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Yang Y, Wang Q, Wang C, Buxbaum J, Ionita-Laza I. KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies. Am J Hum Genet 2024:S0002-9297(24)00166-6. [PMID: 38821058 DOI: 10.1016/j.ajhg.2024.05.003] [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: 09/10/2023] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024] Open
Abstract
Both trio and population designs are popular study designs for identifying risk genetic variants in genome-wide association studies (GWASs). The trio design, as a family-based design, is robust to confounding due to population structure, whereas the population design is often more powerful due to larger sample sizes. Here, we propose KnockoffHybrid, a knockoff-based statistical method for hybrid analysis of both the trio and population designs. KnockoffHybrid provides a unified framework that brings together the advantages of both designs and produces powerful hybrid analysis while controlling the false discovery rate (FDR) in the presence of linkage disequilibrium and population structure. Furthermore, KnockoffHybrid has the flexibility to leverage different types of summary statistics for hybrid analyses, including expression quantitative trait loci (eQTL) and GWAS summary statistics. We demonstrate in simulations that KnockoffHybrid offers power gains over non-hybrid methods for the trio and population designs with the same number of cases while controlling the FDR with complex correlation among variants and population structure among subjects. In hybrid analyses of three trio cohorts for autism spectrum disorders (ASDs) from the Autism Speaks MSSNG, Autism Sequencing Consortium, and Autism Genome Project with GWAS summary statistics from the iPSYCH project and eQTL summary statistics from the MetaBrain project, KnockoffHybrid outperforms conventional methods by replicating several known risk genes for ASDs and identifying additional associations with variants in other genes, including the PRAME family genes involved in axon guidance and which may act as common targets for human speech/language evolution and related disorders.
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Affiliation(s)
- Yi Yang
- Department of Biostatistics, City University of Hong Kong, Hong Kong SAR, China; School of Data Science, City University of Hong Kong, Hong Kong SAR, China.
| | - Qi Wang
- School of Data Science, City University of Hong Kong, Hong Kong SAR, China
| | - Chen Wang
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Joseph Buxbaum
- Departments of Psychiatry, Neuroscience, and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Columbia University, New York, NY 10032, USA; Department of Statistics, Lund University, Lund, Sweden
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2
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Garro-Núñez D, Picado-Martínez MJ, Espinoza-Campos E, Ugalde-Araya D, Macaya G, Raventós H, Chavarría-Soley G. Systematic exploration of a decade of publications on psychiatric genetics in Latin America. Am J Med Genet B Neuropsychiatr Genet 2024; 195:e32960. [PMID: 37860990 DOI: 10.1002/ajmg.b.32960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 08/08/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023]
Abstract
Psychiatric disorders have a great impact in terms of mortality, morbidity, and disability across the lifespan. Considerable effort has been devoted to understanding their complex and heterogeneous genetic architecture, including diverse ancestry populations. Our aim was to review the psychiatric genetics research published with Latin American populations from 2010 to 2019, and classify it according to country of origin, type of analysis, source of funding, and other variables. We found that most publications came from Brazil, Mexico, and Colombia. Also, local funds are generally not large enough for genome-wide studies in Latin America, with the exception of Brazil and Mexico; larger studies are often done in collaboration with international partners, mostly funded by US agencies. In most of the larger studies, the participants are individuals of Latin American ancestry living in the United States, which limits the potential for exploring the complex gene-environment interaction. Family studies, traditionally strong in Latin America, represent about 30% of the total research publications. Scarce local resources for research in Latin America have probably been an important limitation for conducting bigger and more complex studies, contributing to the reduced representation of these populations in global psychiatric genetics studies. Increasing diversity must be a goal to improve generalizability and applicability in clinical settings.
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Affiliation(s)
| | | | | | - Daniela Ugalde-Araya
- Center for Research in Cellular and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica
| | - Gabriel Macaya
- Center for Research in Cellular and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica
| | - Henriette Raventós
- Biology School, Universidad de Costa Rica, San José, Costa Rica
- Center for Research in Cellular and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica
| | - Gabriela Chavarría-Soley
- Biology School, Universidad de Costa Rica, San José, Costa Rica
- Center for Research in Cellular and Molecular Biology, Universidad de Costa Rica, San José, Costa Rica
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Zhong Y, Cook RJ, Yu A. Analysis of secondary failure time responses in studies with response-dependent sampling schemes. Stat Med 2023; 42:4763-4775. [PMID: 37643587 DOI: 10.1002/sim.9887] [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] [Received: 06/01/2022] [Revised: 06/20/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Response-dependent sampling is routinely used as an enrichment strategy in the design of family studies investigating the heritable nature of disease. In addition to the response of primary interest, investigators often wish to investigate the association between biomarkers and secondary responses related to possible comorbidities. Statistical analysis regarding genetic biomarkers and their association with the secondary outcome must address the biased sampling scheme involving the primary response. In this article, we develop composite likelihoods and two-stage estimation procedures for such secondary analyses in which the within-family dependence structure for the primary and secondary outcomes is modeled via a Gaussian copula. The dependence among responses within family members is modeled based on kinship coefficients. Auxiliary data from independent individuals are exploited by augmenting the composite likelihoods to increase precision of marginal parameter estimates and enhance the efficiency of estimators of the dependence parameters. Simulation studies are carried out to evaluate the finite sample performance of the proposed method, and an application to a motivating family study in psoriatic arthritis is given for illustration.
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Affiliation(s)
- Yujie Zhong
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China
- Oncology Statistics, R&D China AstraZeneca, Shanghai, China
| | - Richard J Cook
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Aiai Yu
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China
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4
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Diego VP, Manusov EG, Mao X, Curran JE, Göring H, Almeida M, Mahaney MC, Peralta JM, Blangero J, Williams-Blangero S. Genotype-by-socioeconomic status interaction influences heart disease risk scores and carotid artery thickness in Mexican Americans: the predominant role of education in comparison to household income and socioeconomic index. Front Genet 2023; 14:1132110. [PMID: 37795246 PMCID: PMC10547145 DOI: 10.3389/fgene.2023.1132110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/17/2023] [Indexed: 10/06/2023] Open
Abstract
Background: Socioeconomic status (SES) is a potent environmental determinant of health. To our knowledge, no assessment of genotype-environment interaction has been conducted to consider the joint effects of socioeconomic status and genetics on risk for cardiovascular disease (CVD). We analyzed Mexican American Family Studies (MAFS) data to evaluate the hypothesis that genotype-by-environment interaction (GxE) is an important determinant of variation in CVD risk factors. Methods: We employed a linear mixed model to investigate GxE in Mexican American extended families. We studied two proxies for CVD [Pooled Cohort Equation Risk Scores/Framingham Risk Scores (FRS/PCRS) and carotid artery intima-media thickness (CA-IMT)] in relation to socioeconomic status as determined by Duncan's Socioeconomic Index (SEI), years of education, and household income. Results: We calculated heritability for FRS/PCRS and carotid artery intima-media thickness. There was evidence of GxE due to additive genetic variance heterogeneity and genetic correlation for FRS, PCRS, and CA-IMT measures for education (environment) but not for household income or SEI. Conclusion: The genetic effects underlying CVD are dynamically modulated at the lower end of the SES spectrum. There is a significant change in the genetic architecture underlying the major components of CVD in response to changes in education.
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Affiliation(s)
- Vincent P. Diego
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Eron G. Manusov
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Xi Mao
- Department of Economics, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Joanne E. Curran
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Harald Göring
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Marcio Almeida
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Michael C. Mahaney
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Juan M. Peralta
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - John Blangero
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Sarah Williams-Blangero
- Department of Human Genetics, School of Medicine, University of Texas Rio Grande Valley, Brownsville, TX, United States
- School of Medicine, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX, United States
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Ul Islam Z, Baneen U, Khaliq T, Nurulain SM, Muneer Z, Hussain S. Association analysis of miRNA-146a and miRNA-499 polymorphisms with rheumatoid arthritis: a case-control and trio-family study. Clin Exp Med 2023; 23:1667-1675. [PMID: 36303006 DOI: 10.1007/s10238-022-00916-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/08/2022] [Indexed: 11/03/2022]
Abstract
Single nucleotide polymorphism is known to alter the expression and processing of miRNAs leading to a variety of diseases including rheumatoid arthritis (RA). However, disagreement is present up to date regarding the association of miRNA-146a and miRNA-499 polymorphisms with RA. The goal of this study was to assess the association of polymorphisms at miRNA-146a and miRNA-499 with the pathogenesis of RA in patients originating from Pakistan. Initially, eleven hundred subjects (1100) comprises of 550 RA patients and 550 healthy controls were investigated in the case-control analysis. Spectrophotometric measurement of lipids and C-reactive protein was used, whereas interleukin-1 receptor associated kinase-1 and TNF-receptor associated factor-6 values were quantified by an enzyme-linked immunosorbent assay. Secondly, heritability of susceptible alleles was tested from 70 trio-families. The miRNA-146a rs2910164 and miRNA-499 rs3746444 polymorphisms were genotyped using the polymerase chain reaction followed by restriction digestion. A Significant association of miRNA-146a and miRNA-499 genotypes was observed with RA patients (P < 0.05, respectively). The miRNA-146a rs2910164 G (OR = 1.4, P < 0.05) and miRNA-499 rs3746444 C (OR = 1.6, P < 0.0001) allele was significantly associated with RA in comparison with controls, respectively. Besides, the transmission analysis revealed a significant (P < 0.05) inheritance of rs2910164 G and rs3746444 C allele from parents to affected offspring. The current research concludes that miRNA-146a (rs2910164; C > G) and miRNA-499 (rs3746444; T > C) polymorphisms are linked to RA in the population studied. Furthermore, it was demonstrated for the first time in our high-risk cohort that the rs2910164 G and rs3746444 C allele was strongly related to familial RA.
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Affiliation(s)
- Zia Ul Islam
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad, 45550, Pakistan
| | - Umul Baneen
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad, 45550, Pakistan
| | - Taqdees Khaliq
- Department of Rheumatology, Federal Government Polyclinic Hospital, 44 Luqman Hakeem Road G/6, Islamabad, 46000, Pakistan
| | - Syed Muhammad Nurulain
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad, 45550, Pakistan
| | - Zahid Muneer
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad, 45550, Pakistan
| | - Sabir Hussain
- Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlai Kalan, Islamabad, 45550, Pakistan.
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Vazzana KM, Musolf AM, Bailey-Wilson JE, Hiraki LT, Silverman ED, Scott C, Dalgard CL, Hasni S, Deng Z, Kaplan MJ, Lewandowski LB. Transmission disequilibrium analysis of whole genome data in childhood-onset systemic lupus erythematosus. Genes Immun 2023; 24:200-206. [PMID: 37488248 PMCID: PMC10529982 DOI: 10.1038/s41435-023-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023]
Abstract
Childhood-onset systemic lupus erythematosus (cSLE) patients are unique, with hallmarks of Mendelian disorders (early-onset and severe disease) and thus are an ideal population for genetic investigation of SLE. In this study, we use the transmission disequilibrium test (TDT), a family-based genetic association analysis that employs robust methodology, to analyze whole genome sequencing data. We aim to identify novel genetic associations in an ancestrally diverse, international cSLE cohort. Forty-two cSLE patients and 84 unaffected parents from 3 countries underwent whole genome sequencing. First, we performed TDT with single nucleotide variant (SNV)-based (common variants) using PLINK 1.9, and gene-based (rare variants) analyses using Efficient and Parallelizable Association Container Toolbox (EPACTS) and rare variant TDT (rvTDT), which applies multiple gene-based burden tests adapted for TDT, including the burden of rare variants test. Applying the GWAS standard threshold (5.0 × 10-8) to common variants, our SNV-based analysis did not return any genome-wide significant SNVs. The rare variant gene-based TDT analysis identified many novel genes significantly enriched in cSLE patients, including HNRNPUL2, a DNA repair protein, and DNAH11, a ciliary movement protein, among others. Our approach identifies several novel SLE susceptibility genes in an ancestrally diverse childhood-onset lupus cohort.
