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Maculewicz E, Leońska-Duniec A, Mastalerz A, Szarska E, Garbacz A, Lepionka T, Łakomy R, Anyżewska A, Bertrandt J. The Influence of FTO, FABP2, LEP, LEPR, and MC4R Genes on Obesity Parameters in Physically Active Caucasian Men. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19106030. [PMID: 35627568 PMCID: PMC9141290 DOI: 10.3390/ijerph19106030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/09/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023]
Abstract
Obesity is a complex multifactorial abnormality that has a well-confirmed genetic basis. However, the problem still lies in identifying the polymorphisms linked to body mass and composition. Therefore, this study aimed to analyze associations between FTO (rs9939609), FABP2 (rs1799883), and LEP (rs2167270), LEPR (rs1137101), and MC4R (rs17782313) polymorphisms and obesity-related parameters. Unrelated Caucasian males (n = 165) were recruited. All participants had similar physical activity levels. The participants were divided into two groups depending on their body mass index (BMI) and fat mass index (FMI). All samples were genotyped using real-time polymerase chain reaction (real-time PCR). When tested individually, only one statistically significant result was found. The FTO A/T polymorphism was significantly associated with FMI (p = 0.01). The chance of having increased FMI was >2-fold higher for the FTO A allele carriers (p < 0.01). Gene−gene interaction analyses showed the additional influence of all investigated genes on BMI and FMI. In summary, it was demonstrated that harboring the FTO A allele might be a risk factor for elevated fat mass. Additionally, this study confirmed that all five polymorphisms are involved in the development of common obesity in the studied population and the genetic risk of obesity is linked to the accumulation of numerous variants.
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Affiliation(s)
- Ewelina Maculewicz
- Faculty of Physical Education, Jozef Pilsudski University of Physical Education in Warsaw, 00-809 Warsaw, Poland;
- Correspondence:
| | - Agata Leońska-Duniec
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland;
| | - Andrzej Mastalerz
- Faculty of Physical Education, Jozef Pilsudski University of Physical Education in Warsaw, 00-809 Warsaw, Poland;
| | - Ewa Szarska
- Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland; (E.S.); (T.L.); (R.Ł.)
| | - Aleksandra Garbacz
- Institute of Animal Sciences, Faculty of Animal Breeding, Bioengineering and Conservation, Warsaw University of Life Sciences—SGGW, 02-787 Warsaw, Poland;
| | - Tomasz Lepionka
- Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland; (E.S.); (T.L.); (R.Ł.)
| | - Roman Łakomy
- Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland; (E.S.); (T.L.); (R.Ł.)
| | - Anna Anyżewska
- University of Economics and Human Sciences in Warsaw, Okopowa 59, 01-043 Warsaw, Poland;
| | - Jerzy Bertrandt
- Faculty of Health Sciences, Pope John Paul II State School of Higher Education in Biala Podlaska, 21-500 Biala Podlaska, Poland;
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Peng L, Tan J, Tian X, Zhou L. EnANNDeep: An Ensemble-based lncRNA-protein Interaction Prediction Framework with Adaptive k-Nearest Neighbor Classifier and Deep Models. Interdiscip Sci 2022; 14:209-232. [PMID: 35006529 DOI: 10.1007/s12539-021-00483-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 01/08/2023]
Abstract
lncRNA-protein interactions (LPIs) prediction can deepen the understanding of many important biological processes. Artificial intelligence methods have reported many possible LPIs. However, most computational techniques were evaluated mainly on one dataset, which may produce prediction bias. More importantly, they were validated only under cross validation on lncRNA-protein pairs, and did not consider the performance under cross validations on lncRNAs and proteins, thus fail to search related proteins/lncRNAs for a new lncRNA/protein. Under an ensemble learning framework (EnANNDeep) composed of adaptive k-nearest neighbor classifier and Deep models, this study focuses on systematically finding underlying linkages between lncRNAs and proteins. First, five LPI-related datasets are arranged. Second, multiple source features are integrated to depict an lncRNA-protein pair. Third, adaptive k-nearest neighbor classifier, deep neural network, and deep forest are designed to score unknown lncRNA-protein pairs, respectively. Finally, interaction probabilities from the three predictors are integrated based on a soft voting technique. In comparing to five classical LPI identification models (SFPEL, PMDKN, CatBoost, PLIPCOM, and LPI-SKF) under fivefold cross validations on lncRNAs, proteins, and LPIs, EnANNDeep computes the best average AUCs of 0.8660, 0.8775, and 0.9166, respectively, and the best average AUPRs of 0.8545, 0.8595, and 0.9054, respectively, indicating its superior LPI prediction ability. Case study analyses indicate that SNHG10 may have dense linkage with Q15717. In the ensemble framework, adaptive k-nearest neighbor classifier can separately pick the most appropriate k for each query lncRNA-protein pair. More importantly, deep models including deep neural network and deep forest can effectively learn the representative features of lncRNAs and proteins.
