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Shao Z, Wang T, Qiao J, Zhang Y, Huang S, Zeng P. A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies. BMC Bioinformatics 2022; 23:359. [PMID: 36042399 PMCID: PMC9429742 DOI: 10.1186/s12859-022-04897-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/22/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Multilocus analysis on a set of single nucleotide polymorphisms (SNPs) pre-assigned within a gene constitutes a valuable complement to single-marker analysis by aggregating data on complex traits in a biologically meaningful way. However, despite the existence of a wide variety of SNP-set methods, few comprehensive comparison studies have been previously performed to evaluate the effectiveness of these methods. RESULTS We herein sought to fill this knowledge gap by conducting a comprehensive empirical comparison for 22 commonly-used summary-statistics based SNP-set methods. We showed that only seven methods could effectively control the type I error, and that these well-calibrated approaches had varying power performance under the simulation scenarios. Overall, we confirmed that the burden test was generally underpowered and score-based variance component tests (e.g., sequence kernel association test) were much powerful under the polygenic genetic architecture in both common and rare variant association analyses. We further revealed that two linkage-disequilibrium-free P value combination methods (e.g., harmonic mean P value method and aggregated Cauchy association test) behaved very well under the sparse genetic architecture in simulations and real-data applications to common and rare variant association analyses as well as in expression quantitative trait loci weighted integrative analysis. We also assessed the scalability of these approaches by recording computational time and found that all these methods can be scalable to biobank-scale data although some might be relatively slow. CONCLUSION In conclusion, we hope that our findings can offer an important guidance on how to choose appropriate multilocus association analysis methods in post-GWAS era. All the SNP-set methods are implemented in the R package called MCA, which is freely available at https://github.com/biostatpzeng/ .
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Affiliation(s)
- Zhonghe Shao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Jiahao Qiao
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Yuchen Zhang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Shuiping Huang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
- Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
- Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Key Laboratory of Environment and Health, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
- Engineering Research Innovation Center of Biological Data Mining and Healthcare Transformation, Xuzhou Medical University, Xuzhou, 221004, Jiangsu, China.
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Dutta D, VandeHaar P, Fritsche LG, Zöllner S, Boehnke M, Scott LJ, Lee S. A powerful subset-based method identifies gene set associations and improves interpretation in UK Biobank. Am J Hum Genet 2021; 108:669-681. [PMID: 33730541 DOI: 10.1016/j.ajhg.2021.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
Tests of association between a phenotype and a set of genes in a biological pathway can provide insights into the genetic architecture of complex phenotypes beyond those obtained from single-variant or single-gene association analysis. However, most existing gene set tests have limited power to detect gene set-phenotype association when a small fraction of the genes are associated with the phenotype and cannot identify the potentially "active" genes that might drive a gene set-based association. To address these issues, we have developed Gene set analysis Association Using Sparse Signals (GAUSS), a method for gene set association analysis that requires only GWAS summary statistics. For each significantly associated gene set, GAUSS identifies the subset of genes that have the maximal evidence of association and can best account for the gene set association. Using pre-computed correlation structure among test statistics from a reference panel, our p value calculation is substantially faster than other permutation- or simulation-based approaches. In simulations with varying proportions of causal genes, we find that GAUSS effectively controls type 1 error rate and has greater power than several existing methods, particularly when a small proportion of genes account for the gene set signal. Using GAUSS, we analyzed UK Biobank GWAS summary statistics for 10,679 gene sets and 1,403 binary phenotypes. We found that GAUSS is scalable and identified 13,466 phenotype and gene set association pairs. Within these gene sets, we identify an average of 17.2 (max = 405) genes that underlie these gene set associations.
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Affiliation(s)
- Diptavo Dutta
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Peter VandeHaar
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lars G Fritsche
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sebastian Zöllner
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael Boehnke
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura J Scott
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seunggeun Lee
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; Graduate School of Data Science, Seoul National University, Seoul 08826, Republic of Korea.
