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Zhu DD, Yuan JM, Zhu R, Wang Y, Qian ZY, Zou JG. Pathway-based analysis of genome-wide association study of circadian phenotypes. J Biomed Res 2018; 32:361-370. [PMID: 29784899 PMCID: PMC6163116 DOI: 10.7555/jbr.32.20170102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Sleepiness affects normal social life, which attracts more and more attention. Circadian phenotypes contribute to obvious individual differences in susceptibility to sleepiness. We aimed to identify candidate single nucleotide polymorphisms (SNPs) which may cause circadian phenotypes, elucidate the potential mechanisms, and generate corresponding SNP-gene-pathways. A genome-wide association studies (GWAS) dataset of circadian phenotypes was utilized in the study. Then, the Identify Candidate Causal SNPs and Pathways analysis was employed to the GWAS dataset after quality control filters. Furthermore, genotype-phenotype association analysis was performed with HapMap database. Four SNPs in three different genes were determined to correlate with usual weekday bedtime, totally providing seven hypothetical mechanisms. Eleven SNPs in six genes were identified to correlate with usual weekday sleep duration, which provided six hypothetical pathways. Our results demonstrated that fifteen candidate SNPs in eight genes played vital roles in six hypothetical pathways implicated in usual weekday bedtime and six potential pathways involved in usual weekday sleep duration.
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Affiliation(s)
- Di-di Zhu
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Jia-Min Yuan
- Department of Cardiology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Rui Zhu
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yao Wang
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Zhi-Yong Qian
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Jian-Gang Zou
- Department of Cardiology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, China
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Gumpinger AC, Roqueiro D, Grimm DG, Borgwardt KM. Methods and Tools in Genome-wide Association Studies. Methods Mol Biol 2018; 1819:93-136. [PMID: 30421401 DOI: 10.1007/978-1-4939-8618-7_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many traits, such as height, the response to a given drug, or the susceptibility to certain diseases are presumably co-determined by genetics. Especially in the field of medicine, it is of major interest to identify genetic aberrations that alter an individual's risk to develop a certain phenotypic trait. Addressing this question requires the availability of comprehensive, high-quality genetic datasets. The technological advancements and the decreasing cost of genotyping in the last decade led to an increase in such datasets. Parallel to and in line with this technological progress, an analysis framework under the name of genome-wide association studies was developed to properly collect and analyze these data. Genome-wide association studies aim at finding statistical dependencies-or associations-between a trait of interest and point-mutations in the DNA. The statistical models used to detect such associations are diverse, spanning the whole range from the frequentist to the Bayesian setting.Since genetic datasets are inherently high-dimensional, the search for associations poses not only a statistical but also a computational challenge. As a result, a variety of toolboxes and software packages have been developed, each implementing different statistical methods while using various optimizations and mathematical techniques to enhance the computations.This chapter is devoted to the discussion of widely used methods and tools in genome-wide association studies. We present the different statistical models and the assumptions on which they are based, explain peculiarities of the data that have to be accounted for and, most importantly, introduce commonly used tools and software packages for the different tasks in a genome-wide association study, complemented with examples for their application.
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Affiliation(s)
- Anja C Gumpinger
- Machine Learning and Computational Biology Lab, D-BSSE, ETH Zurich, Basel, Switzerland. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Damian Roqueiro
- Machine Learning and Computational Biology Lab, D-BSSE, ETH Zurich, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Dominik G Grimm
- Machine Learning and Computational Biology Lab, D-BSSE, ETH Zurich, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Karsten M Borgwardt
- Machine Learning and Computational Biology Lab, D-BSSE, ETH Zurich, Basel, Switzerland. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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Wang Y, Wu W, Zhu M, Wang C, Shen W, Cheng Y, Geng L, Li Z, Zhang J, Dai J, Ma H, Chen L, Hu Z, Jin G, Shen H. Integrating expression-related SNPs into genome-wide gene- and pathway-based analyses identified novel lung cancer susceptibility genes. Int J Cancer 2017; 142:1602-1610. [DOI: 10.1002/ijc.31182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Yuzhuo Wang
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Weibing Wu
- Department of Thoracic Surgery; First Affiliated Hospital of Nanjing Medical University; Nanjing 210029 China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Wei Shen
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Yang Cheng
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Liguo Geng
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Zhihua Li
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Jiahui Zhang
