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Hecker J, Chun S, Samiei A, Liu C, Laurie C, Kachroo P, Lutz SM, Lee S, Smith AV, Lasky-Su J, Cho MH, Sharma S, Soto Quirós ME, Avila L, Celedón JC, Raby B, Zhou X, Silverman EK, DeMeo DL, Lange C, Weiss ST. FGF20 and PGM2 variants are associated with childhood asthma in family-based whole-genome sequencing studies. Hum Mol Genet 2023; 32:696-707. [PMID: 36255742 PMCID: PMC9896483 DOI: 10.1093/hmg/ddac258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Asthma is a heterogeneous common respiratory disease that remains poorly understood. The established genetic associations fail to explain the high estimated heritability, and the prevalence of asthma differs between populations and geographic regions. Robust association analyses incorporating different genetic ancestries and whole-genome sequencing data may identify novel genetic associations. METHODS We performed family-based genome-wide association analyses of childhood-onset asthma based on whole-genome sequencing (WGS) data for the 'The Genetic Epidemiology of Asthma in Costa Rica' study (GACRS) and the Childhood Asthma Management Program (CAMP). Based on parent-child trios with children diagnosed with asthma, we performed a single variant analysis using an additive and a recessive genetic model and a region-based association analysis of low-frequency and rare variants. RESULTS Based on 1180 asthmatic trios (894 GACRS trios and 286 CAMP trios, a total of 3540 samples with WGS data), we identified three novel genetic loci associated with childhood-onset asthma: rs4832738 on 4p14 ($P=1.72\ast{10}^{-9}$, recessive model), rs1581479 on 8p22 ($P=1.47\ast{10}^{-8}$, additive model) and rs73367537 on 10q26 ($P=1.21\ast{10}^{-8}$, additive model in GACRS only). Integrative analyses suggested potential novel candidate genes underlying these associations: PGM2 on 4p14 and FGF20 on 8p22. CONCLUSION Our family-based whole-genome sequencing analysis identified three novel genetic loci for childhood-onset asthma. Gene expression data and integrative analyses point to PGM2 on 4p14 and FGF20 on 8p22 as linked genes. Furthermore, region-based analyses suggest independent potential low-frequency/rare variant associations on 8p22. Follow-up analyses are needed to understand the functional mechanisms and generalizability of these associations.
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Affiliation(s)
- Julian Hecker
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmad Samiei
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Cuining Liu
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sharon M Lutz
- Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care, Boston, MA 02215, USA
| | - Sanghun Lee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin-si, 16890, South Korea
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Lydiana Avila
- Department of Pediatrics, Hospital Nacional de Niños, 10101 San José, Costa Rica
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Benjamin Raby
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | - Christoph Lange
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
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2
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Hecker J, Prokopenko D, Lange C, Fier HL. PolyGEE: a generalized estimating equation approach to the efficient and robust estimation of polygenic effects in large-scale association studies. Biostatistics 2019; 19:295-306. [PMID: 28968646 PMCID: PMC5991211 DOI: 10.1093/biostatistics/kxx040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/21/2017] [Indexed: 11/17/2022] Open
Abstract
To quantify polygenic effects, i.e. undetected genetic effects, in large-scale association studies, we propose a generalized estimating equation (GEE) based estimation framework. We develop a marginal model for single-variant association test statistics of complex diseases that generalizes existing approaches such as LD Score regression and that is applicable to population-based designs, to family-based designs or to arbitrary combinations of both. We extend the standard GEE approach so that the parameters of the proposed marginal model can be estimated based on working-correlation/linkage-disequilibrium (LD) matrices from external reference panels. Our method achieves substantial efficiency gains over standard approaches, while it is robust against misspecification of the LD structure, i.e. the LD structure of the reference panel can differ substantially from the true LD structure in the study population. In simulation studies and in applications to population-based and family-based studies, we illustrate the features of the proposed GEE framework. Our results suggest that our approach can be up to 100% more efficient than existing methodology.
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Affiliation(s)
- Julian Hecker
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA and Department of Genomic Mathematics, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA and Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Heide Loehlein Fier
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA and Department of Genomic Mathematics, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
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3
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Hecker J, Laird N, Lange C. A comparison of popular TDT-generalizations for family-based association analysis. Genet Epidemiol 2019; 43:300-317. [PMID: 30609057 DOI: 10.1002/gepi.22181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/26/2018] [Accepted: 11/26/2018] [Indexed: 12/31/2022]
Abstract
The transmission disequilibrium test (TDT) is the gold standard for testing the association between a genetic variant and disease in samples consisting of affected individuals and their parents. In practice, more complex pedigree structures, that is siblings with no parents, or three-generational pedigrees with possibly missing genotypes, are common. There are several generalizations of the TDT that are suitable for use with arbitrary pedigree structures. We consider three such frequently used generalizations, family-based association test, pedigree disequilibrium test, and generalized disequilibrium test, that have accompanying software and compare them regarding validity and power in the single variant setting. We use simulations to study the effects of population admixture, populations whose genotypes are not in Hardy-Weinberg equilibrium (HWE), different pedigree structures, and the presence of linkage. Whereas our results show that some TDT generalizations can have a substantially increased Type 1 error, these tests are often used in substantive research without caveats about the validity of their Type 1 error. For the association analysis of rare variants in sequencing studies, region-based extensions of the TDT generalizations, that rely on the postulated robustness of the single variant tests, have been proposed. We discuss the implications of our results for these region-based extensions.
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Affiliation(s)
- Julian Hecker
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Nan Laird
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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4
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Dizier MH, Margaritte-Jeannin P, Pain L, Sarnowski C, Brossard M, Mohamdi H, Lavielle N, Babron MCC, Just J, Lathrop M, Laprise C, Bouzigon E, Demenais F, Nadif R. Interactive effect between ATPase-related genes and early-life tobacco smoke exposure on bronchial hyper-responsiveness detected in asthma-ascertained families. Thorax 2018; 74:254-260. [PMID: 30282721 DOI: 10.1136/thoraxjnl-2018-211797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/21/2018] [Accepted: 08/20/2018] [Indexed: 01/29/2023]
Abstract
BACKGROUND A positional cloning study of bronchial hyper-responsiveness (BHR) at the 17p11 locus in the French Epidemiological study on the Genetics and Environment of Asthma (EGEA) families showed significant interaction between early-life environmental tobacco smoke (ETS) exposure and genetic variants located in DNAH9. This gene encodes the heavy chain subunit of axonemal dynein, which is involved with ATP in the motile cilia function.Our goal was to identify genetic variants at other genes interacting with ETS in BHR by investigating all genes belonging to the 'ATP-binding' and 'ATPase activity' pathways which include DNAH9, are targets of cigarette smoke and play a crucial role in the airway inflammation. METHODS Family-based interaction tests between ETS-exposed and unexposed BHR siblings were conducted in 388 EGEA families. Twenty single-nucleotide polymorphisms (SNP) showing interaction signals (p≤5.10-3) were tested in the 253 Saguenay-Lac-Saint-Jean (SLSJ) families. RESULTS One of these SNPs was significantly replicated for interaction with ETS in SLSJ families (p=0.003). Another SNP reached the significance threshold after correction for multiple testing in the combined analysis of the two samples (p=10-5). Results were confirmed using both a robust log-linear test and a gene-based interaction test. CONCLUSION The SNPs showing interaction with ETS belong to the ATP8A1 and ABCA1 genes, which play a role in the maintenance of asymmetry and homeostasis of lung membrane lipids.
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Affiliation(s)
- Marie-Hélène Dizier
- INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Patricia Margaritte-Jeannin
- INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Lucile Pain
- Département des Sciences Fondamentales, Université du Québec, Chicoutimi, Quebec, Canada
| | - Chloé Sarnowski
- INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Myriam Brossard
- INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Hamida Mohamdi
- INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Nolwenn Lavielle
- INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Marie-Claude C Babron
- INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Jocelyne Just
- Service d'Allergologie Pédiatrique, Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand-Trousseau (APHP), UPMC Paris 06, Paris, France
| | - Mark Lathrop
- Department of Human Genetics, McGill University and Genome Quebec's Innovation Centre, Montréal, Québec, Canada
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec, Chicoutimi, Quebec, Canada
| | - Emmanuelle Bouzigon
- INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Florence Demenais
- INSERM, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Rachel Nadif
- Aging and Chronic Diseases-Epidemiological and Public Health Approaches (VIMA), Inserm, U1168, Villejuif, France.,UMR-S 1168, Université de Versailles Saint-Quentin-en-Yvelines, Paris, France
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5
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Zhou YH, Marron JS, Wright FA. Computation of ancestry scores with mixed families and unrelated individuals. Biometrics 2017; 74:155-164. [PMID: 28452052 DOI: 10.1111/biom.12708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 03/01/2017] [Accepted: 03/01/2017] [Indexed: 01/03/2023]
Abstract
The issue of robustness to family relationships in computing genotype ancestry scores such as eigenvector projections has received increased attention in genetic association, and is particularly challenging when sets of both unrelated individuals and closely related family members are included. The current standard is to compute loadings (left singular vectors) using unrelated individuals and to compute projected scores for remaining family members. However, projected ancestry scores from this approach suffer from shrinkage toward zero. We consider two main novel strategies: (i) matrix substitution based on decomposition of a target family-orthogonalized covariance matrix, and (ii) using family-averaged data to obtain loadings. We illustrate the performance via simulations, including resampling from 1000 Genomes Project data, and analysis of a cystic fibrosis dataset. The matrix substitution approach has similar performance to the current standard, but is simple and uses only a genotype covariance matrix, while the family-average method shows superior performance. Our approaches are accompanied by novel ancillary approaches that provide considerable insight, including individual-specific eigenvalue scree plots.
