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Hwang JW, Lee JS. Korean Clinical Guideline for Autism Spectrum Disorder - Clinical Features, Course, Epidemiology, and Cause. Soa Chongsonyon Chongsin Uihak 2024; 35:8-14. [PMID: 38204746 PMCID: PMC10774551 DOI: 10.5765/jkacap.230040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/10/2023] [Accepted: 12/03/2023] [Indexed: 01/12/2024] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous developmental disorder characterized by impairments in two core areas: 1) social communication and interaction and 2) restricted and repetitive patterns of behaviors and interests. In general, ASD is known to be a lifelong disorder. Follow-up studies from childhood to adulthood have reported that the severity of the key symptoms ASD decreases over time. However, chronic health problems including mental health occur in many patients with ASD. The prevalence of ASD has increased from around 0.04% in the 1970s to 2.8% at present. The average age of diagnosis in developed countries is 38-120 months of age. Recent evidence suggests that biological factors which include genetic, congenital, immunological, neuroanatomical, biochemical, and environmental ones are important in causing autism. Until now, early signs and various risk factors of ASD have been suggested.
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Affiliation(s)
- Jun-Won Hwang
- Department of Psychiatry, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Jeong-Seop Lee
- Department of Psychiatry, Inha University Hospital, Inha University School of Medicine, Incheon, Korea
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Kim HK, Gonçalves VF, Husain MI, Müller DJ, Mulsant BH, Zai G, Kloiber S. Cross-disorder GWAS meta-analysis of endocannabinoid DNA variations in major depressive disorder, bipolar disorder, attention deficit hyperactivity disorder, autism spectrum disorder, and schizophrenia. Psychiatry Res 2023; 330:115563. [PMID: 37924773 DOI: 10.1016/j.psychres.2023.115563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023]
Abstract
The endocannabinoid system (ECS) is implicated in multiple mental disorders. In this study, we explored DNA variations in the ECS across major depressive disorder (MDD), bipolar disorder, attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), and schizophrenia by performing a cross-disorder genome-wide association study (GWAS) meta-analysis. We obtained six datasets from the Psychiatric Genomics Consortium containing GWAS summary statistics from European cohorts (284,023 cases and 508,515 controls). Effective sample size weighted meta-analysis was performed for 2241 single nucleotide polymorphisms (SNPs) pertaining to gene bodies of 33 endocannabinoid genes using METAL, where an overall z-statistic is calculated for each marker based on a weighted sum of individual statistics. Heterogeneity was examined with I2 and X2 tests. MAGMA gene-based analysis was also performed. We identified nine SNPs significantly associated with a change in risk of having a mental disorder. The lead SNP was rs12805732 (Gene: Diacylglycerol Lipase Alpha; DAGLA). Four SNPs had substantial heterogeneity (I2>60 %). DAGLA had the strongest association with disease risk in gene-based analysis. Our findings suggest that the ECS may be a shared pathway in mental disorders. Future studies validating these findings would contribute to the identification of biomarkers of disease risk across multiple mental disorders.
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Affiliation(s)
- Helena K Kim
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Vanessa F Gonçalves
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada; Molecular Brain Sciences Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada
| | - Muhammad I Husain
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - Daniel J Müller
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - Benoit H Mulsant
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Gwyneth Zai
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Stefan Kloiber
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, Canada; Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Canada.
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Dominguez-Alonso S, Carracedo A, Rodriguez-Fontenla C. eQTL colocalization analysis highlights novel susceptibility genes in Autism Spectrum Disorders (ASD). Transl Psychiatry 2023; 13:336. [PMID: 37907504 PMCID: PMC10618232 DOI: 10.1038/s41398-023-02621-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023] Open
Abstract
Autism Spectrum Disorders (ASD) are a group of neurodevelopmental disorders (NDDs) characterized by difficulties in social interaction and communication, repetitive behavior, and restricted interests. ASD has proven to have a strong genetic component. However, defining causal genes is still one of the main challenges in GWAS, since the vast majority (>90%) of detected signals lie within the non-coding genome. Expression quantitative trait locus (eQTL) colocalization analysis determines whether a specific variant is responsible for both a local eQTL and GWAS association and has helped leverage data and rendering gene discovery for a wide array of diseases. Here we further mine the largest ASD GWAS performed to date (18,381 cases and 27,969 controls) altogether with GWAS summary statistics from the main PGC studies (Schizophrenia, MD (Major Depression) and ADHD (Attention Deficit/Hyperactivity Disorder)), by using eQTpLot, a newly developed tool that illustrates the colocalization of GWAS and eQTL signals in a locus, and the enrichment of and correlation between the candidate gene eQTLs and trait-significant variants. This analysis points up 8 genes with a significant eQTL colocalization signal in ASD (CRHR1, KANSL1, MANBA, MAPT, MMP12, NKX2-2, PTPRE and WNT3) and one gene (SRPK2) with a marginally significant colocalization signal (r = 0.69, p < 1 × 10-6), and specifically highlights the potentially causal role of MAPT (r = 0.76, p < 1 × 10-6), NKX2-2 (r = 0.71, p-value = 2.26-02) and PTPRE (r = 0.97, p-value = 2.63-04) when restricting the analysis to brain tissue.