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China. .,College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China.
| | - Jingwei Tan
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Xiongfei Tian
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, China.
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3
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Rana S, Sultana A, Bhatti AA. Effect of interaction between obesity-promoting genetic variants and behavioral factors on the risk of obese phenotypes. Mol Genet Genomics 2021; 296:919-938. [PMID: 33966103 DOI: 10.1007/s00438-021-01793-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 01/28/2023]
Abstract
The studies investigating gene-gene and gene-environment (or gene-behavior) interactions provide valuable insight into the pathomechanisms underlying obese phenotypes. The Pakistani population due to its unique characteristics offers numerous advantages for conducting such studies. In this view, the current study was undertaken to examine the effects of gene-gene and gene-environment/behavior interactions on the risk of obesity in a sample of Pakistani population. A total of 578 adult participants including 290 overweight/obese cases and 288 normal-weight controls were involved. The five key obesity-associated genetic variants namely MC4R rs17782313, BDNF rs6265, FTO rs1421085, TMEM18 rs7561317, and NEGR1 rs2815752 were genotyped using the TaqMan allelic discrimination assays. The data related to behavioral factors, such as eating pattern, diet consciousness, the tendency toward fat-dense food (TFDF), sleep duration, sleep-wake cycle (SWC), shift work (SW), and physical activity levels were collected via a questionnaire. Gene-gene and gene-behavior interactions were analyzed by multifactor dimensionality reduction and linear regression, respectively. In our study, only TMEM18 rs7561317 was found to be significantly associated with anthropometric traits with no significant effect of gene-gene interactions were observed on obesity-related phenotypes. However, the genetic variants were found to interact with the behavioral factors to significantly influence various obesity-related anthropometric traits including BMI, waist circumference, hip circumference, waist-to-hip ratio, waist-to-height ratio, and percentage of body fat. In conclusion, the interaction between genetic architecture and behavior/environment determines the outcome of obesity-related anthropometric phenotypes. Thus, gene-environment/behavior interaction studies should be promoted to explore the risk of complex and multifactorial disorders, such as obesity.
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Affiliation(s)
- Sobia Rana
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan.