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3
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Ureña-Peralta JR, Pérez-Moraga R, García-García F, Guerri C. Lack of TLR4 modifies the miRNAs profile and attenuates inflammatory signaling pathways. PLoS One 2020; 15:e0237066. [PMID: 32780740 PMCID: PMC7418977 DOI: 10.1371/journal.pone.0237066] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 07/19/2020] [Indexed: 12/12/2022] Open
Abstract
TLR4 is a member of the toll-like receptors (TLR) immune family, which are activated by lipopolysaccharide, ethanol or damaged tissue, among others, by triggering proinflammatory cytokines release and inflammation. Lack of TLR4 protects against inflammatory processes and neuroinflammation linked with several neuropathologies. By considering that miRNAs are key post-transcriptional regulators of the proteins involved in distinct cellular processes, including inflammation, this study aimed to assess the impact of the miRNAs profile in mice cortices lacking the TLR4 response. Using mice cerebral cortices and next-generation sequencing (NGS), the findings showed that lack of TLR4 significantly reduced the quantity and diversity of the miRNAs expressed in WT mice cortices. The results also revealed a significant down-regulation of the miR-200 family, while cluster miR-99b/let-7e/miR-125a was up-regulated in TLR4-KO vs. WT. The bioinformatics and functional analyses demonstrated that TLR4-KO presented the systematic depletion of many pathways closely related to the immune system response, such as cytokine and interleukin signaling, MAPK and ion Channels routes, MyD88 pathways, NF-κβ and TLR7/8 pathways. Our results provide new insights into the molecular and biological processes associated with the protective effects of TLR-KO against inflammatory damage and neuroinflammation, and reveal the relevance of the TLR4 receptors response in many neuropathologies.
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Affiliation(s)
- Juan R. Ureña-Peralta
- Molecular and cellular pathology of Alcohol Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Raúl Pérez-Moraga
- Bioinformatics & Biostatistics Unit, Prince Felipe Research Center, Valencia, Spain
- Biomedical Imaging Unit FISABIO-CIPF, Prince Felipe Research Center, Valencia, Spain
| | | | - Consuelo Guerri
- Molecular and cellular pathology of Alcohol Laboratory, Prince Felipe Research Center, Valencia, Spain
- * E-mail:
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4
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Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges. ENTROPY 2020; 22:e22040427. [PMID: 33286201 PMCID: PMC7516904 DOI: 10.3390/e22040427] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/18/2020] [Accepted: 04/03/2020] [Indexed: 12/22/2022]
Abstract
Over the last decade, gene set analysis has become the first choice for gaining insights into underlying complex biology of diseases through gene expression and gene association studies. It also reduces the complexity of statistical analysis and enhances the explanatory power of the obtained results. Although gene set analysis approaches are extensively used in gene expression and genome wide association data analysis, the statistical structure and steps common to these approaches have not yet been comprehensively discussed, which limits their utility. In this article, we provide a comprehensive overview, statistical structure and steps of gene set analysis approaches used for microarrays, RNA-sequencing and genome wide association data analysis. Further, we also classify the gene set analysis approaches and tools by the type of genomic study, null hypothesis, sampling model and nature of the test statistic, etc. Rather than reviewing the gene set analysis approaches individually, we provide the generation-wise evolution of such approaches for microarrays, RNA-sequencing and genome wide association studies and discuss their relative merits and limitations. Here, we identify the key biological and statistical challenges in current gene set analysis, which will be addressed by statisticians and biologists collectively in order to develop the next generation of gene set analysis approaches. Further, this study will serve as a catalog and provide guidelines to genome researchers and experimental biologists for choosing the proper gene set analysis approach based on several factors.
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Sevim Bayrak C, Zhang P, Tristani-Firouzi M, Gelb BD, Itan Y. De novo variants in exomes of congenital heart disease patients identify risk genes and pathways. Genome Med 2020; 12:9. [PMID: 31941532 PMCID: PMC6961332 DOI: 10.1186/s13073-019-0709-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022] Open
Abstract
Background Congenital heart disease (CHD) affects ~ 1% of live births and is the most common birth defect. Although the genetic contribution to the CHD has been long suspected, it has only been well established recently. De novo variants are estimated to contribute to approximately 8% of sporadic CHD. Methods CHD is genetically heterogeneous, making pathway enrichment analysis an effective approach to explore and statistically validate CHD-associated genes. In this study, we performed novel gene and pathway enrichment analyses of high-impact de novo variants in the recently published whole-exome sequencing (WES) data generated from a cohort of CHD 2645 parent-offspring trios to identify new CHD-causing candidate genes and mutations. We performed rigorous variant- and gene-level filtrations to identify potentially damaging variants, followed by enrichment analyses and gene prioritization. Results Our analyses revealed 23 novel genes that are likely to cause CHD, including HSP90AA1, ROCK2, IQGAP1, and CHD4, and sharing biological functions, pathways, molecular interactions, and properties with known CHD-causing genes. Conclusions Ultimately, these findings suggest novel genes that are likely to be contributing to CHD pathogenesis.