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Affiliation(s)
- Kathleen M Vazzana
- Lupus Genomics and Global Health Disparities Unit, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Anthony M Musolf
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 22124, USA
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 22124, USA
| | - Linda T Hiraki
- Division of Rheumatology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Earl D Silverman
- Division of Rheumatology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Christiaan Scott
- Paediatric Rheumatology, Red Cross War Memorial Children's Hospital and University of Cape Town, Cape Town, South Africa
| | - Clifton L Dalgard
- The American Genome Center, Department of Anatomy, Physiology & Genetics, Uniformed Services University, Bethesda, MD, USA
| | - Sarfaraz Hasni
- Clinical Program, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zuoming Deng
- Biodata Mining and Discovery Section, Office of Science and Technology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Laura B Lewandowski
- Lupus Genomics and Global Health Disparities Unit, Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
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Zheng H, Ye Y, Huang H, Huang C, Gao W, Wang M, Li W, Zhou R, Jiang J, Wang S, Yu C, Lv J, Wu X, Huang X, Cao W, Yan Y, Zheng K, Wu T, Li L. A pedigree-based cohort to study the genetic risk factors for cardiometabolic diseases: study design, baseline characteristics and preliminary results. Front Public Health 2023; 11:1189993. [PMID: 37521988 PMCID: PMC10374840 DOI: 10.3389/fpubh.2023.1189993] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background We initiated the Fujian Tulou Pedigree-based Cohort (FTPC) as the integration of extended pedigrees and prospective cohort to clarify the genetic and environmental risk factors of cardiometabolic diseases. Methods FTPC was carried out in Nanjing County, Fujian Province, China from August 2015 to December 2017 to recruit probands with the same surnames and then enroll their first-degree and more distant relatives. The participants were asked to complete questionnaire interview, physical examination, and blood collection. According to the local genealogical booklets and family registry, we reconstructed extended pedigrees to estimate the heritability of cardiometabolic traits. The follow-up of FTPC is scheduled every 5 years in the future. Results The baseline survey interviewed 2,727 individuals in two clans. A total of 1,563 adult subjects who completed all baseline examinations were used to reconstruct pedigrees and 452 extended pedigrees were finally identified, including one seven-generation pedigree, two five-generation pedigrees, 23 four-generation pedigrees, 186 three-generation pedigrees, and 240 two-generation pedigrees. The average age of the participants was 57.4 years, with 43.6% being males. The prevalence of hypertension, diabetes and dyslipidemia in FTPC were 49.2, 10.0, and 45.2%, respectively. Based on the pedigree structure, the heritability of systolic blood pressure, diastolic blood pressure, fast blood glucose, total cholesterol, triglyceride, high-density lipoprotein, and low-density lipoprotein was estimated at 0.379, 0.306, 0.386, 0.452, 0.568, 0.852, and 0.387, respectively. Conclusion As an extended pedigree cohort in China, FTPC will provide an important source to study both genetic and environmental risk factors prospectively.
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Affiliation(s)
- Hongchen Zheng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ying Ye
- Department of Local Diseases Control and Prevention, Fujian Provincial Center for Disease Control and Prevention, Fuzhou, China
| | - Hui Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Chunlan Huang
- Department of Hygiene, Nanjing Country Center for Disease Control and Prevention, Nanjing, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Wenyong Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Ren Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Jin Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Siyue Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
| | - Xiaoling Wu
- Department of Hygiene, Nanjing Country Center for Disease Control and Prevention, Nanjing, China
| | - Xiaoming Huang
- Department of Hygiene, Nanjing Country Center for Disease Control and Prevention, Nanjing, China
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Yansheng Yan
- Department of Local Diseases Control and Prevention, Fujian Provincial Center for Disease Control and Prevention, Fuzhou, China
| | - Kuicheng Zheng
- Fujian Provincial Center for Disease Control and Prevention, Fuzhou, China
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
- Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
- Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, China
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Yoosefzadeh Najafabadi M, Hesami M, Rajcan I. Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1956. [PMID: 37653871 PMCID: PMC10221147 DOI: 10.3390/plants12101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 07/30/2023]
Abstract
Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties of plants since the 19th century. However, there are several breeding cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, and loss of heterozygosity (LOH), where Mendelian heredity is not applicable, known as non-Mendelian heredity. This type of inheritance can be influenced by several factors besides the genetic architecture of the plant and its breeding potential. Therefore, exploring various non-Mendelian heredity mechanisms, their prevalence in plants, and the implications for plant breeding is of paramount importance to accelerate the pace of crop improvement. In this review, we examine the current understanding of non-Mendelian heredity in plants, including the mechanisms, inheritance patterns, and applications in plant breeding, provide an overview of the various forms of non-Mendelian inheritance (including epigenetic inheritance, cytoplasmic inheritance, hybrid vigor, and LOH), explore insight into the implications of non-Mendelian heredity in plant breeding, and the potential it holds for future research.
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Affiliation(s)
| | | | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.Y.N.); (M.H.)
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9
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Hecker J, Chun S, Samiei A, Liu C, Laurie C, Kachroo P, Lutz SM, Lee S, Smith AV, Lasky-Su J, Cho MH, Sharma S, Soto Quirós ME, Avila L, Celedón JC, Raby B, Zhou X, Silverman EK, DeMeo DL, Lange C, Weiss ST. FGF20 and PGM2 variants are associated with childhood asthma in family-based whole-genome sequencing studies. Hum Mol Genet 2023; 32:696-707. [PMID: 36255742 PMCID: PMC9896483 DOI: 10.1093/hmg/ddac258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Asthma is a heterogeneous common respiratory disease that remains poorly understood. The established genetic associations fail to explain the high estimated heritability, and the prevalence of asthma differs between populations and geographic regions. Robust association analyses incorporating different genetic ancestries and whole-genome sequencing data may identify novel genetic associations. METHODS We performed family-based genome-wide association analyses of childhood-onset asthma based on whole-genome sequencing (WGS) data for the 'The Genetic Epidemiology of Asthma in Costa Rica' study (GACRS) and the Childhood Asthma Management Program (CAMP). Based on parent-child trios with children diagnosed with asthma, we performed a single variant analysis using an additive and a recessive genetic model and a region-based association analysis of low-frequency and rare variants. RESULTS Based on 1180 asthmatic trios (894 GACRS trios and 286 CAMP trios, a total of 3540 samples with WGS data), we identified three novel genetic loci associated with childhood-onset asthma: rs4832738 on 4p14 ($P=1.72\ast{10}^{-9}$, recessive model), rs1581479 on 8p22 ($P=1.47\ast{10}^{-8}$, additive model) and rs73367537 on 10q26 ($P=1.21\ast{10}^{-8}$, additive model in GACRS only). Integrative analyses suggested potential novel candidate genes underlying these associations: PGM2 on 4p14 and FGF20 on 8p22. CONCLUSION Our family-based whole-genome sequencing analysis identified three novel genetic loci for childhood-onset asthma. Gene expression data and integrative analyses point to PGM2 on 4p14 and FGF20 on 8p22 as linked genes. Furthermore, region-based analyses suggest independent potential low-frequency/rare variant associations on 8p22. Follow-up analyses are needed to understand the functional mechanisms and generalizability of these associations.
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Affiliation(s)
- Julian Hecker
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmad Samiei
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Cuining Liu
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sharon M Lutz
- Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care, Boston, MA 02215, USA
| | - Sanghun Lee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin-si, 16890, South Korea
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Lydiana Avila
- Department of Pediatrics, Hospital Nacional de Niños, 10101 San José, Costa Rica
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Benjamin Raby
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | - Christoph Lange
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
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10
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LaPierre N, Fu B, Turnbull S, Eskin E, Sankararaman S. Leveraging family data to design Mendelian Randomization that is provably robust to population stratification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522936. [PMID: 36711635 PMCID: PMC9881984 DOI: 10.1101/2023.01.05.522936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Mendelian Randomization (MR) has emerged as a powerful approach to leverage genetic instruments to infer causality between pairs of traits in observational studies. However, the results of such studies are susceptible to biases due to weak instruments as well as the confounding effects of population stratification and horizontal pleiotropy. Here, we show that family data can be leveraged to design MR tests that are provably robust to confounding from population stratification, assortative mating, and dynastic effects. We demonstrate in simulations that our approach, MR-Twin, is robust to confounding from population stratification and is not affected by weak instrument bias, while standard MR methods yield inflated false positive rates. We applied MR-Twin to 121 trait pairs in the UK Biobank dataset and found that MR-Twin identifies likely causal trait pairs and does not identify trait pairs that are unlikely to be causal. Our results suggest that confounding from population stratification can lead to false positives for existing MR methods, while MR-Twin is immune to this type of confounding.
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Affiliation(s)
| | - Boyang Fu
- Department of Computer Science, UCLA, Los Angeles CA
| | | | - Eleazar Eskin
- Department of Computer Science, UCLA, Los Angeles CA
- Department of Computational Medicine, UCLA, Los Angeles CA
- Department of Human Genetics, UCLA, Los Angeles CA
| | - Sriram Sankararaman
- Department of Computer Science, UCLA, Los Angeles CA
- Department of Computational Medicine, UCLA, Los Angeles CA
- Department of Human Genetics, UCLA, Los Angeles CA
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11
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Yang Y, Wang C, Liu L, Buxbaum J, He Z, Ionita-Laza I. KnockoffTrio: A knockoff framework for the identification of putative causal variants in genome-wide association studies with trio design. Am J Hum Genet 2022; 109:1761-1776. [PMID: 36150388 PMCID: PMC9606389 DOI: 10.1016/j.ajhg.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/24/2022] [Indexed: 01/25/2023] Open
Abstract
Family-based designs can eliminate confounding due to population substructure and can distinguish direct from indirect genetic effects, but these designs are underpowered due to limited sample sizes. Here, we propose KnockoffTrio, a statistical method to identify putative causal genetic variants for father-mother-child trio design built upon a recently developed knockoff framework in statistics. KnockoffTrio controls the false discovery rate (FDR) in the presence of arbitrary correlations among tests and is less conservative and thus more powerful than the conventional methods that control the family-wise error rate via Bonferroni correction. Furthermore, KnockoffTrio is not restricted to family-based association tests and can be used in conjunction with more powerful, potentially nonlinear models to improve the power of standard family-based tests. We show, using empirical simulations, that KnockoffTrio can prioritize causal variants over associations due to linkage disequilibrium and can provide protection against confounding due to population stratification. In applications to 14,200 trios from three study cohorts for autism spectrum disorders (ASDs), including AGP, SPARK, and SSC, we show that KnockoffTrio can identify multiple significant associations that are missed by conventional tests applied to the same data. In particular, we replicate known ASD association signals with variants in several genes such as MACROD2, NRXN1, PRKAR1B, CADM2, PCDH9, and DOCK4 and identify additional associations with variants in other genes including ARHGEF10, SLC28A1, ZNF589, and HINT1 at FDR 10%.