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
| | - Liang Chen
- Department of Thoracic Surgery; First Affiliated Hospital of Nanjing Medical University; Nanjing 210029 China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health; Nanjing Medical University; Nanjing 211166 China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University; Nanjing 211166 China
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4
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Chen G, Doumatey AP, Zhou J, Lei L, Bentley AR, Tekola-Ayele F, Adebamowo SN, Baker JL, Fasanmade O, Okafor G, Eghan B, Agyenim-Boateng K, Amoah A, Adebamowo C, Acheampong J, Johnson T, Oli J, Shriner D, Adeyemo AA, Rotimi CN. Genome-wide analysis identifies an african-specific variant in SEMA4D associated with body mass index. Obesity (Silver Spring) 2017; 25:794-800. [PMID: 28296344 PMCID: PMC5373947 DOI: 10.1002/oby.21804] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 12/23/2022]
Abstract
OBJECTIVE The prevalence of obesity varies between ethnic groups. No genome-wide association study (GWAS) for body mass index (BMI) has been conducted in continental Africans. METHODS We performed a GWAS for BMI in 1,570 West Africans (WA). Replication was conducted in independent samples of WA (n = 1,411) and African Americans (AA) (n = 9,020). RESULTS We identified a novel genome-wide significant African-specific locus for BMI (SEMA4D, rs80068415; minor allele frequency = 0.008, P = 2.10 × 10-8 ). This finding was replicated in independent samples of WA (P = 0.013) and AA (P = 0.017). Individuals with obesity had higher serum SEMA4D levels compared to those without obesity (P < 0.0001), and elevated levels of serum SEMA4D were associated with increased obesity risk (OR = 4.2, P < 1 × 10-4 ). The prevalence of obesity was higher in individuals with the CT versus TT genotypes (55.6% vs. 22.9%). CONCLUSIONS A novel variant in SEMA4D was significantly associated with BMI. Carriers of the C allele were 4.6 BMI units heavier than carriers of the T allele (P = 0.0007). This variant is monomorphic in Europeans and Asians, highlighting the importance of studying diverse populations. While there is evidence for the involvement of SEMA4D in inflammatory processes, this study is the first to implicate SEMA4D in obesity pathophysiology.
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Affiliation(s)
- Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Lin Lei
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Fasil Tekola-Ayele
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Sally N Adebamowo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Jennifer L Baker
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Olufemi Fasanmade
- University of Lagos, College of Medicine, Endocrine and Metabolic Unit, Lagos, Nigeria
| | - Godfrey Okafor
- University of Nigeria Teaching Hospital, Department of Hematology, Enugu, Nigeria
| | - Benjamin Eghan
- University of Science and Technology, Department of Medicine, Kumasi, Ghana
| | | | - Albert Amoah
- University of Ghana Medical School, Department of Medicine and Therapeutics, Accra, Ghana
| | | | - Joseph Acheampong
- University of Science and Technology, Department of Medicine, Kumasi, Ghana
| | - Thomas Johnson
- University of Lagos, College of Medicine, Endocrine and Metabolic Unit, Lagos, Nigeria
| | - Johnnie Oli
- University of Nigeria Teaching Hospital, Department of Hematology, Enugu, Nigeria
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA, 20892
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5
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Valcarcel A, Grinde K, Cook K, Green A, Tintle N. A multistep approach to single nucleotide polymorphism-set analysis: an evaluation of power and type I error of gene-based tests of association after pathway-based association tests. BMC Proc 2016; 10:349-355. [PMID: 27980661 PMCID: PMC5133510 DOI: 10.1186/s12919-016-0055-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The aggregation of functionally associated variants given a priori biological information can aid in the discovery of rare variants associated with complex diseases. Many methods exist that aggregate rare variants into a set and compute a single p value summarizing association between the set of rare variants and a phenotype of interest. These methods are often called gene-based, rare variant tests of association because the variants in the set are often all contained within the same gene. A reasonable extension of these approaches involves aggregating variants across an even larger set of variants (eg, all variants contained in genes within a pathway). Testing sets of variants such as pathways for association with a disease phenotype reduces multiple testing penalties, may increase power, and allows for straightforward biological interpretation. However, a significant variant-set association test does not indicate precisely which variants contained within that set are causal. Because pathways often contain many variants, it may be helpful to follow-up significant pathway tests by conducting gene-based tests on each gene in that pathway to narrow in on the region of causal variants. In this paper, we propose such a multistep approach for variant-set analysis that can also account for covariates and complex pedigree structure. We demonstrate this approach on simulated phenotypes from Genetic Analysis Workshop 19. We find generally better power for the multistep approach when compared to a more conventional, single-step approach that simply runs gene-based tests of association on each gene across the genome. Further work is necessary to evaluate the multistep approach on different data sets with different characteristics.
