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Nieuwoudt C, Farooq FB, Brooks-Wilson A, Bureau A, Graham J. Statistics to prioritize rare variants in family-based sequencing studies with disease subtypes. Genet Epidemiol 2024. [PMID: 38940260 DOI: 10.1002/gepi.22579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/26/2024] [Accepted: 06/13/2024] [Indexed: 06/29/2024]
Abstract
Family-based sequencing studies are increasingly used to find rare genetic variants of high risk for disease traits with familial clustering. In some studies, families with multiple disease subtypes are collected and the exomes of affected relatives are sequenced for shared rare variants (RVs). Since different families can harbor different causal variants and each family harbors many RVs, tests to detect causal variants can have low power in this study design. Our goal is rather to prioritize shared variants for further investigation by, for example, pathway analyses or functional studies. The transmission-disequilibrium test prioritizes variants based on departures from Mendelian transmission in parent-child trios. Extending this idea to families, we propose methods to prioritize RVs shared in affected relatives with two disease subtypes, with one subtype more heritable than the other. Global approaches condition on a variant being observed in the study and assume a known probability of carrying a causal variant. In contrast, local approaches condition on a variant being observed in specific families to eliminate the carrier probability. Our simulation results indicate that global approaches are robust to misspecification of the carrier probability and prioritize more effectively than local approaches even when the carrier probability is misspecified.
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Affiliation(s)
- Christina Nieuwoudt
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Fabiha Binte Farooq
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Angela Brooks-Wilson
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Alexandre Bureau
- Département de Médecine Sociale et Préventive, Université Laval, Québec City, Québec, Canada
- Centre de recherche CERVO, Québec City, Québec, Canada
| | - Jinko Graham
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, British Columbia, Canada
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Lin F, Jun Li, Ziqi Wang, Zhang T, Lu T, Jiang M, Yang K, Jia M, Zhang D, Wang L. Replication of previous autism-GWAS hits suggests the association between NAA1, SORCS3, and GSDME and autism in the Han Chinese population. Heliyon 2024; 10:e23677. [PMID: 38234914 PMCID: PMC10792458 DOI: 10.1016/j.heliyon.2023.e23677] [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: 06/30/2023] [Revised: 11/25/2023] [Accepted: 12/09/2023] [Indexed: 01/19/2024] Open
Abstract
Background Autism is a severe neurodevelopmental disorder characterized by social interaction deficits, impairments in communication, and restricted and repetitive stereotyped behavior and activities. Family and twin studies suggested an essential role of genetic factors in the etiology of autism spectrum disorder (ASD). Also, other studies found SORCS3 and GSDME (DFNA5) might be involved in brain development and susceptible to ASD. Methods In this study, 17 genome-wide significant SNPs reported in previous ASD genome-wide association studies (GWAS) and 7 SNPs in strong linkage disequilibrium with known ASD GWAS hits were selected to investigate the association between these SNPs and autism in the Han Chinese population. Then, 10 tagSNPs in SORCS3 and 11 tagSNPs in GSDME were selected to analyze the association between these SNPs and autism. The selected 24 SNPs and tagSNPs were genotyped using the Agena MassARRAY SNP genotyping assay in 757 Han Chinese autism trios. Results Rs1484144 in NAA11 was significantly associated with autism; significance remained after the Bonferroni correction (P < 0.0022). Also, rs79879286, rs12154597, and rs12540919 near GSDME, as well as rs9787523 and rs3750261 in SORCS3, were nominally associated with autism. Conclusion Our study suggests that rs1484144 in NAA11 is a significant SNP for autism in the Han Chinese population, while SORCS3 and GSDME might be the susceptibility genes for autism in this population.
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Affiliation(s)
- Fen Lin
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Jun Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Ziqi Wang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Tian Zhang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Tianlan Lu
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Miaomiao Jiang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Kang Yang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Meixiang Jia
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Dai Zhang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Guangdong Key Laboratory of Mental Health and Cognitive Science, Institute for Brain Research and Rehabilitation (IBRR), South China Normal University, Guangzhou, China
| | - Lifang Wang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
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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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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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5
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Shang S, Zhou Y, Chen K, Chen L, Li P, Li D, Cui S, Zhang MJ, Chen X, Li Q. A Novel Gene CDC27 Causes SLE and Is Associated With the Disease Activity. Front Immunol 2022; 13:876963. [PMID: 35418986 PMCID: PMC8996071 DOI: 10.3389/fimmu.2022.876963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/17/2022] Open
Abstract
Background As genetic genetic factors are important in SLE, so screening causative genes is of great significance for the prediction and early prevention in people who may develop SLE. At present, it is very difficult to screen causative genes through pedigrees. The analytical method described herein can be used to screen causative genes for SLE and other complex diseases through pedigrees. Methods For the first time, 24 lupus pedigrees were analyzed by combining whole exon sequencing and a variety of biological information tools including common-specific analysis, pVAAST (pedigree variant annotation, analysis and search tool), Exomiser (Combining phenotype and PPI associated analysis), and FARVAT (family based gene burden), and the causative genes of these families with lupus identified. Selected causative genes in peripheral-blood mononuclear cells (PBMCs) were evaluated by quantitative polymerase chain reaction (qPCR). Results Cell division cycle 27 (CDC27) was screened out by common-specific analysis and Exomiser causative gene screening. FARVAT analysis on these families detected only CDC27 at the extremely significant level (false discovery rate <0.05) by three family-based burden analyses (BURDEN, CALPHA, and SKATO). QPCR was performed to detect for CDC27 in the PBMCs of the SLE family patients, sporadic lupus patients, and healthy people. Compared with the healthy control group, CDC27 expression was low in lupus patients (familial and sporadic patients) (P<0.05) and correlated with lupus activity indicators: negatively with C-reactive protein (CRP) (P<0.05) and erythrocyte sedimentation rate (P<0.05) and positively with complement C3 and C4 (P<0.05). The CDC27 expression was upregulated in PBMCs from SLE patients with reduced lupus activity after immunotherapy (P<0.05). Based on Receiver operating characteristic (ROC) curve analysis, the sensitivity and specificity of CDC27 in diagnosing SLE were 82.30% and 94.40%. Conclusion The CDC27 gene, as found through WES combined with multiple analytical method may be a causative gene of lupus. CDC27 may serve as a marker for the diagnosis of SLE and is closely related to the lupus activity. We hope that the analytical method in this study will be used to screen causative genes for other diseases through small pedigrees, especially among non-close relatives.
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Affiliation(s)
- Shunlai Shang
- School of Medicine, Nankai University, Tianjin, China.,Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Yena Zhou
- School of Medicine, Nankai University, Tianjin, China
| | - Keng Chen
- Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, China
| | - Lang Chen
- Medical Technology & Bioinformatics Department, Beijing Mygenostics co., LTD, Beijing, China
| | - Ping Li
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Diangeng Li
- Department of Academic Research, Beijing-Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Shaoyuan Cui
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Mei-Jun Zhang
- Bioinformation Department, Geneis (Beijing) Co., Ltd., Beijing, China
| | - Xiangmei Chen
- School of Medicine, Nankai University, Tianjin, China.,Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Qinggang Li
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
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Identification and selection of healthy spermatozoa in heterozygous carriers of the Phe508del-variant of the CFTR-gene in assisted reproduction. Sci Rep 2022; 12:1866. [PMID: 35115637 PMCID: PMC8814069 DOI: 10.1038/s41598-022-05925-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
The pathogenic variant Phe508del of the CFTR-gene is the most frequent cause of cystic fibrosis (CF). Whereas male CF-patients are infertile due to bilateral agenesis of the efferent ducts, the fertility status of male heterozygous carriers is uncertain. We aimed at demonstrating the involvement of the CFTR-ion channel during sperm capacitation and to potentially select variant-free spermatozoa in heterozygous carriers of the CFTR-variant using flow cytometry (FC). Using FC and sorting, single cell polymerase chain reaction, immuno-fluorescent staining an experimental study was performed on nine fertile semen donors and three heterozygous infertile men carrying the Phe508del gene variant. Chemical inhibition of CFTR interfered with sperm capacitation. Most viable spermatozoa of heterozygous carriers of the Phe508del variant of the CFTR-gene show immune-fluorescent CFTR. Sperm capacitation in Phe508del carriers was similar to that in healthy semen donors. Distribution of the Phe508del allele in trio data of CF-affected families corresponded to the expected recessive inheritance pattern. Infertility in Phe508del heterozygous men is unlikely to be caused by the pathogenic variant although some contribution cannot be excluded. Normal sperm capacitation in carriers of pathogenic variants of the Phe508del-gene may in part explain the high prevalence of a potentially lethal recessive disorder.
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Hershberger RE, Cowan J, Jordan E, Kinnamon DD. The Complex and Diverse Genetic Architecture of Dilated Cardiomyopathy. Circ Res 2021; 128:1514-1532. [PMID: 33983834 DOI: 10.1161/circresaha.121.318157] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Our insight into the diverse and complex nature of dilated cardiomyopathy (DCM) genetic architecture continues to evolve rapidly. The foundations of DCM genetics rest on marked locus and allelic heterogeneity. While DCM exhibits a Mendelian, monogenic architecture in some families, preliminary data from our studies and others suggests that at least 20% to 30% of DCM may have an oligogenic basis, meaning that multiple rare variants from different, unlinked loci, determine the DCM phenotype. It is also likely that low-frequency and common genetic variation contribute to DCM complexity, but neither has been examined within a rare variant context. Other types of genetic variation are also likely relevant for DCM, along with gene-by-environment interaction, now established for alcohol- and chemotherapy-related DCM. Collectively, this suggests that the genetic architecture of DCM is broader in scope and more complex than previously understood. All of this elevates the impact of DCM genetics research, as greater insight into the causes of DCM can lead to interventions to mitigate or even prevent it and thus avoid the morbid and mortal scourge of human heart failure.