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Affiliation(s)
- Yi Yang
- Department of Biostatistics, Columbia University, New York, NY 10032, USA; Department of Biostatistics, City University of Hong Kong, Hong Kong SAR, China; School of Data Science, City University of Hong Kong, Hong Kong SAR, China
| | - Chen Wang
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Linxi Liu
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Joseph Buxbaum
- Departments of Psychiatry, Neuroscience, and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zihuai He
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
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12
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Chen W, Coombes BJ, Larson NB. Recent advances and challenges of rare variant association analysis in the biobank sequencing era. Front Genet 2022; 13:1014947. [PMID: 36276986 PMCID: PMC9582646 DOI: 10.3389/fgene.2022.1014947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022] Open
Abstract
Causal variants for rare genetic diseases are often rare in the general population. Rare variants may also contribute to common complex traits and can have much larger per-allele effect sizes than common variants, although power to detect these associations can be limited. Sequencing costs have steadily declined with technological advancements, making it feasible to adopt whole-exome and whole-genome profiling for large biobank-scale sample sizes. These large amounts of sequencing data provide both opportunities and challenges for rare-variant association analysis. Herein, we review the basic concepts of rare-variant analysis methods, the current state-of-the-art methods in utilizing variant annotations or external controls to improve the statistical power, and particular challenges facing rare variant analysis such as accounting for population structure, extremely unbalanced case-control design. We also review recent advances and challenges in rare variant analysis for familial sequencing data and for more complex phenotypes such as survival data. Finally, we discuss other potential directions for further methodology investigation.
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Affiliation(s)
- Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, United States
- *Correspondence: Wenan Chen, ; Brandon J. Coombes, ; Nicholas B. Larson,
| | - Brandon J. Coombes
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Wenan Chen, ; Brandon J. Coombes, ; Nicholas B. Larson,
| | - Nicholas B. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- *Correspondence: Wenan Chen, ; Brandon J. Coombes, ; Nicholas B. Larson,
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13
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Ray D, Vergara C, Taub MA, Wojcik G, Ladd‐Acosta C, Beaty TH, Duggal P. Benchmarking statistical methods for analyzing parent-child dyads in genetic association studies. Genet Epidemiol 2022; 46:266-284. [PMID: 35451532 PMCID: PMC9356976 DOI: 10.1002/gepi.22453] [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] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/06/2022] [Accepted: 03/15/2022] [Indexed: 11/24/2022]
Abstract
Genetic association studies of child health outcomes often employ family-based study designs. One of the most popular family-based designs is the case-parent trio design that considers the smallest possible nuclear family consisting of two parents and their affected child. This trio design is particularly advantageous for studying relatively rare disorders because it is less prone to type 1 error inflation due to population stratification compared to population-based study designs (e.g., case-control studies). However, obtaining genetic data from both parents is difficult, from a practical perspective, and many large studies predominantly measure genetic variants in mother-child dyads. While some statistical methods for analyzing parent-child dyad data (most commonly involving mother-child pairs) exist, it is not clear if they provide the same advantage as trio methods in protecting against population stratification, or if a specific dyad design (e.g., case-mother dyads vs. case-mother/control-mother dyads) is more advantageous. In this article, we review existing statistical methods for analyzing genome-wide marker data on dyads and perform extensive simulation experiments to benchmark their type I errors and statistical power under different scenarios. We extend our evaluation to existing methods for analyzing a combination of case-parent trios and dyads together. We apply these methods on genotyped and imputed data from multiethnic mother-child pairs only, case-parent trios only or combinations of both dyads and trios from the Gene, Environment Association Studies consortium (GENEVA), where each family was ascertained through a child affected by nonsyndromic cleft lip with or without cleft palate. Results from the GENEVA study corroborate the findings from our simulation experiments. Finally, we provide recommendations for using statistical genetic association methods for dyads.
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Affiliation(s)
- Debashree Ray
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
- Department of Biostatistics, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Candelaria Vergara
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Genevieve Wojcik
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Christine Ladd‐Acosta
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Priya Duggal
- Department of Epidemiology, Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
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14
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Brandes N, Weissbrod O, Linial M. Open problems in human trait genetics. Genome Biol 2022; 23:131. [PMID: 35725481 PMCID: PMC9208223 DOI: 10.1186/s13059-022-02697-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 05/30/2022] [Indexed: 12/21/2022] Open
Abstract
Genetic studies of human traits have revolutionized our understanding of the variation between individuals, and yet, the genetics of most traits is still poorly understood. In this review, we highlight the major open problems that need to be solved, and by discussing these challenges provide a primer to the field. We cover general issues such as population structure, epistasis and gene-environment interactions, data-related issues such as ancestry diversity and rare genetic variants, and specific challenges related to heritability estimates, genetic association studies, and polygenic risk scores. We emphasize the interconnectedness of these problems and suggest promising avenues to address them.
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Affiliation(s)
- Nadav Brandes
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Omer Weissbrod
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michal Linial
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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15
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Burt CH. Challenging the utility of polygenic scores for social science: Environmental confounding, downward causation, and unknown biology. Behav Brain Sci 2022; 46:e207. [PMID: 35551690 PMCID: PMC9653522 DOI: 10.1017/s0140525x22001145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The sociogenomics revolution is upon us, we are told. Whether revolutionary or not, sociogenomics is poised to flourish given the ease of incorporating polygenic scores (or PGSs) as "genetic propensities" for complex traits into social science research. Pointing to evidence of ubiquitous heritability and the accessibility of genetic data, scholars have argued that social scientists not only have an opportunity but a duty to add PGSs to social science research. Social science research that ignores genetics is, some proponents argue, at best partial and likely scientifically flawed, misleading, and wasteful. Here, I challenge arguments about the value of genetics for social science and with it the claimed necessity of incorporating PGSs into social science models as measures of genetic influences. In so doing, I discuss the impracticability of distinguishing genetic influences from environmental influences because of non-causal gene-environment correlations, especially population stratification, familial confounding, and downward causation. I explain how environmental effects masquerade as genetic influences in PGSs, which undermines their raison d'être as measures of genetic propensity, especially for complex socially contingent behaviors that are the subject of sociogenomics. Additionally, I draw attention to the partial, unknown biology, while highlighting the persistence of an implicit, unavoidable reductionist genes versus environments approach. Leaving sociopolitical and ethical concerns aside, I argue that the potential scientific rewards of adding PGSs to social science are few and greatly overstated and the scientific costs, which include obscuring structural disadvantages and cultural influences, outweigh these meager benefits for most social science applications.
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Affiliation(s)
- Callie H Burt
- Department of Criminal Justice & Criminology, Center for Research on Interpersonal Violence (CRIV), Georgia State University, Atlanta, GA, USA ; www.callieburt.org
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16
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Simulation Research on the Methods of Multi-Gene Region Association Analysis Based on a Functional Linear Model. Genes (Basel) 2022; 13:genes13030455. [PMID: 35328009 PMCID: PMC8954869 DOI: 10.3390/genes13030455] [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: 01/30/2022] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 11/16/2022] Open
Abstract
Genome-wide association analysis is an important approach to identify genetic variants associated with complex traits. Complex traits are not only affected by single gene loci, but also by the interaction of multiple gene loci. Studies of association between gene regions and quantitative traits are of great significance in revealing the genetic mechanism of biological development. There have been a lot of studies on single-gene region association analysis, but the application of functional linear models in multi-gene region association analysis is still less. In this paper, a functional multi-gene region association analysis test method is proposed based on the functional linear model. From the three directions of common multi-gene region method, multi-gene region weighted method and multi-gene region loci weighted method, that test method is studied combined with computer simulation. The following conclusions are obtained through computer simulation: (a) The functional multi-gene region association analysis test method has higher power than the functional single gene region association analysis test method; (b) The functional multi-gene region weighted method performs better than the common functional multi-gene region method; (c) the functional multi-gene region loci weighted method is the best method for association analysis on three directions of the common multi-gene region method; (d) the performance of the Step method and Multi-gene region loci weighted Step for multi-gene regions is the best in general. Functional multi-gene region association analysis test method can theoretically provide a feasible method for the study of complex traits affected by multiple genes.
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17
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Prokopenko D, Lee S, Hecker J, Mullin K, Morgan S, Katsumata Y, Weiner MW, Fardo DW, Laird N, Bertram L, Hide W, Lange C, Tanzi RE. Region-based analysis of rare genomic variants in whole-genome sequencing datasets reveal two novel Alzheimer's disease-associated genes: DTNB and DLG2. Mol Psychiatry 2022; 27:1963-1969. [PMID: 35246634 PMCID: PMC9126808 DOI: 10.1038/s41380-022-01475-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 01/25/2022] [Accepted: 02/04/2022] [Indexed: 01/01/2023]
Abstract
Alzheimer's disease (AD) is a genetically complex disease for which nearly 40 loci have now been identified via genome-wide association studies (GWAS). We attempted to identify groups of rare variants (alternate allele frequency <0.01) associated with AD in a region-based, whole-genome sequencing (WGS) association study (rvGWAS) of two independent AD family datasets (NIMH/NIA; 2247 individuals; 605 families). Employing a sliding window approach across the genome, we identified several regions that achieved association p values <10-6, using the burden test or the SKAT statistic. The genomic region around the dystobrevin beta (DTNB) gene was identified with the burden and SKAT test and replicated in case/control samples from the ADSP study reaching genome-wide significance after meta-analysis (pmeta = 4.74 × 10-8). SKAT analysis also revealed region-based association around the Discs large homolog 2 (DLG2) gene and replicated in case/control samples from the ADSP study (pmeta = 1 × 10-6). In conclusion, in a region-based rvGWAS of AD we identified two novel AD genes, DLG2 and DTNB, based on association with rare variants.
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Affiliation(s)
- Dmitry Prokopenko
- grid.32224.350000 0004 0386 9924Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Sanghun Lee
- grid.411982.70000 0001 0705 4288Department of Medical Consilience, Graduate School, Dankook University, Yongin, South Korea ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Julian Hecker
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.62560.370000 0004 0378 8294Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Kristina Mullin
- grid.32224.350000 0004 0386 9924Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA USA
| | - Sarah Morgan
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA USA
| | - Yuriko Katsumata
- grid.266539.d0000 0004 1936 8438Department of Biostatistics, University of Kentucky, Lexington, KY USA ,grid.266539.d0000 0004 1936 8438Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY USA
| | | | - Michael W. Weiner
- grid.266102.10000 0001 2297 6811Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA USA
| | - David W. Fardo
- grid.266539.d0000 0004 1936 8438Department of Biostatistics, University of Kentucky, Lexington, KY USA ,grid.266539.d0000 0004 1936 8438Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY USA
| | - Nan Laird
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Lars Bertram
- grid.4562.50000 0001 0057 2672Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany ,grid.5510.10000 0004 1936 8921Department of Psychology, University of Oslo, Oslo, Norway
| | - Winston Hide
- grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA ,grid.239395.70000 0000 9011 8547Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA USA
| | - Christoph Lange
- grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Rudolph E. Tanzi
- grid.32224.350000 0004 0386 9924Genetics and Aging Research Unit and The Henry and Allison McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
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18
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Leslie EJ. Genetic models and approaches to study orofacial clefts. Oral Dis 2021; 28:1327-1338. [PMID: 34923716 DOI: 10.1111/odi.14109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Orofacial clefts (OFCs) are common craniofacial birth defects with heterogeneous phenotype and etiology. Geneticists have applied nearly every available method and technology to further our understanding of the genetic architectures of OFCs. OBJECTIVE This review describes the evidence for a genetic etiology in OFCs, statistical genetic approaches employed to identify genetic causes, and how the results have shaped our current understanding of the genetic architectures of syndromic and nonsyndromic OFCs. CONCLUSION There has been rapid progress towards elucidating the genetic architectures of OFCs due to the availability of large collections of DNA samples from cases, controls, and families with OFCs and the consistent adoption of new methodologies and novel statistical approaches as they are developed. Genetic studies have identified rare and common variants influencing risk of OFCs in both Mendelian and complex forms of OFCs, blurring the distinctions traditional categories used in genetic studies and clinical medicine.