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Affiliation(s)
- Yi-Hui Zhou
- Department of Biological Sciences, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, U.S.A
| | - James S Marron
- Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, U.S.A
| | - Fred A Wright
- Department of Biological Sciences and Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh, U.S.A
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6
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Association of nsv823469 copy number loss with decreased risk of chronic obstructive pulmonary disease and pulmonary function in Chinese. Sci Rep 2017; 7:40060. [PMID: 28079130 PMCID: PMC5227687 DOI: 10.1038/srep40060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/30/2016] [Indexed: 01/17/2023] Open
Abstract
It is highly possible that copy number variations (CNVs) in susceptible regions have effects on chronic obstructive pulmonary disease (COPD) development, while long noncoding RNA (lncRNAs) have been shown to cause COPD. We hypothesized that the common CNV, named nsv823469 located on 6p22.1, and covering lncRNAs (major histocompatibility complex, class I, A (HLA-A) and HLA complex group 4B (HCG4B)) has an effect on COPD risk. This association was assessed through a two-stage case-control study, and was further confirmed with COPD and pulmonary function-based family analyses, respectively. The copy number loss (0-copy/1-copy) of nsv823469 significantly decreased risk of COPD compared with normal (2-copy) (OR = 0.77, 95% CI = 0.69–0.85). The loss allele, inducing copy number loss of nsv823469, has a tendency to transmit to offspring or siblings (P = 0.010) and is associated with forced expiratory volume in 1 second (FEV1) (P = 0.030). Furthermore, the copy number loss of nsv823469 in normal pulmonary tissue decreases the expression levels of HCG4B (r = 0.315, P = 0.031) and HLA-A (r = 0.296, P = 0.044). Our data demonstrates that nsv823469 plays a role in COPD and pulmonary function inheritance by potentially altering expression of HCG4B.
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Bhatnagar SR, Greenwood CMT, Labbe A. Assessing transmission ratio distortion in extended families: a comparison of analysis methods. BMC Proc 2016; 10:197-202. [PMID: 27980636 PMCID: PMC5133486 DOI: 10.1186/s12919-016-0030-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A statistical departure from Mendel's law of segregation is known as transmission ratio distortion. Although well documented in many other organisms, the extent of transmission ratio distortion and its influence in the human genome remains incomplete. Using Genetic Analysis Workshop 19 whole genome sequence data from 20 large Mexican American pedigrees, our goal was to identify potentially distorted regions in the genome using family-based association methods such as the transmission disequilibrium test, the pedigree disequilibrium test, and the family-based association test. Preliminary results showed an unusually high number of transmission ratio distortion signals identified by the transmission disequilibrium test, but this phenomenon could not be replicated by the pedigree disequilibrium test or family-based association test. Applying these tests to different subsets of the data, we found the transmission disequilibrium test to be very sensitive to imputed genotypes. Regression analysis of transmission ratio distortion test p values controlling for minor allele frequency and quality control checks showed that Hardy Weinberg p values are associated with this inflation. Although the transmission disequilibrium test appears confounded by imputation of single nucleotide polymorphisms, the pedigree disequilibrium test and family-based association test seem to offer more robust alternatives when searching for transmission ratio distortion loci in whole genome sequence data from extended families.
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Affiliation(s)
- Sahir R. Bhatnagar
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Avenue West, Montreal, QC H3A 1A2 Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste. Catherine, Montreal, QC H3T 1E2 Canada
| | - Celia M. T. Greenwood
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Avenue West, Montreal, QC H3A 1A2 Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste. Catherine, Montreal, QC H3T 1E2 Canada
- Departments of Oncology and Human Genetics, McGill University, Montreal, QC Canada
| | - Aurélie Labbe
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Avenue West, Montreal, QC H3A 1A2 Canada
- Department of Psychiatry, McGill University, Montreal, QC Canada
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8
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Xie C, Chen X, Qiu F, Zhang L, Wu D, Chen J, Yang L, Lu J. The role of WWOX polymorphisms on COPD susceptibility and pulmonary function traits in Chinese: a case-control study and family-based analysis. Sci Rep 2016; 6:21716. [PMID: 26902998 PMCID: PMC4763216 DOI: 10.1038/srep21716] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 01/29/2016] [Indexed: 01/21/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) in the WW domain containing oxidoreductase (WWOX) gene were recently identified to be quantitative trait loci for lung function and thus likely to be susceptible biomarkers for COPD. However, the associations between WWOX SNPs and COPD risk are still unclear. Here, by conducting a two-center case-control study including 1511 COPD cases and 1677 controls and a family-based analysis comprising 95 nuclear pedigrees, we tested the associations between five SNPs that are rs10220974C >T, rs3764340C >G, rs12918952G >A, rs383362G >T, rs12828G >A of WWOX and COPD risk as well as the hereditary inclination of these loci among COPD families. We found that the SNP rs383362G >T was significantly associated with an increased risk of COPD in a T allele-number dependent-manner (OR = 1.30, 95%CI = 1.11 - 1.52). The T allele was more prone to over transmit to sick children and sibs than the G allele (Z = 2.900, P = 0.004). Moreover, the forced expiratory volume in one second/forced vital capacity (FEV1/FVC), FEV1/predicted-FEV1 and annual FEV1 also significantly decreased in the rs383362T carriers compared to the rs383362GG carriers. For other SNPs, no significant association was observed for COPD and pulmonary function. Taken together, our data demonstrated that the SNP rs383362G >T of WWOX plays a role in COPD inheritance.
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Affiliation(s)
- Chenli Xie
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China.,Department of respiratory medicine, The Fifth People's Hospital of Dongguan City, Dongguan 523900, China
| | - Xiaoliang Chen
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China.,Shenzhen Guangming district center for disease control and prevention Shenzhen 518106, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Lisha Zhang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Di Wu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Jiansong Chen
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Lei Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
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9
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Fava VM, Manry J, Cobat A, Orlova M, Van Thuc N, Ba NN, Thai VH, Abel L, Alcaïs A, Schurr E. A Missense LRRK2 Variant Is a Risk Factor for Excessive Inflammatory Responses in Leprosy. PLoS Negl Trop Dis 2016; 10:e0004412. [PMID: 26844546 PMCID: PMC4742274 DOI: 10.1371/journal.pntd.0004412] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/08/2016] [Indexed: 12/17/2022] Open
Abstract
Background Depending on the epidemiological setting, a variable proportion of leprosy patients will suffer from excessive pro-inflammatory responses, termed type-1 reactions (T1R). The LRRK2 gene encodes a multi-functional protein that has been shown to modulate pro-inflammatory responses. Variants near the LRRK2 gene have been associated with leprosy in some but not in other studies. We hypothesized that LRRK2 was a T1R susceptibility gene and that inconsistent association results might reflect different proportions of patients with T1R in the different sample settings. Hence, we evaluated the association of LRRK2 variants with T1R susceptibility. Methodology An association scan of the LRRK2 locus was performed using 156 single-nucleotide polymorphisms (SNPs). Evidence of association was evaluated in two family-based samples: A set of T1R-affected and a second set of T1R-free families. Only SNPs significant for T1R-affected families with significant evidence of heterogeneity relative to T1R-free families were considered T1R-specific. An expression quantitative trait locus (eQTL) analysis was applied to evaluate the impact of T1R-specific SNPs on LRRK2 gene transcriptional levels. Principal Findings A total of 18 T1R-specific variants organized in four bins were detected. The core SNP capturing the T1R association was the LRRK2 missense variant M2397T (rs3761863) that affects LRRK2 protein turnover. Additionally, a bin of nine SNPs associated with T1R were eQTLs for LRRK2 in unstimulated whole blood cells but not after exposure to Mycobacterium leprae antigen. Significance The results support a preferential association of LRRK2 variants with T1R. LRRK2 involvement in T1R is likely due to a pathological pro-inflammatory loop modulated by LRRK2 availability. Interestingly, the M2397T variant was reported in association with Crohn’s disease with the same risk allele as in T1R suggesting common inflammatory mechanism in these two distinct diseases. A major challenge of current leprosy control is the management of host pathological immune responses coined Type-1 Reactions (T1R). T1R are characterized by acute inflammatory episodes whereby cellular immune responses are directed against host peripheral nerve cells. T1R affects up half of all leprosy patients and are a major cause of leprosy-associated disabilities. Since there is evidence that host genetic factors predispose leprosy patients to T1R, we have conducted a candidate gene study to test if LRRK2 gene variants are T1R risk factors. The choice of LRRK2 was motivated by the fact that LRRK2 was associated with leprosy per se in some but not in other studies. We reasoned that this may reflect different proportions of leprosy patients with T1R in the different samples and that LRRK2 may in truth be a T1R susceptibility gene. Here, we show that variants overlapping the LRRK2 gene, reported as suggestive leprosy per se susceptibility factors in a previous genome-wide association study, are preferentially associated with T1R. The main SNP carrying most of the association signal is the amino-acid change M2397T (rs3761863) which is known to impact LRRK2 turnover. Interestingly, eQTL SNPs counterbalanced the effect of the M2397T variant but this compensatory mechanism was abrogated by Mycobacterium leprae antigen stimulation.