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Affiliation(s)
- Ray E Hershberger
- Divisions of Cardiovascular Medicine (R.E.H.), The Ohio State University Wexner Medical Center, Columbus.,Human Genetics (R.E.H., J.C., E.J., D.D.K.), The Ohio State University Wexner Medical Center, Columbus.,Department of Internal Medicine and the Davis Heart and Lung Research Institute (R.E.H., J.C., E.J., D.D.K.), The Ohio State University Wexner Medical Center, Columbus
| | - Jason Cowan
- Human Genetics (R.E.H., J.C., E.J., D.D.K.), The Ohio State University Wexner Medical Center, Columbus.,Department of Internal Medicine and the Davis Heart and Lung Research Institute (R.E.H., J.C., E.J., D.D.K.), The Ohio State University Wexner Medical Center, Columbus
| | - Elizabeth Jordan
- Human Genetics (R.E.H., J.C., E.J., D.D.K.), The Ohio State University Wexner Medical Center, Columbus.,Department of Internal Medicine and the Davis Heart and Lung Research Institute (R.E.H., J.C., E.J., D.D.K.), The Ohio State University Wexner Medical Center, Columbus
| | - Daniel D Kinnamon
- Human Genetics (R.E.H., J.C., E.J., D.D.K.), The Ohio State University Wexner Medical Center, Columbus.,Department of Internal Medicine and the Davis Heart and Lung Research Institute (R.E.H., J.C., E.J., D.D.K.), The Ohio State University Wexner Medical Center, Columbus
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8
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Khan MI, Cs P. Case-Parent Trio Studies in Cleft Lip and Palate. Glob Med Genet 2021; 7:75-79. [PMID: 33392609 PMCID: PMC7772012 DOI: 10.1055/s-0040-1722097] [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] [Indexed: 11/15/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is one of the most common congenital malformations in humans involving various genetic and environmental risk factors. The prevalence of CL/P varies according to geographical location, ethnicity, race, gender, and socioeconomic status, affecting approximately 1 in 800 live births worldwide. Genetic studies aim to understand the mechanisms contributory to a phenotype by measuring the association between genetic variants and also between genetic variants and phenotype population. Genome-wide association studies are standard tools used to discover genetic loci related to a trait of interest. Genetic association studies are generally divided into two main design types: population-based studies and family-based studies. The epidemiological population-based studies comprise unrelated individuals that directly compare the frequency of genetic variants between (usually independent) cases and controls. The alternative to population-based studies (case–control designs) includes various family-based study designs that comprise related individuals. An example of such a study is a case–parent trio design study, which is commonly employed in genetics to identify the variants underlying complex human disease where transmission of alleles from parents to offspring is studied. This article describes the fundamentals of case–parent trio study, trio design and its significances, statistical methods, and limitations of the trio studies.
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Affiliation(s)
- Mahamad Irfanulla Khan
- Department of Orthodontics & Dentofacial Orthopedics, The Oxford Dental College, Bangalore, Karnataka, India
| | - Prashanth Cs
- Department of Orthodontics & Dentofacial Orthopedics, DAPM RV Dental College, Bangalore, Karnataka, India
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Piras IS, Picinelli C, Iennaco R, Baccarin M, Castronovo P, Tomaiuolo P, Cucinotta F, Ricciardello A, Turriziani L, Nanetti L, Mariotti C, Gellera C, Lintas C, Sacco R, Zuccato C, Cattaneo E, Persico AM. Huntingtin gene CAG repeat size affects autism risk: Family-based and case-control association study. Am J Med Genet B Neuropsychiatr Genet 2020; 183:341-351. [PMID: 32652810 DOI: 10.1002/ajmg.b.32806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 04/20/2020] [Accepted: 05/04/2020] [Indexed: 11/10/2022]
Abstract
The Huntingtin (HTT) gene contains a CAG repeat in exon 1, whose expansion beyond 39 repeats consistently leads to Huntington's disease (HD), whereas normal-to-intermediate alleles seemingly modulate brain structure, function and behavior. The role of the CAG repeat in Autism Spectrum Disorder (ASD) was investigated applying both family-based and case-control association designs, with the SCA3 repeat as a negative control. Significant overtransmission of "long" CAG alleles (≥17 repeats) to autistic children and of "short" alleles (≤16 repeats) to their unaffected siblings (all p < 10-5 ) was observed in 612 ASD families (548 simplex and 64 multiplex). Surprisingly, both 193 population controls and 1,188 neurological non-HD controls have significantly lower frequencies of "short" CAG alleles compared to 185 unaffected siblings and higher rates of "long" alleles compared to 548 ASD patients from the same families (p < .05-.001). The SCA3 CAG repeat displays no association. "Short" HTT alleles seemingly exert a protective effect from clinically overt autism in families carrying a genetic predisposition for ASD, while "long" alleles may enhance autism risk. Differential penetrance of autism-inducing genetic/epigenetic variants may imply atypical developmental trajectories linked to HTT functions, including excitation/inhibition imbalance, cortical neurogenesis and apoptosis, neuronal migration, synapse formation, connectivity and homeostasis.
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Affiliation(s)
- Ignazio Stefano Piras
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Chiara Picinelli
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Raffaele Iennaco
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy.,Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Marco Baccarin
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Paola Castronovo
- Mafalda Luce Center for Pervasive Developmental Disorders, Milan, Italy
| | - Pasquale Tomaiuolo
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Francesca Cucinotta
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Arianna Ricciardello
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Laura Turriziani
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Lorenzo Nanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Caterina Mariotti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Carla Lintas
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University Campus Bio-Medico, Rome, Italy
| | - Roberto Sacco
- Unit of Child and Adolescent NeuroPsychiatry & Laboratory of Molecular Psychiatry and Neurogenetics, University Campus Bio-Medico, Rome, Italy
| | - Chiara Zuccato
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy.,Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Elena Cattaneo
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy.,Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Antonio M Persico
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
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10
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Hou R, Cole SA, Graff M, Haack K, Laston S, Comuzzie AG, Mehta NR, Ryan K, Cousminer DL, Zemel BS, Grant SFA, Mitchell BD, Shypailo RJ, Gourlay ML, North KE, Butte NF, Voruganti VS. Genetic variants affecting bone mineral density and bone mineral content at multiple skeletal sites in Hispanic children. Bone 2020; 132:115175. [PMID: 31790847 PMCID: PMC7120871 DOI: 10.1016/j.bone.2019.115175] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 12/24/2022]
Abstract
CONTEXT Osteoporosis is a major public health burden with significant economic costs. However, the correlates of bone health in Hispanic children are understudied. OBJECTIVE We aimed to identify genetic variants associated with bone mineral density (BMD) and bone mineral content (BMC) at multiple skeletal sites in Hispanic children. METHODS We conducted a cross-sectional genome-wide linkage analysis, genome-wide and exome-wide association analysis of BMD and BMC. The Viva La Familia Study is a family-based cohort with a total of 1030 Hispanic children (4-19 years old at baseline) conducted in Houston, TX. BMD and BMC were measured by Dual-energy X-ray absorptiometry. RESULTS Significant heritability were observed for BMC and BMD at multiple skeletal sites ranging between 44 and 68% (P < 2.8 × 10-9). Significant evidence for linkage was found for BMD of pelvis and left leg on chromosome 7p14, lumbar spine on 20q13 and left rib on 6p21, and BMC of pelvis on chromosome 20q12 and total body on 14q22-23 (logarithm of odds score > 3). We found genome-wide significant association between BMC of right arm and rs762920 at PVALB (P = 4.6 × 10-8), and between pelvis BMD and rs7000615 at PTK2B (P = 7.4 × 10-8). Exome-wide association analysis revealed novel association of variants at MEGF10 and ABRAXAS2 with left arm and lumber spine BMC, respectively (P < 9 × 10-7). CONCLUSIONS We identified novel loci associated with BMC and BMD in Hispanic children, with strongest evidence for PTK2B. These findings provide better understanding of bone genetics and shed light on biological mechanisms underlying BMD and BMC variation.
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Affiliation(s)
- Ruixue Hou
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sandra Laston
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas the Rio Grande Valley, Brownsville, TX, USA
| | | | - Nitesh R Mehta
- Department of Pediatrics and USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Kathleen Ryan
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Diana L Cousminer
- Division of Human Genetics, Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, USA; Department of Genetics, University of Pennsylvania, USA
| | - Babette S Zemel
- Division of GI, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, USA
| | - Struan F A Grant
- Division of Human Genetics, Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, USA; Department of Pediatrics, University of Pennsylvania, Philadelphia, USA; Department of Genetics, University of Pennsylvania, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Roman J Shypailo
- Department of Pediatrics and USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Margaret L Gourlay
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nancy F Butte
- Department of Pediatrics and USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX, USA
| | - V Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA.