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19
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Qurashi TA, Bhat GA, Khan MS, Rasool R, Sameen F, Hassan I, Mudassar S. Interleukin 4 and Interleukin 4 receptor alpha gene variants and risk of atopy - A case control study based assessment. Clin Immunol 2021; 229:108783. [PMID: 34129931 DOI: 10.1016/j.clim.2021.108783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/12/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
INTRODUCTION IL4 pathway is known to upregulate IgE mediated immune responses and responsible for the manifestation of Atopic disorders. The current study was aimed to elucidate the genetic variations of Interleukin 4 (IL4) and Interleukin 4 receptor alpha (IL4R) genes and their possible association with atopic subjects. METHODS The well-designed questionnaire was used to collect the subject demographic and clinical details. Biochemical parameters were analysed using Chemiluminescent Immunoassay (CLIA) technique. The genotyping was performed using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). RESULTS We observed a statistically significant difference of serum Immunoglobulin-E (IgE) levels among cases and controls (P<0.05). Subjects harbouring the variant genotypes of I50V and Q576R single nucleotide polymorphisms (SNPs) in IL4R gene showed statistically differential risk towards atopic disorders. However, the variants genotype of 70 bp VNTR polymorphism in IL4 gene showed a protective role towards in predisposition to Atopy. On stratification, the above genetic variants had a significant impact on modifiable and non-modifiable factors associated with the disease. CONCLUSION Our study demonstrates that increased IgE levels and IL4 gene variants (I50V and Q576R) are significantly associated towards predisposition to allergic disorders in this study population.
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Affiliation(s)
- Taha Ashraf Qurashi
- Department of Clinical Biochemistry, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, 190011, J&K, India
| | - Gulzar Ahmad Bhat
- Department of Clinical Biochemistry, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, 190011, J&K, India
| | - Mosin Saleem Khan
- Department of Clinical Biochemistry, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, 190011, J&K, India
| | - Roohi Rasool
- Department of Immunology and Molecular Medicine, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, 190011, J&K, India
| | - Farah Sameen
- Department of Dermatology, SKIMS Medical College, Bemina, 190018, J&K, India
| | - Iffat Hassan
- Department of Dermatology & Venereal Diseases, Govt. Medical College Srinagar and Associated Hospitals, Karan Nagar, 190010, J&K, India
| | - Syed Mudassar
- Department of Clinical Biochemistry, Sher-I-Kashmir Institute of Medical Sciences (SKIMS), Soura, 190011, J&K, India.
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20
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Costantino F, Mambu Mambueni H, Said-Nahal R, Garchon HJ, Breban M. What Have We Learned From Family-Based Studies About Spondyloarthritis? Front Genet 2021; 12:671306. [PMID: 34149813 PMCID: PMC8209510 DOI: 10.3389/fgene.2021.671306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/12/2021] [Indexed: 01/31/2023] Open
Abstract
Spondyloarthritis (SpA) is a chronic inflammatory disorder with a high familial aggregation, emphasizing the existence of genetic susceptibility factors. In the last decades, family-based studies have contributed to better understand the genetic background of SpA, in particular by showing that the most likely model of transmission is oligogenic with multiplicative effects. Coexistence of different SpA subtypes within families also highlighted the complex interplay between all subtypes. Several whole-genome linkage analyses using sib-pairs or multiplex families were performed in the 1990s to try to identify genetic susceptibility factors besides HLA-B27. Unfortunately, no consistent results were obtained and family-based studies have been progressively set aside in favor of case-control designs. In particular, case-control genome-wide association studies allowed the identification of more than 40 susceptibility regions. However, all these loci explain only a small fraction of disease predisposition. Several hypotheses have been advanced to account for this unexplained heritability, including rare variants involvement, leading to a renewed interest in family-based designs, which are probably more powerful in the detection of such variants. In this review, our purpose is to summarize what has been learned to date regarding SpA genetics from family-based studies, with a special focus on recent identification of rare associated variants through next-generation sequencing studies.
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Affiliation(s)
- Félicie Costantino
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France.,Rheumatology Division, Ambroise Paré Hospital, Boulogne-Billancourt, France
| | - Hendrick Mambu Mambueni
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France
| | - Roula Said-Nahal
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France.,Rheumatology Division, Ambroise Paré Hospital, Boulogne-Billancourt, France
| | - Henri-Jean Garchon
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France.,Genetics Division, Ambroise Paré Hospital, Boulogne-Billancourt, France
| | - Maxime Breban
- UVSQ, Inserm U1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Montigny-le-Bretonneux, France.,Rheumatology Division, Ambroise Paré Hospital, Boulogne-Billancourt, France
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21
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Goswami C, Chattopadhyay A, Chuang EY. Rare variants: data types and analysis strategies. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:961. [PMID: 34277761 PMCID: PMC8267277 DOI: 10.21037/atm-21-1635] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Chayanika Goswami
- Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei.,Centre of Genomic and Precision Medicine, National Taiwan University, Taipei
| | | | - Eric Y Chuang
- Centre of Genomic and Precision Medicine, National Taiwan University, Taipei.,Department of Electrical Engineering, National Taiwan University, Taipei.,China Medical University, Taichung
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22
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Hecker J, Townes FW, Kachroo P, Laurie C, Lasky-Su J, Ziniti J, Cho MH, Weiss ST, Laird NM, Lange C. A unifying framework for rare variant association testing in family-based designs, including higher criticism approaches, SKATs, and burden tests. Bioinformatics 2021; 36:5432-5438. [PMID: 33367522 PMCID: PMC8016468 DOI: 10.1093/bioinformatics/btaa1055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/20/2020] [Accepted: 12/10/2020] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Analysis of rare variants in family-based studies remains a challenge. Transmission-based approaches provide robustness against population stratification, but the evaluation of the significance of test statistics based on asymptotic theory can be imprecise. Also, power will depend heavily on the choice of the test statistic and on the underlying genetic architecture of the locus, which will be generally unknown. RESULTS In our proposed framework, we utilize the FBAT haplotype algorithm to obtain the conditional offspring genotype distribution under the null hypothesis given the sufficient statistic. Based on this conditional offspring genotype distribution, the significance of virtually any association test statistic can be evaluated based on simulations or exact computations, without the need for asymptotic approximations. Besides standard linear burden-type statistics, this enables our approach to also evaluate other test statistics such as variance components statistics, higher criticism approaches, and maximum-single-variant-statistics, where asymptotic theory might be involved or does not provide accurate approximations for rare variant data. Based on these P-values, combined test statistics such as the aggregated Cauchy association test (ACAT) can also be utilized. In simulation studies, we show that our framework outperforms existing approaches for family-based studies in several scenarios. We also applied our methodology to a TOPMed whole-genome sequencing dataset with 897 asthmatic trios from Costa Rica. AVAILABILITY AND IMPLEMENTATION FBAT software is available at https://sites.google.com/view/fbatwebpage. Simulation code is available at https://github.com/julianhecker/FBAT_rare_variant_test_simulations. Whole-genome sequencing data for 'NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica' is available at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000988.v4.p1. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Julian Hecker
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - F William Townes
- Department of Computer Science, Princeton University, Princeton, NJ 08540-5233, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195-1617, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - John Ziniti
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nan M Laird
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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23
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Lou XY, Hou TT, Liu SY, Xu HM, Lin F, Tang X, MacLeod SL, Cleves MA, Hobbs CA. Innovative approach to identify multigenomic and environmental interactions associated with birth defects in family-based hybrid designs. Genet Epidemiol 2021; 45:171-189. [PMID: 32996630 PMCID: PMC8495752 DOI: 10.1002/gepi.22363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 11/09/2022]
Abstract
Genes, including those with transgenerational effects, work in concert with behavioral, environmental, and social factors via complex biological networks to determine human health. Understanding complex relationships between causal factors underlying human health is an essential step towards deciphering biological mechanisms. We propose a new analytical framework to investigate the interactions between maternal and offspring genetic variants or their surrogate single nucleotide polymorphisms (SNPs) and environmental factors using family-based hybrid study design. The proposed approach can analyze diverse genetic and environmental factors and accommodate samples from a variety of family units, including case/control-parental triads, and case/control-parental dyads, while minimizing potential bias introduced by population admixture. Comprehensive simulations demonstrated that our innovative approach outperformed the log-linear approach, the best available method for case-control family data. The proposed approach had greater statistical power and was capable to unbiasedly estimate the maternal and child genetic effects and the effects of environmental factors, while controlling the Type I error rate against population stratification. Using our newly developed approach, we analyzed the associations between maternal and fetal SNPs and obstructive and conotruncal heart defects, with adjustment for demographic and lifestyle factors and dietary supplements. Fourteen and 11 fetal SNPs were associated with obstructive and conotruncal heart defects, respectively. Twenty-seven and 17 maternal SNPs were associated with obstructive and conotruncal heart defects, respectively. In addition, maternal body mass index was a significant risk factor for obstructive defects. The proposed approach is a powerful tool for interrogating the etiological mechanism underlying complex traits.
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Affiliation(s)
- Xiang-Yang Lou
- Department of Biostatistics, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Ting-Ting Hou
- Department of Biostatistics, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, Florida, USA
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shou-Ye Liu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hai-Ming Xu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Feng Lin
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xinyu Tang
- The US Food and Drug Administration, Silver Spring, Maryland, USA
| | | | - Mario A. Cleves
- Department of Pediatrics, Morsani College of Medicine, Health Informatics Institute, University of South Florida, Tampa, Florida, USA
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, California, USA
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24
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The GGLEAM Study: Understanding Glaucoma in the Ohio Amish. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041551. [PMID: 33561996 PMCID: PMC7915874 DOI: 10.3390/ijerph18041551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022]
Abstract
Glaucoma leads to millions of cases of visual impairment and blindness around the world. Its susceptibility is shaped by both environmental and genetic risk factors. Although over 120 risk loci have been identified for glaucoma, a large portion of its heritability is still unexplained. Here we describe the foundation of the Genetics of GLaucoma Evaluation in the AMish (GGLEAM) study to investigate the genetic architecture of glaucoma in the Ohio Amish, which exhibits lower genetic and environmental heterogeneity compared to the general population. To date, we have enrolled 81 Amish individuals in our study from Holmes County, Ohio. As a part of our enrollment process, 62 GGLEAM study participants (42 glaucoma-affected and 20 unaffected individuals) received comprehensive eye examinations and glaucoma evaluations. Using the data from the Anabaptist Genealogy Database, we found that 80 of the GGLEAM study participants were related to one another through a large, multigenerational pedigree containing 1586 people. We plan to integrate the health and kinship data obtained for the GGLEAM study to interrogate glaucoma genetics and pathophysiology in this unique population.
