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Chang-Brahim I, Koppensteiner LJ, Beltrame L, Bodner G, Saranti A, Salzinger J, Fanta-Jende P, Sulzbachner C, Bruckmüller F, Trognitz F, Samad-Zamini M, Zechner E, Holzinger A, Molin EM. Reviewing the essential roles of remote phenotyping, GWAS and explainable AI in practical marker-assisted selection for drought-tolerant winter wheat breeding. FRONTIERS IN PLANT SCIENCE 2024; 15:1319938. [PMID: 38699541 PMCID: PMC11064034 DOI: 10.3389/fpls.2024.1319938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/13/2024] [Indexed: 05/05/2024]
Abstract
Marker-assisted selection (MAS) plays a crucial role in crop breeding improving the speed and precision of conventional breeding programmes by quickly and reliably identifying and selecting plants with desired traits. However, the efficacy of MAS depends on several prerequisites, with precise phenotyping being a key aspect of any plant breeding programme. Recent advancements in high-throughput remote phenotyping, facilitated by unmanned aerial vehicles coupled to machine learning, offer a non-destructive and efficient alternative to traditional, time-consuming, and labour-intensive methods. Furthermore, MAS relies on knowledge of marker-trait associations, commonly obtained through genome-wide association studies (GWAS), to understand complex traits such as drought tolerance, including yield components and phenology. However, GWAS has limitations that artificial intelligence (AI) has been shown to partially overcome. Additionally, AI and its explainable variants, which ensure transparency and interpretability, are increasingly being used as recognised problem-solving tools throughout the breeding process. Given these rapid technological advancements, this review provides an overview of state-of-the-art methods and processes underlying each MAS, from phenotyping, genotyping and association analyses to the integration of explainable AI along the entire workflow. In this context, we specifically address the challenges and importance of breeding winter wheat for greater drought tolerance with stable yields, as regional droughts during critical developmental stages pose a threat to winter wheat production. Finally, we explore the transition from scientific progress to practical implementation and discuss ways to bridge the gap between cutting-edge developments and breeders, expediting MAS-based winter wheat breeding for drought tolerance.
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Affiliation(s)
- Ignacio Chang-Brahim
- Unit Bioresources, Center for Health & Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Lorenzo Beltrame
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Gernot Bodner
- Department of Crop Sciences, Institute of Agronomy, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Anna Saranti
- Human-Centered AI Lab, Department of Forest- and Soil Sciences, Institute of Forest Engineering, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jules Salzinger
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Phillipp Fanta-Jende
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Christoph Sulzbachner
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Felix Bruckmüller
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Friederike Trognitz
- Unit Bioresources, Center for Health & Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Elisabeth Zechner
- Verein zur Förderung einer nachhaltigen und regionalen Pflanzenzüchtung, Zwettl, Austria
| | - Andreas Holzinger
- Human-Centered AI Lab, Department of Forest- and Soil Sciences, Institute of Forest Engineering, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Eva M. Molin
- Unit Bioresources, Center for Health & Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
- Human-Centered AI Lab, Department of Forest- and Soil Sciences, Institute of Forest Engineering, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
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2
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V RP, Finnell RH, Ross ME, Alarcón P, Suazo J. Neural tube defects and epigenetics: role of histone post-translational histone modifications. Epigenomics 2024; 16:419-426. [PMID: 38410929 DOI: 10.2217/epi-2023-0357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Neural tube defects (NTDs) are the most common congenital anomalies of the CNS. It is widely appreciated that both genetic and environmental factors contribute to their etiology. The inability to ascribe clear genetic patterns of inheritance to various NTD phenotypes suggests it is possible that epigenetic mechanisms are involved in the etiology of NTDs. In this context, the contribution of DNA methylation as an underlying contributing factor to the etiology of NTDs has been extensively reviewed. Here, an updated accounting of the evidence linking post-translational histone modifications to these birth defects, relying heavily upon studies in humans, and the possible molecular implications inferred from reports based on cellular and animal models, are presented.
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Affiliation(s)
- Rosa Pardo V
- Section of Genetics, Hospital Clínico Universidad de Chile, Dr. Carlos Lorca Tobar #999, Santiago, Chile
- Unit of Neonatology, Hospital Clínico Universidad de Chile, Dr. Carlos Lorca Tobar #999, Santiago, Chile
| | - Richard H Finnell
- Center for Precision Environmental Health, Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - M Elizabeth Ross
- Center for Neurogenetics, Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, 407 East 61st Street, NY, USA
| | - Pablo Alarcón
- Section of Genetics, Hospital Clínico Universidad de Chile, Dr. Carlos Lorca Tobar #999, Santiago, Chile
- Section of Genetics, Hospital Sótero del Río, Avenida Concha y Toro #3459, Santiago, Chile
| | - José Suazo
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Olivos #943, Santiago, Chile
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3
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Ortiz GG, Torres-Mendoza BMG, Ramírez-Jirano J, Marquez-Pedroza J, Hernández-Cruz JJ, Mireles-Ramirez MA, Torres-Sánchez ED. Genetic Basis of Inflammatory Demyelinating Diseases of the Central Nervous System: Multiple Sclerosis and Neuromyelitis Optica Spectrum. Genes (Basel) 2023; 14:1319. [PMID: 37510224 PMCID: PMC10379341 DOI: 10.3390/genes14071319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Demyelinating diseases alter myelin or the coating surrounding most nerve fibers in the central and peripheral nervous systems. The grouping of human central nervous system demyelinating disorders today includes multiple sclerosis (MS) and neuromyelitis optica spectrum disorders (NMOSD) as distinct disease categories. Each disease is caused by a complex combination of genetic and environmental variables, many involving an autoimmune response. Even though these conditions are fundamentally similar, research into genetic factors, their unique clinical manifestations, and lesion pathology has helped with differential diagnosis and disease pathogenesis knowledge. This review aims to synthesize the genetic approaches that explain the differential susceptibility between these diseases, explore the overlapping clinical features, and pathological findings, discuss existing and emerging hypotheses on the etiology of demyelination, and assess recent pathogenicity studies and their implications for human demyelination. This review presents critical information from previous studies on the disease, which asks several questions to understand the gaps in research in this field.
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Affiliation(s)
- Genaro Gabriel Ortiz
- Department of Philosophical and Methodological Disciplines and Service of Molecular Biology in Medicine Hospital, Civil University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
- Department of Neurology, High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44329, Jalisco, Mexico
| | - Blanca M G Torres-Mendoza
- Department of Philosophical and Methodological Disciplines and Service of Molecular Biology in Medicine Hospital, Civil University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
- Neurosciences Division, Western Biomedical Research Center, Mexican Social Security Institute (Instituto Mexicano del Seguro Social, IMSS), Guadalajara 44340, Jalisco, Mexico
| | - Javier Ramírez-Jirano
- Neurosciences Division, Western Biomedical Research Center, Mexican Social Security Institute (Instituto Mexicano del Seguro Social, IMSS), Guadalajara 44340, Jalisco, Mexico
| | - Jazmin Marquez-Pedroza
- Neurosciences Division, Western Biomedical Research Center, Mexican Social Security Institute (Instituto Mexicano del Seguro Social, IMSS), Guadalajara 44340, Jalisco, Mexico
- Coordination of Academic Activities, Western Biomedical Research Center, Mexican Social Security Institute (Instituto Mexicano del Seguro Social, IMSS), Guadalajara 44340, Jalisco, Mexico
| | - José J Hernández-Cruz
- Department of Neurology, High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44329, Jalisco, Mexico
| | - Mario A Mireles-Ramirez
- Department of Neurology, High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44329, Jalisco, Mexico
| | - Erandis D Torres-Sánchez
- Department of Medical and Life Sciences, University Center of la Cienega, University of Guadalajara, Ocotlan 47820, Jalisco, Mexico
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García-Sancha N, Corchado-Cobos R, Gómez-Vecino A, Jiménez-Navas A, Pérez-Baena MJ, Blanco-Gómez A, Holgado-Madruga M, Mao JH, Cañueto J, Castillo-Lluva S, Mendiburu-Eliçabe M, Pérez-Losada J. Evolutionary Origins of Metabolic Reprogramming in Cancer. Int J Mol Sci 2022; 23:ijms232012063. [PMID: 36292921 PMCID: PMC9603151 DOI: 10.3390/ijms232012063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/23/2022] Open
Abstract
Metabolic changes that facilitate tumor growth are one of the hallmarks of cancer. These changes are not specific to tumors but also take place during the physiological growth of tissues. Indeed, the cellular and tissue mechanisms present in the tumor have their physiological counterpart in the repair of tissue lesions and wound healing. These molecular mechanisms have been acquired during metazoan evolution, first to eliminate the infection of the tissue injury, then to enter an effective regenerative phase. Cancer itself could be considered a phenomenon of antagonistic pleiotropy of the genes involved in effective tissue repair. Cancer and tissue repair are complex traits that share many intermediate phenotypes at the molecular, cellular, and tissue levels, and all of these are integrated within a Systems Biology structure. Complex traits are influenced by a multitude of common genes, each with a weak effect. This polygenic component of complex traits is mainly unknown and so makes up part of the missing heritability. Here, we try to integrate these different perspectives from the point of view of the metabolic changes observed in cancer.