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11
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Mukhopadhyay N, Bishop M, Mortillo M, Chopra P, Hetmanski JB, Taub MA, Moreno LM, Valencia-Ramirez LC, Restrepo C, Wehby GL, Hecht JT, Deleyiannis F, Butali A, Weinberg SM, Beaty TH, Murray JC, Leslie EJ, Feingold E, Marazita ML. Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21. Hum Genet 2020; 139:215-226. [PMID: 31848685 PMCID: PMC6981325 DOI: 10.1007/s00439-019-02099-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/07/2019] [Indexed: 12/30/2022]
Abstract
Orofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic, and the genetic etiology of non-syndromic OFCs is only partially determined. Here, we analyze whole genome sequence (WGS) data for association with risk of OFCs in European and Colombian families selected from a multicenter family-based OFC study. This is the first large-scale WGS study of OFC in parent-offspring trios, and a part of the Gabriella Miller Kids First Pediatric Research Program created for the study of childhood cancers and structural birth defects. WGS provides deeper and more specific genetic data than using imputation on present-day single nucleotide polymorphic (SNP) marker panels. Genotypes of case-parent trios at single nucleotide variants (SNV) and short insertions and deletions (indels) spanning the entire genome were called from their sequences using human GRCh38 genome assembly, and analyzed for association using the transmission disequilibrium test. Among genome-wide significant associations, we identified a new locus on chromosome 21 in Colombian families, not previously observed in other larger OFC samples of Latin American ancestry. This locus is situated within a region known to be expressed during craniofacial development. Based on deeper investigation of this locus, we concluded that it contributed risk for OFCs exclusively in the Colombians. This study reinforces the ancestry differences seen in the genetic etiology of OFCs, and underscores the need for larger samples when studying for OFCs and other birth defects in populations with diverse ancestry.
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Affiliation(s)
- Nandita Mukhopadhyay
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA
| | - Madison Bishop
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Michael Mortillo
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Lina M Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | | | - Claudia Restrepo
- Fundación Clínica Noel (http://www.clinicanoel.org.co/), Medellín, Colombia
| | - George L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, TX, 77030, USA
| | | | - Azeez Butali
- Iowa Institute of Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Eleanor Feingold
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Biostatistics Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA.
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15219, USA.
- Department of Psychiatry, School of Medicine and Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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12
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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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13
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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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14
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Mei B, Wang Z. A multiple regression method for genomewide association studies using only linkage information. J Genet 2018. [DOI: 10.1007/s12041-018-0936-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Rastas P. Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics 2017; 33:3726-3732. [DOI: 10.1093/bioinformatics/btx494] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/01/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Pasi Rastas
- Department of Zoology, Butterfly Genetics Group, University of Cambridge, Cambridge, UK
- Department of Biosciences, Ecological Genetics Research Unit, University of Helsinki, Helsinki, Finland
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16
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Genetic loci associated with an earlier age at onset in multiplex schizophrenia. Sci Rep 2017; 7:6486. [PMID: 28744025 PMCID: PMC5527118 DOI: 10.1038/s41598-017-06795-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/16/2017] [Indexed: 11/28/2022] Open
Abstract
An earlier age at onset (AAO) has been associated with greater genetic loadings in schizophrenia. This study aimed to identify modifier loci associated with an earlier AAO of schizophrenia. A genome-wide association analysis (GWAS) was conducted in 94 schizophrenia probands with the earliest AAO and 91 with the latest AAO. Candidate single nucleotide polymorphisms (SNPs) were then genotyped in the co-affected siblings and unrelated probands. Multi-SNP genetic risk scores (GRS) composed of the candidate loci were used to distinguish patients with an early or late AAO. The 14-SNP GRS could distinguish the co-affected siblings (n = 90) of the earliest probands from those (n = 91) of the latest probands. When 132 patients with an earlier AAO and 158 patients with a later AAO were included, a significant trend in the 14-SNP GRS was detected among those unrelated probands from 4 family groups with the earliest, earlier, later, and latest AAO. The overall effect of the 14 SNPs on an AAO in schizophrenia was verified using co-affected siblings of the GWAS probands and trend effect across unrelated patients. Preliminary network analysis of these loci revealed the involvement of PARK2, a gene intensively reported in Parkinson’s disease and schizophrenia research.
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17
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Birth weight interacts with a functional variant of the oxytocin receptor gene (OXTR) to predict executive functioning in children. Dev Psychopathol 2017; 30:203-211. [PMID: 28511728 DOI: 10.1017/s0954579417000578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genetic variation in the oxytocin receptor gene (OXTR) is associated with several psychiatric conditions characterized by deficits in executive functioning (EF). A specific OXTR variant, rs2254298, has previously been associated with brain functioning in regions implicated in EF. Moreover, birth weight variation across the entire range is associated with individual differences in cortical structure and function that underlie EF. This is the first study to examine the main and interactive effect between rs2254298 and birth weight on EF in children. The sample consisted of 310 children from an ongoing longitudinal study. EF was measured at age 4.5 using observational tasks indexing working memory, cognitive flexibility, and inhibitory control. A family-based design that controlled for population admixture, stratification, and nongenomic confounds was employed. A significant genetic association between rs2254298 and EF was observed, with more copies of the major allele (G) associated with higher EF. There was also a significant interaction between rs2254298 and birth weight, such that more copies of the major allele in combination with higher birth weight predicted better EF. Findings suggest that OXTR may be associated with discrete neurocognitive abilities in childhood, and these effects may be modulated by intrauterine conditions related to fetal growth and development.
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18
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Beaty TH, Marazita ML, Leslie EJ. Genetic factors influencing risk to orofacial clefts: today's challenges and tomorrow's opportunities. F1000Res 2016; 5:2800. [PMID: 27990279 PMCID: PMC5133690 DOI: 10.12688/f1000research.9503.1] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/18/2016] [Indexed: 12/18/2022] Open
Abstract
Orofacial clefts include cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP), which combined represent the largest group of craniofacial malformations in humans with an overall prevalence of one per 1,000 live births. Each of these birth defects shows strong familial aggregation, suggesting a major genetic component to their etiology. Genetic studies of orofacial clefts extend back centuries, but it has proven difficult to define any single etiologic mechanism because many genes appear to influence risk. Both linkage and association studies have identified several genes influencing risk, but these differ across families and across populations. Genome-wide association studies have identified almost two dozen different genes achieving genome-wide significance, and there are broad classes of 'causal genes' for orofacial clefts: a few genes strongly associated with risk and possibly directly responsible for Mendelian syndromes which include orofacial clefts as a key phenotypic feature of the syndrome, and multiple genes with modest individual effects on risk but capable of disrupting normal craniofacial development under the right circumstances (which may include exposure to environmental risk factors). Genomic sequencing studies are now underway which will no doubt reveal additional genes/regions where variants (sequence and structural) can play a role in controlling risk to orofacial clefts. The real challenge to medicine and public health is twofold: to identify specific genes and other etiologic factors in families with affected members and then to devise effective interventions for these different biological mechanisms controlling risk to complex and heterogeneous birth defects such as orofacial clefts.
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Affiliation(s)
- Terri H Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Mary L Marazita
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Elizabeth J Leslie
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
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19
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Herold C, Hooli BV, Mullin K, Liu T, Roehr JT, Mattheisen M, Parrado AR, Bertram L, Lange C, Tanzi RE. Family-based association analyses of imputed genotypes reveal genome-wide significant association of Alzheimer's disease with OSBPL6, PTPRG, and PDCL3. Mol Psychiatry 2016; 21:1608-1612. [PMID: 26830138 PMCID: PMC4970971 DOI: 10.1038/mp.2015.218] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/25/2015] [Accepted: 12/07/2015] [Indexed: 01/19/2023]
Abstract
The genetic basis of Alzheimer's disease (AD) is complex and heterogeneous. Over 200 highly penetrant pathogenic variants in the genes APP, PSEN1, and PSEN2 cause a subset of early-onset familial AD. On the other hand, susceptibility to late-onset forms of AD (LOAD) is indisputably associated to the ɛ4 allele in the gene APOE, and more recently to variants in more than two-dozen additional genes identified in the large-scale genome-wide association studies (GWAS) and meta-analyses reports. Taken together however, although the heritability in AD is estimated to be as high as 80%, a large proportion of the underlying genetic factors still remain to be elucidated. In this study, we performed a systematic family-based genome-wide association and meta-analysis on close to 15 million imputed variants from three large collections of AD families (~3500 subjects from 1070 families). Using a multivariate phenotype combining affection status and onset age, meta-analysis of the association results revealed three single nucleotide polymorphisms (SNPs) that achieved genome-wide significance for association with AD risk: rs7609954 in the gene PTPRG (P-value=3.98 × 10-8), rs1347297 in the gene OSBPL6 (P-value=4.53 × 10-8), and rs1513625 near PDCL3 (P-value=4.28 × 10-8). In addition, rs72953347 in OSBPL6 (P-value=6.36 × 10-7) and two SNPs in the gene CDKAL1 showed marginally significant association with LOAD (rs10456232, P-value=4.76 × 10-7; rs62400067, P-value=3.54 × 10-7). In summary, family-based GWAS meta-analysis of imputed SNPs revealed novel genomic variants in (or near) PTPRG, OSBPL6, and PDCL3 that influence risk for AD with genome-wide significance.