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Affiliation(s)
- Cigdem Sevim Bayrak
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuval Itan
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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6
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He T, Hill CB, Angessa TT, Zhang XQ, Chen K, Moody D, Telfer P, Westcott S, Li C. Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5603-5616. [PMID: 31504706 PMCID: PMC6812734 DOI: 10.1093/jxb/erz332] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/13/2019] [Indexed: 05/10/2023]
Abstract
Single-marker genome-wide association studies (GWAS) have successfully detected associations between single nucleotide polymorphisms (SNPs) and agronomic traits such as flowering time and grain yield in barley. However, the analysis of individual SNPs can only account for a small proportion of genetic variation, and can only provide limited knowledge on gene network interactions. Gene-based GWAS approaches provide enormous opportunity both to combine genetic information and to examine interactions among genetic variants. Here, we revisited a previously published phenotypic and genotypic data set of 895 barley varieties grown in two years at four different field locations in Australia. We employed statistical models to examine gene-phenotype associations, as well as two-way epistasis analyses to increase the capability to find novel genes that have significant roles in controlling flowering time in barley. Genetic associations were tested between flowering time and corresponding genotypes of 174 putative flowering time-related genes. Gene-phenotype association analysis detected 113 genes associated with flowering time in barley, demonstrating the unprecedented power of gene-based analysis. Subsequent two-way epistasis analysis revealed 19 pairs of gene×gene interactions involved in controlling flowering time. Our study demonstrates that gene-based association approaches can provide higher capacity for future crop improvement to increase crop performance and adaptation to different environments.
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Affiliation(s)
- Tianhua He
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Camilla Beate Hill
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Tefera Tolera Angessa
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Kefei Chen
- SAGI-WEST, Faculty of Science and Engineering, Curtin University, Bentley, WA, Australia
| | | | - Paul Telfer
- Australian Grain Technologies Pty Ltd (AGT), SA, Australia
| | - Sharon Westcott
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Hubei Jingzhou, China
- Correspondence:
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7
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Alag A. Machine learning approach yields epigenetic biomarkers of food allergy: A novel 13-gene signature to diagnose clinical reactivity. PLoS One 2019; 14:e0218253. [PMID: 31216310 PMCID: PMC6584060 DOI: 10.1371/journal.pone.0218253] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 05/29/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Current laboratory tests are less than 50% accurate in distinguishing between people who have food allergies (FA) and those who are merely sensitized to foods, resulting in the use of expensive and potentially dangerous Oral Food Challenges. This study presents a purely-computational machine learning approach, conducted using DNA Methylation (DNAm) data, to accurately diagnose food allergies and potentially find epigenetic targets for the disease. METHODS AND RESULTS An unbiased feature-selection pipeline was created that narrowed down 405,000+ potential CpG biomarkers to 18. Machine-learning models that utilized subsets of this 18-feature aggregate achieved perfect classification accuracy on completely hidden test cohorts (on an 8-fold hidden dataset). Ensemble classification was also shown to be effective for this High Dimension Low Sample Size (HDLSS) DNA methylation dataset. The efficacy of these machine learning classifiers and the 18 CpGs was further validated by their high accuracy on a large number of hidden data permutations, where the samples in the training, cross-validation, and hidden sets were repeatedly randomly allocated. The 18-CpG signature mapped to 13 genes, on which biological insights were collected. Notably, many of the FA-discriminating genes found in this study were strongly associated with the immune system, and seven of the 13 genes were previously associated with FA. CONCLUSIONS Previous studies have also created highly-accurate classifiers for this dataset, using both data-driven and a priori biological insights to construct a 96-CpG signature. This research builds on previous work because it uses a completely computational approach to obtain a perfect classification accuracy while using only 18 highly discriminating CpGs (0.005% of the total available features). In machine learning, simpler models, as used in this study, are generally preferred over more complex ones (other things being equal). Lastly, the completely data-driven methodology presented in this research eliminates the need for a priori biological information and allows for generalizability to other DNAm classification problems.