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Affiliation(s)
- Alessandra Valcarcel
- Department of Statistics, University of Connecticut, 2390 Alumni Drive, Storrs, CT 06269 USA
| | - Kelsey Grinde
- Department of Biostatistics, University of Washington, NE Pacific St, Seattle, WA 98195 USA
| | - Kaitlyn Cook
- Department of Mathematics and Statistics, Carleton College, 1 N College St, Northfield, MN 55057 USA
| | - Alden Green
- Department of Statistics, Harvard University, Massachusetts Hall, Cambridge, MA 02138 USA
| | - Nathan Tintle
- Department of Mathematics, Statistics and Computer Science, Dordt College, 498 4th Ave. NE, Dordt College, Sioux Center, IA 51250 USA
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Mattheisen M, Samuels JF, Wang Y, Greenberg BD, Fyer AJ, McCracken JT, Geller DA, Murphy DL, Knowles JA, Grados MA, Riddle MA, Rasmussen SA, McLaughlin NC, Nurmi E, Askland KD, Qin HD, Cullen BA, Piacentini J, Pauls DL, Bienvenu OJ, Stewart SE, Liang KY, Goes FS, Maher B, Pulver AE, Shugart YY, Valle D, Lange C, Nestadt G. Genome-wide association study in obsessive-compulsive disorder: results from the OCGAS. Mol Psychiatry 2015; 20:337-44. [PMID: 24821223 PMCID: PMC4231023 DOI: 10.1038/mp.2014.43] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 02/07/2023]
Abstract
Obsessive-compulsive disorder (OCD) is a psychiatric condition characterized by intrusive thoughts and urges and repetitive, intentional behaviors that cause significant distress and impair functioning. The OCD Collaborative Genetics Association Study (OCGAS) is comprised of comprehensively assessed OCD patients with an early age of OCD onset. After application of a stringent quality control protocol, a total of 1065 families (containing 1406 patients with OCD), combined with population-based samples (resulting in a total sample of 5061 individuals), were studied. An integrative analyses pipeline was utilized, involving association testing at single-nucleotide polymorphism (SNP) and gene levels (via a hybrid approach that allowed for combined analyses of the family- and population-based data). The smallest P-value was observed for a marker on chromosome 9 (near PTPRD, P=4.13 × 10(-)(7)). Pre-synaptic PTPRD promotes the differentiation of glutamatergic synapses and interacts with SLITRK3. Together, both proteins selectively regulate the development of inhibitory GABAergic synapses. Although no SNPs were identified as associated with OCD at genome-wide significance level, follow-up analyses of genome-wide association study (GWAS) signals from a previously published OCD study identified significant enrichment (P=0.0176). Secondary analyses of high-confidence interaction partners of DLGAP1 and GRIK2 (both showing evidence for association in our follow-up and the original GWAS study) revealed a trend of association (P=0.075) for a set of genes such as NEUROD6, SV2A, GRIA4, SLC1A2 and PTPRD. Analyses at the gene level revealed association of IQCK and C16orf88 (both P<1 × 10(-)(6), experiment-wide significant), as well as OFCC1 (P=6.29 × 10(-)(5)). The suggestive findings in this study await replication in larger samples.