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Affiliation(s)
- Christine Herold
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany, Department of Biostatistics, Harvard T.H Chan School of Public Health, Boston, 02115 Massachusetts, USA
| | - Basavaraj V. Hooli
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, 02114 USA
| | - Kristina Mullin
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, 02114 USA
| | - Tian Liu
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Johannes T Roehr
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Antonio R. Parrado
- Computational Sciences, Janssen Research & Development, Pharmaceutical Company of Johnson & Johnson, Spring House, Pennsylvania, 19477
| | - Lars Bertram
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany, School of Public Health, Faculty of Medicine, The Imperial College of Science, Technology, and Medicine, London, W6 8RP, UK, Platform for Genome Analytics, Institutes of Neurogenetics & Integrative and Experimental Genomics, University of Lübeck, 23552 Lübeck, Germany
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H Chan School of Public Health, Boston, 02115 Massachusetts, USA,To whom correspondence should be addressed: Christoph Lange, Ph.D., Professor of Biostatistics, Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, Tel: +1 (617) 432-4925, , and, Rudolph E. Tanzi, Ph.D., Director, Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA, Joesph P. and Rose F. Kennedy Professor of Neurology, Harvard Medical School, Boston, Massachusetts 02114, USA, Tel: +1 (617) 726-6845,
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, 02114 USA,To whom correspondence should be addressed: Christoph Lange, Ph.D., Professor of Biostatistics, Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, Massachusetts 02115, Tel: +1 (617) 432-4925, , and, Rudolph E. Tanzi, Ph.D., Director, Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA, Joesph P. and Rose F. Kennedy Professor of Neurology, Harvard Medical School, Boston, Massachusetts 02114, USA, Tel: +1 (617) 726-6845,
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Gonzalez S, Gupta J, Villa E, Mallawaarachchi I, Rodriguez M, Ramirez M, Zavala J, Armas R, Dassori A, Contreras J, Flores D, Jerez A, Ontiveros A, Nicolini H, Escamilla M. Replication of genome-wide association study (GWAS) susceptibility loci in a Latino bipolar disorder cohort. Bipolar Disord 2016; 18:520-527. [PMID: 27759212 PMCID: PMC5095871 DOI: 10.1111/bdi.12438] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 09/02/2016] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Recent genome-wide association studies (GWASs) have identified numerous putative genetic polymorphisms associated with bipolar disorder (BD) and/or schizophrenia (SC). We hypothesized that a portion of these polymorphisms would also be associated with BD in the Latino American population. To identify such regions, we tested previously identified genetic variants associated with BD and/or SC and ancestral haploblocks containing these single nucleotide polymorphisms (SNPs) in a sample of Latino subjects with BD. METHODS A total of 2254 Latino individuals were genotyped for 91 SNPs identified in previous BD and/or SC GWASs, along with selected SNPs in strong linkage disequilibrium with these markers. Family-based single marker and haplotype association testing was performed using the PBAT software package. Empirical P-values were derived from 10 000 permutations. RESULTS Associations of eight a priori GWAS SNPs with BD were replicated with nominal (P≤.05) levels of significance. These included SNPs within nuclear factor I A (NFIA), serologically defined colon cancer antigen 8 (SDCCAG8), lysosomal associated membrane protein 3 (LAMP3), nuclear factor kappa B subunit 1 (NFKB1), major histocompatibility complex, class I, B (HLA-B) and 5'-nucleotidase, cytosolic II (NT5C2) and SNPs within intragenic regions microRNA 6828 (MIR6828)-solute carrier family 7 member 14 (SLC7A14) and sonic hedgehog (SHH)-long intergenic non-protein coding RNA 1006 (LINC01006). Of the 76 ancestral haploblocks that were tested for associations with BD, our top associated haploblock was located in LAMP3; however, the association did not meet statistical thresholds of significance following Bonferroni correction. CONCLUSIONS These results indicate that some of the gene variants found to be associated with BD or SC in other populations are also associated with BD risk in Latinos. Variants in six genes and two intragenic regions were associated with BD in our Latino sample and provide additional evidence for overlap in genetic risk between SC and BD.
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Affiliation(s)
- Suzanne Gonzalez
- Center of Excellence in Neurosciences, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA.
| | - Jayanta Gupta
- Department of Health Sciences, College of Health Professions & Social Work, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Erika Villa
- Center of Excellence in Neurosciences, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Indika Mallawaarachchi
- Biostatistics and Epidemiology Consulting Lab, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Marco Rodriguez
- Center of Excellence in Neurosciences, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Mercedes Ramirez
- Center of Excellence in Neurosciences, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
- Department of Psychiatry, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Juan Zavala
- Center of Excellence in Neurosciences, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
- Department of Psychiatry, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
| | - Regina Armas
- Langley Porter Psychiatric Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Albana Dassori
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- South Texas Veterans Health Care System, San Antonio, TX, USA
| | - Javier Contreras
- Centro de Investigación en Biología Celular y Molecular y Escuela de Biologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Deborah Flores
- Los Angeles Biomedical Research Center at Harbor, University of California Los Angeles Medical Center, Torrance, CA, USA
| | - Alvaro Jerez
- Centro Internacional de Trastornos Afectivos y de la Conducta Adictiva, Guatemala City, Guatemala
| | - Alfonso Ontiveros
- Instituto de Información e Investigación en Salud Mental AC, Monterrey, Nuevo Leon, México
| | - Humberto Nicolini
- Grupo de Estudios Médicos y Familiares Carracci S.C., México D.F, México
| | - Michael Escamilla
- Center of Excellence in Neurosciences, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
- Department of Psychiatry, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
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Wade M, Hoffmann TJ, Knafo-Noam A, O'Connor TG, Jenkins JM. Oxytocin and vasopressin hormone genes in children's externalizing problems: A cognitive endophenotype approach. Horm Behav 2016; 82:78-86. [PMID: 27155104 DOI: 10.1016/j.yhbeh.2016.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 03/04/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
Externalizing problems are among the most common mental health problems of children. Research suggests that these problems are heritable, yet little is known about the specific genes involved in their pathophysiology. The current study examined a genotype-endophenotype-phenotype model of externalizing problems in 320 preschool-aged children. Markers of the oxytocin (OXT) and arginine vasopressin (AVP) hormone genes were selected as candidates owing to their known association with psychopathology in other domains. We tested whether OXT and AVP variants were related to children's externalizing problems, as well as two cognitive endophenotypes presumed to underlie these problems: theory of mind (ToM) and executive functioning (EF). Externalizing problems were assessed at age 4.5 using a previously-validated rating scale. ToM and EF were measured with age-appropriate tasks. Using a family-based association design and controlling for non-genomic confounds, support was found for an association between a two-marker OXT haplotype (rs2740210-rs2770378) and a two-marker AVP haplotype (rs1887854-rs3761249) and externalizing problems. Specific associations of these haplotypes with ToM and EF were also observed. Further, ToM and EF were shown to independently and jointly predict externalizing problems, and to partially mediate the effects of OXT and AVP on externalizing problems. This study provides the first evidence that genetic variation in OXT and AVP may contribute to individual differences in childhood externalizing problems, and that these effects may operate through emerging neurocognitive abilities in the preschool period.
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Affiliation(s)
- Mark Wade
- Department of Applied Psychology and Human Development, University of Toronto, Canada.
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, and Institute for Human Genetics, University of California at San Francisco, USA
| | - Ariel Knafo-Noam
- Department of Psychology, The Hebrew University of Jerusalem, Israel
| | | | - Jennifer M Jenkins
- Department of Applied Psychology and Human Development, University of Toronto, Canada.
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22
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Roten LT, Thomsen LCV, Gundersen AS, Fenstad MH, Odland ML, Strand KM, Solberg P, Tappert C, Araya E, Bærheim G, Lyslo I, Tollaksen K, Bjørge L, Austgulen R. The Norwegian preeclampsia family cohort study: a new resource for investigating genetic aspects and heritability of preeclampsia and related phenotypes. BMC Pregnancy Childbirth 2015; 15:319. [PMID: 26625711 PMCID: PMC4666119 DOI: 10.1186/s12884-015-0754-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/21/2015] [Indexed: 12/27/2022] Open
Abstract
Background Preeclampsia is a major pregnancy complication without curative treatment available. A Norwegian Preeclampsia Family Cohort was established to provide a new resource for genetic and molecular studies aiming to improve the understanding of the complex pathophysiology of preeclampsia. Methods Participants were recruited from five Norwegian hospitals after diagnoses of preeclampsia registered in the Medical birth registry of Norway were verified according to the study’s inclusion criteria. Detailed obstetric information and information on personal and family disease history focusing on cardiovascular health was collected. At attendance anthropometric measurements were registered and blood samples were drawn. The software package SPSS 19.0 for Windows was used to compute descriptive statistics such as mean and SD. P-values were computed based on t-test statistics for normally distributed variables. Nonparametrical methods (chi square) were used for categorical variables. Results A cohort consisting of 496 participants (355 females and 141 males) representing 137 families with increased occurrence of preeclampsia has been established, and blood samples are available for 477 participants. Descriptive analyses showed that about 60 % of the index women’s pregnancies with birth data registered were preeclamptic according to modern diagnosis criteria. We also found that about 41 % of the index women experienced more than one preeclamptic pregnancy. In addition, the descriptive analyses confirmed that preeclamptic pregnancies are more often accompanied with delivery complications. Conclusion The data and biological samples collected in this Norwegian Preeclampsia Family Cohort will provide an important basis for future research. Identification of preeclampsia susceptibility genes and new biomarkers may contribute to more efficient strategies to identify mothers “at risk” and contribute to development of novel preventative therapies.