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Affiliation(s)
- Vinicius M. Fava
- Program in Infectious Diseases and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Canada
- The McGill International TB Centre, Departments of Human Genetics and Medicine, McGill University, Montreal, Canada
| | - Jérémy Manry
- Program in Infectious Diseases and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Canada
- The McGill International TB Centre, Departments of Human Genetics and Medicine, McGill University, Montreal, Canada
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
| | - Marianna Orlova
- Program in Infectious Diseases and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Canada
- The McGill International TB Centre, Departments of Human Genetics and Medicine, McGill University, Montreal, Canada
| | | | - Nguyen Ngoc Ba
- Hospital for Dermato-Venerology, Ho Chi Minh City, Vietnam
| | - Vu Hong Thai
- Hospital for Dermato-Venerology, Ho Chi Minh City, Vietnam
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, United States of America
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, New York, United States of America
- Centre d’Investigation Clinique, Unité de Recherche Clinique, Necker and Cochin Hospitals, Paris, France
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Canada
- The McGill International TB Centre, Departments of Human Genetics and Medicine, McGill University, Montreal, Canada
- * E-mail:
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10
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Dizier MH, Nadif R, Margaritte-Jeannin P, Barton SJ, Sarnowski C, Gagné-Ouellet V, Brossard M, Lavielle N, Just J, Lathrop M, Holloway JW, Laprise C, Bouzigon E, Demenais F. Interaction between the DNAH9 gene and early smoke exposure in bronchial hyperresponsiveness. Eur Respir J 2016; 47:1072-81. [PMID: 26797031 DOI: 10.1183/13993003.00849-2015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 11/18/2015] [Indexed: 12/21/2022]
Abstract
A previous genome-wide linkage scan of bronchial hyperresponsiveness (BHR) in the French Epidemiological study on the Genetics and Environment of Asthma (EGEA) families, performed in the presence of a gene×early-life environmental tobacco smoke (ETS) exposure interaction, showed the strongest interaction in the 17p11 region where linkage was detected only among unexposed siblings. Our goal was to conduct fine-scale mapping of 17p11 to identify single nucleotide polymorphisms (SNPs) interacting with ETS that influence BHR.Analyses were performed in 388 French EGEA asthmatic families, using a two-step strategy: 1) selection of SNPs displaying family-based association test (FBAT) association signals (p≤0.01) with BHR in unexposed siblings, and 2) a FBAT homogeneity test between exposed and unexposed siblings plus a robust log-linear interaction test.A single SNP reached the threshold (p≤3×10(-3)) for significant interaction with ETS using both interaction tests, after accounting for multiple testing. Results were replicated in 253 French-Canadian families, but not in 341 UK families, probably due in part to differences in phenotypic features between datasets.The SNP showing significant interaction with ETS belongs toDNAH9(dynein, axonemal, heavy chain 9), a promising candidate gene involved in respiratory cilia mobility and associated with primary ciliary dyskinesia, a disease associated with abnormalities of pulmonary function.
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Affiliation(s)
- Marie-Hélène Dizier
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Rachel Nadif
- INSERM, U1168, Aging and Chronic Diseases, Epidemiological and Public Health Approaches (VIMA), Villejuif, France Université Versailles Saint-Quentin-en-Yvelines, UMR_S 1168, Paris, France These authors contributed equally to this work
| | - Patricia Margaritte-Jeannin
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France These authors contributed equally to this work
| | - Sheila J Barton
- MRC Lifecourse Epidemiology Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Chloé Sarnowski
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France Université Paris-Sud, UMR_S 1018, Villejuif, France
| | | | - Myriam Brossard
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France Université Paris-Sud, UMR_S 1018, Villejuif, France
| | - Nolwenn Lavielle
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France Université Paris-Sud, UMR_S 1018, Villejuif, France
| | - Jocelyne Just
- Service d'Allergologie Pédiatrique, Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand-Trousseau (APHP) - Sorbonne Universités, UPMC Université Paris 06, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Equipe EPAR, Paris, France
| | - Mark Lathrop
- McGill University and Genome Quebec's Innovation Centre, Montréal, Canada
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Catherine Laprise
- Université du Québec, Chicoutimi, Canada These authors contributed equally to this work
| | - Emmanuelle Bouzigon
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France These authors contributed equally to this work
| | - Florence Demenais
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
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11
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Bureau A, Duchesne T. On the validity of within-nuclear-family genetic association analysis in samples of extended families. Stat Appl Genet Mol Biol 2015; 14:533-49. [PMID: 26544107 DOI: 10.1515/sagmb-2015-0056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Splitting extended families into their component nuclear families to apply a genetic association method designed for nuclear families is a widespread practice in familial genetic studies. Dependence among genotypes and phenotypes of nuclear families from the same extended family arises because of genetic linkage of the tested marker with a risk variant or because of familial specificity of genetic effects due to gene-environment interaction. This raises concerns about the validity of inference conducted under the assumption of independence of the nuclear families. We indeed prove theoretically that, in a conditional logistic regression analysis applicable to disease cases and their genotyped parents, the naive model-based estimator of the variance of the coefficient estimates underestimates the true variance. However, simulations with realistic effect sizes of risk variants and variation of this effect from family to family reveal that the underestimation is negligible. The simulations also show the greater efficiency of the model-based variance estimator compared to a robust empirical estimator. Our recommendation is therefore, to use the model-based estimator of variance for inference on effects of genetic variants.
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12
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Zhou S, Shi Z, Cui M, Li J, Ma Z, Shi Y, Zheng Z, Zhang F, Jin T, Geng T, Chen C, Guo Y, Zhou J, Huang S, Guo X, Gao L, Gong P, Gao X, Zhang K. A New Role for LOC101928437 in Non-Syndromic Intellectual Disability: Findings from a Family-Based Association Test. PLoS One 2015; 10:e0135669. [PMID: 26287547 PMCID: PMC4545728 DOI: 10.1371/journal.pone.0135669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/25/2015] [Indexed: 11/19/2022] Open
Abstract
Non-syndromic intellectual disability (NSID) is mental retardation in persons of normal physical appearance who have no recognisable features apart from obvious deficits in intellectual functioning and adaptive ability; however, its genetic etiology of most patients has remained unknown. The main purpose of this study was to fine map and identify specific causal gene(s) by genotyping a NSID family cohort using a panel of markers encompassing a target region reported in a previous work. A total of 139 families including probands, parents and relatives were included in the household survey, clinical examinations and intelligence tests, recruited from the Qinba mountain region of Shannxi province, western China. A collection of 34 tagged single nucleotide polymorphisms (tSNPs) spanning five microsatellite marker (STR) loci were genotyped using an iPLEX Gold assay. The association between tSNPs and patients was analyzed by family-based association testing (FBAT) and haplotype analysis (HBAT). Four markers (rs5974392, rs12164331, rs5929554 and rs3116911) in a block that showed strong linkage disequilibrium within the first three introns of the LOC101928437 locus were found to be significantly associated with NSID (all P<0.01) by the FBAT method for a single marker in additive, dominant and recessive models. The results of haplotype tests of this block also revealed a significant association with NSID (all P<0.05) using 2-window and larger HBAT analyses. These results suggest that LOC101928437 is a novel candidate gene for NSID in Han Chinese individuals of the Qinba region of China. Although the biological function of the gene has not been well studied, knowledge about this gene will provide insights that will increase our understanding of NSID development.