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Affiliation(s)
- Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Aurora Gómez-Vecino
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Alejandro Jiménez-Navas
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Manuel Jesús Pérez-Baena
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Marina Holgado-Madruga
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, 37007 Salamanca, Spain
- Instituto de Neurociencias de Castilla y León (INCyL), 37007 Salamanca, Spain
| | - Jian-Hua Mao
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Javier Cañueto
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Departamento de Dermatología, Hospital Universitario de Salamanca, Paseo de San Vicente 58-182, 37007 Salamanca, Spain
| | - Sonia Castillo-Lluva
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), 28040 Madrid, Spain
| | - Marina Mendiburu-Eliçabe
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (M.M.-E.); (J.P.-L.)
| | - Jesús Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, 37007 Salamanca, Spain
- Instituto de Investigación Biosanitaria de Salamanca (IBSAL), 37007 Salamanca, Spain
- Correspondence: (M.M.-E.); (J.P.-L.)
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Pang H, Lin J, Luo S, Huang G, Li X, Xie Z, Zhou Z. The missing heritability in type 1 diabetes. Diabetes Obes Metab 2022; 24:1901-1911. [PMID: 35603907 PMCID: PMC9545639 DOI: 10.1111/dom.14777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022]
Abstract
Type 1 diabetes (T1D) is a complex autoimmune disease characterized by an absolute deficiency of insulin. It affects more than 20 million people worldwide and imposes an enormous financial burden on patients. The underlying pathogenic mechanisms of T1D are still obscure, but it is widely accepted that both genetics and the environment play an important role in its onset and development. Previous studies have identified more than 60 susceptible loci associated with T1D, explaining approximately 80%-85% of the heritability. However, most identified variants confer only small increases in risk, which restricts their potential clinical application. In addition, there is still a so-called 'missing heritability' phenomenon. While the gap between known heritability and true heritability in T1D is small compared with that in other complex traits and disorders, further elucidation of T1D genetics has the potential to bring novel insights into its aetiology and provide new therapeutic targets. Many hypotheses have been proposed to explain the missing heritability, including variants remaining to be found (variants with small effect sizes, rare variants and structural variants) and interactions (gene-gene and gene-environment interactions; e.g. epigenetic effects). In the following review, we introduce the possible sources of missing heritability and discuss the existing related knowledge in the context of T1D.
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Affiliation(s)
- Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jian Lin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
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6
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Nada D, Julien C, Papillon-Cavanagh S, Majewski J, Elbakry M, Elremaly W, Samuels ME, Moreau A. Identification of FAT3 as a new candidate gene for adolescent idiopathic scoliosis. Sci Rep 2022; 12:12298. [PMID: 35853984 PMCID: PMC9296578 DOI: 10.1038/s41598-022-16620-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
In an effort to identify rare alleles associated with adolescent idiopathic scoliosis (AIS) whole-exome sequencing was performed on a discovery cohort of 73 unrelated patients and 70 age-and sex matched controls, all of French-Canadian ancestry. A collapsing gene burden test was performed to analyze rare protein-altering variants using case–control statistics. Since no single gene achieved statistical significance, targeted exon sequencing was performed for 24 genes with the smallest p values, in an independent replication cohort of unrelated severely affected females with AIS and sex-matched controls (N = 96 each). An excess of rare, potentially protein-altering variants was noted in one particular gene, FAT3, although it did not achieve statistical significance. Independently, we sequenced the exomes of all members of a rare multiplex family of three affected sisters and unaffected parents. All three sisters were compound heterozygous for two rare protein-altering variants in FAT3. The parents were single heterozygotes for each variant. The two variants in the family were also present in our discovery cohort. A second validation step was done, using another independent replication cohort of 258 unrelated AIS patients having reach their skeletal maturity and 143 healthy controls to genotype nine FAT3 gene variants, including the two variants previously identified in the multiplex family: p.L517S (rs139595720) and p.L4544F (rs187159256). Interestingly, two FAT3 variants, rs139595720 (genotype A/G) and rs80293525 (genotype C/T), were enriched in severe scoliosis cases (4.5% and 2.7% respectively) compared to milder cases (1.4% and 0.7%) and healthy controls (1.6% and 0.8%). Our results implicate FAT3 as a new candidate gene in the etiology of AIS.
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Affiliation(s)
- Dina Nada
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Pharmacology and Biochemistry Department, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cédric Julien
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Injury Repair Recovery Program, McGill University Health Center Research Institute, Montreal, QC, Canada
| | | | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Mohamed Elbakry
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Wesam Elremaly
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Mark E Samuels
- Sainte-Justine University Hospital Research Center, Montreal, QC, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Alain Moreau
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada. .,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada. .,Department of Stomatology, Faculty of Dentistry, Université de Montréal, Montreal, QC, Canada.
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7
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Zaidi PH, Shahid M, Seetharam K, Vinayan MT. Genomic Regions Associated With Salinity Stress Tolerance in Tropical Maize ( Zea Mays L.). FRONTIERS IN PLANT SCIENCE 2022; 13:869270. [PMID: 35712555 PMCID: PMC9194767 DOI: 10.3389/fpls.2022.869270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Being a widely cultivated crop globally under diverse climatic conditions and soil types, maize is often exposed to an array of biotic and abiotic stresses. Soil salinity is one of the challenges for maize cultivation in many parts of lowland tropics that significantly affects crop growth and reduces economic yields. Breeding strategies integrated with molecular approach might accelerate the process of identifying and developing salinity-tolerant maize cultivars. In this study, an association mapping panel consisting of 305 diverse maize inbred lines was phenotyped in a managed salinity stress phenotyping facility at International Center for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates (UAE). Wide genotypic variability was observed in the panel under salinity stress for key phenotypic traits viz., grain yield, days to anthesis, anthesis-silking interval, plant height, cob length, cob girth, and kernel number. The panel was genotyped following the genome-based sequencing approach to generate 955,690 SNPs. Total SNPs were filtered to 213,043 at a call rate of 0.85 and minor allele frequency of 0.05 for association analysis. A total of 259 highly significant (P ≤ 1 × 10-5) marker-trait associations (MTAs) were identified for seven phenotypic traits. The phenotypic variance for MTAs ranged between 5.2 and 9%. A total of 64 associations were found in 19 unique putative gene expression regions. Among them, 12 associations were found in gene models with stress-related biological functions.
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Affiliation(s)
- Pervez H. Zaidi
- Asia Regional Maize Program, International Maize & Wheat Improvement Center (CIMMYT), Hyderabad, India
| | - Mohammed Shahid
- International Centre for Biosaline Agriculture (ICBA), Dubai, United Arab Emirates
| | - Kaliyamoorthy Seetharam
- Asia Regional Maize Program, International Maize & Wheat Improvement Center (CIMMYT), Hyderabad, India
| | - Madhumal Thayil Vinayan
- Asia Regional Maize Program, International Maize & Wheat Improvement Center (CIMMYT), Hyderabad, India
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Kim BH, Choi YH, Yang JJ, Kim S, Nho K, Lee JM. Identification of Novel Genes Associated with Cortical Thickness in Alzheimer’s Disease: Systems Biology Approach to Neuroimaging Endophenotype. J Alzheimers Dis 2020; 75:531-545. [DOI: 10.3233/jad-191175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Bo-Hyun Kim
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
| | - Yong-Ho Choi
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
| | - Jin-Ju Yang
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
| | - SangYun Kim
- Department of Neurology, Seoul National University College of Medicine and Clinical Neuroscience Center of Seoul National University Bundang Hospital, Seongnam, Korea
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jong-Min Lee
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
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9
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Determining population stratification and subgroup effects in association studies of rare genetic variants for nicotine dependence. Psychiatr Genet 2020; 29:111-119. [PMID: 31033776 PMCID: PMC6636808 DOI: 10.1097/ypg.0000000000000227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Supplemental Digital Content is available in the text. Background Rare variants (minor allele frequency < 1% or 5 %) can help researchers to deal with the confounding issue of ‘missing heritability’ and have a proven role in dissecting the etiology for human diseases and complex traits. Methods We extended the combined multivariate and collapsing (CMC) and weighted sum statistic (WSS) methods and accounted for the effects of population stratification and subgroup effects using stratified analyses by the principal component analysis, named here as ‘str-CMC’ and ‘str-WSS’. To evaluate the validity of the extended methods, we analyzed the Genetic Architecture of Smoking and Smoking Cessation database, which includes African Americans and European Americans genotyped on Illumina Human Omni2.5, and we compared the results with those obtained with the sequence kernel association test (SKAT) and its modification, SKAT-O that included population stratification and subgroup effect as covariates. We utilized the Cochran–Mantel–Haenszel test to check for possible differences in single nucleotide polymorphism allele frequency between subgroups within a gene. We aimed to detect rare variants and considered population stratification and subgroup effects in the genomic region containing 39 acetylcholine receptor-related genes. Results The Cochran–Mantel–Haenszel test as applied to GABRG2 (P = 0.001) was significant. However, GABRG2 was detected both by str-CMC (P= 8.04E-06) and str-WSS (P= 0.046) in African Americans but not by SKAT or SKAT-O. Conclusions Our results imply that if associated rare variants are only specific to a subgroup, a stratified analysis might be a better approach than a combined analysis.