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25
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Kanzi AM, San JE, Chimukangara B, Wilkinson E, Fish M, Ramsuran V, de Oliveira T. Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Front Genet 2020; 11:544162. [PMID: 33193618 PMCID: PMC7649788 DOI: 10.3389/fgene.2020.544162] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.
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Affiliation(s)
- Aquillah M. Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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26
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Komiyama Y, Koshiji C, Yoshida W, Natsume N, Kawamata H. 5,10-Methylenetetrahydrofolate reductase ( MTHFR) C677T/A1298C polymorphisms in patients with nonsyndromic cleft lip and palate. Biomed Rep 2020; 13:57. [PMID: 33123371 PMCID: PMC7583695 DOI: 10.3892/br.2020.1364] [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: 06/21/2020] [Accepted: 09/21/2020] [Indexed: 11/06/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is considered a multifactorial genetic disorder. Folic acid metabolism has been suggested to underlie the development of CL/P. The gene for the enzyme 5,10-methylentetrahydrofolate reductase (MTHFR) contributes to folic acid metabolism, and polymorphisms of this gene at C677T (rs1801133) and A1298C (rs1801131) are reported to alter its enzyme activity and are suggested to be involved in CL/P development. We investigated C677T and A1298C polymorphisms of the MTHFR gene in Japanese patients with nonsyndromic CL/P and cleft palate only (CPO). We examined 240 patients with CL/P, 103 fathers and 153 mothers of the patients, and 68 healthy controls. Restriction fragment length polymorphisms (RFLPs) of C677T and A1298C of MTHFR were analyzed. We determined the frequencies of the polymorphisms in the patients and controls and performed a transmission equilibrium test and haplotype analysis of both MTHFR C677T and A1298C. There were no significant differences in the frequencies of MTHFR C677T and A1298C polymorphisms between the patients and controls. We did not observe transmission equilibrium or linkage equilibrium among the cases. In this experimental condition, we did not detect an association of MTHFR C677T and/or A1298C polymorphisms with the development of CL/P in this Japanese cohort.
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Affiliation(s)
- Yuske Komiyama
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Mibu, Tochigi 321-0293, Japan
| | - Chikako Koshiji
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Mibu, Tochigi 321-0293, Japan
| | - Waka Yoshida
- Department of Oral Pathology, School of Dentistry, Aichi-Gakuin University, Nagoya, Aichi 464-8650, Japan
| | - Nagato Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, School of Dentistry, Aichi-Gakuin University, Nagoya, Aichi 464-8650, Japan
| | - Hitoshi Kawamata
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine, Mibu, Tochigi 321-0293, Japan
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27
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Xiang X, Wang S, Liu T, Wang M, Li J, Jiang J, Wu T, Hu Y. Exploring gene-gene interaction in family-based data with an unsupervised machine learning method: EPISFA. Genet Epidemiol 2020; 44:811-824. [PMID: 32869348 DOI: 10.1002/gepi.22342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/06/2020] [Accepted: 06/21/2020] [Indexed: 11/06/2022]
Abstract
Gene-gene interaction (G × G) is thought to fill the gap between the estimated heritability of complex diseases and the limited genetic proportion explained by identified single-nucleotide polymorphisms. The current tools for exploring G × G were often developed for case-control designs with less considerations for their applications in families. Family-based studies are robust against bias led from population stratification in genetic studies and helpful in understanding G × G. We proposed a new algorithm epistasis sparse factor analysis (EPISFA) and epistasis sparse factor analysis for linkage disequilibrium (EPISFA-LD) based on unsupervised machine learning to screen G × G. Extensive simulations were performed to compare EPISFA/EPISFA-LD with a classical family-based algorithm FAM-MDR (family-based multifactor dimensionality reduction). The results showed that EPISFA/EPISFA-LD is a tool of both high power and computational efficiency that could be applied in family designs and is applicable within high-dimensionality datasets. Finally, we applied EPISFA/EPISFA-LD to a real dataset drawn from the Fangshan/family-based Ischemic Stroke Study in China. Five pairs of G × G were discovered by EPISFA/EPISFA-LD, including three pairs verified by other algorithms (FAM-MDR and logistic), and an additional two pairs uniquely identified by EPISFA/EPISFA-LD only. The results from EPISFA might offer new insights for understanding the genetic etiology of complex diseases. EPISFA/EPISFA-LD was implemented in R. All relevant source code as well as simulated data could be freely downloaded from https://github.com/doublexism/episfa.
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Affiliation(s)
- Xiao Xiang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Siyue Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Tianyi Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Capital Medical University, Beijing, China
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jiawen Li
- Department of Clinical Medicine, School of Medicine, Peking University, Beijing, China
| | - Jin Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yonghua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
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28
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Turkmen AS, Lin S. Detecting X-linked common and rare variant effects in family-based sequencing studies. Genet Epidemiol 2020; 45:36-45. [PMID: 32864779 DOI: 10.1002/gepi.22352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/26/2020] [Accepted: 08/03/2020] [Indexed: 11/08/2022]
Abstract
The breakthroughs in next generation sequencing have allowed us to access data consisting of both common and rare variants, and in particular to investigate the impact of rare genetic variation on complex diseases. Although rare genetic variants are thought to be important components in explaining genetic mechanisms of many diseases, discovering these variants remains challenging, and most studies are restricted to population-based designs. Further, despite the shift in the field of genome-wide association studies (GWAS) towards studying rare variants due to the "missing heritability" phenomenon, little is known about rare X-linked variants associated with complex diseases. For instance, there is evidence that X-linked genes are highly involved in brain development and cognition when compared with autosomal genes; however, like most GWAS for other complex traits, previous GWAS for mental diseases have provided poor resources to deal with identification of rare variant associations on X-chromosome. In this paper, we address the two issues described above by proposing a method that can be used to test X-linked variants using sequencing data on families. Our method is much more general than existing methods, as it can be applied to detect both common and rare variants, and is applicable to autosomes as well. Our simulation study shows that the method is efficient, and exhibits good operational characteristics. An application to the University of Miami Study on Genetics of Autism and Related Disorders also yielded encouraging results.
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Affiliation(s)
- Asuman S Turkmen
- Statistics Department, The Ohio State University, Columbus, Ohio.,Statistics Department, The Ohio State University, Newark, Ohio
| | - Shili Lin
- Statistics Department, The Ohio State University, Columbus, Ohio
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29
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Pagliaroli L, Vereczkei A, Padmanabhuni SS, Tarnok Z, Farkas L, Nagy P, Rizzo R, Wolanczyk T, Szymanska U, Kapisyzi M, Basha E, Koumoula A, Androutsos C, Tsironi V, Karagiannidis I, Paschou P, Barta C. Association of Genetic Variation in the 3'UTR of LHX6, IMMP2L, and AADAC With Tourette Syndrome. Front Neurol 2020; 11:803. [PMID: 32922348 PMCID: PMC7457023 DOI: 10.3389/fneur.2020.00803] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/29/2020] [Indexed: 01/08/2023] Open
Abstract
Background: Tourette Syndrome (TS) is a neurodevelopmental disorder that presents with motor and vocal tics early in childhood. The aim of this study was to investigate genetic variants in the 3' untranslated region (3'UTR) of TS candidate genes with a putative link to microRNA (miRNA) mediated regulation or gene expression. Methods: We used an in silico approach to identify 32 variants in the 3'UTR of 18 candidate genes putatively changing the binding site for miRNAs. In a sample composed of TS cases and controls (n = 290), as well as TS family trios (n = 148), we performed transmission disequilibrium test (TDT) and meta-analysis. Results: We found positive association of rs3750486 in the LIM homeobox 6 (LHX6) gene (p = 0.021) and rs7795011 in the inner mitochondrial membrane peptidase subunit 2 (IMMP2L) gene (p = 0.029) with TS in our meta-analysis. The TDT showed an over-transmission of the A allele of rs1042201 in the arylacetamide deacetylase (AADAC) gene in TS patients (p = 0.029). Conclusion: This preliminary study provides further support for the involvement of LHX6, IMMP2L, and AADAC genes, as well as epigenetic mechanisms, such as altered miRNA mediated gene expression regulation in the etiology of TS.
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Affiliation(s)
- Luca Pagliaroli
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Andrea Vereczkei
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | | | - Zsanett Tarnok
- Vadaskert Clinic for Child and Adolescent Psychiatry, Budapest, Hungary
| | - Luca Farkas
- Vadaskert Clinic for Child and Adolescent Psychiatry, Budapest, Hungary
| | - Peter Nagy
- Vadaskert Clinic for Child and Adolescent Psychiatry, Budapest, Hungary
| | - Renata Rizzo
- Materno Infantile and Radiological Science Department, University of Catania, Catania, Italy
| | - Tomasz Wolanczyk
- Department of Child Psychiatry, Medical University of Warsaw, Warsaw, Poland
| | - Urszula Szymanska
- Department of Child Psychiatry, Medical University of Warsaw, Warsaw, Poland
| | - Mira Kapisyzi
- University Hospital Center "Mother Theresa," Tirana, Albania
| | - Entela Basha
- University Hospital Center "Mother Theresa," Tirana, Albania
| | - Anastasia Koumoula
- Department of Child and Adolescent Psychiatry, Sismanoglio General Hospital of Attica, Athens, Greece
| | - Christos Androutsos
- Department of Child and Adolescent Psychiatry, Sismanoglio General Hospital of Attica, Athens, Greece
| | - Vaia Tsironi
- Department of Child and Adolescent Psychiatry, Sismanoglio General Hospital of Attica, Athens, Greece
| | - Iordanis Karagiannidis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
| | - Peristera Paschou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
| | - Csaba Barta
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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30
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Liu R, Yuan M, Xu H, Chen P, Xu XS, Yang Y. Adaptive weighted sum tests via LASSO method in multi-locus family-based association analysis. Comput Biol Chem 2020; 88:107320. [PMID: 32711355 DOI: 10.1016/j.compbiolchem.2020.107320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 03/06/2020] [Accepted: 06/22/2020] [Indexed: 01/20/2023]
Abstract
Family based multi-locus tests integrate information from individual loci by weighted averaging of the marginal statistics, and have been proven to be more efficient and robust than the single-locus tests in genetic association studies. The power depends on how much information the weights can extract from data. The currently published weighted sum methods are only applicable to either common or rare variants and may suffer from substantial power loss especially for rare variants. In this paper, we propose a novel data-driven weight to improve the power under both common and rare variant circumstances. We use the l1 regularization in Least Absolute Shrinkage and Selection Operator (LASSO) regression to construct the weight serving as a simultaneously adaptive marker selection process. Simulations for a dichotomous phenotype demonstrated that our LASSO-based approach outperformed the existing multi-locus methods in the sense of providing the highest statistical power while well controlled type I error rate under different scenarios. We also applied our methods to a real dataset for rheumatoid arthritis (GAW15 Problem 2). Two groups of alleles, in which individual SNPs had only modest and non-significant effects, were detected (P < 0.00001) using our proposed methods, whereas traditional multi-locus methods failed to identify them. In conclusion, the novel LASSO-based approach represents a superior weight-choosing strategy for multi-locus tests.