| | - Ayesha Sultana
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
| | - Adil Anwar Bhatti
- Molecular Biology and Human Genetics Laboratory, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, 75270, Pakistan
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Magaña J, Contreras MG, Keys KL, Risse-Adams O, Goddard PC, Zeiger AM, Mak ACY, Elhawary JR, Samedy-Bates LA, Lee E, Thakur N, Hu D, Eng C, Salazar S, Huntsman S, Hu T, Burchard EG, White MJ. An epistatic interaction between pre-natal smoke exposure and socioeconomic status has a significant impact on bronchodilator drug response in African American youth with asthma. BioData Min 2020; 13:7. [PMID: 32636926 PMCID: PMC7333373 DOI: 10.1186/s13040-020-00218-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/23/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Asthma is one of the leading chronic illnesses among children in the United States. Asthma prevalence is higher among African Americans (11.2%) compared to European Americans (7.7%). Bronchodilator medications are part of the first-line therapy, and the rescue medication, for acute asthma symptoms. Bronchodilator drug response (BDR) varies substantially among different racial/ethnic groups. Asthma prevalence in African Americans is only 3.5% higher than that of European Americans, however, asthma mortality among African Americans is four times that of European Americans; variation in BDR may play an important role in explaining this health disparity. To improve our understanding of disparate health outcomes in complex phenotypes such as BDR, it is important to consider interactions between environmental and biological variables. RESULTS We evaluated the impact of pairwise and three-variable interactions between environmental, social, and biological variables on BDR in 233 African American youth with asthma using Visualization of Statistical Epistasis Networks (ViSEN). ViSEN is a non-parametric entropy-based approach able to quantify interaction effects using an information-theory metric known as Information Gain (IG). We performed analyses in the full dataset and in sex-stratified subsets. Our analyses identified several interaction models significantly, and suggestively, associated with BDR. The strongest interaction significantly associated with BDR was a pairwise interaction between pre-natal smoke exposure and socioeconomic status (full dataset IG: 2.78%, p = 0.001; female IG: 7.27%, p = 0.004)). Sex-stratified analyses yielded divergent results for females and males, indicating the presence of sex-specific effects. CONCLUSIONS Our study identified novel interaction effects significantly, and suggestively, associated with BDR in African American children with asthma. Notably, we found that all of the interactions identified by ViSEN were "pure" interaction effects, in that they were not the result of strong main effects on BDR, highlighting the complexity of the network of biological and environmental factors impacting this phenotype. Several associations uncovered by ViSEN would not have been detected using regression-based methods, thus emphasizing the importance of employing statistical methods optimized to detect both additive and non-additive interaction effects when studying complex phenotypes such as BDR. The information gained in this study increases our understanding and appreciation of the complex nature of the interactions between environmental and health-related factors that influence BDR and will be invaluable to biomedical researchers designing future studies.
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Affiliation(s)
- J. Magaña
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - M. G. Contreras
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - K. L. Keys
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Berkeley Institute for Data Science, University of California, Berkeley, CA USA
| | - O. Risse-Adams
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Lowell Science Research Program, Lowell High School, San Francisco, CA USA
- Department of Biology, University of California, Santa Cruz, CA USA
| | - P. C. Goddard
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Department of Genetics, Stanford University, Stanford, CA USA
| | - A. M. Zeiger
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA USA
| | - A. C. Y. Mak
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - J. R. Elhawary
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - L. A. Samedy-Bates
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA USA
| | - E. Lee
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - N. Thakur
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - D. Hu
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - C. Eng
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - S. Salazar
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - S. Huntsman
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
| | - T. Hu
- School of Computing, Queen’s University, Kingston, ON Canada
| | - E. G. Burchard
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA USA
| | - M. J. White
- Department of Medicine, University of California, 1550 4th Street, UCSF Rock Hall, Box 2911, San Francisco, CA 94158 USA
