595 (OR = 0.56, 95% CI 0.35-0.90; Pperm = 0.017) and rs2397147 (OR = 0.54, 95% CI 0.30-0.98; Pperm = 0.05) were associated with susceptibility to psoriasis in males. In the male group, diplotype rs2397147-C/C × rs17883901-G/G was associated with a decreased risk of psoriasis (FDR-adjusted p = 0.014), whereas diplotype rs6933870-G/G × rs17883901-G/G (FDR-adjusted p = 0.045) showed an association with an increased disease risk in females. The joint effects of SNPs with tobacco smoking (rs648595 and rs17883901) and alcohol abuse (rs648595 and rs542914) on psoriasis risk were observed (Pperm ≤ 0.05). We also found multiple sex-independent associations between GCLC gene polymorphisms and various clinical features such as earlier disease onset, the psoriatic triad, and specific localizations of skin lesions. The present study is the first to show that polymorphisms of the GCLC gene are significantly associated with the risk of psoriasis and related to its clinical features.
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Affiliation(s)
- Ekaterina Efanova
- Medvenka Central District Hospital, 68 Sovetskaya Street, 307030 Kursk, Russia
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
| | - Olga Bushueva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
| | - Roman Saranyuk
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
- Center for Medical Examinations and Prevention, 2 Leninsky Komsomol Avenue, 305026 Kursk, Russia
| | - Anna Surovtseva
- Laboratory of Genomic Research, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
| | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State University, 85 Pobedy Street, 308015 Belgorod, Russia
| | - Maria Solodilova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
| | - Alexey Polonikov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, 3 Karl Marx Street, 305041 Kursk, Russia
- Laboratory of Statistical Genetics and Bioinformatics, Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, 18 Yamskaya Street, 305041 Kursk, Russia
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Castellini G, Merola GP, Baccaredda Boy O, Pecoraro V, Bozza B, Cassioli E, Rossi E, Bessi V, Sorbi S, Nacmias B, Ricca V. Emotional dysregulation, alexithymia and neuroticism: a systematic review on the genetic basis of a subset of psychological traits. Psychiatr Genet 2023; 33:79-101. [PMID: 36729042 PMCID: PMC10158611 DOI: 10.1097/ypg.0000000000000335] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/24/2022] [Indexed: 02/03/2023]
Abstract
Neuroticism, alexithymia and emotion dysregulation are key traits and known risk factors for several psychiatric conditions. In this systematic review, the aim is to evaluate the genetic contribution to these psychological phenotypes. A systematic review of articles found in PubMed was conducted. Search terms included 'genetic', 'GWAS', 'neuroticism', 'alexithymia' and 'emotion dysregulation'. Risk of bias was assessed utilizing the STREGA checklist. Two hundred two papers were selected from existing literature based on the inclusion and exclusion criteria. Among these, 27 were genome-wide studies and 175 were genetic association studies. Single gene association studies focused on selected groups of genes, mostly involved in neurotransmission, with conflicting results. GWAS studies on neuroticism, on the other hand, found several relevant and replicated intergenic and intronic loci affecting the expression and regulation of crucial and well-known genes (such as DRD2 and CRHR1). Mutations in genes coding for trascriptional factors were also found to be associated with neuroticism (DCC, XKR6, TCF4, RBFOX1), as well as a noncoding regulatory RNA (LINC00461). On the other hand, little GWAS data are available on alexythima and emotional dysregulation.
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Affiliation(s)
| | | | | | | | | | | | | | - Valentina Bessi
- Neurology Unit, Department of Health Sciences, University of Florence, Florence, Italy
| | - Sandro Sorbi
- Neurology Unit, Department of Health Sciences, University of Florence, Florence, Italy
| | - Benedetta Nacmias
- Neurology Unit, Department of Health Sciences, University of Florence, Florence, Italy
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Belonogova NM, Kirichenko AV, Freidin MB, Williams FMK, Suri P, Aulchenko YS, Axenovich TI, Tsepilov YA. Noncoding rare variants in PANX3 are associated with chronic back pain. Pain 2023; 164:864-869. [PMID: 36448979 PMCID: PMC10014492 DOI: 10.1097/j.pain.0000000000002781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/31/2022] [Indexed: 12/05/2022]
Abstract
ABSTRACT Back pain is the leading cause of years lived with disability worldwide, yet surprisingly, little is known regarding the biology underlying this condition. The impact of genetics is known for chronic back pain: its heritability is estimated to be at least 40%. Large genome-wide association studies have shown that common variation may account for up to 35% of chronic back pain heritability; rare variants may explain a portion of the heritability not explained by common variants. In this study, we performed the first gene-based association analysis of chronic back pain using UK Biobank imputed data including rare variants with moderate imputation quality. We discovered 2 genes, SOX5 and PANX3 , influencing chronic back pain. The SOX5 gene is a well-known back pain gene. The PANX3 gene has not previously been described as having a role in chronic back pain. We showed that the association of PANX3 with chronic back pain is driven by rare noncoding intronic polymorphisms. This result was replicated in an independent sample from UK Biobank and validated using a similar phenotype, dorsalgia, from FinnGen Biobank. We also found that the PANX3 gene is associated with intervertebral disk disorders. We can speculate that a possible mechanism of action of PANX3 on back pain is due to its effect on the intervertebral disks.