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Affiliation(s)
- S Dominguez-Alonso
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - C Rodriguez-Fontenla
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
- Grupo de Medicina Xenómica, Fundación Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS), Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
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4
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Gonzales S, Zhao JZ, Choi NY, Acharya P, Jeong S, Lee MY. SOX7: Novel Autistic Gene Identified by Analysis of Multi-Omics Data. RESEARCH SQUARE 2023:rs.3.rs-3346245. [PMID: 37790478 PMCID: PMC10543249 DOI: 10.21203/rs.3.rs-3346245/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background Despite thousands of variants identified by genome-wide association studies (GWAS) to be associated with autism spectrum disorder (ASD), it is unclear which mutations are causal because most are noncoding. Consequently, reliable diagnostic biomarkers are lacking. RNA-seq analysis captures biomolecular complexity that GWAS cannot by considering transcriptomic patterns. Therefore, integrating DNA and RNA testing may reveal causal genes and useful biomarkers for ASD. Methods We performed gene-based association studies using an adaptive test method with GWAS summary statistics from two large Psychiatric Genomics Consortium (PGC) datasets (ASD2019: 18,382 cases and 27,969 controls; ASD2017: 6,197 cases and 7,377 controls). We also investigated differential expression for genes identified with the adaptive test using an RNA-seq dataset (GSE30573: 3 cases and 3 controls) and DESeq2. Results We identified 5 genes significantly associated with ASD in ASD2019 (KIZ-AS1, p = 8.67×10- 10; KIZ, p = 1.16×10- 9; XRN2, p = 7.73×10- 9; SOX7, p = 2.22×10- 7; LOC101929229 (also known as PINX1-DT), p = 2.14×10- 6). Two of the five genes were replicated in ASD2017: SOX7 (p = 0.00087) and LOC101929229 (p = 0.009), and KIZ was close to the replication boundary of replication (p = 0.06). We identified significant expression differences for SOX7 (p = 0.0017, adjusted p = 0.0085), LOC101929229 (p = 5.83×10- 7, adjusted p = 1.18×10- 5), and KIZ (p = 0.00099, adjusted p = 0.0055). SOX7 encodes a transcription factor that regulates developmental pathways, alterations in which may contribute to ASD. Limitations The limitation of the gene-based analysis is the reliance on a reference population for estimating linkage disequilibrium between variants. The similarity of this reference population to the population of study is crucial to the accuracy of many gene-based analyses, including those performed in this study. As a result, the extent of our findings is limited to European populations, as this was our reference of choice. Future work includes a tighter integration of DNA and RNA information as well as extensions to non-European populations that have been under-researched. Conclusions These findings suggest that SOX7 and its related SOX family genes encode transcription factors that are critical to the downregulation of the canonical Wnt/β-catenin signaling pathway, an important developmental signaling pathway, providing credence to the biologic plausibility of the association between gene SOX7 and autism spectrum disorder.
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Affiliation(s)
| | - Jane Zizhen Zhao
- Miami Dade College Kendall Campus and School for Advanced Studies
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Mio C, Baldan F, Damante G. NK2 homeobox gene cluster: Functions and roles in human diseases. Genes Dis 2023; 10:2038-2048. [PMID: 37492711 PMCID: PMC10363584 DOI: 10.1016/j.gendis.2022.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/15/2022] [Accepted: 10/01/2022] [Indexed: 07/27/2023] Open
Abstract
NK2 genes (NKX2 gene cluster in humans) encode for homeodomain-containing transcription factors that are conserved along the phylogeny. According to the most detailed classifications, vertebrate NKX2 genes are classified into two distinct families, NK2.1 and NK2.2. The former is constituted by NKX2-1 and NKX2-4 genes, which are homologous to the Drosophila scro gene; the latter includes NKX2-2 and NKX2-8 genes, which are homologous to the Drosophila vnd gene. Conservation of these genes is not only related to molecular structure and expression, but also to biological functions. In Drosophila and vertebrates, NK2 genes share roles in the development of ventral regions of the central nervous system. In vertebrates, NKX2 genes have a relevant role in the development of several other organs such as the thyroid, lung, and pancreas. Loss-of-function mutations in NKX2-1 and NKX2-2 are the monogenic cause of the brain-lung-thyroid syndrome and neonatal diabetes, respectively. Alterations in NKX2-4 and NKX2-8 genes may play a role in multifactorial diseases, autism spectrum disorder, and neural tube defects, respectively. NKX2-1, NKX2-2, and NKX2-8 are expressed in various cancer types as either oncogenes or tumor suppressor genes. Several data indicate that evaluation of their expression in tumors has diagnostic and/or prognostic value.
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Affiliation(s)
- Catia Mio
- Dipartimento di Area Medica, Università degli Studi di Udine, Udine 33100, Italy
| | - Federica Baldan
- Istituto di Genetica Medica, Azienda Sanitaria Universitaria Friuli Centrale, Udine 33100, Italy
| | - Giuseppe Damante
- Dipartimento di Area Medica, Università degli Studi di Udine, Udine 33100, Italy
- Istituto di Genetica Medica, Azienda Sanitaria Universitaria Friuli Centrale, Udine 33100, Italy
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Cabana-Domínguez J, Llonga N, Arribas L, Alemany S, Vilar-Ribó L, Demontis D, Fadeuilhe C, Corrales M, Richarte V, Børglum AD, Ramos-Quiroga JA, Soler Artigas M, Ribasés M. Transcriptomic risk scores for attention deficit/hyperactivity disorder. Mol Psychiatry 2023; 28:3493-3502. [PMID: 37537283 PMCID: PMC10618083 DOI: 10.1038/s41380-023-02200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023]
Abstract
Attention deficit/hyperactivity disorder (ADHD) is a highly heritable neurodevelopmental disorder. We performed a transcriptome-wide association study (TWAS) using the latest genome-wide association study (GWAS) meta-analysis, in 38,691 individuals with ADHD and 186,843 controls, and 14 gene-expression reference panels across multiple brain tissues and whole blood. Based on TWAS results, we selected subsets of genes and constructed transcriptomic risk scores (TRSs) for the disorder in peripheral blood mononuclear cells of individuals with ADHD and controls. We found evidence of association between ADHD and TRSs constructed using expression profiles from multiple brain areas, with individuals with ADHD carrying a higher burden of TRSs than controls. TRSs were uncorrelated with the polygenic risk score (PRS) for ADHD and, in combination with PRS, improved significantly the proportion of variance explained over the PRS-only model. These results support the complementary predictive potential of genetic and transcriptomic profiles in blood and underscore the potential utility of gene expression for risk prediction and deeper insight in molecular mechanisms underlying ADHD.
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Affiliation(s)
- Judit Cabana-Domínguez
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain.
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain.
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.
| | - Natalia Llonga
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Lorena Arribas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Silvia Alemany
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Laura Vilar-Ribó
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
| | - Ditte Demontis
- Department of Biomedicine/Human Genetics, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christian Fadeuilhe
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montse Corrales
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vanesa Richarte
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anders D Børglum
- Department of Biomedicine/Human Genetics, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - Josep Antoni Ramos-Quiroga
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain.