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Affiliation(s)
- Manuel Mattheisen
- Department of Biomedicine and Center for Integrated Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
- Harvard School of Public Health, Department of Biostatistics, Boston, MA, USA
- Department of Genomic Mathematics, University of Bonn, Bonn, Germany
| | - Jack F. Samuels
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | - Ying Wang
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | - Benjamin D. Greenberg
- Brown Medical School, Department of Psychiatry and Human Behavior, Providence, RI, USA
| | - Abby J. Fyer
- College of Physicians and Surgeons at Columbia University, New York State Psychiatric Institute, New York, NY, USA
| | - James T. McCracken
- University of California, Los Angeles School of Medicine, Department of Psychiatry and Biobehavioral Sciences, Los Angeles, CA, USA
| | - Daniel A. Geller
- Massachusetts General Hospital and Harvard Medical School, Department of Psychiatry, Boston, MA, USA
| | - Dennis L. Murphy
- National Institute of Mental Health, Laboratory of Clinical Science, Bethesda, MD, USA
| | - James A. Knowles
- Keck School of Medicine at the University of Southern California, Department of Psychiatry and Behavioral Sciences, Los Angeles, CA, USA
| | - Marco A. Grados
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | - Mark A. Riddle
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | - Steven A. Rasmussen
- Brown Medical School, Department of Psychiatry and Human Behavior, Providence, RI, USA
| | - Nicole C. McLaughlin
- Brown Medical School, Department of Psychiatry and Human Behavior, Providence, RI, USA
| | - Erica Nurmi
- University of California, Los Angeles School of Medicine, Department of Psychiatry and Biobehavioral Sciences, Los Angeles, CA, USA
| | - Kathleen D. Askland
- Brown Medical School, Department of Psychiatry and Human Behavior, Providence, RI, USA
| | - Hai-De Qin
- National Institute of Mental Health, Unit of Statistical Genomics, Intramural Research Program, Division of Intramural Research Program, Bethesda, MD, USA
| | - Bernadette A. Cullen
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | - John Piacentini
- University of California, Los Angeles School of Medicine, Department of Psychiatry and Biobehavioral Sciences, Los Angeles, CA, USA
| | - David L. Pauls
- Massachusetts General Hospital and Harvard Medical School, Department of Psychiatry, Boston, MA, USA
| | - O. Joseph Bienvenu
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | - S. Evelyn Stewart
- Massachusetts General Hospital and Harvard Medical School, Department of Psychiatry, Boston, MA, USA
- University of British Columbia, Department of Psychiatry, Vancouver, BC, Canada
| | - Kung-Yee Liang
- Johns Hopkins University Bloomberg School of Public Health, Department of Mental Health, Baltimore, MD, USA
| | - Fernando S. Goes
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | - Brion Maher
- Johns Hopkins University Bloomberg School of Public Health, Department of Mental Health, Baltimore, MD, USA
| | - Ann E. Pulver
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
| | - Yin-Yao Shugart
- National Institute of Mental Health, Unit of Statistical Genomics, Intramural Research Program, Division of Intramural Research Program, Bethesda, MD, USA
| | - David Valle
- Johns Hopkins University School of Medicine, Institute of Human Genetics, Baltimore, MD, USA
| | - Cristoph Lange
- Harvard School of Public Health, Department of Biostatistics, Boston, MA, USA
- Department of Genomic Mathematics, University of Bonn, Bonn, Germany
| | - Gerald Nestadt
- Johns Hopkins University School of Medicine, Department of Psychiatry and Behavioral Sciences, Baltimore, MD, USA
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7
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Rajkumar AP, Christensen JH, Mattheisen M, Jacobsen I, Bache I, Pallesen J, Grove J, Qvist P, McQuillin A, Gurling HM, Tümer Z, Mors O, Børglum AD. Analysis of t(9;17)(q33.2;q25.3) chromosomal breakpoint regions and genetic association reveals novel candidate genes for bipolar disorder. Bipolar Disord 2015; 17:205-11. [PMID: 25053281 DOI: 10.1111/bdi.12239] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 04/29/2014] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Breakpoints of chromosomal abnormalities facilitate identification of novel candidate genes for psychiatric disorders. Genome-wide significant evidence supports the linkage between chromosome 17q25.3 and bipolar disorder (BD). Co-segregation of translocation t(9;17)(q33.2;q25.3) with psychiatric disorders has been reported. We aimed to narrow down these chromosomal breakpoint regions and to investigate the associations between single nucleotide polymorphisms within these regions and BD as well as schizophrenia (SZ) in large genome-wide association study samples. METHODS We cross-linked Danish psychiatric and cytogenetic case registers to identify an individual with both t(9;17)(q33.2;q25.3) and BD. Fluorescent in situ hybridization was employed to map the chromosomal breakpoint regions of this proband. We accessed the Psychiatric Genomics Consortium BD (n = 16,731) and SZ (n = 21,856) data. Genetic associations between these disorders and single nucleotide polymorphisms within these breakpoint regions were analysed by BioQ, FORGE, and RegulomeDB programmes. RESULTS Four protein-coding genes [coding for (endonuclease V (ENDOV), neuronal pentraxin I (NPTX1), ring finger protein 213 (RNF213), and regulatory-associated protein of mammalian target of rapamycin (mTOR) (RPTOR)] were found to be located within the 17q25.3 breakpoint region. NPTX1 was significantly associated with BD (p = 0.004), while ENDOV was significantly associated with SZ (p = 0.0075) after Bonferroni correction. CONCLUSIONS Prior linkage evidence and our findings suggest NPTX1 as a novel candidate gene for BD.