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El Hajj Chehadeh S, Osman W, Nazar S, Jerman L, Alghafri A, Sajwani A, Alawlaqi M, AlObeidli M, Jelinek HF, AlAnouti F, Khalaf K, Alsafar H. Implication of genetic variants in overweight and obesity susceptibility among the young Arab population of the United Arab Emirates. Gene 2020; 739:144509. [PMID: 32109558 DOI: 10.1016/j.gene.2020.144509] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/22/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Overweight and obesity are major risk factors for Type 2 Diabetes Mellitus (T2DM), cardiovascular disease (CVD) and cancer. Genetic predisposition has been shown to play a key role in obesity, and genome-wide association studies (GWAS) have identified multiple loci linked with obesity in various ethnic groups. The aim of this study was to validate the reported genetic variants associated with obesity and overweight in a young UAE Arab population. METHODS Twenty-two associated single nucleotide polymorphisms (SNPs) at 11 loci (FTO, MC4R, TMEM18, KCTD15, MTCH2, SH2B1, TFAP2B, GNPDA2, NEGR1, PCSK1 and BDNF) were studied in 392 controls and 318 overweight/obese young Emiratis (aged 18-35 years). RESULTS After adjusting for age and smoking, rs3751812 of the FTO gene was associated with overweight/obesity in male participants (p-value < 0.016), while SNPs rs17782313, rs571312 of the MC4R gene and rs12463617 of the TMEM18 gene were significantly associated with overweight/obesity in female participants (p-value = 0.001, 0.028, 0.044, respectively). Follow-up association tests and logistic regression revealed the contribution of the FTO rs3751812 and MC4R rs571213 SNPs to the risk of overweight/obesity after adjusting for age, sex and smoking (p-value = 0.044, 0.049, respectively). In addition, the FTO rs3751812 was associated with the risk of overweight/obesity after adjusting for the effect of other markers (rs17782313, rs571312, rs2867125, rs6548238 and rs12463617) (p-value = 0.035). A significant gene-gene interaction was seen between FTO, MCR4 and TMEM18 (p-value = 0.013). CONCLUSIONS Our data demonstrates that rs3751812 of the FTO gene is the key SNP associated with risk of overweight/obesity among the young UAE Arab population, in alignment with previous findings. Our results also indicate that the identified genes stratify with sex and risk of overweight/obesity. In addition to their direct association with overweight/obesity, rs17782313 and rs571312, as well as rs2867125 and rs6548238, may have a modifying effect on the risk of overweight/obesity caused by the rs3751812. Population-specific, sex-specific genetic profiling is important in understanding the heritability of obesity.
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Affiliation(s)
| | - Wael Osman
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates; College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Suna Nazar
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Laila Jerman
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Ameera Alghafri
- College of Medicine, Mohammad Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ali Sajwani
- College of Medicine, Mohammad Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mohamed Alawlaqi
- School of Medicine, The Royal College of Surgeons, Dublin, Ireland
| | - Mohamed AlObeidli
- College of Medicine and Health Sciences, United Arab Emirates University, AlAin, United Arab Emirates
| | - Herbert F Jelinek
- School of Community Health, Charles Sturt University, Albury, Australia; Department of Biomedical Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Fatme AlAnouti
- College of Natural and Health Sciences, Zayed University, Abu Dhabi, United Arab Emirates
| | - Kinda Khalaf
- Department of Biomedical Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates; Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.
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Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. Transl Psychiatry 2019; 9:256. [PMID: 31624234 PMCID: PMC6797775 DOI: 10.1038/s41398-019-0596-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
Both heritability and environment contribute to risk for schizophrenia. However, the molecular mechanisms of interactions between genetic and non-genetic factors remain unclear. Epigenetic regulation of neuronal genome may be a presumable mechanism in pathogenesis of schizophrenia. Here, we performed analysis of open chromatin landscape of gene promoters in prefrontal cortical (PFC) neurons from schizophrenic patients. We cataloged cell-type-based epigenetic signals of transcriptional start sites (TSS) marked by histone H3-K4 trimethylation (H3K4me3) across the genome in PFC from multiple schizophrenia subjects and age-matched control individuals. One of the top-ranked chromatin alterations was found in the major histocompatibility (MHC) locus on chromosome 6 highlighting the overlap between genetic and epigenetic risk factors in schizophrenia. The chromosome conformation capture (3C) analysis in human brain cells revealed the architecture of multipoint chromatin interactions between the schizophrenia-associated genetic and epigenetic polymorphic sites and distantly located HLA-DRB5 and BTNL2 genes. In addition, schizophrenia-specific chromatin modifications in neurons were particularly prominent for non-coding RNA genes, including an uncharacterized LINC01115 gene and recently identified BNRNA_052780. Notably, protein-coding genes with altered epigenetic state in schizophrenia are enriched for oxidative stress and cell motility pathways. Our results imply the rare individual epigenetic alterations in brain neurons are involved in the pathogenesis of schizophrenia.