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Affiliation(s)
- Shaohe Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Institute of Population and Health, Northwest University, Xi’an, China
| | - Zhangyan Shi
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Institute of Population and Health, Northwest University, Xi’an, China
| | - Meng Cui
- Xi’an Institute of Mental Health, Xi’an, China
| | - Junlin Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Institute of Population and Health, Northwest University, Xi’an, China
| | - Zhe Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Institute of Population and Health, Northwest University, Xi’an, China
| | - Yuanyu Shi
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Institute of Population and Health, Northwest University, Xi’an, China
| | - Zijian Zheng
- College of Public Management, Institute of Application Psychology, Northwest University, Xi’an, China
| | - Fuchang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Institute of Population and Health, Northwest University, Xi’an, China
- College of Public Management, Institute of Application Psychology, Northwest University, Xi’an, China
| | - Tianbo Jin
- School of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- National Engineering Research Center for Miniaturized Detection Systems, Xi’an, Shaanxi, China
| | - Tingting Geng
- School of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- National Engineering Research Center for Miniaturized Detection Systems, Xi’an, Shaanxi, China
| | - Chao Chen
- School of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- National Engineering Research Center for Miniaturized Detection Systems, Xi’an, Shaanxi, China
| | - Yale Guo
- The 2 Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Jianping Zhou
- The 2 Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Shaoping Huang
- The 2 Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Xingli Guo
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an Shaanxi, China
| | - Pingyuan Gong
- Laboratory of Medical Molecular Biology, Henan University of Science and Technology, Luoyang, China
| | - Xiaocai Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Institute of Population and Health, Northwest University, Xi’an, China
- College of Public Management, Institute of Application Psychology, Northwest University, Xi’an, China
- * E-mail: (XG); (KZ)
| | - Kejin Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Institute of Population and Health, Northwest University, Xi’an, China
- * E-mail: (XG); (KZ)
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13
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A powerful nonparametric statistical framework for family-based association analyses. Genetics 2015; 200:69-78. [PMID: 25745024 DOI: 10.1534/genetics.115.175174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/23/2015] [Indexed: 01/04/2023] Open
Abstract
Family-based study design is commonly used in genetic research. It has many ideal features, including being robust to population stratification (PS). With the advance of high-throughput technologies and ever-decreasing genotyping cost, it has become common for family studies to examine a large number of variants for their associations with disease phenotypes. The yield from the analysis of these family-based genetic data can be enhanced by adopting computationally efficient and powerful statistical methods. We propose a general framework of a family-based U-statistic, referred to as family-U, for family-based association studies. Unlike existing parametric-based methods, the proposed method makes no assumption of the underlying disease models and can be applied to various phenotypes (e.g., binary and quantitative phenotypes) and pedigree structures (e.g., nuclear families and extended pedigrees). By using only within-family information, it can offer robust protection against PS. In the absence of PS, it can also utilize additional information (i.e., between-family information) for power improvement. Through simulations, we demonstrated that family-U attained higher power over a commonly used method, family-based association tests, under various disease scenarios. We further illustrated the new method with an application to large-scale family data from the Framingham Heart Study. By utilizing additional information (i.e., between-family information), family-U confirmed a previous association of CHRNA5 with nicotine dependence.
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14
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Wei Q, Chen Y, Zeng Z, Shu C, Long L, Lu J, Huang Y, Yin P. Transmission/disequilibrium tests incorporating unaffected offspring. PLoS One 2014; 9:e114892. [PMID: 25535968 PMCID: PMC4275232 DOI: 10.1371/journal.pone.0114892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 11/14/2014] [Indexed: 11/18/2022] Open
Abstract
We propose a new method for family-based tests of association and linkage called transmission/disequilibrium tests incorporating unaffected offspring (TDTU). This new approach, constructed based on transmission/disequilibrium tests for quantitative traits (QTDT), provides a natural extension of the transmission/disequilibrium test (TDT) to utilize transmission information from heterozygous parents to their unaffected offspring as well as the affected offspring from ascertained nuclear families. TDTU can be used in various study designs and can accommodate all types of independent nuclear families with at least one affected offspring. When the study sample contains only case-parent trios, the TDTU is equivalent to TDT. Informative-transmission disequilibrium test (i-TDT) and generalized disequilibrium test(GDT) are another two methods that can use information of both unaffected offspring and affected offspring. In contract to i-TDT and GDT, the test statistic of TDTU is simpler and more explicit, and can be implemented more easily. Through computer simulations, we demonstrate that power of the TDTU is slightly higher compared to i-TDT and GDT. All the three methods are more powerful than method that uses affected offspring only, suggesting that unaffected siblings also provide information about linkage and association.
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Affiliation(s)
- Qinyu Wei
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanli Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chang Shu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lu Long
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianhua Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yangxin Huang
- Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Ping Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail:
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15
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NOD2 and CCDC122-LACC1 genes are associated with leprosy susceptibility in Brazilians. Hum Genet 2014; 133:1525-32. [PMID: 25367361 DOI: 10.1007/s00439-014-1502-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 10/19/2014] [Indexed: 01/07/2023]
Abstract
Leprosy is a complex disease with phenotypes strongly influenced by genetic variation. A Chinese genome-wide association study (GWAS) depicted novel genes and pathways associated with leprosy susceptibility, only partially replicated by independent studies in different ethnicities. Here, we describe the results of a validation and replication study of the Chinese GWAS in Brazilians, using a stepwise strategy that involved two family-based and three independent case-control samples, resulting in 3,614 individuals enrolled. First, we genotyped a family-based sample for 36 tag single-nucleotide polymorphisms (SNPs) of five genes located in four different candidate loci: CCDC122-LACC1, NOD2, TNFSF15 and RIPK2. Association between leprosy and tag SNPs at NOD2 (rs8057431) and CCDC122-LACC1 (rs4942254) was then replicated in three additional, independent samples (combined OR(AA) = 0.49, P = 1.39e-06; OR(CC) = 0.72, P = 0.003, respectively). These results clearly implicate the NOD2 pathway in the regulation of leprosy susceptibility across diverse populations.
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16
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Fodil M, Teixeira VH, Chaudru V, Hilliquin P, Bombardieri S, Balsa A, Westhovens R, Barrera P, Alves H, Migliorin P, Bardin T, Cornelis F, Boudjema A, Petit-Teixeira E. Relationship between SNPs and expression level for candidate genes in rheumatoid arthritis. Scand J Rheumatol 2014; 44:2-7. [PMID: 25221852 DOI: 10.3109/03009742.2014.918175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
OBJECTIVES The study of polymorphisms of genes differentially expressed may lead to the identification of putative causal genetic variants in multifactorial diseases such as rheumatoid arthritis (RA). Based on preceding transcriptomic results, we genotyped 10 single nucleotide polymorphisms (SNPs) belonging to six genes (S100A8, RNASE2, PGLYRP1, RUNX3, IL2RB, and LY96) showing the highest fold change (> 1.9) when level of expression was compared between RA patients and controls. These SNPs were then analysed to evaluate their role in RA. METHOD The relationship between gene expression and genotypes of SNPs was first investigated by Kruskal-Wallis and Mann-Whitney tests in RA patients and controls. The genetic association of these SNPs with RA were then analysed using family-based association tests in trio families. RESULTS We found that RNASE2 gene expression was related to rs2013109 genotypes in 14 RA patients (p = 0.030). The association study in a discovery sample of 200 French trio families revealed a significant association with RA for one SNP, PGLYRP1-rs2041992 (p = 0.019); this association was stronger in trios where RA patients carried the HLA-DRB1 shared epitope (SE) (p = 0.003). However, this association was not found in a replication sample of 240 European trio families (p = 0.6). CONCLUSIONS Family-based association tests did not reveal an association between RA and any SNP of the candidate genes tested. However, RNASE2 gene expression was differentially expressed in RA patients considering a sequence polymorphism. This result led us to highlight the potential disease-specific regulation for this candidate gene in RA.
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Affiliation(s)
- M Fodil
- GenHotel-EA3886, Evry-Val d'Essonne University, Evry-Genopole , France
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17
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Eu-ahsunthornwattana J, Miller EN, Fakiola M, Jeronimo SMB, Blackwell JM, Cordell HJ. Comparison of methods to account for relatedness in genome-wide association studies with family-based data. PLoS Genet 2014; 10:e1004445. [PMID: 25033443 PMCID: PMC4102448 DOI: 10.1371/journal.pgen.1004445] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 05/02/2014] [Indexed: 11/23/2022] Open
Abstract
Approaches based on linear mixed models (LMMs) have recently gained popularity for modelling population substructure and relatedness in genome-wide association studies. In the last few years, a bewildering variety of different LMM methods/software packages have been developed, but it is not always clear how (or indeed whether) any newly-proposed method differs from previously-proposed implementations. Here we compare the performance of several LMM approaches (and software implementations, including EMMAX, GenABEL, FaST-LMM, Mendel, GEMMA and MMM) via their application to a genome-wide association study of visceral leishmaniasis in 348 Brazilian families comprising 3626 individuals (1972 genotyped). The implementations differ in precise details of methodology implemented and through various user-chosen options such as the method and number of SNPs used to estimate the kinship (relatedness) matrix. We investigate sensitivity to these choices and the success (or otherwise) of the approaches in controlling the overall genome-wide error-rate for both real and simulated phenotypes. We compare the LMM results to those obtained using traditional family-based association tests (based on transmission of alleles within pedigrees) and to alternative approaches implemented in the software packages MQLS, ROADTRIPS and MASTOR. We find strong concordance between the results from different LMM approaches, and all are successful in controlling the genome-wide error rate (except for some approaches when applied naively to longitudinal data with many repeated measures). We also find high correlation between LMMs and alternative approaches (apart from transmission-based approaches when applied to SNPs with small or non-existent effects). We conclude that LMM approaches perform well in comparison to competing approaches. Given their strong concordance, in most applications, the choice of precise LMM implementation cannot be based on power/type I error considerations but must instead be based on considerations such as speed and ease-of-use. Recently, statistical approaches known as linear mixed models (LMMs) have become popular for analysing data from genome-wide association studies. In the last few years, a bewildering variety of different LMM methods/software packages have been developed, but it has not always been clear how (or indeed whether) any newly-proposed method differs from previously-proposed implementations. Here we compare the performance of several different LMM approaches (and software implementations) via their application to a genome-wide association study of visceral leishmaniasis in 348 Brazilian families comprising 3626 individuals. We also compare the LMM results to those obtained using alternative analysis methods. Overall, we find strong concordance between the results from the different LMM approaches and high correlation between the results from LMMs and most alternative approaches. We conclude that LMM approaches perform well in comparison to competing approaches and, in most applications, the precise LMM implementation will not be too important, and can be chosen on the basis of speed or convenience.