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Affiliation(s)
- Rui Liu
- Department of Statistics and Finance, University of Science and Technology of China, Hefei 230026, China
| | - Min Yuan
- School of Public Health Administration, Anhui Medical School, Hefei 230032, China
| | - Huang Xu
- Department of Statistics and Finance, University of Science and Technology of China, Hefei 230026, China
| | - Pinzhong Chen
- Jiangyin Hospital of Traditional Chinese Medicine, Wuxi 214401, China
| | - Xu Steven Xu
- Janssen Research and Development, 920 Route 202, Raritan, NJ 08869, USA.
| | - Yaning Yang
- Department of Statistics and Finance, University of Science and Technology of China, Hefei 230026, China.
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31
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Prokopenko D, Hecker J, Kirchner R, Chapman BA, Hoffman O, Mullin K, Hide W, Bertram L, Laird N, DeMeo DL, Lange C, Tanzi RE. Identification of Novel Alzheimer's Disease Loci Using Sex-Specific Family-Based Association Analysis of Whole-Genome Sequence Data. Sci Rep 2020; 10:5029. [PMID: 32193444 PMCID: PMC7081222 DOI: 10.1038/s41598-020-61883-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/17/2020] [Indexed: 11/21/2022] Open
Abstract
With the advent of whole genome-sequencing (WGS) studies, family-based designs enable sex-specific analysis approaches that can be applied to only affected individuals; tests using family-based designs are attractive because they are completely robust against the effects of population substructure. These advantages make family-based association tests (FBATs) that use siblings as well as parents especially suited for the analysis of late-onset diseases such as Alzheimer's Disease (AD). However, the application of FBATs to assess sex-specific effects can require additional filtering steps, as sensitivity to sequencing errors is amplified in this type of analysis. Here, we illustrate the implementation of robust analysis approaches and additional filtering steps that can minimize the chances of false positive-findings due to sex-specific sequencing errors. We apply this approach to two family-based AD datasets and identify four novel loci (GRID1, RIOK3, MCPH1, ZBTB7C) showing sex-specific association with AD risk. Following stringent quality control filtering, the strongest candidate is ZBTB7C (Pinter = 1.83 × 10-7), in which the minor allele of rs1944572 confers increased risk for AD in females and protection in males. ZBTB7C encodes the Zinc Finger and BTB Domain Containing 7C, a transcriptional repressor of membrane metalloproteases (MMP). Members of this MMP family were implicated in AD neuropathology.
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Affiliation(s)
- Dmitry Prokopenko
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Julian Hecker
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rory Kirchner
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brad A Chapman
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Oliver Hoffman
- Department of Clinical Pathology, University of Melbourne, Victoria, 3000, Melbourne, Australia
| | - Kristina Mullin
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Winston Hide
- Harvard Medical School, Boston, MA, USA
- Department of Neuroscience, Sheffield Institute for Translational Neurosciences, University of Sheffield, Sheffield, UK
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, US
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Nan Laird
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Dawn L DeMeo
- Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Rudolph E Tanzi
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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Jiang S, Cook RJ. A Mixture Model for Bivariate Interval-Censored Failure Times with Dependent Susceptibility. STATISTICS IN BIOSCIENCES 2020. [DOI: 10.1007/s12561-020-09270-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Pyhäjärvi T, Kujala ST, Savolainen O. 275 years of forestry meets genomics in Pinus sylvestris. Evol Appl 2020; 13:11-30. [PMID: 31988655 PMCID: PMC6966708 DOI: 10.1111/eva.12809] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA-seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long-term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.
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Affiliation(s)
- Tanja Pyhäjärvi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| | | | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
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Maili L, Letra A, Silva R, Buchanan EP, Mulliken JB, Greives MR, Teichgraeber JF, Blackwell SJ, Ummer R, Weber R, Chiquet B, Blanton SH, Hecht JT. PBX-WNT-P63-IRF6 pathway in nonsyndromic cleft lip and palate. Birth Defects Res 2019; 112:234-244. [PMID: 31825181 DOI: 10.1002/bdr2.1630] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/18/2019] [Accepted: 11/21/2019] [Indexed: 01/01/2023]
Abstract
Nonsyndromic cleft lip and palate (NSCLP) is one of the most common craniofacial anomalies in humans, affecting more than 135,000 newborns worldwide. NSCLP has a multifactorial etiology with more than 50 genes postulated to play an etiologic role. The genetic pathway comprised of Pbx-Wnt-p63-Irf6 genes was shown to control facial morphogenesis in mice and proposed as a regulatory pathway for NSCLP. Based on these findings, we investigated whether variation in PBX1, PBX2, and TP63, and their proposed interactions were associated with NSCLP. Fourteen single nucleotide variants (SNVs) in/nearby PBX1, PBX2, and TP63 were genotyped in 780 NSCLP families of nonHispanic white (NHW) and Hispanic ethnicities. Family-based association tests were performed for individual SNVs stratified by ethnicity and family history of NSCLP. Gene-gene interactions were also tested. A significant association was found for PBX2 rs3131300 and NSCLP in combined Hispanic families (p = .003) while nominal association was found for TP63 rs9332461 in multiplex Hispanic families (p = .005). Significant haplotype associations were observed for PBX2 in NHW (p = .0002) and Hispanic families (p = .003), and for TP63 in multiplex Hispanic families (.003). An independent case-control group was used to validate findings, and significant associations were found with PBX1 rs6426870 (p = .007) and TP63 rs9332461 (p = .03). Gene-gene interactions were detected between PBX1/PBX2/TP63 with IRF6 in NHW families, and between PBX1 with WNT9B in both NHW and Hispanic families (p < .0018). This study provides the first evidence for a role of PBX1 and PBX2, additional evidence for the role of TP63, and support for the proposed PBX-WNT-TP63-IRF6 regulatory pathway in the etiology of NSCLP.
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Affiliation(s)
- Lorena Maili
- Department of Pediatrics, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | - Ariadne Letra
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Renato Silva
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Department of Endodontics, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Edward P Buchanan
- Department of Plastic Surgery, Texas Children's Hospital, Houston, Texas
| | | | - Matthew R Greives
- Department of Pediatric Surgery, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | - John F Teichgraeber
- Department of Pediatric Surgery, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | | | - Rohit Ummer
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Ryan Weber
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Brett Chiquet
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Department of Pediatric Dentistry, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Susan H Blanton
- Dr. John T. MacDonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas.,Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
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Kachroo P, Hecker J, Chawes BL, Ahluwalia TS, Cho MH, Qiao D, Kelly RS, Chu SH, Virkud YV, Huang M, Barnes KC, Burchard EG, Eng C, Hu D, Celedón JC, Daya M, Levin AM, Gui H, Williams LK, Forno E, Mak ACY, Avila L, Soto-Quiros ME, Cloutier MM, Acosta-Pérez E, Canino G, Bønnelykke K, Bisgaard H, Raby BA, Lange C, Weiss ST, Lasky-Su JA. Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma. Chest 2019; 156:1068-1079. [PMID: 31557467 PMCID: PMC6904857 DOI: 10.1016/j.chest.2019.08.2202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/02/2019] [Accepted: 08/22/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Asthma is a common respiratory disorder with a highly heterogeneous nature that remains poorly understood. The objective was to use whole genome sequencing (WGS) data to identify regions of common genetic variation contributing to lung function in individuals with a diagnosis of asthma. METHODS WGS data were generated for 1,053 individuals from trios and extended pedigrees participating in the family-based Genetic Epidemiology of Asthma in Costa Rica study. Asthma affection status was defined through a physician's diagnosis of asthma, and most participants with asthma also had airway hyperresponsiveness (AHR) to methacholine. Family-based association tests for single variants were performed to assess the associations with lung function phenotypes. RESULTS A genome-wide significant association was identified between baseline FEV1/FVC ratio and a single-nucleotide polymorphism in the top hit cysteine-rich secretory protein LCCL domain-containing 2 (CRISPLD2) (rs12051168; P = 3.6 × 10-8 in the unadjusted model) that retained suggestive significance in the covariate-adjusted model (P = 5.6 × 10-6). Rs12051168 was also nominally associated with other related phenotypes: baseline FEV1 (P = 3.3 × 10-3), postbronchodilator (PB) FEV1 (7.3 × 10-3), and PB FEV1/FVC ratio (P = 2.7 × 10-3). The identified baseline FEV1/FVC ratio and rs12051168 association was meta-analyzed and replicated in three independent cohorts in which most participants with asthma also had confirmed AHR (combined weighted z-score P = .015) but not in cohorts without information about AHR. CONCLUSIONS These findings suggest that using specific asthma characteristics, such as AHR, can help identify more genetically homogeneous asthma subgroups with genotype-phenotype associations that may not be observed in all children with asthma. CRISPLD2 also may be important for baseline lung function in individuals with asthma who also may have AHR.
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Affiliation(s)
- Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Julian Hecker
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bo L Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Tarunveer S Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Rachel S Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Su H Chu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Yamini V Virkud
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Department of Pediatrics, Massachusetts General Hospital for Children and Harvard Medical School, Boston, MA
| | - Mengna Huang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Colorado, CO
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Colorado, CO
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI; Center for Bioinformatics, Henry Ford Health System, Detroit, MI
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI; Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Henry Ford Health System, Detroit, MI; Department of Internal Medicine, Henry Ford Health System, Detroit, MI
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, Allergy and Immunology, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA
| | - Angel C Y Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Lydiana Avila
- Department of Pediatrics, Hospital Nacional de Niños, San José, Costa Rica
| | | | | | - Edna Acosta-Pérez
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA; Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.
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Genetic Variation Underpinning ADHD Risk in a Caribbean Community. Cells 2019; 8:cells8080907. [PMID: 31426340 PMCID: PMC6721689 DOI: 10.3390/cells8080907] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/07/2019] [Accepted: 08/12/2019] [Indexed: 12/13/2022] Open
Abstract
Attention Deficit Hyperactivity Disorder (ADHD) is a highly heritable and prevalent neurodevelopmental disorder that frequently persists into adulthood. Strong evidence from genetic studies indicates that single nucleotide polymorphisms (SNPs) harboured in the ADGRL3 (LPHN3), SNAP25, FGF1, DRD4, and SLC6A2 genes are associated with ADHD. We genotyped 26 SNPs harboured in genes previously reported to be associated with ADHD and evaluated their potential association in 386 individuals belonging to 113 nuclear families from a Caribbean community in Barranquilla, Colombia, using family-based association tests. SNPs rs362990-SNAP25 (T allele; p = 2.46 × 10−4), rs2282794-FGF1 (A allele; p = 1.33 × 10−2), rs2122642-ADGRL3 (C allele, p = 3.5 × 10−2), and ADGRL3 haplotype CCC (markers rs1565902-rs10001410-rs2122642, OR = 1.74, Ppermuted = 0.021) were significantly associated with ADHD. Our results confirm the susceptibility to ADHD conferred by SNAP25, FGF1, and ADGRL3 variants in a community with a significant African American component, and provide evidence supporting the existence of specific patterns of genetic stratification underpinning the susceptibility to ADHD. Knowledge of population genetics is crucial to define risk and predict susceptibility to disease.