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Affiliation(s)
- Nadezhda M. Belonogova
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
| | - Anatoly V. Kirichenko
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
- Kurchatov genomics center of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Maxim B. Freidin
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Frances M. K. Williams
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Pradeep Suri
- Seattle Epidemiologic Research and Information Center, VA Puget Sound Health Care System, 1660 S. Columbian Way, Seattle, WA 98108, USA
- Division of Rehabilitation Care Services, 1660 S. Columbian Way, Seattle, WA 98108, USA
- Clinical Learning, Evidence, and Research Center, University of Washington, 325 Ninth Avenue, Box 359612 Seattle, WA 98104, USA
| | - Yurii S. Aulchenko
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
- PolyOmica, Het Vlaggeschip 61, 5237 PA ‘s-Hertogenbosch, the Netherlands
| | - Tatiana I. Axenovich
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
| | - Yakov A. Tsepilov
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
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Bastos CR, Bock BB, Xavier J, Camerini L, Dewes SS, Grellert M, de Carvalho HW, Jansen K, da Silva RA, Pinheiro RT, de Mattos Souza L, Oses JP, Portela LV, Lara DR, Tovo-Rodrigues L, Ghisleni G. Temperament traits mediate the relationship between CACNA1C polymorphisms and bipolar disorder in cisgender women. Eur Arch Psychiatry Clin Neurosci 2023; 273:41-50. [PMID: 36181558 DOI: 10.1007/s00406-022-01493-7] [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: 04/23/2022] [Accepted: 09/13/2022] [Indexed: 11/03/2022]
Abstract
The influence of temperament traits on bipolar disorder (BD) has been investigated. Both temperament traits and BD are partially genetically determined and seem to be influenced by variations in the CACNA1C gene. These variations presented a significant interactive effect with biological sex, although studies that evaluate this relationship are scarce. Here, we assessed the mediation effect of temperament traits on the relationship between two polymorphisms in the CACNA1C gene (rs1006737 and rs4765913) and BD according to sex. This is a cross-sectional study consisting of 878 Caucasian individuals (508 women and 370 men), aged 18-35, enrolled in a population-based study in the city of Pelotas, Southern Brazil. BD diagnosis was evaluated using the clinical interview MINI 5.0, and temperament traits were assessed via the application of the Affective and Emotional Composite Temperament Scale (AFECTS). Mediation models were tested using the modeling tool PROCESS (version 3.3) for SPSS. Bootstrapping-enhanced mediation analyses in women indicated that traits anger (39%) and caution (27%) mediated the association between the rs4765913 SNP and BD, while traits volition (29%), anger (35%), and caution (29%) mediated the association between the AA haplotype (rs1006737-rs4765913) and the BD. No effect was encountered for cisgender men. Our model revealed that paths from CACNA1C SNPs to BD are mediated by specific temperament traits in women, reinforcing the definition of temperament traits as endophenotypes.
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Affiliation(s)
- Clarissa Ribeiro Bastos
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Bertha Bueno Bock
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil
| | - Janaina Xavier
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil
| | - Laísa Camerini
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil
| | - Samantha Seibt Dewes
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil
| | - Mateus Grellert
- Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | | | - Karen Jansen
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil
| | - Ricardo Azevedo da Silva
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil
| | - Ricardo Tavares Pinheiro
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil
| | - Luciano de Mattos Souza
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil
| | - Jean Pierre Oses
- Institute of Biological Sciences, Federal University of Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Luis Valmor Portela
- Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diogo Rizzato Lara
- Department of Cellular and Molecular Biology, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Luciana Tovo-Rodrigues
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Gabriele Ghisleni
- Post-Graduation Program in Health and Behavior, Center of Health Science, Catholic University of Pelotas, 373, 324C Gonçalves Chaves Street, Pelotas, Rio Grande do Sul, CEP 96015-560, Brazil.