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Affiliation(s)
- Jakris Eu-ahsunthornwattana
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
- Division of Medical Genetics, Department of Internal Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Ratchathevi, Bangkok, Thailand
| | - E. Nancy Miller
- Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Michaela Fakiola
- Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, United Kingdom
| | | | - Selma M. B. Jeronimo
- Department of Biochemistry, Center for Biosciences, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Jenefer M. Blackwell
- Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, United Kingdom
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Subiaco, Western Australia, Australia
| | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
- * E-mail:
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18
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Cobat A, Abel L, Alcaïs A, Schurr E. A general efficient and flexible approach for genome-wide association analyses of imputed genotypes in family-based designs. Genet Epidemiol 2014; 38:560-71. [PMID: 25044438 DOI: 10.1002/gepi.21842] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 05/13/2014] [Accepted: 05/19/2014] [Indexed: 01/10/2023]
Abstract
Genotype imputation is a critical technique for following up genome-wide association studies. Efficient methods are available for dealing with the probabilistic nature of imputed single nucleotide polymorphisms (SNPs) in population-based designs, but not for family-based studies. We have developed a new analytical approach (FBATdosage), using imputed allele dosage in the general framework of family-based association tests to bridge this gap. Simulation studies showed that FBATdosage yielded highly consistent type I error rates, whatever the level of genotype uncertainty, and a much higher power than the best-guess genotype approach. FBATdosage allows fast linkage and association testing of several million of imputed variants with binary or quantitative phenotypes in nuclear families of arbitrary size with arbitrary missing data for the parents. The application of this approach to a family-based association study of leprosy susceptibility successfully refined the association signal at two candidate loci, C1orf141-IL23R on chromosome 1 and RAB32-C6orf103 on chromosome 6.
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Affiliation(s)
- Aurélie Cobat
- Departments of Human Genetics and Medicine, McGill International TB Center, McGill University Health Center, Montreal, QC, Canada
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Preston MD, Dudbridge F. Utilising family-based designs for detecting rare variant disease associations. Ann Hum Genet 2014; 78:129-40. [PMID: 24571231 PMCID: PMC4292528 DOI: 10.1111/ahg.12051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 11/17/2013] [Indexed: 01/04/2023]
Abstract
Rare genetic variants are thought to be important components in the causality of many diseases but discovering these associations is challenging. We demonstrate how best to use family-based designs to improve the power to detect rare variant disease associations. We show that using genetic data from enriched families (those pedigrees with greater than one affected member) increases the power and sensitivity of existing case-control rare variant tests. However, we show that transmission- (or within-family-) based tests do not benefit from this enrichment. This means that, in studies where a limited amount of genotyping is available, choosing a single case from each of many pedigrees has greater power than selecting multiple cases from fewer pedigrees. Finally, we show how a pseudo-case-control design allows a greater range of statistical tests to be applied to family data.
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Affiliation(s)
- Mark D Preston
- London School of Hygiene and Tropical MedicineKeppel Street, London, WC1E 7HT, UK
| | - Frank Dudbridge
- London School of Hygiene and Tropical MedicineKeppel Street, London, WC1E 7HT, UK
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Dizier MH, Margaritte-Jeannin P, Madore AM, Moffatt M, Brossard M, Lavielle N, Sarnowski C, Just J, Cookson W, Lathrop M, Laprise C, Bouzigon E, Demenais F. The nuclear factor I/A (NFIA) gene is associated with the asthma plus rhinitis phenotype. J Allergy Clin Immunol 2014; 134:576-582.e1. [PMID: 24560411 DOI: 10.1016/j.jaci.2013.12.1074] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 11/20/2013] [Accepted: 12/19/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND A previous genome-wide linkage scan in 295 families of the French Epidemiological Study on the Genetics and Environment of Asthma (EGEA) showed strong evidence of linkage of the 1p31 region to the combined asthma plus allergic rhinitis (AR) phenotype. OBJECTIVE Our purpose was to conduct fine-scale mapping of the 1p31 linkage region to identify the genetic variants associated with asthma plus AR. METHODS Association analyses with the asthma plus rhinitis phenotype were first conducted in the EGEA family sample using the family-based association method (FBAT) and logistic regression. The test of homogeneity of association between asthma plus AR versus asthma alone or AR alone was also applied. Replication of EGEA findings was sought in French-Canadian and United Kingdom family samples. RESULTS We found a significant association between asthma plus rhinitis and a 1p31 genetic variant (P = 2 × 10(-5) for rs12122228, which reached the multiple testing-corrected threshold) in EGEA using FBAT. There was evidence of heterogeneity of association between asthma plus AR versus asthma alone or AR alone (P = .03). A Meta-analysis of FBAT results from EGEA and French-Canadian families improved evidence for both association and heterogeneity (P = 5 × 10(-6) and P = .008, respectively), whereas a meta-analysis of EGEA, French-Canadian, and United Kingdom samples based on logistic regression slightly increased the evidence for heterogeneity. CONCLUSION The single nucleotide polymorphism specifically associated to asthma plus rhinitis is located in the flanking 5' untranslated region of the nuclear factor I/A (NFIA) gene, a strong candidate gene for asthma and AR.
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Affiliation(s)
- Marie-Hélène Dizier
- INSERM U946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France.
| | - Patricia Margaritte-Jeannin
- INSERM U946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | | | - Miriam Moffatt
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Myriam Brossard
- INSERM U946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Nolwenn Lavielle
- INSERM U946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Chloé Sarnowski
- INSERM U946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Jocelyne Just
- Centre de l'Asthme et des Allergies, APHP, Hôpital Trousseau, UMPC, Paris, France
| | - William Cookson
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | | | | | - Emmanuelle Bouzigon
- INSERM U946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Florence Demenais
- INSERM U946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
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Lu ATH, Yoon J, Geschwind DH, Cantor RM. QTL replication and targeted association highlight the nerve growth factor gene for nonverbal communication deficits in autism spectrum disorders. Mol Psychiatry 2013; 18:226-35. [PMID: 22105621 PMCID: PMC3586745 DOI: 10.1038/mp.2011.155] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Autism Spectrum Disorder (ASD) has a heterogeneous etiology that is genetically complex. It is defined by deficits in communication and social skills and the presence of restricted and repetitive behaviors. Genetic analyses of heritable quantitative traits that correlate with ASD may reduce heterogeneity. With this in mind, deficits in nonverbal communication (NVC) were quantified based on items from the Autism Diagnostic Interview Revised. Our previous analysis of 228 families from the Autism Genetics Research Exchange (AGRE) repository reported 5 potential quantitative trait loci (QTL). Here we report an NVC QTL replication study in an independent sample of 213 AGRE families. One QTL was replicated (P<0.0004). It was investigated using a targeted-association analysis of 476 haplotype blocks with 708 AGRE families using the Family Based Association Test (FBAT). Blocks in two QTL genes were associated with NVC with a P-value of 0.001. Three associated haplotype blocks were intronic to the Nerve Growth Factor (NGF) gene (P=0.001, 0.001, 0.002), and one was intronic to KCND3 (P=0.001). Individual haplotypes within the associated blocks drove the associations (0.003, 0.0004 and 0.0002) for NGF and 0.0001 for KCND3. Using the same methods, these genes were tested for association with NVC in an independent sample of 1517 families from an Autism Genome Project (AGP). NVC was associated with a haplotype in an adjacent NGF block (P=0.0005) and one 46 kb away from the associated block in KCND3 (0.008). These analyses illustrate the value of QTL and targeted association studies for genetically complex disorders such as ASD. NGF is a promising risk gene for NVC deficits.