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Abstract
OBJECTIVE The Developmental Origins of Disease hypothesis has spurred increased interest in how prenatal exposures affect lifelong health, while mechanisms such as epigenetics may explain the multigenerational influences on health. Such factors are not well captured within conventional epidemiologic study designs. We explored the feasibility of collecting information on the offspring and grand-offspring of participants in a long-running study. DESIGN The Bogalusa Heart Study is a study, begun in 1973, of life-course cardiovascular health in a semirural population (65% white and 35% black). MAIN MEASURES Female participants who had previously provided information on their pregnancies were contacted to obtain contact information for their daughters aged 12 and older. Daughters were then contacted to obtain reproductive histories, and invited for a clinic or lab visit to measure cardiovascular risk factors. RESULTS Two hundred seventy-four daughters of 208 mothers were recruited; 81% (223) had a full clinic visit and 19% (51) a phone interview only. Forty-five percent of the daughters were black, and 55% white. Mean and median age at interview was 27, with 15% under the age of 18. The strongest predictors of participation were black race, recent maternal participation in the parent study, and living in or near Bogalusa. Simple correlations for cardiovascular risk factors across generations were between r = 0.19 (systolic blood pressure) and r = 0.39 (BMI, LDL). CONCLUSION It is feasible to contact the children of study participants even when participants are adults, and initial information on the grandchildren can also be determined in this manner.
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Torres JB. Race, Rare Genetic Variants, and the Science of Human Difference in the Post‐Genomic Age. TRANSFORMING ANTHROPOLOGY 2019. [DOI: 10.1111/traa.12144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jada Benn Torres
- Genetic Anthropology and Biocultural Studies Laboratory Department of Anthropology Vanderbilt University Nashville TN 37235
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12
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Trifonova EA, Swarovskaya MG, Ganzha OA, Voronkova OV, Gabidulina TV, Stepanov VA. The interaction effect of angiogenesis and endothelial dysfunction-related gene variants increases the susceptibility of recurrent pregnancy loss. J Assist Reprod Genet 2019; 36:717-726. [PMID: 30680517 DOI: 10.1007/s10815-019-01403-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/09/2019] [Indexed: 01/08/2023] Open
Abstract
PURPOSE The role of genetic polymorphisms in the pathogenesis of recurrent pregnancy loss (RPL) has been studied intensively. Complex diseases, including miscarriage, are believed to have a polygenic basis, and gene-gene interactions can play a significant role in the etiology of the disease. This study was conducted to investigate the association of gene-gene interactions with angiogenesis, endothelial dysfunction-related gene polymorphisms, and RPL. METHODS A case-control study was conducted with 253 unrelated RPL patients with 2 or more spontaneous pregnancy losses and 339 healthy women with no history of pregnancy complications. Genotyping of single-nucleotide polymorphisms (SNPs) was performed using real-time polymerase chain reaction (real-time PCR), restriction fragment length polymorphism (RFLP), or allele-specific polymerase chain reaction methods. RESULTS The genotypes 677TT of the MTHFR gene, 936TT, 936CT, and 634CC, 634GC of the VEGF gene, and allele 894T of the NOS3 gene were associated with a predisposition to RPL in the Russian population. A significant role of additive and epistatic effects in the gene-gene interactions of the SNPs of SERPINE-1, ACE, NOS3, MTHFR, and VEGF genes in RPL was demonstrated. CONCLUSIONS The results showed that gene-gene interactions are important for RPL susceptibility. Additionally, analysis of the genotype combinations of several allelic variants provides more information on RPL risk than analysis of independent polymorphic markers.
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Affiliation(s)
- E A Trifonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia.,Siberian State Medical University, Tomsk, Russia
| | - M G Swarovskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia. .,Siberian State Medical University, Tomsk, Russia.
| | - O A Ganzha
- Siberian State Medical University, Tomsk, Russia
| | | | | | - V A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
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13
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Awany D, Allali I, Dalvie S, Hemmings S, Mwaikono KS, Thomford NE, Gomez A, Mulder N, Chimusa ER. Host and Microbiome Genome-Wide Association Studies: Current State and Challenges. Front Genet 2019; 9:637. [PMID: 30723493 PMCID: PMC6349833 DOI: 10.3389/fgene.2018.00637] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/27/2018] [Indexed: 12/20/2022] Open
Abstract
The involvement of the microbiome in health and disease is well established. Microbiome genome-wide association studies (mGWAS) are used to elucidate the interaction of host genetic variation with the microbiome. The emergence of this relatively new field has been facilitated by the advent of next generation sequencing technologies that enable the investigation of the complex interaction between host genetics and microbial communities. In this paper, we review recent studies investigating host-microbiome interactions using mGWAS. Additionally, we highlight the marked disparity in the sampling population of mGWAS carried out to date and draw attention to the critical need for inclusion of diverse populations.
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Affiliation(s)
- Denis Awany
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shareefa Dalvie
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Sian Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kilaza S Mwaikono
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nicholas E Thomford
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Andres Gomez
- Department of Animal Science, University of Minnesota-Twin Cities, St. Paul, MN, United States
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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14
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Evolving Ecosystems: Inheritance and Selection in the Light of the Microbiome. Arch Med Res 2017; 48:780-789. [DOI: 10.1016/j.arcmed.2018.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 01/12/2018] [Indexed: 02/06/2023]
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15
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Sharafeldin N, Slattery ML, Liu Q, Franco-Villalobos C, Caan BJ, Potter JD, Yasui Y. Multiple Gene-Environment Interactions on the Angiogenesis Gene-Pathway Impact Rectal Cancer Risk and Survival. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14101146. [PMID: 28956832 PMCID: PMC5664647 DOI: 10.3390/ijerph14101146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/06/2017] [Accepted: 09/23/2017] [Indexed: 12/25/2022]
Abstract
Characterization of gene-environment interactions (GEIs) in cancer is limited. We aimed at identifying GEIs in rectal cancer focusing on a relevant biologic process involving the angiogenesis pathway and relevant environmental exposures: cigarette smoking, alcohol consumption, and animal protein intake. We analyzed data from 747 rectal cancer cases and 956 controls from the Diet, Activity and Lifestyle as a Risk Factor for Rectal Cancer study. We applied a 3-step analysis approach: first, we searched for interactions among single nucleotide polymorphisms on the pathway genes; second, we searched for interactions among the genes, both steps using Logic regression; third, we examined the GEIs significant at the 5% level using logistic regression for cancer risk and Cox proportional hazards models for survival. Permutation-based test was used for multiple testing adjustment. We identified 8 significant GEIs associated with risk among 6 genes adjusting for multiple testing: TNF (OR = 1.85, 95% CI: 1.10, 3.11), TLR4 (OR = 2.34, 95% CI: 1.38, 3.98), and EGR2 (OR = 2.23, 95% CI: 1.04, 4.78) with smoking; IGF1R (OR = 1.69, 95% CI: 1.04, 2.72), TLR4 (OR = 2.10, 95% CI: 1.22, 3.60) and EGR2 (OR = 2.12, 95% CI: 1.01, 4.46) with alcohol; and PDGFB (OR = 1.75, 95% CI: 1.04, 2.92) and MMP1 (OR = 2.44, 95% CI: 1.24, 4.81) with protein. Five GEIs were associated with survival at the 5% significance level but not after multiple testing adjustment: CXCR1 (HR = 2.06, 95% CI: 1.13, 3.75) with smoking; and KDR (HR = 4.36, 95% CI: 1.62, 11.73), TLR2 (HR = 9.06, 95% CI: 1.14, 72.11), EGR2 (HR = 2.45, 95% CI: 1.42, 4.22), and EGFR (HR = 6.33, 95% CI: 1.95, 20.54) with protein. GEIs between angiogenesis genes and smoking, alcohol, and animal protein impact rectal cancer risk. Our results support the importance of considering the biologic hypothesis to characterize GEIs associated with cancer outcomes.