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain.
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.
| | - Marta Ribasés
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain.
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain.
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.
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Sahana G, Cai Z, Sanchez MP, Bouwman AC, Boichard D. Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle. J Dairy Sci 2023:S0022-0302(23)00357-0. [PMID: 37349208 DOI: 10.3168/jds.2022-22694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/01/2023] [Indexed: 06/24/2023]
Abstract
Genotype data from dairy cattle selection programs have greatly facilitated GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models that go beyond additive effects, elucidate the genetic architecture of a trait, and finally, decipher the underlying biology of traits. The entire process, comprising data generation, quality control, statistical analyses, interpretation of association results, and linking results to biology should be designed and executed to minimize the generation of false-positive and false-negative associations and misleading links to biological processes. This review aims to provide general guidelines for data analysis that address data quality control, association tests, adjustment for population stratification, and significance evaluation to improve the reliability of conclusions. We also provide guidance on post-GWAS strategy and the interpretation of results. These guidelines are tailored to dairy cattle, which are characterized by long-range linkage disequilibrium, large half-sib families, and routinely collected phenotypes, requiring different approaches than those applied in human GWAS. We discuss common limitations and challenges that have been overlooked in the analysis and interpretation of GWAS to identify candidate sequence variants in dairy cattle.
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Affiliation(s)
- G Sahana
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark.
| | - Z Cai
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark
| | - M P Sanchez
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - A C Bouwman
- Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, the Netherlands
| | - D Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
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Gonzales S, Zhao JZ, Choi NY, Acharya P, Jeong S, Lee MY. SOX7: Novel Autistic Gene Identified by Analysis of Multi-Omics Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.26.542456. [PMID: 37292933 PMCID: PMC10245991 DOI: 10.1101/2023.05.26.542456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background Genome-wide association studies and next generation sequencing data analyses based on DNA information have identified thousands of mutations associated with autism spectrum disorder (ASD). However, more than 99% of identified mutations are non-coding. Thus, it is unclear which of these mutations might be functional and thus potentially causal variants. Transcriptomic profiling using total RNA-sequencing has been one of the most utilized approaches to link protein levels to genetic information at the molecular level. The transcriptome captures molecular genomic complexity that the DNA sequence solely does not. Some mutations alter a gene's DNA sequence but do not necessarily change expression and/or protein function. To date, few common variants reliably associated with the diagnosis status of ASD despite consistently high estimates of heritability. In addition, reliable biomarkers used to diagnose ASD or molecular mechanisms to define the severity of ASD do not exist. Objectives It is necessary to integrate DNA and RNA testing together to identify true causal genes and propose useful biomarkers for ASD. Methods We performed gene-based association studies with adaptive test using genome-wide association studies (GWAS) summary statistics with two large GWAS datasets (ASD 2019 data: 18,382 ASD cases and 27,969 controls [discovery data]; ASD 2017 data: 6,197 ASD cases and 7,377 controls [replication data]) which were obtained from the Psychiatric Genomics Consortium (PGC). In addition, we investigated differential expression for genes identified in gene-based GWAS with a RNA-seq dataset (GSE30573: 3 cases and 3 controls) using the DESeq2 package. Results We identified 5 genes significantly associated with ASD in ASD 2019 data (KIZ-AS1, p=8.67×10-10; KIZ, p=1.16×10-9; XRN2, p=7.73×10-9; SOX7, p=2.22×10-7; PINX1-DT, p=2.14×10-6). Among these 5 genes, gene SOX7 (p=0.00087), LOC101929229 (p=0.009), and KIZ-AS1 (p=0.059) were replicated in ASD 2017 data. KIZ (p=0.06) was close to the boundary of replication in ASD 2017 data. Genes SOX7 (p=0.0017, adjusted p=0.0085), LOC101929229 (also known as PINX1-DT, p=5.83×10-7, adjusted p=1.18×10-5), and KIZ (p=0.00099, adjusted p=0.0055) indicated significant expression differences between cases and controls in the RNA-seq data. SOX7 encodes a member of the SOX (SRY-related HMG-box) family of transcription factors pivotally contributing to determining of the cell fate and identity in many lineages. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins leading to autism. Conclusion Gene SOX7 in the transcription factor family could be associated with ASD. This finding may provide new diagnostic and therapeutic strategies for ASD.
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Affiliation(s)
- Samantha Gonzales
- Department of Biostatistics, Florida International University, Miami, FL 33199
| | - Jane Zizhen Zhao
- Miami Dade College Kendall Campus and School for Advanced Studies, Miami, FL 33176
| | - Na Young Choi
- Department of Biomedical Engineering, University of North Texas, Denton, TX 76207
| | - Prabha Acharya
- Department of Biomedical Engineering, University of North Texas, Denton, TX 76207
| | - Sehoon Jeong
- Department of Healthcare Information Technology Inje University, Gimhae, South Korea, 50834
| | - Moo-Yeal Lee
- Department of Biomedical Engineering, University of North Texas, Denton, TX 76207
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9
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Nam YW, Downey M, Rahman MA, Cui M, Zhang M. Channelopathy of small- and intermediate-conductance Ca 2+-activated K + channels. Acta Pharmacol Sin 2023; 44:259-267. [PMID: 35715699 PMCID: PMC9889811 DOI: 10.1038/s41401-022-00935-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/31/2022] [Indexed: 02/04/2023] Open
Abstract
Small- and intermediate-conductance Ca2+-activated K+ (KCa2.x/KCa3.1 also called SK/IK) channels are gated exclusively by intracellular Ca2+. The Ca2+ binding protein calmodulin confers sub-micromolar Ca2+ sensitivity to the channel-calmodulin complex. The calmodulin C-lobe is constitutively associated with the proximal C-terminus of the channel. Interactions between calmodulin N-lobe and the channel S4-S5 linker are Ca2+-dependent, which subsequently trigger conformational changes in the channel pore and open the gate. KCNN genes encode four subtypes, including KCNN1 for KCa2.1 (SK1), KCNN2 for KCa2.2 (SK2), KCNN3 for KCa2.3 (SK3), and KCNN4 for KCa3.1 (IK). The three KCa2.x channel subtypes are expressed in the central nervous system and the heart. The KCa3.1 subtype is expressed in the erythrocytes and the lymphocytes, among other peripheral tissues. The impact of dysfunctional KCa2.x/KCa3.1 channels on human health has not been well documented. Human loss-of-function KCa2.2 mutations have been linked with neurodevelopmental disorders. Human gain-of-function mutations that increase the apparent Ca2+ sensitivity of KCa2.3 and KCa3.1 channels have been associated with Zimmermann-Laband syndrome and hereditary xerocytosis, respectively. This review article discusses the physiological significance of KCa2.x/KCa3.1 channels, the pathophysiology of the diseases linked with KCa2.x/KCa3.1 mutations, the structure-function relationship of the mutant KCa2.x/KCa3.1 channels, and potential pharmacological therapeutics for the KCa2.x/KCa3.1 channelopathy.