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Affiliation(s)
- AT-H Lu
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - J Yoon
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - DH Geschwind
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA,Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA,Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - RM Cantor
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA,Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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The ANO3/MUC15 locus is associated with eczema in families ascertained through asthma. J Allergy Clin Immunol 2013; 129:1547-53.e3. [PMID: 22657408 DOI: 10.1016/j.jaci.2012.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 04/05/2012] [Accepted: 04/09/2012] [Indexed: 12/11/2022]
Abstract
BACKGROUND A previous genome-wide linkage scan in 295 families of the French Epidemiological Study on the Genetics and Environment of Asthma (EGEA) reported strong evidence of linkage of 11p14 to eczema. OBJECTIVE Our purpose was to conduct fine-scale mapping of the 11p14 region to identify the genetic variants associated with eczema. METHODS Association analyses were first conducted in the family sample from the French EGEA by using 2 methods: the family-based association method and logistic regression. Replication of the EGEA findings was sought in French Canadian and United Kingdom family samples, which, similarly to EGEA samples, were ascertained through asthma. We also tested for association in 2 German samples ascertained through eczema. RESULTS We found significant association of eczema with 11p14 genetic variants in the vicinity of the linkage peak in EGEA (P = 10(-4) for rs1050153 by using the family-based association method, which reached the multiple testing-corrected threshold of 10(-4); P = .003 with logistic regression). Pooled analysis of the 3 asthma-ascertained samples showed strong improvement in the evidence for association (P = 6 × 10(-6) for rs293974, P = 3 × 10(-5) for rs1050153, and P = 8 × 10(-5) for rs15783). No association was observed in the eczema-ascertained samples. CONCLUSION The significant single nucleotide polymorphisms are located within the overlapping anoctamin 3 (ANO3) and mucin 15 (MUC15) genes. Several lines of evidence suggest that MUC15 is a strong candidate for eczema. Further investigation is needed to confirm our findings and to better understand the role of the ANO3/MUC15 locus in eczema and its relationship with respect to asthma.
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A family-based association study after genome-wide linkage analysis identified two genetic loci for renal function in a Mongolian population. Kidney Int 2012; 83:285-92. [PMID: 23254893 DOI: 10.1038/ki.2012.389] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The estimated glomerular filtration rate is a well-known measure of renal function and is widely used to follow the course of disease. Although there have been several investigations establishing the genetic background contributing to renal function, Asian populations have rarely been used in these genome-wide studies. Here, we aimed to find candidate genetic determinants of renal function in 1007 individuals from 73 extended families of Mongolian origin. Linkage analysis found two suggestive regions near 9q21 (logarithm of odds (LOD) 2.82) and 15q15 (LOD 2.70). The subsequent family-based association study found 2 and 10 significant single-nucleotide polymorphisms (SNPs) in each region, respectively. The strongest SNPs on chromosome 9 and 15 were rs17400257 and rs1153831 with P-values of 7.21 × 10(-9) and 2.47 × 10(-11), respectively. Genes located near these SNPs are considered candidates for determining renal function and include FRMD3, GATM, and SPATA5L1. Thus, we identified possible loci that determine renal function in an isolated Asian population. Consistent with previous reports, our study found genes linked and associated with renal function in other populations.
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Lu ATH, Dai X, Martinez-Agosto JA, Cantor RM. Support for calcium channel gene defects in autism spectrum disorders. Mol Autism 2012; 3:18. [PMID: 23241247 PMCID: PMC3558437 DOI: 10.1186/2040-2392-3-18] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 10/31/2012] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED BACKGROUND Alternation of synaptic homeostasis is a biological process whose disruption might predispose children to autism spectrum disorders (ASD). Calcium channel genes (CCG) contribute to modulating neuronal function and evidence implicating CCG in ASD has been accumulating. We conducted a targeted association analysis of CCG using existing genome-wide association study (GWAS) data and imputation methods in a combined sample of parent/affected child trios from two ASD family collections to explore this hypothesis. METHODS A total of 2,176 single-nucleotide polymorphisms (SNP) (703 genotyped and 1,473 imputed) covering the genes that encode the α1 subunit proteins of 10 calcium channels were tested for association with ASD in a combined sample of 2,781 parent/affected child trios from 543 multiplex Caucasian ASD families from the Autism Genetics Resource Exchange (AGRE) and 1,651 multiplex and simplex Caucasian ASD families from the Autism Genome Project (AGP). SNP imputation using IMPUTE2 and a combined reference panel from the HapMap3 and the 1,000 Genomes Project increased coverage density of the CCG. Family-based association was tested using the FBAT software which controls for population stratification and accounts for the non-independence of siblings within multiplex families. The level of significance for association was set at 2.3E-05, providing a Bonferroni correction for this targeted 10-gene panel. RESULTS Four SNPs in three CCGs were associated with ASD. One, rs10848653, is located in CACNA1C, a gene in which rare de novo mutations are responsible for Timothy syndrome, a Mendelian disorder that features ASD. Two others, rs198538 and rs198545, located in CACN1G, and a fourth, rs5750860, located in CACNA1I, are in CCGs that encode T-type calcium channels, genes with previous ASD associations. CONCLUSIONS These associations support a role for common CCG SNPs in ASD.
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Affiliation(s)
- Ake Tzu-Hui Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90024-7088, USA.
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Vaillancourt VT, Bordeleau M, Laviolette M, Laprise C. From expression pattern to genetic association in asthma and asthma-related phenotypes. BMC Res Notes 2012; 5:630. [PMID: 23148572 PMCID: PMC3532380 DOI: 10.1186/1756-0500-5-630] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 11/06/2012] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Asthma is a complex disease characterized by hyperresponsiveness, obstruction and inflammation of the airways. To date, several studies using different approaches as candidate genes approach, genome wide association studies, linkage analysis and genomic expression leaded to the identification of over 300 genes involved in asthma pathophysiology. Combining results from two studies of genomic expression, this study aims to perform an association analysis between genes differently expressed in bronchial biopsies of asthmatics compared to controls and asthma-related phenotypes using the same French-Canadian Caucasian population. RESULTS Before correction, 31 of the 85 genes selected were associated with at least one asthma-related phenotype. We found four genes that survived the correction for multiple testing. The rs11630178 in aggrecan gene (AGC1) is associated with atopy (p=0.0003) and atopic asthma (p=0.0001), the rs1247653 in the interferon alpha-inducible protein 6 (IFI6), the rs1119529 in adrenergic, alpha-2A-, receptor (ADRA2A) and the rs13103321 in the alcohol dehydrogenase 1B (class I), beta polypeptide (ADH1B), are associated with asthma (p=0.019; 0.01 and 0.002 respectively). CONCLUSION To our knowledge, this is the first time those genes are associated with asthma and related traits. Consequently, our study confirms that genetic and expression studies are complementary to identify new candidate genes and to investigate their role to improve the comprehension of the complexity of asthma pathophysiology.
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Affiliation(s)
- Vanessa T Vaillancourt
- Département des sciences fondamentales, Université du Québec à Chicoutimi, 555 boulevard de l'Université, Chicoutimi, Saguenay, Québec, G7H 2B1, Canada
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Miller NH, Justice CM, Marosy B, Swindle K, Kim Y, Roy-Gagnon MH, Sung H, Behneman D, Doheny KF, Pugh E, Wilson AF. Intra-familial tests of association between familial idiopathic scoliosis and linked regions on 9q31.3-q34.3 and 16p12.3-q22.2. Hum Hered 2012; 74:36-44. [PMID: 23154503 PMCID: PMC4123546 DOI: 10.1159/000343751] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 09/07/2012] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Custom genotyping of markers in families with familial idiopathic scoliosis were used to fine-map candidate regions on chromosomes 9 and 16 in order to identify candidate genes that contribute to this disorder and prioritize them for next-generation sequence analysis. METHODS Candidate regions on 9q and 16p-16q, previously identified as linked to familial idiopathic scoliosis in a study of 202 families, were genotyped with a high-density map of single nucleotide polymorphisms. Tests of linkage for fine-mapping and intra-familial tests of association, including tiled regression, were performed on scoliosis as both a qualitative and quantitative trait. RESULTS AND CONCLUSIONS Nominally significant linkage results were found for markers in both candidate regions. Results from intra-familial tests of association and tiled regression corroborated the linkage findings and identified possible candidate genes suitable for follow-up with next-generation sequencing in these same families. Candidate genes that met our prioritization criteria included FAM129B and CERCAM on chromosome 9 and SYT1, GNAO1, and CDH3 on chromosome 16.
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Affiliation(s)
- Nancy H Miller
- Department of Orthopaedic Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Wason J, Dudbridge F. A general framework for two-stage analysis of genome-wide association studies and its application to case-control studies. Am J Hum Genet 2012; 90:760-73. [PMID: 22560088 DOI: 10.1016/j.ajhg.2012.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 02/17/2012] [Accepted: 03/09/2012] [Indexed: 02/03/2023] Open
Abstract
Two-stage analyses of genome-wide association studies have been proposed as a means to improving power for designs including family-based association and gene-environment interaction testing. In these analyses, all markers are first screened via a statistic that may not be robust to an underlying assumption, and the markers thus selected are then analyzed in a second stage with a test that is independent from the first stage and is robust to the assumption in question. We give a general formulation of two-stage designs and show how one can use this formulation both to derive existing methods and to improve upon them, opening up a range of possible further applications. We show how using simple regression models in conjunction with external data such as average trait values can improve the power of genome-wide association studies. We focus on case-control studies and show how it is possible to use allele frequencies derived from an external reference to derive a powerful two-stage analysis. An illustration involving the Wellcome Trust Case-Control Consortium data shows several genome-wide-significant associations, subsequently validated, that were not significant in the standard analysis. We give some analytic properties of the methods and discuss some underlying principles.