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Affiliation(s)
- Noha Sharafeldin
- School of Public Health, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA.
| | - Qi Liu
- School of Public Health, University of Alberta, Edmonton, AB T6G 2R3, Canada.
| | | | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, CA 94612, USA.
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA 98195, USA.
- Centre for Public Health Research, Massey University, P.O. Box 756, Wellington 6140, New Zealand.
| | - Yutaka Yasui
- School of Public Health, University of Alberta, Edmonton, AB T6G 2R3, Canada.
- Department of Epidemiology & Cancer Control, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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16
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Mayhew AJ, Meyre D. Assessing the Heritability of Complex Traits in Humans: Methodological Challenges and Opportunities. Curr Genomics 2017; 18:332-340. [PMID: 29081689 PMCID: PMC5635617 DOI: 10.2174/1389202918666170307161450] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/29/2016] [Accepted: 01/29/2017] [Indexed: 02/08/2023] Open
Abstract
The goal of this review article is to provide a conceptual based summary of how heritability estimates for complex traits such as obesity are determined and to explore the future directions of research in the heritability field. The target audience are researchers who use heritability data rather than those conducting heritability studies. The article provides an introduction to key concepts critical to understanding heritability studies including: i) definitions of heritability: broad sense versus narrow sense heritability; ii) how data for heritability studies are collected: twin, adoption, family and population-based studies; and iii) analytical techniques: path analysis, structural equations and mixed or regressive models of complex segregation analysis. For each section, a discussion of how the different definitions and methodologies influence heritability estimates is provided. The general limitations of heritability studies are discussed including the issue of “missing heritability” in which heritability estimates are significantly higher than the variance explained by known genetic variants. Potential causes of missing heritability include restriction of many genetic association studies to single nucleotide polymorphisms, gene by gene interactions, epigenetics, and gene by environment interactions. Innovative strategies of accounting for missing heritability including modeling techniques and improved software are discussed.
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Affiliation(s)
- Alexandra J Mayhew
- Department of Health Research Methods, McMaster University, Evidence and Impact, Hamilton, Ontario, Canada
| | - David Meyre
- Department of Health Research Methods, McMaster University, Evidence and Impact, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
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17
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Sandoval-Motta S, Aldana M, Martínez-Romero E, Frank A. The Human Microbiome and the Missing Heritability Problem. Front Genet 2017; 8:80. [PMID: 28659968 PMCID: PMC5468393 DOI: 10.3389/fgene.2017.00080] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 05/29/2017] [Indexed: 12/13/2022] Open
Abstract
The "missing heritability" problem states that genetic variants in Genome-Wide Association Studies (GWAS) cannot completely explain the heritability of complex traits. Traditionally, the heritability of a phenotype is measured through familial studies using twins, siblings and other close relatives, making assumptions on the genetic similarities between them. When this heritability is compared to the one obtained through GWAS for the same traits, a substantial gap between both measurements arise with genome wide studies reporting significantly smaller values. Several mechanisms for this "missing heritability" have been proposed, such as epigenetics, epistasis, and sequencing depth. However, none of them are able to fully account for this gap in heritability. In this paper we provide evidence that suggests that in order for the phenotypic heritability of human traits to be broadly understood and accounted for, the compositional and functional diversity of the human microbiome must be taken into account. This hypothesis is based on several observations: (A) The composition of the human microbiome is associated with many important traits, including obesity, cancer, and neurological disorders. (B) Our microbiome encodes a second genome with nearly a 100 times more genes than the human genome, and this second genome may act as a rich source of genetic variation and phenotypic plasticity. (C) Human genotypes interact with the composition and structure of our microbiome, but cannot by themselves explain microbial variation. (D) Microbial genetic composition can be strongly influenced by the host's behavior, its environment or by vertical and horizontal transmissions from other hosts. Therefore, genetic similarities assumed in familial studies may cause overestimations of heritability values. We also propose a method that allows the compositional and functional diversity of our microbiome to be incorporated to genome wide association studies.
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Affiliation(s)
- Santiago Sandoval-Motta
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico City, Mexico
| | - Maximino Aldana
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico City, Mexico.,Instituto de Ciencias Físicas, Universidad Nacional Autónoma de MéxicoMorelos, Mexico
| | | | - Alejandro Frank
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de MéxicoMexico City, Mexico.,Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de MéxicoMexico City, Mexico.,Member of El Colegio NacionalMexico City, Mexico
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18
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Liu X, Wang H, Cui Y. Statistical Identification of Gene-gene Interactions Triggered By Nonlinear Environmental Modulation. Curr Genomics 2016; 17:388-395. [PMID: 28479867 PMCID: PMC5320540 DOI: 10.2174/1389202917666160726150417] [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: 02/16/2015] [Revised: 09/26/2015] [Accepted: 10/30/2015] [Indexed: 11/22/2022] Open
Abstract
Complex diseases are often caused by the function of multiple genes, gene-gene
(G×G) interactions as well as gene-environment (G×E) interactions.
G×G and G×E interactions are ubiquitous in nature. Empirical evidences have
shown that the effect of G×G interaction on disease risk could be largely modified
by environmental changes. Such a G×G×E triple interaction could be a
potential contributing factor to phenotypic plasticity. Although the role of environmental
factors moderating genetic influences on disease risk has been broadly recognized, no
statistical method has been developed to rigorously assess how environmental changes
modify G×G interactions to affect disease risk. To address this issue, we developed
a G×G×E triple interaction model in this work. We modeled the environmental
modification effect via a varying-coefficient model where the structure of the varying
effect is determined by data. Thus the model has the flexibility to assess nonlinear
environmental moderation effect on G×G interaction. Simulation and real data
analysis were conducted to show the utility of the method. Our approach provides a
quantitative framework to assess triple interactions hypothesized in literature.
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Affiliation(s)
- Xu Liu
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824,USA
| | - Honglang Wang
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824,USA
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, MI 48824,USA.,Division of Health Statistics, School of Public Health, Shanxi Medical University, Shanxi, 030001,P.R. China
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19
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Yashin AI, Arbeev KG, Wu D, Arbeeva L, Kulminski A, Kulminskaya I, Akushevich I, Ukraintseva SV. How Genes Modulate Patterns of Aging-Related Changes on the Way to 100: Biodemographic Models and Methods in Genetic Analyses of Longitudinal Data. NORTH AMERICAN ACTUARIAL JOURNAL : NAAJ 2016; 20:201-232. [PMID: 27773987 PMCID: PMC5070546 DOI: 10.1080/10920277.2016.1178588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND AND OBJECTIVE To clarify mechanisms of genetic regulation of human aging and longevity traits, a number of genome-wide association studies (GWAS) of these traits have been performed. However, the results of these analyses did not meet expectations of the researchers. Most detected genetic associations have not reached a genome-wide level of statistical significance, and suffered from the lack of replication in the studies of independent populations. The reasons for slow progress in this research area include low efficiency of statistical methods used in data analyses, genetic heterogeneity of aging and longevity related traits, possibility of pleiotropic (e.g., age dependent) effects of genetic variants on such traits, underestimation of the effects of (i) mortality selection in genetically heterogeneous cohorts, (ii) external factors and differences in genetic backgrounds of individuals in the populations under study, the weakness of conceptual biological framework that does not fully account for above mentioned factors. One more limitation of conducted studies is that they did not fully realize the potential of longitudinal data that allow for evaluating how genetic influences on life span are mediated by physiological variables and other biomarkers during the life course. The objective of this paper is to address these issues. DATA AND METHODS We performed GWAS of human life span using different subsets of data from the original Framingham Heart Study cohort corresponding to different quality control (QC) procedures and used one subset of selected genetic variants for further analyses. We used simulation study to show that approach to combining data improves the quality of GWAS. We used FHS longitudinal data to compare average age trajectories of physiological variables in carriers and non-carriers of selected genetic variants. We used stochastic process model of human mortality and aging to investigate genetic influence on hidden biomarkers of aging and on dynamic interaction between aging and longevity. We investigated properties of genes related to selected variants and their roles in signaling and metabolic pathways. RESULTS We showed that the use of different QC procedures results in different sets of genetic variants associated with life span. We selected 24 genetic variants negatively associated with life span. We showed that the joint analyses of genetic data at the time of bio-specimen collection and follow up data substantially improved significance of associations of selected 24 SNPs with life span. We also showed that aging related changes in physiological variables and in hidden biomarkers of aging differ for the groups of carriers and non-carriers of selected variants. CONCLUSIONS . The results of these analyses demonstrated benefits of using biodemographic models and methods in genetic association studies of these traits. Our findings showed that the absence of a large number of genetic variants with deleterious effects may make substantial contribution to exceptional longevity. These effects are dynamically mediated by a number of physiological variables and hidden biomarkers of aging. The results of these research demonstrated benefits of using integrative statistical models of mortality risks in genetic studies of human aging and longevity.