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Affiliation(s)
- Young-Woo Nam
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Myles Downey
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Mohammad Asikur Rahman
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University School of Pharmacy, Boston, MA, 02115, USA
| | - Miao Zhang
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA.
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10
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Hooshmand K, Goldstein D, Timmins HC, Li T, Harrison M, Friedlander ML, Lewis CR, Lees JG, Moalem-Taylor G, Guennewig B, Park SB, Kwok JB. Polygenic risk of paclitaxel-induced peripheral neuropathy: a genome-wide association study. J Transl Med 2022; 20:564. [PMID: 36474270 PMCID: PMC9724416 DOI: 10.1186/s12967-022-03754-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genetic risk factors for chemotherapy-induced peripheral neuropathy (CIPN), a major dose-limiting side-effect of paclitaxel, are not well understood. METHODS We performed a genome-wide association study (GWAS) in 183 paclitaxel-treated patients to identify genetic loci associated with CIPN assessed via comprehensive neuropathy phenotyping tools (patient-reported, clinical and neurological grading scales). Bioinformatic analyses including pathway enrichment and polygenic risk score analysis were used to identify mechanistic pathways of interest. RESULTS In total, 77% of the cohort were classified with CIPN (n = 139), with moderate/severe neuropathy in 36%. GWAS was undertaken separately for the three measures of CIPN. GWAS of patient-reported CIPN identified 4 chromosomal regions that exceeded genome-wide significance (rs9846958, chromosome 3; rs117158921, chromosome 18; rs4560447, chromosome 4; rs200091415, chromosome 10). rs4560447 is located within a protein-coding gene, LIMCH1, associated with actin and neural development and expressed in the dorsal root ganglia (DRG). There were additional risk loci that exceeded the statistical threshold for suggestive genome-wide association (P < 1 × 10-5) for all measures. A polygenic risk score calculated from the top 46 ranked SNPs was highly correlated with patient-reported CIPN (r2 = 0.53; P = 1.54 × 10-35). Overlap analysis was performed to identify 3338 genes which were in common between the patient-reported CIPN, neurological grading scale and clinical grading scale GWAS. The common gene set was subsequently analysed for enrichment of gene ontology (GO) and Reactome pathways, identifying a number of pathways, including the axon development pathway (GO:0061564; P = 1.78 × 10-6) and neuronal system (R-HSA-112316; adjusted P = 3.33 × 10-7). CONCLUSIONS Our findings highlight the potential role of axon development and regeneration pathways in paclitaxel-induced CIPN.
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Affiliation(s)
- Kosar Hooshmand
- grid.1013.30000 0004 1936 834XSchool of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia ,grid.1013.30000 0004 1936 834XBrain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia
| | - David Goldstein
- grid.1005.40000 0004 4902 0432Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Hannah C. Timmins
- grid.1013.30000 0004 1936 834XSchool of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia ,grid.1013.30000 0004 1936 834XBrain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia
| | - Tiffany Li
- grid.1013.30000 0004 1936 834XSchool of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia ,grid.1013.30000 0004 1936 834XBrain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia
| | | | - Michael L. Friedlander
- grid.1005.40000 0004 4902 0432Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Craig R. Lewis
- grid.1005.40000 0004 4902 0432Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Justin G. Lees
- grid.1005.40000 0004 4902 0432School of Biomedical Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW Australia
| | - Gila Moalem-Taylor
- grid.1005.40000 0004 4902 0432School of Biomedical Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW Australia
| | - Boris Guennewig
- grid.1013.30000 0004 1936 834XSchool of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia ,grid.1013.30000 0004 1936 834XBrain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia
| | - Susanna B. Park
- grid.1013.30000 0004 1936 834XSchool of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia ,grid.1013.30000 0004 1936 834XBrain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia
| | - John B. Kwok
- grid.1013.30000 0004 1936 834XSchool of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia ,grid.1013.30000 0004 1936 834XBrain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW Australia
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11
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Lynall ME, Soskic B, Hayhurst J, Schwartzentruber J, Levey DF, Pathak GA, Polimanti R, Gelernter J, Stein MB, Trynka G, Clatworthy MR, Bullmore E. Genetic variants associated with psychiatric disorders are enriched at epigenetically active sites in lymphoid cells. Nat Commun 2022; 13:6102. [PMID: 36243721 PMCID: PMC9569335 DOI: 10.1038/s41467-022-33885-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 10/06/2022] [Indexed: 02/06/2023] Open
Abstract
Multiple psychiatric disorders have been associated with abnormalities in both the innate and adaptive immune systems. The role of these abnormalities in pathogenesis, and whether they are driven by psychiatric risk variants, remains unclear. We test for enrichment of GWAS variants associated with multiple psychiatric disorders (cross-disorder or trans-diagnostic risk), or 5 specific disorders (cis-diagnostic risk), in regulatory elements in immune cells. We use three independent epigenetic datasets representing multiple organ systems and immune cell subsets. Trans-diagnostic and cis-diagnostic risk variants (for schizophrenia and depression) are enriched at epigenetically active sites in brain tissues and in lymphoid cells, especially stimulated CD4+ T cells. There is no evidence for enrichment of either trans-risk or cis-risk variants for schizophrenia or depression in myeloid cells. This suggests a possible model where environmental stimuli activate T cells to unmask the effects of psychiatric risk variants, contributing to the pathogenesis of mental health disorders.