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Odgerel Z, Sonti S, Hernandez N, Park J, Ottman R, Louis ED, Clark LN. Whole genome sequencing and rare variant analysis in essential tremor families. PLoS One 2019; 14:e0220512. [PMID: 31404076 PMCID: PMC6690583 DOI: 10.1371/journal.pone.0220512] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/17/2019] [Indexed: 11/19/2022] Open
Abstract
Essential tremor (ET) is one of the most common movement disorders. The etiology of ET remains largely unexplained. Whole genome sequencing (WGS) is likely to be of value in understanding a large proportion of ET with Mendelian and complex disease inheritance patterns. In ET families with Mendelian inheritance patterns, WGS may lead to gene identification where WES analysis failed to identify the causative single nucleotide variant (SNV) or indel due to incomplete coverage of the entire coding region of the genome, in addition to accurate detection of larger structural variants (SVs) and copy number variants (CNVs). Alternatively, in ET families with complex disease inheritance patterns with gene x gene and gene x environment interactions enrichment of functional rare coding and non-coding variants may explain the heritability of ET. We performed WGS in eight ET families (n = 40 individuals) enrolled in the Family Study of Essential Tremor. The analysis included filtering WGS data based on allele frequency in population databases, rare SNV and indel classification and association testing using the Mixed-Model Kernel Based Adaptive Cluster (MM-KBAC) test. A separate analysis of rare SV and CNVs segregating within ET families was also performed. Prioritization of candidate genes identified within families was performed using phenolyzer. WGS analysis identified candidate genes for ET in 5/8 (62.5%) of the families analyzed. WES analysis in a subset of these families in our previously published study failed to identify candidate genes. In one family, we identified a deleterious and damaging variant (c.1367G>A, p.(Arg456Gln)) in the candidate gene, CACNA1G, which encodes the pore forming subunit of T-type Ca(2+) channels, CaV3.1, and is expressed in various motor pathways and has been previously implicated in neuronal autorhythmicity and ET. Other candidate genes identified include SLIT3 which encodes an axon guidance molecule and in three families, phenolyzer prioritized genes that are associated with hereditary neuropathies (family A, KARS, family B, KIF5A and family F, NTRK1). Functional studies of CACNA1G and SLIT3 suggest a role for these genes in ET disease pathogenesis.
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Affiliation(s)
- Zagaa Odgerel
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, United States of America
| | - Shilpa Sonti
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, United States of America
| | - Nora Hernandez
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States of America
| | - Jemin Park
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States of America
| | - Ruth Ottman
- G.H Sergievsky Center, Columbia University, New York, NY, United States of America
- Department of Neurology, College of Physicians and Surgeons, Columbia University New York, NY, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, NY, United States of America
- Division of Epidemiology, New York State Psychiatric Institute, New York, NY, United States of America
| | - Elan D. Louis
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT, United States of America
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States of America
| | - Lorraine N. Clark
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, United States of America
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, United States of America
- * E-mail:
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Yin Q, Sun K, Xiang X, Juan J, Cao Y, Song J, Yang Y, Shi M, Tian Y, Liu K, Fang K, Li J, Tang X, Wu Y, Qin X, Wu T, Chen D, Hu Y. Identification of Novel CXCL12 Genetic Polymorphisms Associated with Type 2 Diabetes Mellitus: A Chinese Sib-Pair Study. Genet Test Mol Biomarkers 2019; 23:435-441. [PMID: 31294628 DOI: 10.1089/gtmb.2018.0149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aims: To discover possible relationships between CXCL12 single nucleotide polymorphisms (SNPs) and type 2 diabetes mellitus (T2DM) and its risk factors. Methods: The present sib-pair study was conducted in a rural community of Beijing, China. SNPs rs2297630, rs1746048, and rs1801157 located within or nearby the CXCL12 gene were genotyped using the allele-specific polymerase chain reaction method. Haseman-Elston regression was used to investigate linkages between these SNPs and T2DM. A generalized estimating equation logistic regression model was used to discover associations between the SNPs, T2DM, and its risk factors. Results: A total of 3171 participants were recruited, comprising 2277 sib pairs. After Bonferroni correction (α = 0.016), rs2297630 was found to be significantly linked to (p = 0.003) and associated with T2DM (AA vs. GG/GA: OR = 2.26, 95% CI: 1.31-3.88, p = 0.003). There were interactions between rs2297630 and dyslipidemia (p < 0.001) and between rs1746048 and hypertension (p = 0.011). Compared to dyslipidemia-free subjects with rs2297630 GG/GA genotypes, dyslipidemia patients with rs2297630 AA had a higher risk of T2DM (OR = 4.15, 95% CI: 2.24-7.67, p < 0.001). Compared to hypertension-free subjects with rs1746048 CC genotypes, hypertension-free subjects with rs1746048 CT/TT had a decreased risk of T2DM (OR = 0.77, 95% CI: 0.60-0.99, p = 0.045). Conclusions: A novel linkage and association was found between rs2297630 and T2DM. Moreover, novel interactions were found between rs2297630 and dyslipidemia as well as rs1746048 and hypertension. These findings will help identify individuals at higher risk of developing T2DM.
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Affiliation(s)
- Qiongzhou Yin
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Kexin Sun
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Xiao Xiang
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Juan Juan
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Yaying Cao
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Jing Song
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Yanfen Yang
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Moye Shi
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Yaohua Tian
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Kuo Liu
- 2 Department of Epidemiology & Biostatistics, Capital Medical University, Beijing, China
| | - Kai Fang
- 3 Beijing Center for Disease Prevention and Control, Beijing, China
| | - Jing Li
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Xun Tang
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Yiqun Wu
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Xueying Qin
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Tao Wu
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Dafang Chen
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
| | - Yonghua Hu
- 1 Department of Epidemiology and Biostatistics, School of Public Public Health, Peking University, Beijing, China
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Rediscovering the value of families for psychiatric genetics research. Mol Psychiatry 2019; 24:523-535. [PMID: 29955165 PMCID: PMC7028329 DOI: 10.1038/s41380-018-0073-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/11/2018] [Accepted: 03/26/2018] [Indexed: 01/09/2023]
Abstract
As it is likely that both common and rare genetic variation are important for complex disease risk, studies that examine the full range of the allelic frequency distribution should be utilized to dissect the genetic influences on mental illness. The rate limiting factor for inferring an association between a variant and a phenotype is inevitably the total number of copies of the minor allele captured in the studied sample. For rare variation, with minor allele frequencies of 0.5% or less, very large samples of unrelated individuals are necessary to unambiguously associate a locus with an illness. Unfortunately, such large samples are often cost prohibitive. However, by using alternative analytic strategies and studying related individuals, particularly those from large multiplex families, it is possible to reduce the required sample size while maintaining statistical power. We contend that using whole genome sequence (WGS) in extended pedigrees provides a cost-effective strategy for psychiatric gene mapping that complements common variant approaches and WGS in unrelated individuals. This was our impetus for forming the "Pedigree-Based Whole Genome Sequencing of Affective and Psychotic Disorders" consortium. In this review, we provide a rationale for the use of WGS with pedigrees in modern psychiatric genetics research. We begin with a focused review of the current literature, followed by a short history of family-based research in psychiatry. Next, we describe several advantages of pedigrees for WGS research, including power estimates, methods for studying the environment, and endophenotypes. We conclude with a brief description of our consortium and its goals.
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40
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Statistical methods for genome-wide association studies. Semin Cancer Biol 2019; 55:53-60. [DOI: 10.1016/j.semcancer.2018.04.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 12/12/2022]
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Lan T, Yang B, Zhang X, Wang T, Lu Q. Statistical Methods and Software for Substance Use and Dependence Genetic Research. Curr Genomics 2019; 20:172-183. [PMID: 31929725 PMCID: PMC6935956 DOI: 10.2174/1389202920666190617094930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Accepted: 05/24/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Substantial substance use disorders and related health conditions emerged dur-ing the mid-20th century and continue to represent a remarkable 21st century global burden of disease. This burden is largely driven by the substance-dependence process, which is a complex process and is influenced by both genetic and environmental factors. During the past few decades, a great deal of pro-gress has been made in identifying genetic variants associated with Substance Use and Dependence (SUD) through linkage, candidate gene association, genome-wide association and sequencing studies. METHODS Various statistical methods and software have been employed in different types of SUD ge-netic studies, facilitating the identification of new SUD-related variants. CONCLUSION In this article, we review statistical methods and software that are currently available for SUD genetic studies, and discuss their strengths and limitations.
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Affiliation(s)
| | | | | | - Tong Wang
- Address correspondence to these authors at the Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Tel/ Fax: ++1-517-353-8623; E-mails: ;
| | - Qing Lu
- Address correspondence to these authors at the Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Tel/ Fax: ++1-517-353-8623; E-mails: ;
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Song J, Jiang X, Cao Y, Juan J, Wu T, Hu Y. Interaction between an ATP-Binding Cassette A1 (ABCA1) Variant and Egg Consumption for the Risk of Ischemic Stroke and Carotid Atherosclerosis: a Family-Based Study in the Chinese Population. J Atheroscler Thromb 2019; 26:835-845. [PMID: 30828007 PMCID: PMC6753237 DOI: 10.5551/jat.46615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aims: ATP-binding cassette A1 (ABCA1) plays an important role in reducing the risk of stroke. Egg is the major source of dietary cholesterol and is known to be associated with the risk of stroke and atherosclerosis. We aimed to assess the effects of interaction between an ABCA1 variant (rs2066715) and egg consumption on the risk of ischemic stroke (IS), carotid plaque, and carotid-intima media thickness (CIMT) in the Chinese population. Methods: In total, 5869 subjects (including 1213 IS cases) across 1128 families were enrolled and divided into two groups based on the median egg consumption (4 eggs per week). In the analyses for the presence of carotid plaque and CIMT, 3171 out of 4656 IS-free controls without self-reported history of coronary heart disease and lipid-lowering medications were included. Multilevel logistic regression models were used to model the genetic association of rs2066715 with the risk of IS, and mixed-effect linear regression for the genetic association of rs2066715 with carotid plaque, and CIMT. The gene-by-egg cross-product term was included in the regression model for interaction analysis. Results: We found that rs2066715 was associated with the increased risk of carotid plaque among those who consumed < 4 eggs per week after adjustment (odds ratio [95% confidence interval]: 1.61 [1.08, 2.39], P = 0.019). A significant effect of interaction between rs2066715 and egg consumption on the risk of carotid plaque was identified (P = 0.011). Conclusion: rs2066715 was found to interact with egg consumption in modifying the risk of carotid plaque in the Chinese population.
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Affiliation(s)
- Jing Song
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University
| | - Xia Jiang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health.,Unit of Cardiovascular Epidemiology, Institute of Environmental Health, Karolinska Institute
| | - Yaying Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University
| | - Juan Juan
- Department of Obstetrics and Gynecology, Peking University First Hospital
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University
| | - Yonghua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University
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43
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Najafi A, Janghorbani S, Motahari SA, Fatemizadeh E. Statistical Association Mapping of Population-Structured Genetic Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:638-649. [PMID: 29990264 DOI: 10.1109/tcbb.2017.2786239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Association mapping of genetic diseases has attracted extensive research interest during the recent years. However, most of the methodologies introduced so far suffer from spurious inference of the associated sites due to population inhomogeneities. In this paper, we introduce a statistical framework to compensate for this shortcoming by equipping the current methodologies with a state-of-the-art clustering algorithm being widely used in population genetics applications. The proposed framework jointly infers the disease-associated factors and the hidden population structures. In this regard, a Markov Chain-Monte Carlo (MCMC) procedure has been employed to assess the posterior probability distribution of the model parameters. We have implemented our proposed framework on a software package whose performance is extensively evaluated on a number of synthetic datasets, and compared to some of the well-known existing methods such as STRUCTURE. It has been shown that in extreme scenarios, up to $10-15$10-15 percent of improvement in the inference accuracy is achieved with a moderate increase in computational complexity.