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Affiliation(s)
- Anatoliy I. Yashin
- Professor, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102E, Durham, NC 27705, USA. Tel.: (+1) 919-668-2713; Fax: (+1) 919-684-3861
| | - Konstantin G. Arbeev
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102F, Durham, NC 27705, USA. Tel.: (+1) 919-668-2707; Fax: (+1) 919-684-3861
| | - Deqing Wu
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A104, Durham, NC 27705, USA. Tel.: (+1) 919-684-6126; Fax: (+1) 919-684-3861
| | - Liubov Arbeeva
- Statistician, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102G, Durham, NC 27705, USA. Tel.: (+1) 919-613-0715; Fax: (+1) 919-684-3861
| | - Alexander Kulminski
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A106, Durham, NC 27705, USA. Tel.: (+1) 919-684-4962; Fax: (+1) 919-684-3861
| | - Irina Kulminskaya
- Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102D, Durham, NC 27705, USA. Tel.: (+1) 919-681-8232; Fax: (+1) 919-684-3861
| | - Igor Akushevich
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A107, Durham, NC 27705, USA. Tel.: (+1) 919-668-2715; Fax: (+1) 919-684-3861
| | - Svetlana V. Ukraintseva
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A105, Durham, NC 27705, USA. Tel.: (+1) 919-668-2712; Fax: (+1) 919-684-3861
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20
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Blanco-Gómez A, Castillo-Lluva S, Del Mar Sáez-Freire M, Hontecillas-Prieto L, Mao JH, Castellanos-Martín A, Pérez-Losada J. Missing heritability of complex diseases: Enlightenment by genetic variants from intermediate phenotypes. Bioessays 2016; 38:664-73. [PMID: 27241833 DOI: 10.1002/bies.201600084] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Diseases of complex origin have a component of quantitative genetics that contributes to their susceptibility and phenotypic variability. However, after several studies, a major part of the genetic component of complex phenotypes has still not been found, a situation known as "missing heritability." Although there have been many hypotheses put forward to explain the reasons for the missing heritability, its definitive causes remain unknown. Complex diseases are caused by multiple intermediate phenotypes involved in their pathogenesis and, very often, each one of these intermediate phenotypes also has a component of quantitative inheritance. Here we propose that at least part of the missing heritability can be explained by the genetic component of intermediate phenotypes that is not detectable at the level of the main complex trait. At the same time, the identification of the genetic component of intermediate phenotypes provides an opportunity to identify part of the missing heritability of complex diseases.
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Affiliation(s)
- Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca/CSIC, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Sonia Castillo-Lluva
- Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca/CSIC, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - María Del Mar Sáez-Freire
- Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca/CSIC, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Lourdes Hontecillas-Prieto
- Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca/CSIC, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Jian Hua Mao
- Life Sciences Division, Lawrence Berkeley National Laboratory (LBNL), University of California, Berkeley, CA, USA
| | - Andrés Castellanos-Martín
- Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca/CSIC, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Jesus Pérez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (CIC-IBMCC), Universidad de Salamanca/CSIC, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
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21
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Visvikis-Siest S, Stathopoulou MG. Beyond genome-wide association studies: identifying variants using -omics approaches. Per Med 2015; 12:529-531. [PMID: 29750611 DOI: 10.2217/pme.15.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Sophie Visvikis-Siest
- INSERM UMR U1122; IGE-PCV "Interactions Gène-Environnement en Physiopathologie CardioVasculaire", Université de Lorraine, Faculté de Pharmacie, 30 Rue Lionnois, 54000 Nancy, France
| | - Maria G Stathopoulou
- INSERM UMR U1122; IGE-PCV "Interactions Gène-Environnement en Physiopathologie CardioVasculaire", Université de Lorraine, Faculté de Pharmacie, 30 Rue Lionnois, 54000 Nancy, France
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22
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Grieshammer U, Shepard KA. Proceedings: consideration of genetics in the design of induced pluripotent stem cell-based models of complex disease. Stem Cells Transl Med 2015; 3:1253-8. [PMID: 25359995 DOI: 10.5966/sctm.2014-0191] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The goal of exploiting induced pluripotent stem cell (iPSC) technology for the discovery of new mechanisms and treatments of disease is being pursued by many laboratories, and analyses of rare monogenic diseases have already provided ample evidence that this approach has merit. Considering the enormous medical burden imposed by common chronic diseases, successful implementation of iPSC-based models has the potential for major impact on these diseases as well. Since common diseases represent complex traits with varying genetic and environmental contributions to disease manifestation, the use of iPSC technology poses unique challenges. In this perspective, we will consider how the genetics of complex disease and mechanisms underlying phenotypic variation affect experimental design.
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Affiliation(s)
- Uta Grieshammer
- California Institute for Regenerative Medicine, 210 King Street, San Francisco, CA 94107 USA
| | - Kelly A Shepard
- California Institute for Regenerative Medicine, 210 King Street, San Francisco, CA 94107 USA
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23
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Heritabilities, proportions of heritabilities explained by GWAS findings, and implications of cross-phenotype effects on PR interval. Hum Genet 2015; 134:1211-9. [PMID: 26385552 PMCID: PMC4628620 DOI: 10.1007/s00439-015-1595-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/21/2015] [Indexed: 12/04/2022]
Abstract
Electrocardiogram (ECG) measurements are a powerful tool for evaluating cardiac function and are widely used for the diagnosis and prediction of a variety of conditions, including myocardial infarction, cardiac arrhythmias, and sudden cardiac death. Recently, genome-wide association studies (GWASs) identified a large number of genes related to ECG parameter variability, specifically for the QT, QRS, and PR intervals. The aims of this study were to establish the heritability of ECG traits, including indices of left ventricular hypertrophy, and to directly assess the proportion of those heritabilities explained by GWAS variants. These analyses were conducted in a large, Dutch family-based cohort study, the Erasmus Rucphen Family study using variance component methods implemented in the SOLAR (Sequential Oligogenic Linkage Analysis Routines) software package. Heritability estimates ranged from 34 % for QRS and Cornell voltage product to 49 % for 12-lead sum. Trait-specific GWAS findings for each trait explained a fraction of their heritability (17 % for QRS, 4 % for QT, 2 % for PR, 3 % for Sokolow–Lyon index, and 4 % for 12-lead sum). The inclusion of all ECG-associated single nucleotide polymorphisms explained an additional 6 % of the heritability of PR. In conclusion, this study shows that, although GWAS explain a portion of ECG trait variability, a large amount of heritability remains to be explained. In addition, larger GWAS for PR are likely to detect loci already identified, particularly those observed for QRS and 12-lead sum.
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Abstract
Genome-wide association studies of complex physiological traits and diseases consistently found that associated genetic factors, such as allelic polymorphisms or DNA mutations, only explained a minority of the expected heritable fraction. This discrepancy is known as “missing heritability”, and its underlying factors and molecular mechanisms are not established. Epigenetic programs may account for a significant fraction of the “missing heritability.” Epigenetic modifications, such as DNA methylation and chromatin assembly states, reflect the high plasticity of the genome and contribute to stably alter gene expression without modifying genomic DNA sequences. Consistent components of complex traits, such as those linked to human stature/height, fertility, and food metabolism or to hereditary defects, have been shown to respond to environmental or nutritional condition and to be epigenetically inherited. The knowledge acquired from epigenetic genome reprogramming during development, stem cell differentiation/de-differentiation, and model organisms is today shedding light on the mechanisms of (a) mitotic inheritance of epigenetic traits from cell to cell, (b) meiotic epigenetic inheritance from generation to generation, and (c) true transgenerational inheritance. Such mechanisms have been shown to include incomplete erasure of DNA methylation, parental effects, transmission of distinct RNA types (mRNA, non-coding RNA, miRNA, siRNA, piRNA), and persistence of subsets of histone marks.
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Affiliation(s)
- Marco Trerotola
- Unit of Cancer Pathology, CeSI, Foundation University 'G. d'Annunzio', Chieti, Italy.
| | - Valeria Relli
- Unit of Cancer Pathology, CeSI, Foundation University 'G. d'Annunzio', Chieti, Italy.
| | - Pasquale Simeone
- Unit of Cancer Pathology, CeSI, Foundation University 'G. d'Annunzio', Chieti, Italy.
| | - Saverio Alberti
- Unit of Cancer Pathology, CeSI, Foundation University 'G. d'Annunzio', Chieti, Italy. .,Department of Neuroscience, Imaging and Clinical Sciences, Unit of Physiology and Physiopathology, 'G. d'Annunzio' University, Chieti, Italy.