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Affiliation(s)
- Mary-Ellen Lynall
- Department of Psychiatry, Herchel Smith Building of Brain & Mind Sciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0SZ, UK.
- Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK.
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK.
| | - Blagoje Soskic
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- Human Technopole, Milan, Italy
| | | | | | - Daniel F Levey
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Gita A Pathak
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Renato Polimanti
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Joel Gelernter
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Murray B Stein
- VA San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Ed Bullmore
- Department of Psychiatry, Herchel Smith Building of Brain & Mind Sciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0SZ, UK
- Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK
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12
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Baranova A, Wang J, Cao H, Chen JH, Chen J, Chen M, Ni S, Xu X, Ke X, Xie S, Sun J, Zhang F. Shared genetics between autism spectrum disorder and attention-deficit/hyperactivity disorder and their association with extraversion. Psychiatry Res 2022; 314:114679. [PMID: 35717853 DOI: 10.1016/j.psychres.2022.114679] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/31/2022] [Accepted: 06/10/2022] [Indexed: 12/22/2022]
Abstract
BACKGROUND Deciphering the genetic relationships between autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD) may uncover underlining shared pathophysiology as well as inform treatment. METHODS The summary results of genome-wide association studies on ADHD, ASD, and extraversion were utilized for the analyzes. Genetic correlations between ADHD, ASD, and extraversion were tested using linkage disequilibrium score regression. Causal relationships between ADHD, ASD, and extraversion were investigated using Mendelian randomization (MR) analysis. Novel pleiotropic genomic loci shared by ADHD and ASD were identified using a cross-trait meta-analysis. RESULTS Extraversion was positively correlated with ADHD (rg = 0.205) and negatively correlated with ASD (rg = -0.193). The MR analysis showed that ADHD confers a causal effect on ASD (OR: 1.35, 95% confidence interval (CI):1.20-1.52) and vice versa (1.46, 1.38-1.55). Extraversion exerts a causal effect on ADHD only (1.19, 1.05-1.33). The cross-trait meta-analysis identified three novel pleiotropic genomic loci for ADHD and ASD, involving two pleiotropic genes, LINC00461 and KIZ. CONCLUSIONS Our study provides new insights into the shared genetics of ADHD and ASD and their connections with extraversion.
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Affiliation(s)
- Ancha Baranova
- School of Systems Biology, George Mason University, Manassas 20110, USA; Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Jun Wang
- Department of Psychiatry, Wuxi Mental Health Center of Nanjing Medical University, Wuxi 214151, China
| | - Hongbao Cao
- School of Systems Biology, George Mason University, Manassas 20110, USA
| | - Jiang-Huan Chen
- Laboratory of Genomic and Precision Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Jiu Chen
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, 264 Guangzhou Road, Nanjing 210029, China
| | - Miao Chen
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Sulin Ni
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xijia Xu
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Xiaoyan Ke
- Child Mental Health Research Center, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Shiping Xie
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jing Sun
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Fuquan Zhang
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, 264 Guangzhou Road, Nanjing 210029, China; Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing 210029, China.
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13
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Peyre H, Schoeler T, Liu C, Williams CM, Hoertel N, Havdahl A, Pingault JB. Combining multivariate genomic approaches to elucidate the comorbidity between autism spectrum disorder and attention deficit hyperactivity disorder. J Child Psychol Psychiatry 2021; 62:1285-1296. [PMID: 34235737 DOI: 10.1111/jcpp.13479] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) are two highly heritable neurodevelopmental disorders. Several lines of evidence point towards the presence of shared genetic factors underlying ASD and ADHD. We conducted genomic analyses of common risk variants (i.e. single nucleotide polymorphisms, SNPs) shared by ASD and ADHD, and those specific to each disorder. METHODS With the summary data from two GWAS, one on ASD (N = 46,350) and another on ADHD (N = 55,374) individuals, we used genomic structural equation modelling and colocalization analysis to identify SNPs shared by ASD and ADHD and SNPs specific to each disorder. Functional genomic analyses were then conducted on shared and specific common genetic variants. Finally, we performed a bidirectional Mendelian randomization analysis to test whether the shared genetic risk between ASD and ADHD was interpretable in terms of reciprocal relationships between ASD and ADHD. RESULTS We found that 37.5% of the SNPs associated with ASD (at p < 1e-6) colocalized with ADHD SNPs and that 19.6% of the SNPs associated with ADHD colocalized with ASD SNPs. We identified genes mapped to SNPs that are specific to ASD or ADHD and that are shared by ASD and ADHD, including two novel genes INSM1 and PAX1. Our bidirectional Mendelian randomization analyses indicated that the risk of ASD was associated with an increased risk of ADHD and vice versa. CONCLUSIONS Using multivariate genomic analyses, the present study uncovers shared and specific genetic variants associated with ASD and ADHD. Further functional investigation of genes mapped to those shared variants may help identify pathophysiological pathways and new targets for treatment.