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Affiliation(s)
- Linda Tømmerdal Roten
- Department of Laboratory Medicine, Children's and Women's Health, the Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway. .,Central Norway Regional Health Authority, 7501, Stjørdal, Norway.
| | - Liv Cecilie Vestrheim Thomsen
- Department of Obstetrics and Gynecology, Haukeland University Hospital, 5058, Bergen, Norway. .,Department of Clinical Medicine, University of Bergen, 5020, Bergen, Norway.
| | - Astrid Solberg Gundersen
- The Regional Biobank of Central Norway, St. Olavs Hospital, Trondheim, Norway. .,Department of Cancer Research and Molecular Medicine, NTNU, 7491, Trondheim, Norway.
| | - Mona Høysæter Fenstad
- Department of Cancer Research and Molecular Medicine, NTNU, 7491, Trondheim, Norway. .,Department of Immunology and Transfusion Medicine, St. Olavs Hospital, 7006, Trondheim, Norway.
| | - Maria Lisa Odland
- Department of Cancer Research and Molecular Medicine, NTNU, 7491, Trondheim, Norway.
| | - Kristin Melheim Strand
- Department of Laboratory Medicine, Children's and Women's Health, the Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
| | - Per Solberg
- Department of Obstetrics and Gynecology, Levanger Hospital, 7601, Levanger, Norway.
| | - Christian Tappert
- Department of Obstetrics and Gynecology, St. Olavs Hospital, 7006, Trondheim, Norway.
| | - Elisabeth Araya
- Department of Obstetrics and Gynecology, St. Olavs Hospital, 7006, Trondheim, Norway.
| | - Gunhild Bærheim
- Department of Obstetrics and Gynecology, Stavanger University Hospital, 4068, Stavanger, Norway.
| | - Ingvill Lyslo
- Department of Obstetrics and Gynecology, Stavanger University Hospital, 4068, Stavanger, Norway.
| | - Kjersti Tollaksen
- Department of Obstetrics and Gynecology, Stavanger University Hospital, 4068, Stavanger, Norway.
| | - Line Bjørge
- Department of Obstetrics and Gynecology, Haukeland University Hospital, 5058, Bergen, Norway. .,Department of Clinical Medicine, University of Bergen, 5020, Bergen, Norway.
| | - Rigmor Austgulen
- Department of Cancer Research and Molecular Medicine, NTNU, 7491, Trondheim, Norway.
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23
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Wade M, Hoffmann TJ, Jenkins JM. Gene-environment interaction between the oxytocin receptor (OXTR) gene and parenting behaviour on children's theory of mind. Soc Cogn Affect Neurosci 2015; 10:1749-57. [PMID: 25977357 PMCID: PMC4666114 DOI: 10.1093/scan/nsv064] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 04/27/2015] [Accepted: 05/08/2015] [Indexed: 12/13/2022] Open
Abstract
Theory of mind (ToM) is the ability to interpret and understand human behaviour by representing the mental states of others. Like many human capacities, ToM is thought to develop through both complex biological and socialization mechanisms. However, no study has examined the joint effect of genetic and environmental influences on ToM. This study examined how variability in the oxytocin receptor gene (OXTR) and parenting behavior--two widely studied factors in ToM development-interacted to predict ToM in pre-school-aged children. Participants were 301 children who were part of an ongoing longitudinal birth cohort study. ToM was assessed at age 4.5 using a previously validated scale. Parenting was assessed through observations of mothers' cognitively sensitive behaviours. Using a family-based association design, it was suggestive that a particular variant (rs11131149) interacted with maternal cognitive sensitivity on children's ToM (P = 0.019). More copies of the major allele were associated with higher ToM as a function of increasing cognitive sensitivity. A sizeable 26% of the variability in ToM was accounted for by this interaction. This study provides the first empirical evidence of gene-environment interactions on ToM, supporting the notion that genetic factors may be modulated by potent environmental influences early in development.
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Affiliation(s)
- Mark Wade
- Department of Applied Psychology and Human Development, University of Toronto, 252 Bloor Street West, Toronto, Ontario, Canada M5S 1V6 and
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California at San Francisco, UCSF Box 0794, 513 Parnassus Avenue, S965, San Francisco, CA 94143-0794, USA
| | - Jennifer M Jenkins
- Department of Applied Psychology and Human Development, University of Toronto, 252 Bloor Street West, Toronto, Ontario, Canada M5S 1V6 and
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Abstract
For many years, linkage analysis was the primary tool used for the genetic mapping of Mendelian and complex traits with familial aggregation. Linkage analysis was largely supplanted by the wide adoption of genome-wide association studies (GWASs). However, with the recent increased use of whole-genome sequencing (WGS), linkage analysis is again emerging as an important and powerful analysis method for the identification of genes involved in disease aetiology, often in conjunction with WGS filtering approaches. Here, we review the principles of linkage analysis and provide practical guidelines for carrying out linkage studies using WGS data.
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Affiliation(s)
- Jurg Ott
- 1] Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China. [2] Laboratory of Statistical Genetics, Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Jing Wang
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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25
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Feng S, Pistis G, Zhang H, Zawistowski M, Mulas A, Zoledziewska M, Holmen OL, Busonero F, Sanna S, Hveem K, Willer C, Cucca F, Liu DJ, Abecasis GR. Methods for association analysis and meta-analysis of rare variants in families. Genet Epidemiol 2015; 39:227-38. [PMID: 25740221 DOI: 10.1002/gepi.21892] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/03/2015] [Accepted: 01/26/2015] [Indexed: 11/09/2022]
Abstract
Advances in exome sequencing and the development of exome genotyping arrays are enabling explorations of association between rare coding variants and complex traits. To ensure power for these rare variant analyses, a variety of association tests that group variants by gene or functional unit have been proposed. Here, we extend these tests to family-based studies. We develop family-based burden tests, variable frequency threshold tests and sequence kernel association tests. Through simulations, we compare the performance of different tests. We describe situations where family-based studies provide greater power than studies of unrelated individuals to detect rare variants associated with moderate to large changes in trait values. Broadly speaking, we find that when sample sizes are limited and only a modest fraction of all trait-associated variants can be identified, family samples are more powerful. Finally, we illustrate our approach by analyzing the relationship between coding variants and levels of high-density lipoprotein (HDL) cholesterol in 11,556 individuals from the HUNT and SardiNIA studies, demonstrating association for coding variants in the APOC3, CETP, LIPC, LIPG, and LPL genes and illustrating the value of family samples, meta-analysis, and gene-level tests. Our methods are implemented in freely available C++ code.
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Affiliation(s)
- Shuang Feng
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America
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26
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Laston SL, Voruganti VS, Haack K, Shah VO, Bobelu A, Bobelu J, Ghahate D, Harford AM, Paine SS, Tentori F, Cole SA, MacCluer JW, Comuzzie AG, Zager PG. Genetics of kidney disease and related cardiometabolic phenotypes in Zuni Indians: the Zuni Kidney Project. Front Genet 2015; 6:6. [PMID: 25688259 PMCID: PMC4311707 DOI: 10.3389/fgene.2015.00006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/08/2015] [Indexed: 12/31/2022] Open
Abstract
The objective of this study is to identify genetic factors associated with chronic kidney disease (CKD) and related cardiometabolic phenotypes among participants of the Genetics of Kidney Disease in Zuni Indians study. The study was conducted as a community-based participatory research project in the Zuni Indians, a small endogamous tribe in rural New Mexico. We recruited 998 members from 28 extended multigenerational families, ascertained through probands with CKD who had at least one sibling with CKD. We used the Illumina Infinium Human1M-Duo version 3.0 BeadChips to type 1.1 million single nucleotide polymorphisms (SNPs). Prevalence estimates for CKD, hyperuricemia, diabetes, and hypertension were 24%, 30%, 17% and 34%, respectively. We found a significant (p < 1.58 × 10-7) association for a SNP in a novel gene for serum creatinine (PTPLAD2). We replicated significant associations for genes with serum uric acid (SLC2A9), triglyceride levels (APOA1, BUD13, ZNF259), and total cholesterol (PVRL2). We found novel suggestive associations (p < 1.58 × 10-6) for SNPs in genes with systolic (OLFML2B), and diastolic blood pressure (NFIA). We identified a series of genes associated with CKD and related cardiometabolic phenotypes among Zuni Indians, a population with a high prevalence of kidney disease. Illuminating genetic variations that modulate the risk for these disorders may ultimately provide a basis for novel preventive strategies and therapeutic interventions.
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Affiliation(s)
- Sandra L Laston
- South Texas Diabetes and Obesity Institute, Regional Academic Health Center, University of Texas at San Antonio Harlingen, TX, USA
| | - V Saroja Voruganti
- Department of Nutrition, University of North Carolina at Chapel Hill Kannapolis, NC, USA ; University of North Carolina Nutrition Research Institute, University of North Carolina at Chapel Hill Kannapolis, NC, USA
| | - Karin Haack
- Department of Genetics, Texas Biomedical Research Institute San Antonio, TX, USA
| | - Vallabh O Shah
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | - Arlene Bobelu
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | - Jeanette Bobelu
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | - Donica Ghahate
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | - Antonia M Harford
- Department of Biochemistry, University of New Mexico School of Medicine Albuquerque, NM, USA
| | | | | | - Shelley A Cole
- Department of Genetics, Texas Biomedical Research Institute San Antonio, TX, USA
| | - Jean W MacCluer
- Department of Genetics, Texas Biomedical Research Institute San Antonio, TX, USA
| | - Anthony G Comuzzie
- Department of Genetics, Texas Biomedical Research Institute San Antonio, TX, USA ; Southwest National Primate Research Center San Antonio, TX, USA
| | - Philip G Zager
- Dialysis Clinic, Inc., Albuquerque, NM USA ; Department of Medicine, Division of Nephrology, University of New Mexico School of Medicine Albuquerque, NM, USA
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Wade M, Hoffmann TJ, Jenkins JM. Association between the arginine vasopressin receptor 1A (AVPR1A) gene and preschoolers’ executive functioning. Brain Cogn 2014; 90:116-23. [DOI: 10.1016/j.bandc.2014.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 01/08/2023]
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Wade M, Hoffmann TJ, Wigg K, Jenkins JM. Association between the oxytocin receptor (OXTR) gene and children's social cognition at 18 months. GENES BRAIN AND BEHAVIOR 2014; 13:603-10. [DOI: 10.1111/gbb.12148] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 06/05/2014] [Accepted: 06/09/2014] [Indexed: 11/26/2022]
Affiliation(s)
- M. Wade
- Department of Applied Psychology and Human Development; University of Toronto; Toronto ON Canada
| | - T. J. Hoffmann
- Department of Epidemiology and Biostatistics and Institute for Human Genetics; University of California at San Francisco; San Francisco CA USA
| | - K. Wigg
- Genetics and Development Division; Toronto Western Research Institute; Toronto ON Canada
| | - J. M. Jenkins
- Department of Applied Psychology and Human Development; University of Toronto; Toronto ON Canada
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29
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Chiu YF, Chung RH, Lee CY, Kao HY, Hou L, Hsu FC. Identification of rare variants for hypertension with incorporation of linkage information. BMC Proc 2014; 8:S109. [PMID: 25519312 PMCID: PMC4144469 DOI: 10.1186/1753-6561-8-s1-s109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We conducted linkage analysis using the genome-wide association study data on chromosome 3, and then assessed association between hypertension and rare variants of genes located in the regions showing evidence of linkage. The rare variants were collapsed if their minor allele frequencies were less than or equal to the thresholds: 0.01, 0.03, or 0.05. In the collapsing process, they were either unweighted or weighted by the nonparametric linkage log of odds scores in 2 different schemes: exponential weighting and cumulative weighting. Logistic regression models using the generalized estimating equations approach were used to assess association between the collapsed rare variants and hypertension adjusting for age and gender. Evidence of association from the weighted and unweighted collapsing schemes with minor allele frequencies ≤0.01, after accounting for multiple testing, was found for genes DOCK3 (p = 0.0090), ARMC8 (p = 1.29E-5), KCNAB1 (p = 5.8E-4), and MYRIP (p = 5.79E-6). DOCK3 and MYRIP are newly discovered. Incorporating linkage scores as weights was found to help identify rare causal variants with a large effect size.