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sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics. PLoS Comput Biol 2022; 18:e1010172. [PMID: 35653402 PMCID: PMC9197066 DOI: 10.1371/journal.pcbi.1010172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 06/14/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022] Open
Abstract
Gene-based association analysis is an effective gene-mapping tool. Many gene-based methods have been proposed recently. However, their power depends on the underlying genetic architecture, which is rarely known in complex traits, and so it is likely that a combination of such methods could serve as a universal approach. Several frameworks combining different gene-based methods have been developed. However, they all imply a fixed set of methods, weights and functional annotations. Moreover, most of them use individual phenotypes and genotypes as input data. Here, we introduce sumSTAAR, a framework for gene-based association analysis using summary statistics obtained from genome-wide association studies (GWAS). It is an extended and modified version of STAAR framework proposed by Li and colleagues in 2020. The sumSTAAR framework offers a wider range of gene-based methods to combine. It allows the user to arbitrarily define a set of these methods, weighting functions and probabilities of genetic variants being causal. The methods used in the framework were adapted to analyse genes with large number of SNPs to decrease the running time. The framework includes the polygene pruning procedure to guard against the influence of the strong GWAS signals outside the gene. We also present new improved matrices of correlations between the genotypes of variants within genes. These matrices estimated on a sample of 265,000 individuals are a state-of-the-art replacement of widely used matrices based on the 1000 Genomes Project data. Gene-based association analysis is an effective gene mapping tool. Quite a few frameworks have been proposed recently for gene-based association analysis using a combination of different methods. However, all of these frameworks have at least one of the disadvantages: they use a fixed set of methods, they cannot use functional annotations, or they use individual phenotypes and genotypes as input data. To overcome these limitations, we propose sumSTAAR, a framework for gene-based association analysis using GWAS summary statistics. Our framework allows the user to arbitrarily define a set of the methods and functional annotations. Moreover, we adopted the methods for the analysis of genes with a large number of SNPs to decrease the running time. The framework includes the polygene pruning procedure to guard against the influence of the strong GWAS signals outside the gene. We also present new improved matrices of correlations between the genotypes of variants within genes, which now allows to include ultra-rare variants (MAF < 10−4) in analysis.
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Katsonis P, Wilhelm K, Williams A, Lichtarge O. Genome interpretation using in silico predictors of variant impact. Hum Genet 2022; 141:1549-1577. [PMID: 35488922 PMCID: PMC9055222 DOI: 10.1007/s00439-022-02457-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/17/2022] [Indexed: 02/06/2023]
Abstract
Estimating the effects of variants found in disease driver genes opens the door to personalized therapeutic opportunities. Clinical associations and laboratory experiments can only characterize a tiny fraction of all the available variants, leaving the majority as variants of unknown significance (VUS). In silico methods bridge this gap by providing instant estimates on a large scale, most often based on the numerous genetic differences between species. Despite concerns that these methods may lack reliability in individual subjects, their numerous practical applications over cohorts suggest they are already helpful and have a role to play in genome interpretation when used at the proper scale and context. In this review, we aim to gain insights into the training and validation of these variant effect predicting methods and illustrate representative types of experimental and clinical applications. Objective performance assessments using various datasets that are not yet published indicate the strengths and limitations of each method. These show that cautious use of in silico variant impact predictors is essential for addressing genome interpretation challenges.
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Affiliation(s)
- Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Kevin Wilhelm
- Graduate School of Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Amanda Williams
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Biochemistry, Human Genetics and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Computational and Integrative Biomedical Research Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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Zorkoltseva I, Shadrina A, Belonogova N, Kirichenko A, Tsepilov Y, Axenovich T. In silico genome-wide gene-based association analysis reveals new genes predisposing to coronary artery disease. Clin Genet 2021; 101:78-86. [PMID: 34687547 DOI: 10.1111/cge.14073] [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: 07/19/2021] [Revised: 09/29/2021] [Accepted: 10/13/2021] [Indexed: 11/30/2022]
Abstract
Genome-wide association study (GWAS) have identified more than 300 single nucleotide polymorphisms at 163 independent loci associated with coronary artery disease (CAD). However, there is no full understanding about the causal genes for CAD and the mechanisms of their action. We aimed to perform a post GWAS analysis to identify genes whose polymorphism may influence the risk of CAD. Using the UK Biobank GWAS summary statistics, we performed a gene-based association analysis. We found 63 genes significantly associated with CAD due to their within-gene polymorphisms. Many of these genes are well known. Some known CAD genes such as FURIN and SORT1 did not show the gene-based association because their variants had low GWAS signals or gene-based association was inflated by the strong GWAS signal outside the gene. For several known CAD genes, we demonstrated that their effects could be explained not only or not at all by their own variants but by the variants within the neighboring genes controlling their expression. Using several bioinformatics techniques, we suggested potential mechanisms underlying gene-CAD associations. Three genes, CDK19, NCALD, and ARHGEF12 were not previously associated with CAD. The role of these genes should be clarified in further studies.
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Affiliation(s)
- Irina Zorkoltseva
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Alexandra Shadrina
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Nadezhda Belonogova
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Anatoly Kirichenko
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Yakov Tsepilov
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Tatiana Axenovich
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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Axenovich TI, Belonogova NM, Zorkoltseva IV, Tsepilov YA. Number of Genes Associated with Neuroticism due to Their Polymorphisms. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421070024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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