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Stallmeyer B, Schulze-Bahr E. Cardiovascular disease and sudden cardiac death: between genetics and genomics. Eur Heart J 2015; 36:1643-5. [DOI: 10.1093/eurheartj/ehv173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Apalasamy YD, Mohamed Z. Obesity and genomics: role of technology in unraveling the complex genetic architecture of obesity. Hum Genet 2015; 134:361-74. [PMID: 25687726 DOI: 10.1007/s00439-015-1533-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/02/2015] [Indexed: 01/15/2023]
Abstract
Obesity is a complex and multifactorial disease that occurs as a result of the interaction between "obesogenic" environmental factors and genetic components. Although the genetic component of obesity is clear from the heritability studies, the genetic basis remains largely elusive. Successes have been achieved in identifying the causal genes for monogenic obesity using animal models and linkage studies, but these approaches are not fruitful for polygenic obesity. The developments of genome-wide association approach have brought breakthrough discovery of genetic variants for polygenic obesity where tens of new susceptibility loci were identified. However, the common SNPs only accounted for a proportion of heritability. The arrival of NGS technologies and completion of 1000 Genomes Project have brought other new methods to dissect the genetic architecture of obesity, for example, the use of exome genotyping arrays and deep sequencing of candidate loci identified from GWAS to study rare variants. In this review, we summarize and discuss the developments of these genetic approaches in human obesity.
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Affiliation(s)
- Yamunah Devi Apalasamy
- Department of Pharmacology, Pharmacogenomics Laboratory, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia,
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Alexander ES, Martin LJ, Collins MH, Kottyan LC, Sucharew H, He H, Mukkada VA, Succop PA, Abonia JP, Foote H, Eby MD, Grotjan TM, Greenler AJ, Dellon ES, Demain JG, Furuta GT, Gurian LE, Harley JB, Hopp RJ, Kagalwalla A, Kaul A, Nadeau KC, Noel RJ, Putnam PE, von Tiehl KF, Rothenberg ME. Twin and family studies reveal strong environmental and weaker genetic cues explaining heritability of eosinophilic esophagitis. J Allergy Clin Immunol 2014; 134:1084-1092.e1. [PMID: 25258143 PMCID: PMC4253562 DOI: 10.1016/j.jaci.2014.07.021] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/27/2014] [Accepted: 07/03/2014] [Indexed: 02/08/2023]
Abstract
BACKGROUND Eosinophilic esophagitis (EoE) is a chronic antigen-driven allergic inflammatory disease, likely involving the interplay of genetic and environmental factors, yet their respective contributions to heritability are unknown. OBJECTIVE To quantify the risk associated with genes and environment on familial clustering of EoE. METHODS Family history was obtained from a hospital-based cohort of 914 EoE probands (n = 2192 first-degree "Nuclear-Family" relatives) and an international registry of monozygotic and dizygotic twins/triplets (n = 63 EoE "Twins" probands). Frequencies, recurrence risk ratios (RRRs), heritability, and twin concordance were estimated. Environmental exposures were preliminarily examined. RESULTS Analysis of the Nuclear-Family-based cohort revealed that the rate of EoE, in first-degree relatives of a proband, was 1.8% (unadjusted) and 2.3% (sex-adjusted). RRRs ranged from 10 to 64, depending on the family relationship, and were higher in brothers (64.0; P = .04), fathers (42.9; P = .004), and males (50.7; P < .001) than in sisters, mothers, and females, respectively. The risk of EoE for other siblings was 2.4%. In the Nuclear-Family cohort, combined gene and common environment heritability was 72.0% ± 2.7% (P < .001). In the Twins cohort, genetic heritability was 14.5% ± 4.0% (P < .001), and common family environment contributed 81.0% ± 4% (P < .001) to phenotypic variance. Probandwise concordance in monozygotic co-twins was 57.9% ± 9.5% compared with 36.4% ± 9.3% in dizygotic co-twins (P = .11). Greater birth weight difference between twins (P = .01), breast-feeding (P = .15), and fall birth season (P = .02) were associated with twin discordance in disease status. CONCLUSIONS EoE RRRs are increased 10- to 64-fold compared with the general population. EoE in relatives is 1.8% to 2.4%, depending on relationship and sex. Nuclear-Family heritability appeared to be high (72.0%). However, the Twins cohort analysis revealed a powerful role for common environment (81.0%) compared with additive genetic heritability (14.5%).
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Affiliation(s)
- Eileen S Alexander
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Health Services Administration, Xavier University, Cincinnati, Ohio
| | - Lisa J Martin
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Margaret H Collins
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Leah C Kottyan
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Heidi Sucharew
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hua He
- Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Vincent A Mukkada
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Paul A Succop
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - J Pablo Abonia
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Heather Foote
- Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Michael D Eby
- Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Tommie M Grotjan
- Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Alexandria J Greenler
- Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Evan S Dellon
- Division of Gastroenterology and Hepatology, Center for Esophageal Diseases and Swallowing, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Jeffrey G Demain
- Allergy, Asthma and Immunology Center of Alaska, Anchorage, Alaska
| | - Glenn T Furuta
- Gastrointestinal Eosinophilic Diseases Program, Children's Hospital Colorado, Digestive Health Institute, University of Colorado School of Medicine, Aurora, Colo
| | | | - John B Harley
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; US Department of Veterans Affairs Medical Center, Cincinnati, Ohio
| | - Russell J Hopp
- Division of Allergy and Immunology, Department of Pediatrics, Creighton University, Omaha, Neb
| | - Amir Kagalwalla
- Division of Gastroenterology, Hepatology & Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill; Northwestern University-Feinberg School of Medicine, Chicago, Ill
| | - Ajay Kaul
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kari C Nadeau
- Stanford Medical School, Stanford, Calif; Division of Allergy and Immunology, Stanford Medical Center and Lucille Packard Children's Hospital, Stanford, Calif
| | - Richard J Noel
- Children's Hospital of Wisconsin, Milwaukee, Wis; Medical College of Wisconsin, Milwaukee, Wis
| | - Philip E Putnam
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Karl F von Tiehl
- BowTie Allergy Specialists, Huntington Memorial Hospital, Pasadena, Calif
| | - Marc E Rothenberg
- Departments of Environmental Health, Pediatrics, Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Divisions of Biostatistics and Epidemiology; Human Genetics; Pathology; Rheumatology, Center for Autoimmune Genomics and Etiology; Gastroenterology, Hepatology and Nutrition; Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
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Lekman M, Hössjer O, Andrews P, Källberg H, Uvehag D, Charney D, Manji H, Rush JA, McMahon FJ, Moore JH, Kockum I. The genetic interacting landscape of 63 candidate genes in Major Depressive Disorder: an explorative study. BioData Min 2014; 7:19. [PMID: 25279001 PMCID: PMC4181757 DOI: 10.1186/1756-0381-7-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/28/2014] [Indexed: 12/17/2022] Open
Abstract
Background Genetic contributions to major depressive disorder (MDD) are thought to result from multiple genes interacting with each other. Different procedures have been proposed to detect such interactions. Which approach is best for explaining the risk of developing disease is unclear. This study sought to elucidate the genetic interaction landscape in candidate genes for MDD by conducting a SNP-SNP interaction analysis using an exhaustive search through 3,704 SNP-markers in 1,732 cases and 1,783 controls provided from the GAIN MDD study. We used three different methods to detect interactions, two logistic regressions models (multiplicative and additive) and one data mining and machine learning (MDR) approach. Results Although none of the interaction survived correction for multiple comparisons, the results provide important information for future genetic interaction studies in complex disorders. Among the 0.5% most significant observations, none had been reported previously for risk to MDD. Within this group of interactions, less than 0.03% would have been detectable based on main effect approach or an a priori algorithm. We evaluated correlations among the three different models and conclude that all three algorithms detected the same interactions to a low degree. Although the top interactions had a surprisingly large effect size for MDD (e.g. additive dominant model Puncorrected = 9.10E-9 with attributable proportion (AP) value = 0.58 and multiplicative recessive model with Puncorrected = 6.95E-5 with odds ratio (OR estimated from β3) value = 4.99) the area under the curve (AUC) estimates were low (< 0.54). Moreover, the population attributable fraction (PAF) estimates were also low (< 0.15). Conclusions We conclude that the top interactions on their own did not explain much of the genetic variance of MDD. The different statistical interaction methods we used in the present study did not identify the same pairs of interacting markers. Genetic interaction studies may uncover previously unsuspected effects that could provide novel insights into MDD risk, but much larger sample sizes are needed before this strategy can be powerfully applied.