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Affiliation(s)
- Anto P Rajkumar
- Department of Biomedicine, Institute of Human Genetics, Aarhus University, Aarhus, Denmark; Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Risskov, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark; Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
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8
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Predicting the phenotypic values of physiological traits using SNP genotype and gene expression data in mice. PLoS One 2014; 9:e115532. [PMID: 25541966 PMCID: PMC4277360 DOI: 10.1371/journal.pone.0115532] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 11/25/2014] [Indexed: 01/22/2023] Open
Abstract
Predicting phenotypes using genome-wide genetic variation and gene expression data is useful in several fields, such as human biology and medicine, as well as in crop and livestock breeding. However, for phenotype prediction using gene expression data for mammals, studies remain scarce, as the available data on gene expression profiling are currently limited. By integrating a few sources of relevant data that are available in mice, this study investigated the accuracy of phenotype prediction for several physiological traits. Gene expression data from two tissues as well as single nucleotide polymorphisms (SNPs) were used. For the studied traits, the variance of the effects of the expression levels was more likely to differ among the genes than were the effects of SNPs. For the glucose concentration, the total cholesterol amount, and the total tidal volume, the accuracy by cross validation tended to be higher when the gene expression data rather than the SNP genotype data were used, and a statistically significant increase in the accuracy was obtained when the gene expression data from the liver were used alone or jointly with the SNP genotype data. For these traits, there were no additional gains in accuracy from using the gene expression data of both the liver and lung compared to that of individual use. The accuracy of prediction using genes that were selected differently was examined; the use of genes with a higher tissue specificity tended to result in an accuracy that was similar to or greater than that associated with the use of all of the available genes for traits such as the glucose concentration and total cholesterol amount. Although relatively few animals were evaluated, the current results suggest that gene expression levels could be used as explanatory variables. However, further studies are essential to confirm our findings using additional animal samples.
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9
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McDonald MLN, Mattheisen M, Cho MH, Liu YY, Harshfield B, Hersh CP, Bakke P, Gulsvik A, Lange C, Beaty TH, Silverman EK. Beyond GWAS in COPD: probing the landscape between gene-set associations, genome-wide associations and protein-protein interaction networks. Hum Hered 2014; 78:131-9. [PMID: 25171373 PMCID: PMC4415367 DOI: 10.1159/000365589] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/01/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES To use a systems biology approach to integrate genotype and protein-protein interaction (PPI) data to identify disease network modules associated with chronic obstructive pulmonary disease (COPD) and to perform traditional pathway analysis. METHODS We utilized a standard gene-set association approach (FORGE) using gene-based association analysis and gene-set definitions from the molecular signatures database (MSigDB). As a discovery step, we analyzed GWAS results from 2 well-characterized COPD cohorts: COPDGene and GenKOLS. We used a third well-characterized COPD case-control cohort for replication: ECLIPSE. Next, we used dmGWAS, a method that integrates GWAS results with PPI, to identify COPD disease modules. RESULTS No gene-sets reached experiment-wide significance in either discovery population. We identified a consensus network of 10 genes identified in modules by integrating GWAS results with PPI that replicated in COPDGene, GenKOLS, and ECLIPSE. Members of 4 gene-sets were enriched among these 10 genes: (i) lung adenocarcinoma tumor-sequencing genes, (ii) IL-7 pathway genes, (iii) kidney cell response to arsenic, and (iv) CD4 T-cell responses. Further, several genes have also been associated with pathophysiology relevant to COPD including KCNK3, NEDD4L, and RIN3. In particular, KCNK3 has been associated with pulmonary arterial hypertension, a common complication in advanced COPD. CONCLUSION We report a set of new genes that may influence the etiology of COPD that would not have been identified using traditional GWAS and pathway analyses alone.