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Affiliation(s)
- Yen-Feng Chiu
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Rd., Zhunan, Miaoli 35053, Taiwan, ROC
| | - Ren-Hua Chung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Rd., Zhunan, Miaoli 35053, Taiwan, ROC
| | - Chun-Yi Lee
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Rd., Zhunan, Miaoli 35053, Taiwan, ROC
| | - Hui-Yi Kao
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Rd., Zhunan, Miaoli 35053, Taiwan, ROC
| | - Lin Hou
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, Connecticut 06520, USA
| | - Fang-Chi Hsu
- Department of Biostatistical Sciences, Division of Public Health Sciences, 1834 Wake Forest Rd., Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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30
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Rastas P, Paulin L, Hanski I, Lehtonen R, Auvinen P. Lep-MAP: fast and accurate linkage map construction for large SNP datasets. ACTA ACUST UNITED AC 2013; 29:3128-34. [PMID: 24078685 DOI: 10.1093/bioinformatics/btt563] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Current high-throughput sequencing technologies allow cost-efficient genotyping of millions of single nucleotide polymorphisms (SNPs) for hundreds of samples. However, the tools that are currently available for constructing linkage maps are not well suited for large datasets. Linkage maps of large datasets would be helpful in de novo genome assembly by facilitating comprehensive genome validation and refinement by enabling chimeric scaffold detection, as well as in family-based linkage and association studies, quantitative trait locus mapping, analysis of genome synteny and other complex genomic data analyses. RESULTS We describe a novel tool, called Lepidoptera-MAP (Lep-MAP), for constructing accurate linkage maps with ultradense genome-wide SNP data. Lep-MAP is fast and memory efficient and largely automated, requiring minimal user interaction. It uses simultaneously data on multiple outbred families and can increase linkage map accuracy by taking into account achiasmatic meiosis, a special feature of Lepidoptera and some other taxa with no recombination in one sex (no recombination in females in Lepidoptera). We demonstrate that Lep-MAP outperforms other methods on real and simulated data. We construct a genome-wide linkage map of the Glanville fritillary butterfly (Melitaea cinxia) with over 40 000 SNPs. The data were generated with a novel in-house SOLiD restriction site-associated DNA tag sequencing protocol, which is described in the online supplementary material. AVAILABILITY AND IMPLEMENTATION Java source code under GNU general public license with the compiled classes and the datasets are available from http://sourceforge.net/users/lep-map.
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Affiliation(s)
- Pasi Rastas
- Department of Biosciences, Metapopulation Research Group, University of Helsinki, P.O. Box 65, FI-00014, Finland and Institute of Biotechnology, University of Helsinki, P.O. Box 56, FI-00014, Finland
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31
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Zhang Z, Wang JC, Howells W, Lin P, Agrawal A, Edenberg HJ, Tischfield JA, Schuckit MA, Bierut LJ, Goate A, Rice JP. Dosage transmission disequilibrium test (dTDT) for linkage and association detection. PLoS One 2013; 8:e63526. [PMID: 23691058 PMCID: PMC3653954 DOI: 10.1371/journal.pone.0063526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 04/06/2013] [Indexed: 11/26/2022] Open
Abstract
Both linkage and association studies have been successfully applied to identify disease susceptibility genes with genetic markers such as microsatellites and Single Nucleotide Polymorphisms (SNPs). As one of the traditional family-based studies, the Transmission/Disequilibrium Test (TDT) measures the over-transmission of an allele in a trio from its heterozygous parents to the affected offspring and can be potentially useful to identify genetic determinants for complex disorders. However, there is reduced information when complete trio information is unavailable. In this study, we developed a novel approach to "infer" the transmission of SNPs by combining both the linkage and association data, which uses microsatellite markers from families informative for linkage together with SNP markers from the offspring who are genotyped for both linkage and a Genome-Wide Association Study (GWAS). We generalized the traditional TDT to process these inferred dosage probabilities, which we name as the dosage-TDT (dTDT). For evaluation purpose, we developed a simulation procedure to assess its operating characteristics. We applied the dTDT to the simulated data and documented the power of the dTDT under a number of different realistic scenarios. Finally, we applied our methods to a family study of alcohol dependence (COGA) and performed individual genotyping on complete families for the top signals. One SNP (rs4903712 on chromosome 14) remained significant after correcting for multiple testing Methods developed in this study can be adapted to other platforms and will have widespread applicability in genomic research when case-control GWAS data are collected in families with existing linkage data.
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Affiliation(s)
- Zhehao Zhang
- Washington University School of Medicine, Department of Psychiatry, St. Louis, Missouri, United States of America
| | - Jen-Chyong Wang
- Washington University School of Medicine, Department of Psychiatry, St. Louis, Missouri, United States of America
| | - William Howells
- Washington University School of Medicine, Department of Psychiatry, St. Louis, Missouri, United States of America
| | - Peng Lin
- Washington University School of Medicine, Department of Psychiatry, St. Louis, Missouri, United States of America
| | - Arpana Agrawal
- Washington University School of Medicine, Department of Psychiatry, St. Louis, Missouri, United States of America
| | - Howard J. Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Jay A. Tischfield
- LSB 136, Rutgers University, Piscataway, New Jersey, United States of America
| | - Marc A. Schuckit
- Department of Psychiatry, University of California San Diego, La Jolla, California, United States of America
| | - Laura J. Bierut
- Washington University School of Medicine, Department of Psychiatry, St. Louis, Missouri, United States of America
| | - Alison Goate
- Washington University School of Medicine, Department of Psychiatry, St. Louis, Missouri, United States of America
| | - John P. Rice
- Washington University School of Medicine, Department of Psychiatry, St. Louis, Missouri, United States of America
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Li Q, Schwender H, Louis TA, Fallin MD, Ruczinski I. Efficient simulation of epistatic interactions in case-parent trios. Hum Hered 2013; 75:12-22. [PMID: 23548797 DOI: 10.1159/000348789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 02/11/2013] [Indexed: 12/26/2022] Open
Abstract
Statistical approaches to evaluate interactions between single nucleotide polymorphisms (SNPs) and SNP-environment interactions are of great importance in genetic association studies, as susceptibility to complex disease might be related to the interaction of multiple SNPs and/or environmental factors. With these methods under active development, algorithms to simulate genomic data sets are needed to ensure proper type I error control of newly proposed methods and to compare power with existing methods. In this paper we propose an efficient method for a haplotype-based simulation of case-parent trios when the disease risk is thought to depend on possibly higher-order epistatic interactions or gene-environment interactions with binary exposures.
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Affiliation(s)
- Qing Li
- Statistical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
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Gonzalez S, Xu C, Ramirez M, Zavala J, Armas R, Contreras SA, Contreras J, Dassori A, Leach RJ, Flores D, Jerez A, Raventós H, Ontiveros A, Nicolini H, Escamilla M. Suggestive evidence for association between L-type voltage-gated calcium channel (CACNA1C) gene haplotypes and bipolar disorder in Latinos: a family-based association study. Bipolar Disord 2013; 15:206-14. [PMID: 23437964 PMCID: PMC3781018 DOI: 10.1111/bdi.12041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVES Through recent genome-wide association studies (GWASs), several groups have reported significant association between variants in the calcium channel, voltage-dependent, L-type, alpha 1C subunit (CACNA1C) and bipolar disorder (BP) in European and European-American cohorts. We performed a family-based association study to determine whether CACNA1C is associated with BP in the Latino population. METHODS This study included 913 individuals from 215 Latino pedigrees recruited from the USA, Mexico, Guatemala, and Costa Rica. The Illumina GoldenGate Genotyping Assay was used to genotype 58 single-nucleotide polymorphisms (SNPs) that spanned a 602.9-kb region encompassing the CACNA1C gene including two SNPs (rs7297582 and rs1006737) previously shown to associate with BP. Individual SNP and haplotype association analyses were performed using Family-Based Association Test (version 2.0.3) and Haploview (version 4.2) software. RESULTS An eight-locus haplotype block that included these two markers showed significant association with BP (global marker permuted p = 0.0018) in the Latino population. For individual SNPs, this sample had insufficient power (10%) to detect associations with SNPs with minor effect (odds ratio = 1.15). CONCLUSIONS Although we were not able to replicate findings of association between individual CACNA1C SNPs rs7297582 and rs1006737 and BP, we were able to replicate the GWAS signal reported for CACNA1C through a haplotype analysis that encompassed these previously reported significant SNPs. These results provide additional evidence that CACNA1C is associated with BP and provides the first evidence that variations in this gene might play a role in the pathogenesis of this disorder in the Latino population.