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Epi-GTBN: an approach of epistasis mining based on genetic Tabu algorithm and Bayesian network. BMC Bioinformatics 2019; 20:444. [PMID: 31455207 PMCID: PMC6712799 DOI: 10.1186/s12859-019-3022-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 08/07/2019] [Indexed: 12/31/2022] Open
Abstract
Background Mining epistatic loci which affects specific phenotypic traits is an important research issue in the field of biology. Bayesian network (BN) is a graphical model which can express the relationship between genetic loci and phenotype. Until now, it has been widely used into epistasis mining in many research work. However, this method has two disadvantages: low learning efficiency and easy to fall into local optimum. Genetic algorithm has the excellence of rapid global search and avoiding falling into local optimum. It is scalable and easy to integrate with other algorithms. This work proposes an epistasis mining approach based on genetic tabu algorithm and Bayesian network (Epi-GTBN). It uses genetic algorithm into the heuristic search strategy of Bayesian network. The individual structure can be evolved through the genetic operations of selection, crossover and mutation. It can help to find the optimal network structure, and then further to mine the epistasis loci effectively. In order to enhance the diversity of the population and obtain a more effective global optimal solution, we use the tabu search strategy into the operations of crossover and mutation in genetic algorithm. It can help to accelerate the convergence of the algorithm. Results We compared Epi-GTBN with other recent algorithms using both simulated and real datasets. The experimental results demonstrate that our method has much better epistasis detection accuracy in the case of not affecting the efficiency for different datasets. Conclusions The presented methodology (Epi-GTBN) is an effective method for epistasis detection, and it can be seen as an interesting addition to the arsenal used in complex traits analyses. Electronic supplementary material The online version of this article (10.1186/s12859-019-3022-z) contains supplementary material, which is available to authorized users.
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Cinelli M, Ferraro G, Iovanella A. Evaluating relevance and redundancy to quantify how binary node metadata interplay with the network structure. Sci Rep 2019; 9:11404. [PMID: 31388045 PMCID: PMC6684645 DOI: 10.1038/s41598-019-47717-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 07/18/2019] [Indexed: 11/22/2022] Open
Abstract
Networks are real systems modelled through mathematical objects made up of nodes and links arranged into peculiar and deliberate (or partially deliberate) topologies. Studying these real-world topologies allows for several properties of interest to be revealed. In real networks, nodes are also identified by a certain number of non-structural features or metadata. Given the current possibility of collecting massive quantity of such metadata, it becomes crucial to identify automatically which are the most relevant for the observed structure. We propose a new method that, independently from the network size, is able to not only report the relevance of binary node metadata, but also rank them. Such a method can be applied to networks from any domain, and we apply it in two heterogeneous cases: a temporal network of technology transfer and a protein-protein interaction network. Together with the relevance of node metadata, we investigate the redundancy of these metadata displaying by the results on a Redundancy-Relevance diagram, which is able to highlight the differences among vectors of metadata from both a structural and a non-structural point of view. The obtained results provide insights of a practical nature into the importance of the observed node metadata for the actual network structure.
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Affiliation(s)
- Matteo Cinelli
- Department of Enterprise Engineering, University of Rome Tor Vergata, Via del Politecnico, 1, Rome, 00133, Italy. .,ISC-CNR Uos "Sapienza", Via dei Taurini, 19, Rome, 00185, Italy.
| | - Giovanna Ferraro
- Department of Enterprise Engineering, University of Rome Tor Vergata, Via del Politecnico, 1, Rome, 00133, Italy
| | - Antonio Iovanella
- Department of Enterprise Engineering, University of Rome Tor Vergata, Via del Politecnico, 1, Rome, 00133, Italy
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Rodríguez-Pardo C, Segura A, Zamorano-León JJ, Martínez-Santos C, Martínez D, Collado-Yurrita L, Giner M, García-García JM, Rodríguez-Pardo JM, López-Farre A. Decision tree learning to predict overweight/obesity based on body mass index and gene polymporphisms. Gene 2019; 699:88-93. [DOI: 10.1016/j.gene.2019.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/26/2022]
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10
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Kafaie S, Chen Y, Hu T. A network approach to prioritizing susceptibility genes for genome-wide association studies. Genet Epidemiol 2019; 43:477-491. [PMID: 30859622 DOI: 10.1002/gepi.22198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/31/2019] [Accepted: 02/25/2019] [Indexed: 12/22/2022]
Abstract
The heritability of complex diseases including cancer is often attributed to multiple interacting genetic alterations. Such a non-linear, non-additive gene-gene interaction effect, that is, epistasis, renders univariable analysis methods ineffective for genome-wide association studies. In recent years, network science has seen increasing applications in modeling epistasis to characterize the complex relationships between a large number of genetic variations and the phenotypic outcome. In this study, by constructing a statistical epistasis network of colorectal cancer (CRC), we proposed to use multiple network measures to prioritize genes that influence the disease risk of CRC through synergistic interaction effects. We computed and analyzed several global and local properties of the large CRC epistasis network. We utilized topological properties of network vertices such as the edge strength, vertex centrality, and occurrence at different graphlets to identify genes that may be of potential biological relevance to CRC. We found 512 top-ranked single-nucleotide polymorphisms, among which COL22A1, RGS7, WWOX, and CELF2 were the four susceptibility genes prioritized by all described metrics as the most influential on CRC.