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Affiliation(s)
- Merry-Lynn Noelle McDonald
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Manuel Mattheisen
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedicine and Centre for integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin Harshfield
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Craig P. Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Terri H. Beaty
- Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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Lee YH, Song GG. Genome-wide pathway analysis of a genome-wide association study on Alzheimer's disease. Neurol Sci 2014; 36:53-9. [PMID: 25037741 DOI: 10.1007/s10072-014-1885-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 07/12/2014] [Indexed: 11/30/2022]
Abstract
The aims of this study were to identify candidate single nucleotide polymorphisms (SNPs) and mechanisms of Alzheimer's disease (AD) and to generate SNP to gene to pathway hypotheses. An AD genome-wide association study (GWAS) dataset that included 370,542 SNPs in 1,000 cases and 1,000 controls of European descent was used in this study. Identify Candidate Causal SNPs and Pathway (ICSNPathway) analysis was applied to the GWAS dataset. ICSNPathway analysis identified 3 candidate SNPs and 2 pathways, which provided 3 hypothetical biological mechanisms. The strongest hypothetical biological mechanism was rs8076604 [non-synonymous coding (deleterious)] to MYO18A to negative regulation of programmed cell death [nominal P < 0.001, false discovery rate (FDR) <0.043]. The second was rs2811226 (regulatory region) to ANXA1 to negative regulation of programmed cell death (nominal P < 0.001, FDR 0.043). The third was rs3734166 (non-synonymous coding) to CDC25C to M phase of the mitotic cell cycle (nominal P < 0.001, FDR 0.049). By applying the ICSNPathway analysis to the AD GWAS meta-analysis data, three candidate SNPs, three genes (MYO18A, ANXA1, CDC25C), 2 pathways involving negative regulation of programmed cell death and 1 pathway involving the M phase of the mitotic cell cycle were identified, which may contribute to AD susceptibility.
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Affiliation(s)
- Young Ho Lee
- Division of Rheumatology, Department of Internal Medicine Korea University Anam Hospital, Korea University College of Medicine, 126-1 5 ga, Anam-dong, Seongbuk-gu, Seoul, 136-705, Korea,
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Juraeva D, Haenisch B, Zapatka M, Frank J, Witt SH, Mühleisen TW, Treutlein J, Strohmaier J, Meier S, Degenhardt F, Giegling I, Ripke S, Leber M, Lange C, Schulze TG, Mössner R, Nenadic I, Sauer H, Rujescu D, Maier W, Børglum A, Ophoff R, Cichon S, Nöthen MM, Rietschel M, Mattheisen M, Brors B. Integrated pathway-based approach identifies association between genomic regions at CTCF and CACNB2 and schizophrenia. PLoS Genet 2014; 10:e1004345. [PMID: 24901509 PMCID: PMC4046913 DOI: 10.1371/journal.pgen.1004345] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 03/20/2014] [Indexed: 11/19/2022] Open
Abstract
In the present study, an integrated hierarchical approach was applied to: (1) identify pathways associated with susceptibility to schizophrenia; (2) detect genes that may be potentially affected in these pathways since they contain an associated polymorphism; and (3) annotate the functional consequences of such single-nucleotide polymorphisms (SNPs) in the affected genes or their regulatory regions. The Global Test was applied to detect schizophrenia-associated pathways using discovery and replication datasets comprising 5,040 and 5,082 individuals of European ancestry, respectively. Information concerning functional gene-sets was retrieved from the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and the Molecular Signatures Database. Fourteen of the gene-sets or pathways identified in the discovery dataset were confirmed in the replication dataset. These include functional processes involved in transcriptional regulation and gene expression, synapse organization, cell adhesion, and apoptosis. For two genes, i.e. CTCF and CACNB2, evidence for association with schizophrenia was available (at the gene-level) in both the discovery study and published data from the Psychiatric Genomics Consortium schizophrenia study. Furthermore, these genes mapped to four of the 14 presently identified pathways. Several of the SNPs assigned to CTCF and CACNB2 have potential functional consequences, and a gene in close proximity to CACNB2, i.e. ARL5B, was identified as a potential gene of interest. Application of the present hierarchical approach thus allowed: (1) identification of novel biological gene-sets or pathways with potential involvement in the etiology of schizophrenia, as well as replication of these findings in an independent cohort; (2) detection of genes of interest for future follow-up studies; and (3) the highlighting of novel genes in previously reported candidate regions for schizophrenia.