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Atkinson A, Garnier S, Afridi S, Fumoux F, Rihet P. Genetic variations in genes involved in heparan sulphate biosynthesis are associated with Plasmodium falciparum parasitaemia: a familial study in Burkina Faso. Malar J 2012; 11:108. [PMID: 22475533 PMCID: PMC3364897 DOI: 10.1186/1475-2875-11-108] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 04/04/2012] [Indexed: 12/18/2022] Open
Abstract
Background There is accumulating evidence that host heparan sulphate proteoglycans play an important role in the life cycle of Plasmodium through their heparan sulphate chains, suggesting that genetic variations in genes involved in heparan sulphate biosynthesis may influence parasitaemia. Interestingly, Hs3st3a1 and Hs3st3b1 encoding enzymes involved in the biosynthesis of heparan sulphate are located within a chromosomal region linked to Plasmodium chabaudi parasitaemia in mice. This suggests that HS3ST3A1 and HS3ST3B1 may influence P. falciparum parasitaemia in humans. Methods Polymorphisms within HS3ST3A1 and HS3ST3B1 were identified in 270 individuals belonging to 44 pedigrees and living in Burkina Faso. Linkage and association between parasitaemia and the polymorphisms were assessed with MERLIN and FBAT. A genetic interaction analysis was also conducted based on the PGMDR approach. Results Linkage between P. falciparum parasitaemia and the chromosomal region containing HS3ST3A1 and HS3ST3B1 was detected on the basis of the 20 SNPs identified. In addition, rs28470223 located within the promoter of HS3ST3A1 was associated with P. falciparum parasitaemia, whereas the PGMDR analysis revealed a genetic interaction between HS3ST3A1 and HS3ST3B1. Seventy-three significant multi-locus models were identified after correcting for multiple tests; 37 significant multi-locus models included rs28470223, whereas 38 multi-locus models contained at least one mis-sense mutation within HS3ST3B1. Conclusion Genetic variants of HS3ST3A1 and HS3ST3B1 are associated with P. falciparum parasitaemia. This suggests that those variants alter both the function of heparan sulphate proteoglycans and P. falciparum parasitaemia.
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Abstract
Family-based association studies have been widely used to identify association between diseases and genetic markers. It is known that genotyping uncertainty is inherent in both directly genotyped or sequenced DNA variations and imputed data in silico. The uncertainty can lead to genotyping errors and missingness and can negatively impact the power and Type I error rates of family-based association studies even if the uncertainty is independent of disease status. Compared with studies using unrelated subjects, there are very few methods that address the issue of genotyping uncertainty for family-based designs. The limited attempts have mostly been made to correct the bias caused by genotyping errors. Without properly addressing the issue, the conventional testing strategy, i.e. family-based association tests using called genotypes, can yield invalid statistical inferences. Here, we propose a new test to address the challenges in analyzing case-parents data by using calls with high accuracy and modeling genotype-specific call rates. Our simulations show that compared with the conventional strategy and an alternative test, our new test has an improved performance in the presence of substantial uncertainty and has a similar performance when the uncertainty level is low. We also demonstrate the advantages of our new method by applying it to imputed markers from a genome-wide case-parents association study.
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Affiliation(s)
- Zhaoxia Yu
- Department of Statistics, University of California, Irvine, CA 92697, USA.
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Poon AH, Chouiali F, Tse SM, Litonjua AA, Hussain SNA, Baglole CJ, Eidelman DH, Olivenstein R, Martin JG, Weiss ST, Hamid Q, Laprise C. Genetic and histologic evidence for autophagy in asthma pathogenesis. J Allergy Clin Immunol 2011; 129:569-71. [PMID: 22040902 DOI: 10.1016/j.jaci.2011.09.035] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/27/2011] [Accepted: 09/29/2011] [Indexed: 10/15/2022]
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Wimmers K, Khoa DVA, Schütze S, Murani E, Ponsuksili S. The three-way relationship of polymorphisms of porcine genes encoding terminal complement components, their differential expression, and health-related phenotypes. BMC Proc 2011; 5 Suppl 4:S19. [PMID: 21645298 PMCID: PMC3108213 DOI: 10.1186/1753-6561-5-s4-s19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background The complement system is an evolutionary ancient mechanism that plays an essential role in innate immunity and contributes to the acquired immune response. Three modes of activation, known as classical, alternative and lectin pathway, lead to the initiation of a common terminal lytic pathway. The terminal complement components (TCCs: C6, C7, C8A, C8B, and C9) are encoded by the genes C6, C7, C8A, C8B, C8G, and C9. We aimed at experimentally testing the porcine genes encoding TCCs as candidate genes for immune competence and disease resistance by addressing the three-way relationship of genotype, health related phenotype, and mRNA expression. Results Comparative sequencing of cDNAs of animals of the breeds German Landrace, Piétrain, Hampshire, Duroc, Vietnamese Potbelly Pig, and Berlin Miniature Pig (BMP) revealed 30 SNPs (21 in protein domains, 12 with AA exchange). The promoter regions (each ~1.5 kb upstream the transcription start sites) of C6, C7, C8A, C8G, and C9 exhibited 29 SNPs. Significant effects of the TCC encoding genes on hemolytic complement activity were shown in a cross of Duroc and BMP after vaccination against Mycoplasma hyopneumoniae, Aujeszky disease virus and PRRSV by analysis of variance using repeated measures mixed models. Family based association tests (FBAT) confirmed the associations. The promoter SNPs were associated with the relative abundance of TCC transcripts obtained by real time RT-PCR of 311 liver samples of commercial slaughter pigs. Complement gene expression showed significant relationship with the prevalence of acute and chronic lung lesions. Conclusions The analyses point to considerable variation of the porcine TCC genes and promote the genes as candidate genes for disease resistance.
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Affiliation(s)
- Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
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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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Liu X, Cheng I, Plummer SJ, Suarez B, Casey G, Catalona WJ, Witte JS. Fine-mapping of prostate cancer aggressiveness loci on chromosome 7q22-35. Prostate 2011; 71:682-9. [PMID: 20945404 PMCID: PMC3027848 DOI: 10.1002/pros.21284] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 08/31/2010] [Indexed: 01/10/2023]
Abstract
BACKGROUND Deciphering the genetic basis of prostate cancer aggressiveness could provide valuable information for the screening and treatment of this common but complex disease. We previously detected linkage between a broad region on chromosome 7q22-35 and Gleason score-a strong predictor of prostate cancer aggressiveness. To further clarify this finding and focus on the potentially causative gene, we undertook a fine-mapping study across the 7q22-35 region. METHODS Our study population encompassed 698 siblings diagnosed with prostate cancer. 3,072 single nucleotide polymorphisms (SNPs) spanning the chromosome 7q22-35 region were genotyped using the Illumina GoldenGate assay. The impact of SNPs on Gleason scores were evaluated using affected sibling pair linkage and family-based association tests. RESULTS We confirmed the previous linkage signal and narrowed the 7q22-35 prostate cancer aggressiveness locus to a 370 kb region. Centered under the linkage peak is the gene KLRG2 (killer cell lectin-like receptor subfamily G, member 2). Association tests indicated that the potentially functional non-synonymous SNP rs17160911 in KLRG2 was significantly associated with Gleason score (P = 0.0007). CONCLUSIONS These findings suggest that genetic variants in the gene KLRG2 may affect Gleason score at diagnosis and hence the aggressiveness of prostate cancer.
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Affiliation(s)
- Xin Liu
- Mary Ann and J. Milburn Smith Child Health Research Program, Department of Pediatrics, Northwestern University Feinberg School of Medicine and Children's Memorial Hospital and Children's Memorial Research Center, Chicago, IL, USA
| | - Iona Cheng
- Epidemiology Program, Cancer Research Center of Hawai`i, University of Hawai`i, Honolulu, HI 96813, USA
| | - Sarah J Plummer
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Brian Suarez
- Department of Genetics, Washington University, 660 South Euclid, St. Louis, Missouri 63110, USA
| | - Graham Casey
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - William J. Catalona
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - John S. Witte
- Departments of Epidemiology & Biostatistics and Urology, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158-9001, USA
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Korvatska O, Estes A, Munson J, Dawson G, Bekris LM, Kohen R, Yu CE, Schellenberg GD, Raskind WH. Mutations in the TSGA14 gene in families with autism spectrum disorders. Am J Med Genet B Neuropsychiatr Genet 2011; 156B:303-11. [PMID: 21438139 PMCID: PMC3552624 DOI: 10.1002/ajmg.b.31162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 11/30/2010] [Indexed: 11/11/2022]
Abstract
Linkage to 7q has been the most robust genetic finding in familial autism. A previous scan of multiplex families with autism spectrum disorders found a linkage signal of genome-wide significance at D7S530 on 7q32. We searched a candidate imprinted region at this location for genetic variants in families with positive linkage scores. Using exon resequencing, we identified three rare potentially pathogenic variants in the TSGA14 gene, which encodes a centrosomal protein. Two variants were missense mutations (c.664C>G; p.P206A and c.766T>G; p.C240G) that changed conserved residues in the same protein domain; the third variant (c.192+5G>A) altered splicing, which resulted in a protein with an internal deletion of 16 residues and a G33D substitution. These rare TSGA14 variants are enriched in the affected subjects (6/348 patients versus 2/670 controls, Fisher's exact two tailed P = 0.022). This is the first report of a possible link of a gene with a centrosomal function with familial autism.