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Affiliation(s)
- Hugo Peyre
- Department of Clinical, Educational and Health Psychology, University College London, London, UK.,Laboratoire de Sciences Cognitives et Psycholinguistique (ENS, EHESS, CNRS), Ecole Normale Supérieure, PSL University, Paris, France.,Neurodiderot, INSERM UMR 1141, Paris Diderot University, Paris, France.,Department of Child and Adolescent Psychiatry, Robert Debré Hospital, APHP, Paris, France
| | - Tabea Schoeler
- Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Chaoyu Liu
- Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Camille Michèle Williams
- Laboratoire de Sciences Cognitives et Psycholinguistique (ENS, EHESS, CNRS), Ecole Normale Supérieure, PSL University, Paris, France
| | - Nicolas Hoertel
- INSERM UMR 894, Psychiatry and Neurosciences Center, Paris Descartes University, PRES Sorbonne Paris Cité, Paris, France.,Department of Psychiatry, Corentin Celton Hospital, APHP, Issy-les-Moulineaux, Paris Descartes University, PRES Sorbonne Paris Cité, Paris, France
| | - Alexandra Havdahl
- Nic Waals Institute, Lovisenberg Diaconal Hospital, Oslo, Norway.,Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Jean-Baptiste Pingault
- Department of Clinical, Educational and Health Psychology, University College London, London, UK.,Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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14
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Liu X, Tian G, Liu Z. Identification of novel genes for triple-negative breast cancer with semiparametric gene-based analysis. J Appl Stat 2021; 50:691-702. [PMID: 36819073 PMCID: PMC9930760 DOI: 10.1080/02664763.2021.1973387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Triple-negative breast cancer (TNBC) is generally considered an aggressive breast cancer subtype associated with poor prognostic outcomes. Up to now, the molecular and cellular mechanisms underlying TNBC pathology have not been fully understood. In this manuscript, we propose a novel semiparametric model with kernel for gene-based analysis with a breast cancer GWAS data. The software of SPMGBA (semiparametric method for gene-based analysis) in MATLAB is available at GitHub (https://github.com/zliu3/SPMGBA). Genetic signatures associated with breast cancer are discovered. We further validate the prognostic power of the identified genes with a large cohort of expression data from the European Genome-Phenome Archive, and discover that SEL1L is associated with the overall survival of TNBC with the p-value of .0002. We conclude that gene SEL1L is down-regulated in TNBC and the expression of SEL1L is positively associated with patient survival.
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Affiliation(s)
- Xiaotong Liu
- Department of Statistics and Data Science, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Guoliang Tian
- Department of Statistics and Data Science, Southern University of Science and Technology, Shenzhen, People's Republic of China
| | - Zhenqiu Liu
- Department of Public Health Sciences, Pennsylvania State University, Hershey, PA, USA, Zhenqiu Liu Department of Public Health Sciences, Pennsylvania State University, Hershey, PA17033, USA
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15
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Gill PS, Clothier JL, Veerapandiyan A, Dweep H, Porter-Gill PA, Schaefer GB. Molecular Dysregulation in Autism Spectrum Disorder. J Pers Med 2021; 11:848. [PMID: 34575625 PMCID: PMC8466026 DOI: 10.3390/jpm11090848] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Autism Spectrum Disorder (ASD) comprises a heterogeneous group of neurodevelopmental disorders with a strong heritable genetic component. At present, ASD is diagnosed solely by behavioral criteria. Advances in genomic analysis have contributed to numerous candidate genes for the risk of ASD, where rare mutations and s common variants contribute to its susceptibility. Moreover, studies show rare de novo variants, copy number variation and single nucleotide polymorphisms (SNPs) also impact neurodevelopment signaling. Exploration of rare and common variants involved in common dysregulated pathways can provide new diagnostic and therapeutic strategies for ASD. Contributions of current innovative molecular strategies to understand etiology of ASD will be explored which are focused on whole exome sequencing (WES), whole genome sequencing (WGS), microRNA, long non-coding RNAs and CRISPR/Cas9 models. Some promising areas of pharmacogenomic and endophenotype directed therapies as novel personalized treatment and prevention will be discussed.
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Affiliation(s)
- Pritmohinder S. Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA;
| | - Jeffery L. Clothier
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Aravindhan Veerapandiyan
- Pediatric Neurology, Arkansas Children’s Hospital, 1 Children’s Way, Little Rock, AR 72202, USA;
| | - Harsh Dweep
- The Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA;
| | | | - G. Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Genetics and Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Hospital NW, Springdale, AR 72762, USA
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16
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Rodriguez-Fontenla C, Carracedo A. UTMOST, a single and cross-tissue TWAS (Transcriptome Wide Association Study), reveals new ASD (Autism Spectrum Disorder) associated genes. Transl Psychiatry 2021; 11:256. [PMID: 33931583 PMCID: PMC8087708 DOI: 10.1038/s41398-021-01378-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/22/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Autism spectrum disorders (ASD) is a complex neurodevelopmental disorder that may significantly impact on the affected individual's life. Common variation (SNPs) could explain about 50% of ASD heritability. Despite this fact and the large size of the last GWAS meta-analysis, it is believed that hundreds of risk genes in ASD have yet to be discovered. New tools, such as TWAS (Transcriptome Wide Association Studies) which integrate tissue expression and genetic data, are a great approach to identify new ASD susceptibility genes. The main goal of this study is to use UTMOST with the publicly available summary statistics from the largest ASD GWAS meta-analysis as genetic input. In addition, an in silico biological characterization for the novel associated loci was performed. Our results have shown the association of 4 genes at the brain level (CIPC, PINX1, NKX2-2, and PTPRE) and have highlighted the association of NKX2-2, MANBA, ERI1, and MITF at the gastrointestinal level. The gastrointestinal associations are quite relevant given the well-established but unexplored relationship between ASD and gastrointestinal symptoms. Cross-tissue analysis has shown the association of NKX2-2 and BLK. UTMOST-associated genes together with their in silico biological characterization seems to point to different biological mechanisms underlying ASD etiology. Thus, it would not be restricted to brain tissue and it will involve the participation of other body tissues such as the gastrointestinal.