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Affiliation(s)
- Dilafruz Juraeva
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Britta Haenisch
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | | | | | - Stephanie H. Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Thomas W. Mühleisen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute for Neuroscience and Medicine (INM-1), Research Centre Juelich, Juelich, Germany
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Sandra Meier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
- National Centre for Integrated Register-based Research (NCRR), Department of Economics and Business, Aarhus University, Aarhus, Denmark
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Ina Giegling
- Division of Molecular and Clinical Neurobiology, Department of Psychiatry, Ludwig-Maximilians-University, Munich, Germany
- Department of Psychiatry, University of Halle-Wittenberg, Halle, Germany
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Markus Leber
- Institute for Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
| | - Christoph Lange
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Genomic Mathematics, University of Bonn, Bonn, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Thomas G. Schulze
- Department of Psychiatry and Psychotherapy, University Medical Center Georg-August-Universität, Göttingen, Germany
| | | | - Igor Nenadic
- Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany
| | - Heinrich Sauer
- Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany
| | - Dan Rujescu
- Division of Molecular and Clinical Neurobiology, Department of Psychiatry, Ludwig-Maximilians-University, Munich, Germany
- Department of Psychiatry, University of Halle-Wittenberg, Halle, Germany
| | - Wolfgang Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - Anders Børglum
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark and Center for Integrated Sequencing, iSEQ, Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
- Centre for Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
| | - Roel Ophoff
- UCLA Center for Neurobehavioral Genetics, Los Angeles, California, United States of America
- Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Institute for Neuroscience and Medicine (INM-1), Research Centre Juelich, Juelich, Germany
- Department of Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Manuel Mattheisen
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
- Department of Genomic Mathematics, University of Bonn, Bonn, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark and Center for Integrated Sequencing, iSEQ, Aarhus, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Lee YH, Kim JH, Song GG. Genome-wide pathway analysis of breast cancer. Tumour Biol 2014; 35:7699-705. [PMID: 24805830 DOI: 10.1007/s13277-014-2027-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/28/2014] [Indexed: 12/15/2022] Open
Abstract
The aim of this study was to identify candidate single-nucleotide polymorphisms (SNPs) that might affect susceptibility to breast cancer and then elucidate their potential mechanisms and generate SNP-to-gene-to-pathway hypotheses. A genome-wide association study (GWAS) dataset of breast cancer that included 453,852 SNPs from 1,145 breast cancer patients and 1,142 control subjects of European descent was used in this study. The identify candidate causal SNPs and pathways (ICSNPathway) method was applied to the GWAS dataset. ICSNPathway analysis identified 16 candidate SNPs, 13 genes, and 7 pathways, which together revealed 7 hypothetical biological mechanisms. The strongest hypothetical biological mechanism was that rs3168891 and rs2899849 alter the role of MBIP in the inactivation of mitogen-activated protein kinase (MAPK) (p < 0.001; false discovery rate (FDR) = 0.038). The second strongest mechanism was that rs2229714 modulates RPS6KA1 to affect its role in growth hormone signaling (p = 0.001; FDR = 0.039). The third strongest mechanism was that rs2230394 modulates ITGB1 to regulate the PTEN pathway and hsa04360 (axon guidance pathway) (p < 0.001; FDR = 0.039, 0.041). Use of the ICSNPathway to analyze breast cancer GWAS data identified 16 candidate SNPs, 13 genes (including MBIP, RPS6KA1, and ITGB1), and 7 pathways that might contribute to the susceptibility of patients to breast cancer.
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Affiliation(s)
- Young Ho Lee
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 126-1 5 ga, Anam-dong, Seongbuk-gu, Seoul, 136-705, Korea,
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Genome-wide pathway analysis in neuroblastoma. Tumour Biol 2013; 35:3471-85. [PMID: 24293394 DOI: 10.1007/s13277-013-1459-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 11/19/2013] [Indexed: 01/16/2023] Open
Abstract
The aim of this study was to identify candidate single-nucleotide polymorphisms (SNPs) that might play a role in susceptibility to neuroblastoma, elucidate their potential mechanisms, and generate SNP-to-gene-to-pathway hypotheses. A genome-wide association study (GWAS) dataset of neuroblastoma that included 442,976 SNPs from 1,627 neuroblastoma patients and 3,254 control subjects of European descent was used in this study. The identify candidate causal SNPs and pathways (ICSNPathway) analysis was applied to the GWAS dataset. ICSNPathway analysis identified 15 candidate SNPs, 10 genes, and 31 pathways, which revealed 10 hypothetical biological mechanisms. The strongest hypothetical biological mechanism was one wherein SNPrs40401 modulates the role of IL3 in several pathways and conditions, including the stem pathway, asthma (hsa05310), the dendritic cell pathway, and development (0.001 < p < 0.004; 0.001 < FDR < 0.033). The second strongest mechanism identified was that in which rs1048108 and rs16852600 alter the function of BARD1, which negatively regulates developmental process and modulates processes including cell development and programmed cell death (0.001 < p < 0.004; 0.001 < FDR < 0.033). The third mechanism identified was one wherein rs1939212 modulated CFL1, resulting in negative regulation of development, cell death, neural crest cell migration, and apoptosis (0.001 < p < 0.004; 0.001 < FDR < 0.033). By using the ICSNPathway to analyze neuroblastoma GWAS data, 15 candidate SNPs, 10 genes including IL3, BARD1, and CFL, and 31 pathways were identified that might contribute to the susceptibility of patients to neuroblastoma.