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Affiliation(s)
- Ayush Alag
- The Harker School, San Jose, CA, United States of America
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8
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Sun R, Hui S, Bader GD, Lin X, Kraft P. Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic. PLoS Genet 2019; 15:e1007530. [PMID: 30875371 PMCID: PMC6436759 DOI: 10.1371/journal.pgen.1007530] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 03/27/2019] [Accepted: 02/28/2019] [Indexed: 11/19/2022] Open
Abstract
A common complementary strategy in Genome-Wide Association Studies (GWAS) is to perform Gene Set Analysis (GSA), which tests for the association between one phenotype of interest and an entire set of Single Nucleotide Polymorphisms (SNPs) residing in selected genes. While there exist many tools for performing GSA, popular methods often include a number of ad-hoc steps that are difficult to justify statistically, provide complicated interpretations based on permutation inference, and demonstrate poor operating characteristics. Additionally, the lack of gold standard gene set lists can produce misleading results and create difficulties in comparing analyses even across the same phenotype. We introduce the Generalized Berk-Jones (GBJ) statistic for GSA, a permutation-free parametric framework that offers asymptotic power guarantees in certain set-based testing settings. To adjust for confounding introduced by different gene set lists, we further develop a GBJ step-down inference technique that can discriminate between gene sets driven to significance by single genes and those demonstrating group-level effects. We compare GBJ to popular alternatives through simulation and re-analysis of summary statistics from a large breast cancer GWAS, and we show how GBJ can increase power by incorporating information from multiple signals in the same gene. In addition, we illustrate how breast cancer pathway analysis can be confounded by the frequency of FGFR2 in pathway lists. Our approach is further validated on two other datasets of summary statistics generated from GWAS of height and schizophrenia.
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Affiliation(s)
- Ryan Sun
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Shirley Hui
- The Donnelly Center, University of Toronto, Toronto, Ontario, Canada
| | - Gary D. Bader
- The Donnelly Center, University of Toronto, Toronto, Ontario, Canada
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Peter Kraft
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
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9
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Reijnders MRF, Kousi M, van Woerden GM, Klein M, Bralten J, Mancini GMS, van Essen T, Proietti-Onori M, Smeets EEJ, van Gastel M, Stegmann APA, Stevens SJC, Lelieveld SH, Gilissen C, Pfundt R, Tan PL, Kleefstra T, Franke B, Elgersma Y, Katsanis N, Brunner HG. Variation in a range of mTOR-related genes associates with intracranial volume and intellectual disability. Nat Commun 2017; 8:1052. [PMID: 29051493 PMCID: PMC5648772 DOI: 10.1038/s41467-017-00933-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/08/2017] [Indexed: 11/09/2022] Open
Abstract
De novo mutations in specific mTOR pathway genes cause brain overgrowth in the context of intellectual disability (ID). By analyzing 101 mMTOR-related genes in a large ID patient cohort and two independent population cohorts, we show that these genes modulate brain growth in health and disease. We report the mTOR activator gene RHEB as an ID gene that is associated with megalencephaly when mutated. Functional testing of mutant RHEB in vertebrate animal models indicates pathway hyperactivation with a concomitant increase in cell and head size, aberrant neuronal migration, and induction of seizures, concordant with the human phenotype. This study reveals that tight control of brain volume is exerted through a large community of mTOR-related genes. Human brain volume can be altered, by either rare disruptive events causing hyperactivation of the pathway, or through the collective effects of common alleles.
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Affiliation(s)
- M R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - M Kousi
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - G M van Woerden
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - M Klein
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - J Bralten
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - G M S Mancini
- Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, 3000 CA, Rotterdam, The Netherlands
| | - T van Essen
- Department of Genetics, University of Groningen, University Medical Center of Groningen, 9700 RB, Groningen, The Netherlands
| | - M Proietti-Onori
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - E E J Smeets
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - M van Gastel
- Department of Medical Care, SWZ zorg, 5691 AG, Son, The Netherlands
| | - A P A Stegmann
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - S J C Stevens
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - S H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 GA, Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - R Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - P L Tan
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - B Franke
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands.,Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 GA, Nijmegen, The Netherlands
| | - Y Elgersma
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - N Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - H G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands. .,Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands.
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