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Affiliation(s)
- Magnus Lekman
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Ola Hössjer
- Department of Mathematics, Stockholm University, Stockholm, Sweden
| | - Peter Andrews
- Institute of Quantitative Biomedical Science, Department of Genetics and Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Henrik Källberg
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Uvehag
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Dennis Charney
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - Husseini Manji
- Laboratory of Molecular Pathophysiology, NIMH, NIH, Department of Health & Human Services (DHHS), Bethesda, USA
| | - John A Rush
- Academic Medical Research Institute, Duke-National University of Singapore, Singapore, Singapore
| | - Francis J McMahon
- Genetic Basis of Mood & Anxiety Disorders Section, Human Genetic Branch, NIMH, NIH, Department of Health & Human Services (DHHS), Bethesda, USA
| | - Jason H Moore
- Institute of Quantitative Biomedical Science, Department of Genetics and Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
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Eskola PJ, Männikkö M, Samartzis D, Karppinen J. Genome-wide association studies of lumbar disc degeneration--are we there yet? Spine J 2014; 14:479-82. [PMID: 24210639 DOI: 10.1016/j.spinee.2013.07.437] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/14/2013] [Indexed: 02/03/2023]
Affiliation(s)
- Pasi J Eskola
- Department of Physical and Rehabilitation Medicine, Institute of Clinical Medicine, University of Oulu, and Medical Research Center Oulu, Box 5000, 90014 Oulu, Finland
| | - Minna Männikkö
- Institute of Health Sciences, Biocenter Oulu, University of Oulu, Box 5000, 90014 Oulu, Finland
| | - Dino Samartzis
- Department of Orthopaedics and Traumatology, University of Hong Kong, Professorial Block, 5th Floor, 102 Pokfulam Rd, Pokfulam, Hong Kong, SAR, China
| | - Jaro Karppinen
- Department of Physical and Rehabilitation Medicine, Institute of Clinical Medicine, University of Oulu, and Medical Research Center Oulu, Box 5000, 90014 Oulu, Finland.
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Brodziak A, Brewczyński PZ. Letter to the Editor regarding: epistatic effects in pathophysiology of asthma and the "missing heritability" of this disease. Med Sci Monit 2014; 20:274-5. [PMID: 24549280 PMCID: PMC3937018 DOI: 10.12659/msm.890506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Andrzej Brodziak
- Independent researcher, Institute of Occupational Medicine and Environmental Health, Sosnowiec, Poland
| | - Piotr Z Brewczyński
- Independent researcher, Institute of Occupational Medicine and Environmental Health, Sosnowiec, Poland
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Irvin MR, Aslibekyan S, Hidalgo B, Arnett D. CPT1A: the future of heart disease detection and personalized medicine? ACTA ACUST UNITED AC 2014; 9:9-12. [PMID: 25774225 DOI: 10.2217/clp.13.75] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- M Ryan Irvin
- Department of Epidemiology, University of Alabama at Birmingham
| | | | - Bertha Hidalgo
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham
| | - Donna Arnett
- Department of Epidemiology, University of Alabama at Birmingham
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Murphy NM, Pouton CW, Irving HR. Human leukocyte antigen haplotype phasing by allele-specific enrichment with peptide nucleic acid probes. Mol Genet Genomic Med 2014; 2:245-53. [PMID: 24936514 PMCID: PMC4049365 DOI: 10.1002/mgg3.65] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/10/2013] [Accepted: 12/17/2013] [Indexed: 12/22/2022] Open
Abstract
Targeted capture of large fragments of genomic DNA that enrich for human leukocyte antigen (HLA) system haplotypes has utility in haematopoietic stem cell transplantation. Current methods of HLA matching are based on inference or familial studies of inheritance; and each approach has its own inherent limitations. We have designed and tested a probe–target-extraction method for capturing specific HLA haplotypes by hybridization of peptide nucleic acid (PNA) probes to alleles of the HLA-DRB1 gene. Short target fragments contained in plasmids were initially used to optimize the method followed by testing samples of genomic DNA from human subjects with preselected HLA haplotypes and obtained approximately 10% enrichment for the specific haplotype. When performed with high-molecular-weight genomic DNA, 99.0% versus 84.0% alignment match was obtained for the specific haplotype probed. The allele-specific target enrichment that we obtained can facilitate the elucidation of haplotypes between the 65 kb separating the HLA-DRB1 and the HLA-DQA1 genes, potentially spanning a total distance of at least 130 kb. Allele-specific target enrichment with PNA probes is a straightforward technique that has the capability to improve the resolution of DNA and whole genome sequencing technologies by allowing haplotyping of enriched DNA and crucially, retaining the DNA methylation profile.
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Affiliation(s)
- Nicholas M Murphy
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) Melbourne, Victoria, 3052, Australia ; Department of Preimplantation Genetic Diagnosis, Melbourne IVF 344 Victoria Parade, East Melbourne, Australia
| | - Colin W Pouton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) Melbourne, Victoria, 3052, Australia
| | - Helen R Irving
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) Melbourne, Victoria, 3052, Australia
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A gene pathway analysis highlights the role of cellular adhesion molecules in multiple sclerosis susceptibility. Genes Immun 2014; 15:126-32. [PMID: 24430173 DOI: 10.1038/gene.2013.70] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/29/2013] [Accepted: 12/03/2013] [Indexed: 12/22/2022]
Abstract
Genome-wide association studies (GWASs) perform per-SNP association tests to identify variants involved in disease or trait susceptibility. However, such an approach is not powerful enough to unravel genes that are not individually contributing to the disease/trait, but that may have a role in interaction with other genes as a group. Pathway analysis is an alternative way to highlight such group of genes. Using SNP association P-values from eight multiple sclerosis (MS) GWAS data sets, we performed a candidate pathway analysis for MS susceptibility by considering genes interacting in the cell adhesion molecule (CAMs) biological pathway using Cytoscape software. This network is a strong candidate, as it is involved in the crossing of the blood-brain barrier by the T cells, an early event in MS pathophysiology, and is used as an efficient therapeutic target. We drew up a list of 76 genes belonging to the CAM network. We highlighted 64 networks enriched with CAM genes with low P-values. Filtering by a percentage of CAM genes up to 50% and rejecting enriched signals mainly driven by transcription factors, we highlighted five networks associated with MS susceptibility. One of them, constituted of ITGAL, ICAM1 and ICAM3 genes, could be of interest to develop novel therapeutic targets.
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Chuang LY, Lane HY, Lin YD, Lin MT, Yang CH, Chang HW. Identification of SNP barcode biomarkers for genes associated with facial emotion perception using particle swarm optimization algorithm. Ann Gen Psychiatry 2014; 13:15. [PMID: 24955105 PMCID: PMC4050220 DOI: 10.1186/1744-859x-13-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 04/23/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Facial emotion perception (FEP) can affect social function. We previously reported that parts of five tested single-nucleotide polymorphisms (SNPs) in the MET and AKT1 genes may individually affect FEP performance. However, the effects of SNP-SNP interactions on FEP performance remain unclear. METHODS This study compared patients with high and low FEP performances (n = 89 and 93, respectively). A particle swarm optimization (PSO) algorithm was used to identify the best SNP barcodes (i.e., the SNP combinations and genotypes that revealed the largest differences between the high and low FEP groups). RESULTS The analyses of individual SNPs showed no significant differences between the high and low FEP groups. However, comparisons of multiple SNP-SNP interactions involving different combinations of two to five SNPs showed that the best PSO-generated SNP barcodes were significantly associated with high FEP score. The analyses of the joint effects of the best SNP barcodes for two to five interacting SNPs also showed that the best SNP barcodes had significantly higher odds ratios (2.119 to 3.138; P < 0.05) compared to other SNP barcodes. In conclusion, the proposed PSO algorithm effectively identifies the best SNP barcodes that have the strongest associations with FEP performance. CONCLUSIONS This study also proposes a computational methodology for analyzing complex SNP-SNP interactions in social cognition domains such as recognition of facial emotion.