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44
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Yan W, Hao Z, Tang S, Dai J, Zheng L, Yu P, Yan W, Han X, Xu X, Shi D, Ikegawa S, Teng H, Jiang Q. A genome-wide association study identifies new genes associated with developmental dysplasia of the hip. Clin Genet 2019; 95:345-355. [PMID: 30511388 DOI: 10.1111/cge.13483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/03/2018] [Accepted: 11/17/2018] [Indexed: 11/30/2022]
Abstract
Developmental dysplasia of the hip (DDH) is one of the most common congenital malformations and covers a spectrum of hip disorders from mild dysplasia to irreducible dislocation. The pathological mechanisms of DDH are poorly understood, which hampers the development of diagnostic tools and treatments. To gain insight into its disease mechanism, we explored the potential biological processes that underlie DDH by integrating pathway analysis tools and performing a genome-wide association study (GWAS). A total of 406 DDH-associated genes (P < 0.001) were identified by our GWAS using a Chinese Han cohort consisting of 386 DDH cases and 500 healthy controls (Set A). We verified the significant loci (P < 10-5 ) in another Chinese Han cohort consisting of 574 DDH patients and 569 healthy controls (Set B). An intronic Single Nucleotide Polymorphism (SNP) (rs61930502) showed significant association in Set A and Set B (P = 2.65 × 10-7 and 2.0 × 10-4 , respectively). The minor allele, rs61930502-A, which tended to prevent DDH showed a dominant effect. Heat shock 70 kDa protein 8 (HSPA8) showed the most direct interactions with other proteins which were coded by DDH-associated genes in the protein-protein interaction analysis. Interestingly, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested a relation between DDH and the genes involved in type II diabetes mellitus pathway (P = 0.0067). Our genetic and protein interaction evidence could open avenues for future studies of DDH.
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Affiliation(s)
- Wenjin Yan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Zheng Hao
- Center of Diagnosis and Treatment for Developmental Dysplasia of the Hip, Nanjing Zhongyangmen Community Health Service Center, Kang'ai Hospital, Nanjing, China
| | - Shuyan Tang
- Obstetrics and Gynecology Hospital, Institute of Metabolism and Integrative Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jin Dai
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Liming Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Pengjun Yu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Wenqiang Yan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiao Han
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xingquan Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Dongquan Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Huajian Teng
- Laboratory for Bone and Joint Disease, Model Animal Research Center (MARC), Nanjing University, Nanjing, China
| | - Qing Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,Laboratory for Bone and Joint Disease, Model Animal Research Center (MARC), Nanjing University, Nanjing, China
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45
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Hecker J, Laird N, Lange C. A comparison of popular TDT-generalizations for family-based association analysis. Genet Epidemiol 2019; 43:300-317. [PMID: 30609057 DOI: 10.1002/gepi.22181] [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: 06/12/2018] [Revised: 09/26/2018] [Accepted: 11/26/2018] [Indexed: 12/31/2022]
Abstract
The transmission disequilibrium test (TDT) is the gold standard for testing the association between a genetic variant and disease in samples consisting of affected individuals and their parents. In practice, more complex pedigree structures, that is siblings with no parents, or three-generational pedigrees with possibly missing genotypes, are common. There are several generalizations of the TDT that are suitable for use with arbitrary pedigree structures. We consider three such frequently used generalizations, family-based association test, pedigree disequilibrium test, and generalized disequilibrium test, that have accompanying software and compare them regarding validity and power in the single variant setting. We use simulations to study the effects of population admixture, populations whose genotypes are not in Hardy-Weinberg equilibrium (HWE), different pedigree structures, and the presence of linkage. Whereas our results show that some TDT generalizations can have a substantially increased Type 1 error, these tests are often used in substantive research without caveats about the validity of their Type 1 error. For the association analysis of rare variants in sequencing studies, region-based extensions of the TDT generalizations, that rely on the postulated robustness of the single variant tests, have been proposed. We discuss the implications of our results for these region-based extensions.
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Affiliation(s)
- Julian Hecker
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Nan Laird
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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46
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Robust Rare-Variant Association Tests for Quantitative Traits in General Pedigrees. STATISTICS IN BIOSCIENCES 2018; 10:491-505. [DOI: 10.1007/s12561-017-9197-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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47
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Zhang BH, Shi JY, Lin YS, Shi B, Jia ZL. VAX1 gene associated non-syndromic cleft lip with or without palate in Western Han Chinese. Arch Oral Biol 2018; 95:40-43. [DOI: 10.1016/j.archoralbio.2018.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023]
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48
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Lee JJ, McGue M, Iacono WG, Chow CC. The accuracy of LD Score regression as an estimator of confounding and genetic correlations in genome-wide association studies. Genet Epidemiol 2018; 42:783-795. [PMID: 30251275 DOI: 10.1002/gepi.22161] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 01/03/2023]
Abstract
To infer that a single-nucleotide polymorphism (SNP) either affects a phenotype or is linkage disequilibrium with a causal site, we must have some assurance that any SNP-phenotype correlation is not the result of confounding with environmental variables that also affect the trait. In this study, we study the properties of linkage disequilibrium (LD) Score regression, a recently developed method for using summary statistics from genome-wide association studies to ensure that confounding does not inflate the number of false positives. We do not treat the effects of genetic variation as a random variable and thus are able to obtain results about the unbiasedness of this method. We demonstrate that LD Score regression can produce estimates of confounding at null SNPs that are unbiased or conservative under fairly general conditions. This robustness holds in the case of the parent genotype affecting the offspring phenotype through some environmental mechanism, despite the resulting correlation over SNPs between LD Scores and the degree of confounding. Additionally, we demonstrate that LD Score regression can produce reasonably robust estimates of the genetic correlation, even when its estimates of the genetic covariance and the two univariate heritabilities are substantially biased.
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Affiliation(s)
- James J Lee
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, Minnesota
| | - Matt McGue
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, Minnesota
| | - William G Iacono
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, Minnesota
| | - Carson C Chow
- Mathematical Biology Section, Laboratory of Biological Modeling, NIDDK, National Institutes of Health, Bethesda, Maryland
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49
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Kruzel-Davila E, Wasser WG, Skorecki K. APOL1 Nephropathy: A Population Genetics and Evolutionary Medicine Detective Story. Semin Nephrol 2018; 37:490-507. [PMID: 29110756 DOI: 10.1016/j.semnephrol.2017.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Common DNA sequence variants rarely have a high-risk association with a common disease. When such associations do occur, evolutionary forces must be sought, such as in the association of apolipoprotein L1 (APOL1) gene risk variants with nondiabetic kidney diseases in populations of African ancestry. The variants originated in West Africa and provided pathogenic resistance in the heterozygous state that led to high allele frequencies owing to an adaptive evolutionary selective sweep. However, the homozygous state is disadvantageous and is associated with a markedly increased risk of a spectrum of kidney diseases encompassing hypertension-attributed kidney disease, focal segmental glomerulosclerosis, human immunodeficiency virus nephropathy, sickle cell nephropathy, and progressive lupus nephritis. This scientific success story emerged with the help of the tools developed over the past 2 decades in human genome sequencing and population genomic databases. In this introductory article to a timely issue dedicated to illuminating progress in this area, we describe this unique population genetics and evolutionary medicine detective story. We emphasize the paradox of the inheritance mode, the missing heritability, and unresolved associations, including cardiovascular risk and diabetic nephropathy. We also highlight how genetic epidemiology elucidates mechanisms and how the principles of evolution can be used to unravel conserved pathways affected by APOL1 that may lead to novel therapies. The APOL1 gene provides a compelling example of a common variant association with common forms of nondiabetic kidney disease occurring in a continental population isolate with subsequent global admixture. Scientific collaboration using multiple experimental model systems and approaches should further clarify pathomechanisms further, leading to novel therapies.
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Affiliation(s)
| | - Walter G Wasser
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Department of Nephrology, Mayanei HaYeshua Medical Center, Bnei Brak, Israel
| | - Karl Skorecki
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute Technion-Israel Institute of Technology, Rambam Health Care Campus, Haifa, Israel.
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50
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Chiquet BT, Yuan Q, Swindell EC, Maili L, Plant R, Dyke J, Boyer R, Teichgraeber JF, Greives MR, Mulliken JB, Letra A, Blanton SH, Hecht JT. Knockdown of Crispld2 in zebrafish identifies a novel network for nonsyndromic cleft lip with or without cleft palate candidate genes. Eur J Hum Genet 2018; 26:1441-1450. [PMID: 29899370 DOI: 10.1038/s41431-018-0192-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/10/2018] [Accepted: 05/08/2018] [Indexed: 11/09/2022] Open
Abstract
Orofacial development is a multifaceted process involving tightly regulated genetic signaling networks, that when perturbed, lead to orofacial abnormalities including cleft lip and/or cleft palate. We and others have shown an association between the cysteine-rich secretory protein LCCL domain containing 2 (CRISPLD2) gene and nonsyndromic cleft lip with or without cleft palate (NSCLP). Further, we demonstrated that knockdown of Crispld2 in zebrafish alters neural crest cell migration patterns resulting in abnormal jaw and palate development. In this study, we performed RNA profiling in zebrafish embryos and identified 249 differentially expressed genes following knockdown of Crispld2. In silico pathway analysis identified a network of seven genes previously implicated in orofacial development for which differential expression was validated in three of the seven genes (CASP8, FOS, and MMP2). Single nucleotide variant (SNV) genotyping of these three genes revealed significant associations between NSCLP and FOS/rs1046117 (GRCh38 chr14:g.75746690 T > C, p = 0.0005) in our nonHispanic white (NHW) families and MMP2/rs243836 (GRCh38 chr16:g.55534236 G > A; p = 0.002) in our Hispanic families. Nominal association was found between NSCLP and CASP8/rs3769825 (GRCh38 chr2:g.202111380 C > A; p < 0.007). Overtransmission of MMP2 haplotypes were identified in the Hispanic families (p < 0.002). Significant gene-gene interactions were identified for FOS-MMP2 in the NHW families and for CASP8-FOS in the NHW simplex family subgroup (p < 0.004). Additional in silico analysis revealed a novel gene regulatory network including five of these newly identified and 23 previously reported NSCLP genes. Our results demonstrate that animal models of orofacial clefting can be powerful tools to identify novel candidate genes and gene regulatory networks underlying NSCLP.
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Affiliation(s)
- Brett T Chiquet
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA. .,Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.
| | - Qiuping Yuan
- Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Eric C Swindell
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.,Department of Biochemistry and Molecular Biology, UTHealth McGovern Medical School, Houston, Texas, 77030, USA
| | - Lorena Maili
- Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Robert Plant
- Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Jeffrey Dyke
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA
| | - Ryan Boyer
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA
| | - John F Teichgraeber
- Divison of Pediatric Plastic Surgery, Department of Pediatric Surgery, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Matthew R Greives
- Divison of Pediatric Plastic Surgery, Department of Pediatric Surgery, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | | | - Ariadne Letra
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA.,Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Susan H Blanton
- Dr. John T. Macdonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Jacqueline T Hecht
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA.,Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
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