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Genome-Wide Pathway Analysis in Major Depressive Disorder. J Mol Neurosci 2013; 51:428-36. [DOI: 10.1007/s12031-013-0047-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 06/06/2013] [Indexed: 01/23/2023]
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Genome-wide pathway analysis of a genome-wide association study on multiple sclerosis. Mol Biol Rep 2012; 40:2557-64. [DOI: 10.1007/s11033-012-2341-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 12/09/2012] [Indexed: 11/27/2022]
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Abstract
OBJECTIVE The aims of this study were to identify the candidate causal single nucleotide polymorphisms (SNPs) and candidate causal mechanisms of asthma and to generate SNP to gene to pathway hypotheses. METHODS SNPs that met a threshold of p ≤ 0.001 in a genome-wide association study (GWAS) dataset of asthma, which included 292,443 SNPs in 473 asthma cases and 1892 controls, were used in the present study. Identify candidate causal SNPs and pathway (ICSNPathway) analysis was applied to this dataset. RESULTS ICSNPathway analysis identified four candidate causal SNPs, four genes, and 21 candidate causal pathways, which in total provided four hypothetical biologic mechanisms: (1) rs7192 (nonsynonymous coding) to HLA-DRA to 21 pathways, such as, the role of eosinophils in the chemokine network of allergy, Th1/Th2 differentiation, and asthma (nominal p ≤ 0.001, FDR p ≤ 0.01); (2) rs20541 (nonsynonymous coding) to IL13 to asthma and cytokines and inflammatory response (nominal p<0.001, FDR p ≤ 0.008); (3) rs1058808 (frameshift coding) to ERBB2 to transmembrane receptor activity (nominal p=0.001, FDR p=0.01); (4) rs17350764 (nonsynonymous coding (deleterious)) to OR52J3 to transmembrane receptor activity (nominal p=0.001, FDR p=0.01). CONCLUSION By applying ICSNPathway analysis to asthma GWAS data, we found four candidate causal SNPs, four genes involving HLA-DRA and IL-13, and four hypotheses, which may contribute to asthma susceptibility.
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Genome-wide pathway analysis of a genome-wide association study on psoriasis and Behcet's disease. Mol Biol Rep 2011; 39:5953-9. [PMID: 22201026 DOI: 10.1007/s11033-011-1407-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/17/2011] [Indexed: 02/07/2023]
Abstract
The aim of this study was to identify candidate causal single nucleotide polymorphisms (SNPs) and candidate causal mechanisms of psoriasis and Behcets's disease (BD) and to generate an SNP → gene → pathway hypothesis. A psoriasis genome-wide association study (GWAS) dataset that included 436,192 SNPs in 1,409 psoriasis cases and 1,436 controls of European descent and a BD GWAS dataset that contained 310,324 SNPs in 1,215 BD cases and 1,278 controls were used in this study. Identify candidate causal SNPs and pathways (ICSNPathway) analysis was applied to the GWAS datasets. ICSNPathway analysis identified 15 candidate causal SNPs and 28 candidate causal pathways. The top five candidate causal SNPs were rs1063478 (P = 1.45E-10), rs8084 (P = 2.20E-08), rs7192 (P = 5.18E-08), rs20541 (P = 5.30E-06), and rs1130838 (P = 5.65E-06), which with the exception of rs20541 [interleukin (IL)-13] are at human leukocyte antigen (HLA) loci. These candidate causal SNPs and pathways provided ten hypothetical biological mechanisms. The most strongly associated pathway concerned HLA. When HLA loci were excluded, ICSNPathway analysis provided one hypothetical biological mechanism. rs20541 (non_synonymous_coding) → IL-13 → dendritic cell involvement in the regulation of Th1 and Th2 development, and the GATA3 pathway. ICSNPathway analysis identified four candidate causal SNPs, eleven candidate causal pathways, and three hypothetical biological mechanisms. One of them was as follows: rs2072895 (non_synonymous_coding & splice-site) and rs2735059 (non_synonymous_coding) → HLA-F → type I diabetes mellitus, antigen processing and presentation, and autoimmune thyroid disease. The application of ICSNPathway analysis to GWAS dataset of psoriasis and BD resulted in the identification of candidate causal SNPs and candidate pathways that might contribute to psoriasis susceptibility.
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