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Affiliation(s)
- Suzanne Gonzalez
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
| | - Chun Xu
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
| | - Mercedes Ramirez
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
| | - Juan Zavala
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
| | - Regina Armas
- Langley Porter Psychiatric Institute, University of California at San Francisco, San Francisco, CA
| | - Salvador A Contreras
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Javier Contreras
- Centro de Investigación en Biología Celular y Molecular y Escuela de Biologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Albana Dassori
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA,South Texas Veterans Health Care System, San Antonio, TX
| | - Robin J Leach
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Deborah Flores
- Los Angeles Biomedical Research Center at Harbor, University of California Los Angeles Medical Center, Torrance, CA, USA
| | - Alvaro Jerez
- Centro Internacional de Trastornos Afectivos y de la Conducta Adictiva, Guatemala City, Guatemala
| | - Henriette Raventós
- Centro de Investigación en Biología Celular y Molecular y Escuela de Biologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Alfonso Ontiveros
- Instituto de Información e Investigación en Salud Mental AC, Monterrey, Nuevo Leon
| | - Humberto Nicolini
- Grupo de Estudios Médicos y Familiares Carracci, S.C., México, D.F., México
| | - Michael Escamilla
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
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Lutz S, Yip WK, Hokanson J, Laird N, Lange C. A general semi-parametric approach to the analysis of genetic association studies in population-based designs. BMC Genet 2013; 14:13. [PMID: 23448186 PMCID: PMC3648382 DOI: 10.1186/1471-2156-14-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 02/01/2013] [Indexed: 12/03/2022] Open
Abstract
Background For genetic association studies in designs of unrelated individuals, current statistical methodology typically models the phenotype of interest as a function of the genotype and assumes a known statistical model for the phenotype. In the analysis of complex phenotypes, especially in the presence of ascertainment conditions, the specification of such model assumptions is not straight-forward and is error-prone, potentially causing misleading results. Results In this paper, we propose an alternative approach that treats the genotype as the random variable and conditions upon the phenotype. Thereby, the validity of the approach does not depend on the correctness of assumptions about the phenotypic model. Misspecification of the phenotypic model may lead to reduced statistical power. Theoretical derivations and simulation studies demonstrate both the validity and the advantages of the approach over existing methodology. In the COPDGene study (a GWAS for Chronic Obstructive Pulmonary Disease (COPD)), we apply the approach to a secondary, quantitative phenotype, the Fagerstrom nicotine dependence score, that is correlated with COPD affection status. The software package that implements this method is available. Conclusions The flexibility of this approach enables the straight-forward application to quantitative phenotypes and binary traits in ascertained and unascertained samples. In addition to its robustness features, our method provides the platform for the construction of complex statistical models for longitudinal data, multivariate data, multi-marker tests, rare-variant analysis, and others.
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Affiliation(s)
- Sharon Lutz
- Department of Biostatistics, University of Colorado Anschutz Medical Campus, Aurora, USA.
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Family-based studies to the rescue of genome-wide association studies in renal function. Kidney Int 2013; 83:196-8. [DOI: 10.1038/ki.2012.398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Teyssèdre S, Elsen JM, Ricard A. Statistical distributions of test statistics used for quantitative trait association mapping in structured populations. Genet Sel Evol 2012; 44:32. [PMID: 23146127 PMCID: PMC3817592 DOI: 10.1186/1297-9686-44-32] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 10/31/2012] [Indexed: 11/25/2022] Open
Abstract
Background Spurious associations between single nucleotide polymorphisms and phenotypes are a major issue in genome-wide association studies and have led to underestimation of type 1 error rate and overestimation of the number of quantitative trait loci found. Many authors have investigated the influence of population structure on the robustness of methods by simulation. This paper is aimed at developing further the algebraic formalization of power and type 1 error rate for some of the classical statistical methods used: simple regression, two approximate methods of mixed models involving the effect of a single nucleotide polymorphism (SNP) and a random polygenic effect (GRAMMAR and FASTA) and the transmission/disequilibrium test for quantitative traits and nuclear families. Analytical formulae were derived using matrix algebra for the first and second moments of the statistical tests, assuming a true mixed model with a polygenic effect and SNP effects. Results The expectation and variance of the test statistics and their marginal expectations and variances according to the distribution of genotypes and estimators of variance components are given as a function of the relationship matrix and of the heritability of the polygenic effect. These formulae were used to compute type 1 error rate and power for any kind of relationship matrix between phenotyped and genotyped individuals for any level of heritability. For the regression method, type 1 error rate increased with the variability of relationships and with heritability, but decreased with the GRAMMAR method and was not affected with the FASTA and quantitative transmission/disequilibrium test methods. Conclusions The formulae can be easily used to provide the correct threshold of type 1 error rate and to calculate the power when designing experiments or data collection protocols. The results concerning the efficacy of each method agree with simulation results in the literature but were generalized in this work. The power of the GRAMMAR method was equal to the power of the FASTA method at the same type 1 error rate. The power of the quantitative transmission/disequilibrium test was low. In conclusion, the FASTA method, which is very close to the full mixed model, is recommended in association mapping studies.
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Affiliation(s)
- Simon Teyssèdre
- INRA, UR 631 Station d’Amélioration Génétique des Animaux, Castanet-Tolosan F-31326, France
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Follow-up association study of linkage regions reveals multiple candidate genes for carotid plaque in Dominicans. Atherosclerosis 2012; 223:177-83. [PMID: 22503546 DOI: 10.1016/j.atherosclerosis.2012.03.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/14/2012] [Accepted: 03/16/2012] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Carotid plaque is a marker of subclinical atherosclerosis with a genetic component. The aim of this follow-up fine mapping study was to identify candidate genes for carotid plaque within four linkage regions. METHODS We successfully genotyped 3712 single nucleotide polymorphisms (SNPs) under the four linkage regions that were previously identified in 100 extended Dominican families. Family-based association tests were performed to investigate their associations with carotid plaque. Promising SNPs were evaluated in an independent population-based subcohort (N=941, 384 Dominicans) from the Northern Manhattan Study (NOMAS). RESULTS In the family study, evidence for association (p<0.0005) was found regarding several genes (NAV2, EFCAB11/TDP1, AGBL1, PTPN9, LINGO1 and LOC730118), with the strongest association at rs4143999 near EFCAB11/TDP1 (p=0.00001 for carotid presence and 0.00003 for plaque area, multiple testing corrected p≤0.02). The association in AGBL1 and PTPN9 was mainly driven by the families with linkage evidence (p=0.00008-0.00001 and 0.76-0.32, respectively, in the families with and without linkage evidence). However, these associations explained only a small portion of the observed linkage. In NOMAS, replication (p<0.05 in the whole NOMAS subcohort and p<0.10 in the smaller Dominican subcohort) was found for SNPs within/near EFCAB11, NAV2, AGBL1 and other genes. CONCLUSION This follow-up study has identified multiple candidate genes for carotid plaque in the Dominican population. Many of these genes have been implicated in neurodegenerative and cardiovascular diseases. Further studies with in-depth re-sequencing are needed to uncover both rare and common functional variants that contribute to the susceptibility to atherosclerosis.
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Design and rationale of a genetic cohort study on congenital cardiac disease: experiences from a multi-institutional platform in Quebec. Cardiol Young 2011; 21:654-64. [PMID: 21729494 DOI: 10.1017/s1047951111000813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Congenital cardiac disease is the most common malformation, and a substantial source of mortality and morbidity in children and young adults. A role for genetic factors is recognised for these malformations, but overall few predisposing loci have been identified. Here we report the rationale, design, and first results of a multi-institutional congenital cardiac disease cohort, assembled mainly from the French-Canadian population of the province of Quebec and centred on families with multiple affected members afflicted by cardiac malformations. METHODS Families were recruited into the study, phenotyped and sampled for DNA in cardiology clinics over the first 3 years of enrolment. We performed segregation analysis and linkage simulations in the subgroup of families with left ventricular outflow tract obstruction (LVOTO). RESULTS A total of 1603 participants from 300 families were recruited, with 169 out of 300 (56.3%) families having more than one affected member. For the LVOTO group, we estimate heritability to be 0.46-0.52 in our cohort. Simulation analysis demonstrated sufficient power to carry out linkage analyses, with an expected mean log-of-odds (LOD) score of 3.8 in 67 pedigrees with LVOTO. CONCLUSION We show feasibility and usefulness of a population-based biobank for genetic investigations into the causes of congenital cardiac disease. Heritability of LVOTO is high and could be accounted for by multiple loci. This platform is ideally suited for multiple analysis approaches, including linkage analysis and novel gene sequencing approaches, and will allow to establish segregation of risk alleles at family and population levels.