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Affiliation(s)
- Cristina Rodriguez-Fontenla
- Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain.
| | - Angel Carracedo
- grid.11794.3a0000000109410645Grupo de Medicina Xenómica, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain ,grid.11794.3a0000000109410645Fundación Pública Galega de Medicina Xenómica (FPGMX), Centro de Investigación Biomédica en Red, Enfermedades Raras (CIBERER), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
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17
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Kim N, Kim KH, Lim WJ, Kim J, Kim SA, Yoo HJ. Whole Exome Sequencing Identifies Novel De Novo Variants Interacting with Six Gene Networks in Autism Spectrum Disorder. Genes (Basel) 2020; 12:genes12010001. [PMID: 33374967 PMCID: PMC7822011 DOI: 10.3390/genes12010001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable condition caused by a combination of environmental and genetic factors such as de novo and inherited variants, as well as rare or common variants among hundreds of related genes. Previous genome-wide association studies have identified susceptibility genes; however, most ASD-associated genes remain undiscovered. This study aimed to examine rare de novo variants to identify genetic risk factors of ASD using whole exome sequencing (WES), functional characterization, and genetic network analyses of identified variants using Korean familial dataset. We recruited children with ASD and their biological parents. The clinical best estimate diagnosis of ASD was made according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5TM), using comprehensive diagnostic instruments. The final analyses included a total of 151 individuals from 51 families. Variants were identified and filtered using the GATK Best Practices for bioinformatics analysis, followed by genome alignments and annotation to the reference genome assembly GRCh37 (liftover to GRCh38), and further annotated using dbSNP 154 build databases. To evaluate allele frequencies of de novo variants, we used the dbSNP, gnomAD exome v2.1.1, and genome v3.0. We used Ingenuity Pathway Analysis (IPA, Qiagen) software to construct networks using all identified de novo variants with known autism-related genes to find probable relationships. We identified 36 de novo variants with potential relations to ASD; 27 missense, two silent, one nonsense, one splice region, one splice site, one 5′ UTR, and one intronic SNV and two frameshift deletions. We identified six networks with functional relationships. Among the interactions between de novo variants, the IPA assay found that the NF-κB signaling pathway and its interacting genes were commonly observed at two networks. The relatively small cohort size may affect the results of novel ASD genes with de novo variants described in our findings. We did not conduct functional experiments in this study. Because of the diversity and heterogeneity of ASD, the primary purpose of this study was to investigate probable causative relationships between novel de novo variants and known autism genes. Additionally, we based functional relationships with known genes on network analysis rather than on statistical analysis. We identified new variants that may underlie genetic factors contributing to ASD in Korean families using WES and genetic network analyses. We observed novel de novo variants that might be functionally linked to ASD, of which the variants interact with six genetic networks.
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Affiliation(s)
- Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (N.K.); (K.H.K.); (W.-J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (N.K.); (K.H.K.); (W.-J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (N.K.); (K.H.K.); (W.-J.L.)
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141, Korea
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Soon Ae Kim
- Department of Pharmacology, School of Medicine, Eulji University, Daejeon 34824, Korea
- Correspondence: (S.A.K.); (H.J.Y.); Tel.: +82-42-259-1672 (S.A.K.); +82-31-787-7436 (H.J.Y.)
| | - Hee Jeong Yoo
- Department of Psychiatry, College of Medicine, Seoul National University, Seoul 03080, Korea
- Department of Psychiatry, Seoul National University Bundang Hospital, Gyeonggi 13620, Korea
- Correspondence: (S.A.K.); (H.J.Y.); Tel.: +82-42-259-1672 (S.A.K.); +82-31-787-7436 (H.J.Y.)
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18
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Mochel F, Rastetter A, Ceulemans B, Platzer K, Yang S, Shinde DN, Helbig KL, Lopergolo D, Mari F, Renieri A, Benetti E, Canitano R, Waisfisz Q, Plomp AS, Huisman SA, Wilson GN, Cathey SS, Louie RJ, Gaudio DD, Waggoner D, Kacker S, Nugent KM, Roeder ER, Bruel AL, Thevenon J, Ehmke N, Horn D, Holtgrewe M, Kaiser FJ, Kamphausen SB, Abou Jamra R, Weckhuysen S, Dalle C, Depienne C. Variants in the SK2 channel gene (KCNN2) lead to dominant neurodevelopmental movement disorders. Brain 2020; 143:3564-3573. [PMID: 33242881 DOI: 10.1093/brain/awaa346] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/17/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
KCNN2 encodes the small conductance calcium-activated potassium channel 2 (SK2). Rodent models with spontaneous Kcnn2 mutations show abnormal gait and locomotor activity, tremor and memory deficits, but human disorders related to KCNN2 variants are largely unknown. Using exome sequencing, we identified a de novo KCNN2 frameshift deletion in a patient with learning disabilities, cerebellar ataxia and white matter abnormalities on brain MRI. This discovery prompted us to collect data from nine additional patients with de novo KCNN2 variants (one nonsense, one splice site, six missense variants and one in-frame deletion) and one family with a missense variant inherited from the affected mother. We investigated the functional impact of six selected variants on SK2 channel function using the patch-clamp technique. All variants tested but one, which was reclassified to uncertain significance, led to a loss-of-function of SK2 channels. Patients with KCNN2 variants had motor and language developmental delay, intellectual disability often associated with early-onset movement disorders comprising cerebellar ataxia and/or extrapyramidal symptoms. Altogether, our findings provide evidence that heterozygous variants, likely causing a haploinsufficiency of the KCNN2 gene, lead to novel autosomal dominant neurodevelopmental movement disorders mirroring phenotypes previously described in rodents.