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Affiliation(s)
- Li-Yeh Chuang
- Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 84001, Taiwan
| | - Hsien-Yuan Lane
- Institute of Clinical Medical Science, China Medical University, Taichung 40402, Taiwan ; Department of Psychiatry, China Medical University Hospital, Taichung 40402, Taiwan
| | - Yu-Da Lin
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan
| | - Ming-Teng Lin
- Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 84001, Taiwan ; Department of Psychiatry, Taipei Veterans General Hospital, Hsinchu Branch, Hsinchu 31064, Taiwan
| | - Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan ; Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan ; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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Hogan KJ. Hereditary vulnerabilities to post-operative cognitive dysfunction and dementia. Prog Neuropsychopharmacol Biol Psychiatry 2013; 47:128-34. [PMID: 23562862 DOI: 10.1016/j.pnpbp.2013.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 11/18/2022]
Abstract
In view of multiple prospective investigations reporting an incidence of 10% or greater in elderly patients after cardiac and non-cardiac procedures, it is surprising that no families, twins or even individual cases have been reported with persistent post-operative cognitive dysfunction (POCD) or post-operative dementia (POD) that is otherwise unexplained. As POCD and POD research has shifted in recent years from surgical and anesthetic variables to predictors of intrinsic, patient-specific susceptibility, a number of markers based on DNA sequence variation have been investigated. Nevertheless, no heritable, genomic indices of persistent POCD or post-operative dementia lasting 3 months or longer after surgery have been identified to date. The present manuscript surveys challenges confronting the search for markers of heritable vulnerability to POCD and POD, and proposes steps forward to be taken now, including the addition of surgical and anesthetic descriptors to ongoing longitudinal dementia protocols and randomized clinical trials (RCTs) comprising serial psychometric testing, and a fresh focus on phenotypes and genotypes shared between outliers with "extreme" POCD and POD traits.
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Affiliation(s)
- Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, B6/319 Clinical Sciences Center, 600 Highland Avenue, Madison, WI 53792, USA.
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Abstract
PURPOSE OF REVIEW Common obesity is widely regarded as a complex, multifactorial trait influenced by the 'obesogenic' environment, sedentary behavior, and genetic susceptibility contributed by common and rare genetic variants. This review describes the recent advances in understanding the role of genetics in obesity. RECENT FINDINGS New susceptibility loci and genetic variants are being uncovered, but the collective effect is relatively small and could not explain most of the BMI heritability. Yet-to-be identified common and rare variants, epistasis, and heritable epigenetic changes may account for part of the 'missing heritability'. Evidence is emerging about the role of epigenetics in determining obesity susceptibility, mediating developmental plasticity, which confers obesity risk from early life experiences. Genetic prediction scores derived from selected genetic variants, and also differential DNA methylation levels and methylation scores, have been shown to correlate with measures of obesity and response to weight loss intervention. Genetic variants, which confer susceptibility to obesity-related morbidities like nonalcoholic fatty liver disease, were also discovered recently. SUMMARY We can expect discovery of more rare genetic variants with the advent of whole exome and genome sequencing, and also greater understanding of epigenetic mechanisms by which environment influences genetic expression and which mediate the gene-environment interaction.
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Recent Developments in Cardiovascular Genetics. Circ Res 2013; 113:e88-91. [DOI: 10.1161/circresaha.113.302634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Novel insights into autoimmune liver diseases provided by genome-wide association studies. J Autoimmun 2013; 46:41-54. [DOI: 10.1016/j.jaut.2013.07.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 12/14/2022]
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Meethal SV, Hogan KJ, Mayanil CS, Iskandar BJ. Folate and epigenetic mechanisms in neural tube development and defects. Childs Nerv Syst 2013; 29:1427-33. [PMID: 24013316 DOI: 10.1007/s00381-013-2162-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 05/13/2013] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Multiple genetic and epigenetic factors involved in central nervous system (CNS) development influence the incidence of neural tube defects (NTDs). DISCUSSION The beneficial effect of periconceptional folic acid on NTD prevention denotes a vital role for the single-carbon biochemical pathway in NTD genesis. Indeed, NTDs are associated with polymorphisms in a diversity of genes that encode folate pathway enzymes. Recent evidence suggests that CNS development and function, and consequently NTDs, are also associated with epigenetic mechanisms, many of which participate in the folate cycle and its input and output pathways. We provide an overview with select examples drawn from the authors' research.
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Affiliation(s)
- Sivan Vadakkadath Meethal
- Department of Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, WI 53792, USA
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Abstract
The elucidation of genes implicated in Mendelian forms of hypertension demonstrates rare variants with substantial effects are responsible, and often these genes lie within pathways managing sodium homeostasis. More recently with advances in affordable high-throughput genotyping strategies, multiple common genetic variants with modest effects on blood pressure (<1 mmHg systolic) have been discovered in the population. In aggregate, these common variants explain <3% of the variance of blood pressure. Although these findings may offer new mechanistic insights into the biology of blood pressure, a key question is can these findings translate into patient benefit? It is timely to reflect on recent advances in genomics, and the use of new resources, such as the 1000 Genomes Project and the Encyclopedia of DNA Elements, to annotate likely causal variants, and their relevance to cardiovascular disease. In this review, we discuss the advances in relation to our knowledge of the genetic architecture of blood pressure, and whether gene discoveries might influence cardiovascular risk assessment, help to stratify patient response to medicine, or identify new biological pathways for novel therapeutic targets.
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Affiliation(s)
- Patricia B Munroe
- William Harvey Research Institute and Barts National Institute for Health Research Cardiovascular Biomedical Research Unit, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ United Kingdom
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Avatars of information: towards an inclusive evolutionary synthesis. Trends Ecol Evol 2013; 28:351-8. [DOI: 10.1016/j.tree.2013.02.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 02/21/2013] [Accepted: 02/24/2013] [Indexed: 01/12/2023]
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Brookes K. The VNTR in complex disorders: The forgotten polymorphisms? A functional way forward? Genomics 2013; 101:273-81. [DOI: 10.1016/j.ygeno.2013.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/08/2013] [Accepted: 03/11/2013] [Indexed: 12/16/2022]
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Circulation Research
Thematic Synopsis. Circ Res 2013. [DOI: 10.1161/circresaha.113.300982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Coronary atherosclerosis is a complex heritable trait with an enigmatic genetic etiology. Genome-wide association studies (GWAS) have successfully led to identification of over 100 different loci for susceptibility to coronary atherosclerosis. Most identified single nucleotide polymorphisms (SNP)s and genes have not been previously implicated in the pathogenesis of atherosclerosis and hence, have modest biological plausibility. The novel discoveries, however, might provide the opportunity for identification of new pathways and consequently novel preventive and therapeutic targets. A notable outcome of GWAS is relatively modest effect sizes of the associated SNPs. Collectively, the identified SNPs account for a relatively small fraction of heritability of coronary atherosclerosis, which raises the question of "missing heritability". Because GWAS test the common disease-comment variant hypothesis, a plausible explanation might be the presence of uncommon and rare variants in the genome that are untested in GWAS but that might exert large effect sizes on the risk of atherosclerosis. The latter, however, remains an empiric question pending validation through experimentation. Alternative mechanisms, such as transgenerational epigenetics including microRNAs, might in part account for the heritability of coronary atherosclerosis. Collectively, the recent findings are indicative of the etiological complexity of coronary atherosclerosis. Hence, it is expected that genetic etiology of coronary atherosclerosis will remain enigmatic in the foreseeable future.
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Affiliation(s)
- A J Marian
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, 77030, USA.
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Uhl EW, Whitley E, Galbreath E, McArthur M, Oglesbee MJ. Evolutionary aspects of animal models. Vet Pathol 2012; 49:876-8. [PMID: 22983990 DOI: 10.1177/0300985812456214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- E W Uhl
- Department of Pathology, College of Veterinary Medicine, 501 DW Brooks Drive, The University of Georgia, Athens, GA 30602, USA.
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Abstract
Despite the well-documented influence of genetics on susceptibility to cardiovascular diseases, delineation of the full spectrum of the risk alleles had to await the development of modern next-generation sequencing technologies. The techniques provide unbiased approaches for identification of the DNA sequence variants (DSVs) in the entire genome (whole genome sequencing [WGS]) or the protein-coding exons (whole exome sequencing [WES]). Each genome contains approximately 4 million DSVs and each exome approximately 13,000 single nucleotide variants. The challenge facing researchers and clinicians alike is to decipher the biological and clinical significance of these variants and harness the information for the practice of medicine. The common DSVs typically exert modest effect sizes, as evidenced by the results of genome-wide association studies, and hence have modest or negligible clinical implications. The focus is on the rare variants with large effect sizes, which are expected to have stronger clinical implications, as in single gene disorders with Mendelian patterns of inheritance. However, the clinical implications of the rare variants for common complex cardiovascular diseases remain to be established. The most important contribution of WES or WGS is in delineation of the novel molecular pathways involved in the pathogenesis of the phenotype, which would be expected to provide for preventive and therapeutic opportunities.
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Affiliation(s)
- Ali J Marian
- Center for Cardiovascular Genetics, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center and Texas Heart Institute, Houston, TX 77030, USA.
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