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Yip WK, De G, Raby BA, Laird N. Identifying causal rare variants of disease through family-based analysis of Genetics Analysis Workshop 17 data set. BMC Proc 2011; 5 Suppl 9:S21. [PMID: 22373204 PMCID: PMC3287856 DOI: 10.1186/1753-6561-5-s9-s21] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Linkage- and association-based methods have been proposed for mapping disease-causing rare variants. Based on the family information provided in the Genetic Analysis Workshop 17 data set, we formulate a two-pronged approach that combines both methods. Using the identity-by-descent information provided for eight extended pedigrees (n = 697) and the simulated quantitative trait Q1, we explore various traditional nonparametric linkage analysis methods; the best result is obtained by assuming between-family heterogeneity and applying the Haseman-Elston regression to each pedigree separately. We discover strong signals from two genes in two different families and weaker signals for a third gene from two other families. As an exploratory approach, we apply an association test based on a modified family-based association test statistic to all rare variants (frequency < 1% or < 3%) designated as causal for Q1. Family-based association tests correctly identified causal single-nucleotide polymorphisms for four genes (KDR, VEGFA, VEGFC, and FLT1). Our results suggest that both linkage and association tests with families show promise for identifying rare variants.
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Affiliation(s)
- Wai-Ki Yip
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Building II, Boston, MA 02115, USA
| | - Gourab De
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Building II, Boston, MA 02115, USA
| | - Benjamin A Raby
- Brigham and Women Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Nan Laird
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Building II, Boston, MA 02115, USA
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Abstract
Association mapping has successfully identified common SNPs associated with many diseases. However, the inability of this class of variation to account for most of the supposed heritability has led to a renewed interest in methods - primarily linkage analysis - to detect rare variants. Family designs allow for control of population stratification, investigations of questions such as parent-of-origin effects and other applications that are imperfectly or not readily addressed in case-control association studies. This article guides readers through the interface between linkage and association analysis, reviews the new methodologies and provides useful guidelines for applications. Just as effective SNP-genotyping tools helped to realize the potential of association studies, next-generation sequencing tools will benefit genetic studies by improving the power of family-based approaches.
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Peloso GM, Dupuis J, Lunetta KL. Evaluation of methods accounting for population structure with pedigree data and continuous outcomes. Genet Epidemiol 2011; 35:427-36. [PMID: 21618600 DOI: 10.1002/gepi.20590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/09/2011] [Accepted: 04/14/2011] [Indexed: 01/01/2023]
Abstract
Methods to account for population structure (PS) in genome-wide association studies have been well developed in samples of unrelated individuals, but when a sample is composed of families, the task of finding and accounting for PS is not as straight forward. Family-based tests that condition on parental genotypes or their sufficient statistics are immune to biases due to PS, but are known to have low power, particularly for unselected samples. Population-based approaches that use all available data are an attractive alternative, but the methods have not been evaluated for continuous outcomes when a sample has both family and PS. Therefore, we compare through simulation the performance of population-based regression models that account for family and PS with continuous outcomes using a range of family sizes and structures, including two and three generational families with admixed and discrete PS. We find that when computation time is a concern, the Dupuis et al. efficient score test performs very well. When computational time is not an issue, a linear mixed effects model adjusting for genetic principal components tends to have slightly better power than the score test and may be preferred.
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Affiliation(s)
- Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
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Van Steen K. Perspectives on genome-wide multi-stage family-based association studies. Stat Med 2011; 30:2201-21. [DOI: 10.1002/sim.4259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 03/07/2011] [Indexed: 01/03/2023]
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Tang H, Siegmund DO, Johnson NA, Romieu I, London SJ. Joint testing of genotype and ancestry association in admixed families. Genet Epidemiol 2011; 34:783-91. [PMID: 21031451 DOI: 10.1002/gepi.20520] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Current genome-wide association studies (GWAS) often involve populations that have experienced recent genetic admixture. Genotype data generated from these studies can be used to test for association directly, as in a non-admixed population. As an alternative, these data can be used to infer chromosomal ancestry, and thus allow for admixture mapping. We quantify the contribution of allele-based and ancestry-based association testing under a family-design, and demonstrate that the two tests can provide non-redundant information. We propose a joint testing procedure, which efficiently integrates the two sources information. The efficiencies of the allele, ancestry and combined tests are compared in the context of a GWAS. We discuss the impact of population history and provide guidelines for future design and analysis of GWAS in admixed populations.
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Affiliation(s)
- Hua Tang
- Department of Genetics, School of Medicine, Stanford University, Stanford, California 94305, USA.
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45
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Benke KS, Fallin MD. Methods: genetic epidemiology. Clin Lab Med 2010; 30:795-814. [PMID: 20832653 DOI: 10.1016/j.cll.2010.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Given the potential benefits of gene identification in psychiatry, genetic epidemiology has become a mainstream discipline within the field. This article discusses the main tools for gene discovery. The focus is on the designs and analytic approaches for each of these methods. Because most gene discovery has now moved to genetic association studies, and most recently to genome-wide association studies, the focus is on methods for this design. Also highlighted are the current challenges of genetic epidemiology as a prelude to future approaches that may be applied to psychiatric disorders in the coming years.
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Affiliation(s)
- Kelly S Benke
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, W6033, Baltimore, MD 21205, USA
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Madore AM, Laprise C. Immunological and genetic aspects of asthma and allergy. J Asthma Allergy 2010; 3:107-21. [PMID: 21437045 PMCID: PMC3047903 DOI: 10.2147/jaa.s8970] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Indexed: 12/21/2022] Open
Abstract
Prevalence of allergy and allergic asthma are increasing worldwide. More than half of the US population has a positive skin prick test and approximately 10% are asthmatics. Many studies have been conducted to define immunological pathways underlying allergy and asthma development and to identify the main genetic determinants. In the effort to find missing pieces of the puzzle, new genomic approaches and more standardized ones, such as the candidate gene approach, have been used collectively. This article proposes an overview of the actual knowledge about immunological and genetic aspects of allergy and asthma. Special attention has been drawn to the challenges linked to genetic research in complex traits such as asthma and to the contribution of new genomic approaches.
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Affiliation(s)
- Anne-Marie Madore
- Université du Québec à Chicoutimi, Département des sciences fondamentales, Saguenay, Canada
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Xu T, Cheng Y, Guo Y, Zhang L, Pei YF, Redger K, Liu YJ, Deng HW. Design and Interpretation of Linkage and Association Studies on Osteoporosis. Clin Rev Bone Miner Metab 2010. [DOI: 10.1007/s12018-010-9070-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet 2010; 42:525-9. [PMID: 20436469 DOI: 10.1038/ng.580] [Citation(s) in RCA: 452] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 04/06/2010] [Indexed: 01/10/2023]
Abstract
Case-parent trios were used in a genome-wide association study of cleft lip with and without cleft palate. SNPs near two genes not previously associated with cleft lip with and without cleft palate (MAFB, most significant SNP rs13041247, with odds ratio (OR) per minor allele = 0.704, 95% CI 0.635-0.778, P = 1.44 x 10(-11); and ABCA4, most significant SNP rs560426, with OR = 1.432, 95% CI 1.292-1.587, P = 5.01 x 10(-12)) and two previously identified regions (at chromosome 8q24 and IRF6) attained genome-wide significance. Stratifying trios into European and Asian ancestry groups revealed differences in statistical significance, although estimated effect sizes remained similar. Replication studies from several populations showed confirming evidence, with families of European ancestry giving stronger evidence for markers in 8q24, whereas Asian families showed stronger evidence for association with MAFB and ABCA4. Expression studies support a role for MAFB in palatal development.
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Campbell DB, Warren D, Sutcliffe JS, Lee EB, Levitt P. Association of MET with social and communication phenotypes in individuals with autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:438-446. [PMID: 19548256 PMCID: PMC7076810 DOI: 10.1002/ajmg.b.30998] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Autism is a complex neurodevelopmental disorder diagnosed by impairments in social interaction, communication, and behavioral flexibility. Autism is highly heritable, but it is not known whether a genetic risk factor contributes to all three core domains of the disorder or autism results from the confluence of multiple genetic risk factors for each domain. We and others reported previously association of variants in the gene encoding the MET receptor tyrosine kinase in five independent samples. We further described enriched association of the MET promoter variant rs1858830 C allele in families with co-occurring autism and gastrointestinal conditions. To test the contribution of this functional MET promoter variant to the domains of autism, we analyzed its association with quantitative scores derived from three instruments used to diagnose and describe autism phenotypes: the Autism Diagnostic Interview-Revised (ADI-R), the Autism Diagnostic Observation Schedule (ADOS), and both the parent and the teacher report forms of the Social Responsiveness Scale (SRS). In 748 individuals from 367 families, the transmission of the MET C allele from parent to child was consistently associated with both social and communication phenotypes of autism. Stratification by gastrointestinal conditions revealed a similar pattern of association with both social and communication phenotypes in 242 individuals with autism from 118 families with co-occurring gastrointestinal conditions, but a lack of association with any domain in 181 individuals from 96 families with ASD and no co-occurring gastrointestinal condition. These data indicate that the MET C allele influences at least two of the three domains of the autism triad.
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Affiliation(s)
- Daniel B. Campbell
- Department of Pharmacology, Vanderbilt University, Nashville, TN,Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN
| | - Dana Warren
- Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN
| | - James S. Sutcliffe
- Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Evon Batey Lee
- Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN,Department of Pediatrics, Vanderbilt University, Nashville, TN
| | - Pat Levitt
- Department of Pharmacology, Vanderbilt University, Nashville, TN,Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN
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50
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Benke KS, Fallin MD. Methods: genetic epidemiology. Psychiatr Clin North Am 2010; 33:15-34. [PMID: 20159338 DOI: 10.1016/j.psc.2009.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Given the potential benefits of gene identification in psychiatry, genetic epidemiology has become a mainstream discipline within the field. This article discusses the main tools for gene discovery. The focus is on the designs and analytic approaches for each of these methods. Because most gene discovery has now moved to genetic association studies, and most recently to genome-wide association studies, the focus is on methods for this design. Also highlighted are the current challenges of genetic epidemiology as a prelude to future approaches that may be applied to psychiatric disorders in the coming years.
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Affiliation(s)
- Kelly S Benke
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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