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Affiliation(s)
- Fanny Mochel
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique and Centre de Référence Neurométabolique Adulte, F-75013, Paris, France
| | - Agnès Rastetter
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France
| | - Berten Ceulemans
- Division of Paediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Deepali N Shinde
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Diego Lopergolo
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Benetti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Roberto Canitano
- Division of Child and Adolescent Neuropsychiatry, University Hospital of Siena, Siena, Italy
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sylvia A Huisman
- Department of Pediatrics, Amsterdam UMC, Amsterdam, The Netherlands.,Prinsenstichting, Purmerend, The Netherlands
| | - Golder N Wilson
- Department of Pediatrics, Texas Tech University Health Science Center, Lubbock, Texas, USA
| | - Sara S Cathey
- Greenwood Genetic Center, Greenwood, South Carolina, 29646, USA
| | - Raymond J Louie
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Daniela Del Gaudio
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Darrel Waggoner
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Shawn Kacker
- Department of Pediatrics, Section of Child Neurology, University of Chicago, Chicago, IL, 60637, USA
| | - Kimberly M Nugent
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ange-Line Bruel
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de référence maladies rares 'déficiences intellectuelles de causes rares', Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Julien Thevenon
- Service de Génétique, Génomique, et Procréation, Centre Hospitalier Universitaire Grenoble Alpes, 38700 La Tronche, France.,INSERM 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Université Grenoble Alpes, 38706 Grenoble, France
| | - Nadja Ehmke
- Institute for Human Genetics and Medical Genetics, Charité - Universitaetsmedizin Berlin, Berlin, Germany
| | - Denise Horn
- Institute for Human Genetics and Medical Genetics, Charité - Universitaetsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics - CUBI, Berlin Institute of Health (BIH), Berlin, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Carine Dalle
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France
| | - Christel Depienne
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France.,Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany
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19
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Khalid M, Raza H, M. Driessen T, J. Lee P, Tejwani L, Sami A, Nawaz M, Mehmood Baig S, Lim J, Kaukab Raja G. Genetic Risk of Autism Spectrum Disorder in a Pakistani Population. Genes (Basel) 2020; 11:genes11101206. [PMID: 33076578 PMCID: PMC7602870 DOI: 10.3390/genes11101206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/29/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Autism spectrum disorder (ASD) is a group of complex multifactorial neurodevelopmental and neuropsychiatric disorders in children characterized by impairment of communication and social interaction. Several genes with associated single nucleotide polymorphisms (SNPs) have been identified for ASD in different genetic association studies, meta-analyses, and genome-wide association studies (GWAS). However, associations between different SNPs and ASD vary from population to population. Four SNPs in genes CNTNAP2, EIF4E, ATP2B2, CACNA1C, and SNP rs4307059 (which is found between CDH9 and CDH10 genes) have been identified and reported as candidate risk factors for ASD. The aim of the present study was, for the first time, to assess the association of SNPs in these genes with ASD in the Pakistani population. PCR-based genotyping was performed using allele-specific primers in 93 ASD and 93 control Pakistani individuals. All genetic associations, genotype frequencies, and allele frequencies were computed as odds’ ratios (ORs) using logistic regression with a threshold of p ≤ 0.01 to determine statistical significance. We found that the homozygous genotypes of mutant T alleles of CNTNAP2 and ATP2B2 were significantly associated with Pakistani ASD patients in unadjusted ORs (p < 0.01), but their significance score was lost in the adjusted model. Other SNPs such as rs4307059, rs17850950 of EIF4E, and rs1006737 of CACNA1C were not statistically significant. Based on this, we conclude that SNPs are not associated with, or are not the main cause of, autism in the Pakistani population, indicating the involvement of additional players, which need to be investigated in future studies in a large population size. One of the limitations of present study is its small sample size. However, this study, being the first on Pakistani ASD patients, may lay the foundations for future studies in larger samples.
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Affiliation(s)
- Madiha Khalid
- Department of Biochemistry, University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University, Rawalpindi 46000, Pakistan; (M.K.); (A.S.)
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Hashim Raza
- Pakistan Institute of Medical Sciences, Islamabad 44000, Pakistan;
| | - Terri M. Driessen
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Paul J. Lee
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; (P.J.L.); (L.T.)
| | - Leon Tejwani
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; (P.J.L.); (L.T.)
| | - Abdul Sami
- Department of Biochemistry, University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University, Rawalpindi 46000, Pakistan; (M.K.); (A.S.)
| | - Muhammad Nawaz
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 41346 Gothenburg, Sweden;
| | - Shahid Mehmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan;
| | - Janghoo Lim
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA;
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, USA; (P.J.L.); (L.T.)
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06510, USA
- Correspondence: (J.L.); (G.K.R.); Tel.: +1-203-737-6268 (J.L.); +92-(051)-9062-742 (G.K.R.)
| | - Ghazala Kaukab Raja
- Department of Biochemistry, University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University, Rawalpindi 46000, Pakistan; (M.K.); (A.S.)
- Correspondence: (J.L.); (G.K.R.); Tel.: +1-203-737-6268 (J.L.); +92-(051)-9062-742 (G.K.R.)
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20
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Lin WY, Lin YS, Chan CC, Liu YL, Tsai SJ, Kuo PH. Using Genetic Risk Score Approaches to Infer Whether an Environmental Factor Attenuates or Exacerbates the Adverse Influence of a Candidate Gene. Front Genet 2020; 11:331. [PMID: 32457790 PMCID: PMC7225361 DOI: 10.3389/fgene.2020.00331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/20/2020] [Indexed: 11/18/2022] Open
Abstract
Some candidate genes have been robustly reported to be associated with complex traits, such as the fat mass and obesity-associated (FTO) gene on body mass index (BMI), and the fibroblast growth factor 5 (FGF5) gene on blood pressure levels. It is of interest to know whether an environmental factor (E) can attenuate or exacerbate the adverse influence of a candidate gene. To this end, we here evaluate the performance of “genetic risk score” (GRS) approaches to detect “gene-environment interactions” (G × E). In the first stage, a GRS is calculated according to the genotypes of variants in a candidate gene. In the second stage, we test whether E can significantly modify this GRS effect. This two-stage procedure can not only provide a p-value for a G × E test but also guide inferences on how E modifies the adverse effect of a gene. With systematic simulations, we compared several ways to construct a GRS. If E exacerbates the adverse influence of a gene, GRS formed by the elastic net (ENET) or the least absolute shrinkage and selection operator (LASSO) is recommended. However, the performance of ENET or LASSO will be compromised if E attenuates the adverse influence of a gene, and using the ridge regression (RIDGE) can be more powerful in this situation. Applying RIDGE to 18,424 subjects in the Taiwan Biobank, we showed that performing regular exercise can attenuate the adverse influence of the FTO gene on four obesity measures: BMI (p = 0.0009), body fat percentage (p = 0.0031), waist circumference (p = 0.0052), and hip circumference (p = 0.0001). As another example, we used RIDGE and found the FGF5 gene has a stronger effect on blood pressure in Han Chinese with a higher waist-to-hip ratio [p = 0.0013 for diastolic blood pressure (DBP) and p = 0.0027 for systolic blood pressure (SBP)]. This study provides an evaluation on the GRS approaches, which is important to infer whether E attenuates or exacerbates the adverse influence of a candidate gene.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yu-Shun Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chang-Chuan Chan
- Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan.,Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan.,Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan.,Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan
| | - Po-Hsiu Kuo
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
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