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Affiliation(s)
- Somayeh Kafaie
- Department of Computer Science, Memorial University, St. John's, NL, Canada
| | - Yuanzhu Chen
- Department of Computer Science, Memorial University, St. John's, NL, Canada
| | - Ting Hu
- Department of Computer Science, Memorial University, St. John's, NL, Canada
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11
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Park DS, Eskin I, Kang EY, Gamazon ER, Eng C, Gignoux CR, Galanter JM, Burchard E, Ye CJ, Aschard H, Eskin E, Halperin E, Zaitlen N. An ancestry-based approach for detecting interactions. Genet Epidemiol 2018; 42:49-63. [PMID: 29114909 PMCID: PMC6065511 DOI: 10.1002/gepi.22087] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND Epistasis and gene-environment interactions are known to contribute significantly to variation of complex phenotypes in model organisms. However, their identification in human association studies remains challenging for myriad reasons. In the case of epistatic interactions, the large number of potential interacting sets of genes presents computational, multiple hypothesis correction, and other statistical power issues. In the case of gene-environment interactions, the lack of consistently measured environmental covariates in most disease studies precludes searching for interactions and creates difficulties for replicating studies. RESULTS In this work, we develop a new statistical approach to address these issues that leverages genetic ancestry, defined as the proportion of ancestry derived from each ancestral population (e.g., the fraction of European/African ancestry in African Americans), in admixed populations. We applied our method to gene expression and methylation data from African American and Latino admixed individuals, respectively, identifying nine interactions that were significant at P<5×10-8. We show that two of the interactions in methylation data replicate, and the remaining six are significantly enriched for low P-values (P<1.8×10-6). CONCLUSION We show that genetic ancestry can be a useful proxy for unknown and unmeasured covariates in the search for interaction effects. These results have important implications for our understanding of the genetic architecture of complex traits.
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Affiliation(s)
- Danny S. Park
- Department of Bioengineering and Therapeutic Sciences. University of California San Francisco. San Francisco, CA
| | - Itamar Eskin
- The Blavatnik School of Computer Science. Tel-Aviv University. Tel Aviv, Israel
| | - Eun Yong Kang
- Department of Computer Science. University of California Los Angeles. Los Angeles, CA
| | - Eric R. Gamazon
- Division of Genetic Medicine, Department of Medicine. Vanderbilt University. Nashville, TN
- Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Celeste Eng
- Department of Medicine. University of California San Francisco. San Francisco, CA
| | - Christopher R. Gignoux
- Department of Bioengineering and Therapeutic Sciences. University of California San Francisco. San Francisco, CA
- Department of Genetics. Stanford University. Palo Alto, CA
| | - Joshua M. Galanter
- Department of Medicine. University of California San Francisco. San Francisco, CA
| | - Esteban Burchard
- Department of Bioengineering and Therapeutic Sciences. University of California San Francisco. San Francisco, CA
- Department of Medicine. University of California San Francisco. San Francisco, CA
| | - Chun J. Ye
- Institute of Human Genetics. University of California San Francisco. San Francisco, CA
| | - Hugues Aschard
- Department of Epidemiology. Harvard School of Public Health. Boston, MA
| | - Eleazar Eskin
- Department of Computer Science. University of California Los Angeles. Los Angeles, CA
| | - Eran Halperin
- The Blavatnik School of Computer Science. Tel-Aviv University. Tel Aviv, Israel
| | - Noah Zaitlen
- Department of Bioengineering and Therapeutic Sciences. University of California San Francisco. San Francisco, CA
- Department of Medicine. University of California San Francisco. San Francisco, CA
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12
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Cirillo E, Parnell LD, Evelo CT. A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants. Front Genet 2017; 8:174. [PMID: 29163640 PMCID: PMC5681904 DOI: 10.3389/fgene.2017.00174] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/24/2017] [Indexed: 01/04/2023] Open
Abstract
Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological processes in which the affected genes and proteins are involved. Such analyses support an interactive evaluation of the possible effects of variations on function, regulation or interaction of gene products. Current pathway analysis software often does not support data visualization of variants in pathways as an alternate method to interpret genetic association results, and specific statistical methods for pathway analysis of SNP data are not combined with these visualization features. In this review, we first describe the visualization options of the tools that were identified by a literature review, in order to provide insight for improvements in this developing field. Tool evaluation was performed using a computational epistatic dataset of gene–gene interactions for obesity risk. Next, we report the necessity to include in these tools statistical methods designed for the pathway-based analysis with SNP data, expressly aiming to define features for more comprehensive pathway-based analysis tools. We conclude by recognizing that pathway analysis of genetic variations data requires a sophisticated combination of the most useful and informative visual aspects of the various tools evaluated.
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Affiliation(s)
- Elisa Cirillo
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, Netherlands
| | - Laurence D Parnell
- Jean Mayer-USDA Human Nutrition Research Center on Aging at Tufts University, Agricultural Research Service, USDA, Boston, MA, United States
| | - Chris T Evelo
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, Netherlands
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13
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Wang S, Jeong HH, Kim D, Wee K, Park HS, Kim SH, Sohn KA. Integrative information theoretic network analysis for genome-wide association study of aspirin exacerbated respiratory disease in Korean population. BMC Med Genomics 2017; 10:31. [PMID: 28589859 PMCID: PMC5461529 DOI: 10.1186/s12920-017-0266-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Aspirin Exacerbated Respiratory Disease (AERD) is a chronic medical condition that encompasses asthma, nasal polyposis, and hypersensitivity to aspirin and other non-steroidal anti-inflammatory drugs. Several previous studies have shown that part of the genetic effects of the disease may be induced by the interaction of multiple genetic variants. However, heavy computational cost as well as the complexity of the underlying biological mechanism has prevented a thorough investigation of epistatic interactions and thus most previous studies have typically considered only a small number of genetic variants at a time. METHODS In this study, we propose a gene network based analysis framework to identify genetic risk factors from a genome-wide association study dataset. We first derive multiple single nucleotide polymorphisms (SNP)-based epistasis networks that consider marginal and epistatic effects by using different information theoretic measures. Each SNP epistasis network is converted into a gene-gene interaction network, and the resulting gene networks are combined as one for downstream analysis. The integrated network is validated on existing knowledgebase of DisGeNET for known gene-disease associations and GeneMANIA for biological function prediction. RESULTS We demonstrated our proposed method on a Korean GWAS dataset, which has genotype information of 440,094 SNPs for 188 cases and 247 controls. The topological properties of the generated networks are examined for scale-freeness, and we further performed various statistical analyses in the Allergy and Asthma Portal (AAP) using the selected genes from our integrated network. CONCLUSIONS Our result reveals that there are several gene modules in the network that are of biological significance and have evidence for controlling susceptibility and being related to the treatment of AERD.
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Affiliation(s)
- Sehee Wang
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Hyun-Hwan Jeong
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, 77030, USA.,Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Dokyoon Kim
- Department of Biomedical & Translational Informatics, Geisinger Health System, Danville, PA, 17822, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Kyubum Wee
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea
| | - Hae-Sim Park
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea
| | - Seung-Hyun Kim
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea. .,Translational Research Laboratory for Inflammatory Disease, Clinical Trial Center, Ajou University Medical Center, Suwon, South Korea.
| | - Kyung-Ah Sohn
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea.
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