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Affiliation(s)
- O Korvatska
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, 98195, USA.
| | - A Estes
- Department of Speech and Hearing Sciences, University of Washington, Seattle, WA, USA
| | - J Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - G Dawson
- Autism Speaks, New York, NY, USA,Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - L M Bekris
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - R Kohen
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - C-E Yu
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - G D Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - W H Raskind
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
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Bureau A, Croteau J, Tayeb A, Mérette C, Labbe A. Latent class model with familial dependence to address heterogeneity in complex diseases: adapting the approach to family-based association studies. Genet Epidemiol 2011; 35:182-9. [PMID: 21308764 DOI: 10.1002/gepi.20566] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/29/2010] [Accepted: 01/04/2011] [Indexed: 11/10/2022]
Abstract
Clinical diagnoses of complex diseases may often encompass multiple genetically heterogeneous disorders. One way of dissecting this heterogeneity is to apply latent class (LC) analysis to measurements related to the diagnosis, such as detailed symptoms, to define more homogeneous disease sub-types, influenced by a smaller number of genes that will thus be more easily detectable. We have previously developed a LC model allowing dependence between the latent disease class status of relatives within families. We have also proposed a strategy to incorporate the posterior probability of class membership of each subject in parametric linkage analysis, which is not directly transferable to genetic association methods. Under the framework of family-based association tests (FBAT), we now propose to make the contribution of an affected subject to the FBAT statistic proportional to his or her posterior class membership probability. Simulations showed a modest but robust power advantage compared to simply assigning each subject to his or her most probable class, and important power gains over the analysis of the disease diagnosis without LC modeling under certain scenarios. The use of LC analysis with FBAT is illustrated using autism spectrum disorder (ASD) symptoms on families from the Autism Genetics Research Exchange, where we examined eight regions previously associated to autism in this sample. The analysis using the posterior probability of membership to an LC detected an association in the JARID2 gene as significant as that for ASD (P = 3 × 10(-5)) but with a larger effect size (odds ratio = 2.17 vs. 1.55).
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Affiliation(s)
- Alexandre Bureau
- Centre de recherche Université Laval Robert-Giffard, Quebec City, Quebec, Canada.
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Dudbridge F, Holmans PA, Wilson SG. A flexible model for association analysis in sibships with missing genotype data. Ann Hum Genet 2011; 75:428-38. [PMID: 21241274 DOI: 10.1111/j.1469-1809.2010.00636.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A common design in family-based association studies consists of siblings without parents. Several methods have been proposed for analysis of sibship data, but they mostly do not allow for missing data, such as haplotype phase or untyped markers. On the other hand, general methods for nuclear families with missing data are computationally intensive when applied to sibships, since every family has missing parents that could have many possible genotypes. We propose a computationally efficient model for sibships by conditioning on the sets of alleles transmitted into the sibship by each parent. This means that the likelihood can be written only in terms of transmitted alleles and we do not have to sum over all possible untransmitted alleles when they cannot be deduced from the siblings. The model naturally accommodates missing data and admits standard theory of estimation, testing, and inclusion of covariates. Our model is quite robust to population stratification and can test for association in the presence of linkage. We show that our model has similar power to FBAT for single marker analysis and improved power for haplotype analysis. Compared to summing over all possible untransmitted alleles, we achieve similar power with considerable reductions in computation time.
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Murphy A, Won S, Rogers A, Chu JH, Raby BA, Lange C. On the genome-wide analysis of copy number variants in family-based designs: methods for combining family-based and population-based information for testing dichotomous or quantitative traits, or completely ascertained samples. Genet Epidemiol 2011; 34:582-90. [PMID: 20718041 DOI: 10.1002/gepi.20515] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We propose a new approach for the analysis of copy number variants (CNVs)for genome-wide association studies in family-based designs. Our new overall association test combines the between-family component and the within-family component of the family-based data so that the new test statistic is fully efficient and, at the same time, maintains robustness against population-admixture and stratification, like classical family-based association tests that are based only on the within-family component. Although all data are incorporated into the test statistic, an adjustment for genetic confounding is not needed, even for the between-family component. The new test statistic is valid for testing either quantitative or dichotomous phenotypes. If external CNV data are available, the approach can also be applied to completely ascertained samples. Similar to the approach by Ionita-Laza et al. ([2008]. Genet Epidemiol 32:273-284), the proposed test statistic does not require a CNV-calling algorithm and is based directly on the CNV probe intensities. We show, via simulation studies, that our methodology increases the power of the FBAT statistic to levels comparable to those of population-based designs. The advantages of the approach in practice are demonstrated by an application to a genome-wide association study for body mass index.
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Affiliation(s)
- Amy Murphy
- Channing Laboratory, Brigham and Women's Hospital, Boston, Massachusetts, USA
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Family-based association studies. Methods Mol Biol 2010. [PMID: 21153615 DOI: 10.1007/978-1-60327-416-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Family-based association methods are useful because they offer improved matching of controls to cases, with the result that they are not susceptible to confounding by population stratification. They also allow analysis of parent-of-origin effects and maternal-fetal interactions. The transmission/disequilibrium test (TDT) is a test of linkage and association that is equivalent to a matched case/control analysis, from which various extensions are possible. A logistic regression formulation leads to modifications for multiallelic markers, haplotypes, and quantitative traits. Some pitfalls are described, for the situations in which one parent is missing, genotyping errors have occurred, and haplotype phase is uncertain. The problem of testing association in general pedigrees is discussed, with particular reference to sib pairs without parents.
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Milet J, Nuel G, Watier L, Courtin D, Slaoui Y, Senghor P, Migot-Nabias F, Gaye O, Garcia A. Genome wide linkage study, using a 250K SNP map, of Plasmodium falciparum infection and mild malaria attack in a Senegalese population. PLoS One 2010; 5:e11616. [PMID: 20657648 PMCID: PMC2904701 DOI: 10.1371/journal.pone.0011616] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 06/06/2010] [Indexed: 12/22/2022] Open
Abstract
Multiple factors are involved in the variability of host's response to P. falciparum infection, like the intensity and seasonality of malaria transmission, the virulence of parasite and host characteristics like age or genetic make-up. Although admitted nowadays, the involvement of host genetic factors remains unclear. Discordant results exist, even concerning the best-known malaria resistance genes that determine the structure or function of red blood cells. Here we report on a genome-wide linkage and association study for P. falciparum infection intensity and mild malaria attack among a Senegalese population of children and young adults from 2 to 18 years old. A high density single nucleotide polymorphisms (SNP) genome scan (Affimetrix GeneChip Human Mapping 250K-nsp) was performed for 626 individuals: i.e. 249 parents and 377 children out of the 504 ones included in the follow-up. The population belongs to a unique ethnic group and was closely followed-up during 3 years. Genome-wide linkage analyses were performed on four clinical and parasitological phenotypes and association analyses using the family based association tests (FBAT) method were carried out in regions previously linked to malaria phenotypes in literature and in the regions for which we identified a linkage peak. Analyses revealed three strongly suggestive evidences for linkage: between mild malaria attack and both the 6p25.1 and the 12q22 regions (empirical p-value = 5×10−5 and 9×10−5 respectively), and between the 20p11q11 region and the prevalence of parasite density in asymptomatic children (empirical p-value = 1.5×10−4). Family based association analysis pointed out one significant association between the intensity of plasmodial infection and a polymorphism located in ARHGAP26 gene in the 5q31–q33 region (p-value = 3.7×10−5). This study identified three candidate regions, two of them containing genes that could point out new pathways implicated in the response to malaria infection. Furthermore, we detected one gene associated with malaria infection in the 5q31–q33 region.
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Affiliation(s)
- Jacqueline Milet
- UMR 216 - Mère et Enfant face aux infections tropicales, Institut de Recherche pour le Développement (IRD), Paris, France
- Laboratoire de parasitologie, Université Paris Descartes, Paris, France
| | - Gregory Nuel
- UMR CNRS 8145 - Mathématiques Appliquées Paris 5 (MAP5), Université Paris Descartes, Paris, France
| | - Laurence Watier
- U 657, Institut National de la Santé et de la Recherche Médicale (INSERM), Garches, France
| | - David Courtin
- UMR 216 - Mère et Enfant face aux infections tropicales, Institut de Recherche pour le Développement (IRD), Paris, France
- Laboratoire de parasitologie, Université Paris Descartes, Paris, France
| | - Yousri Slaoui
- UMR CNRS 8145 - Mathématiques Appliquées Paris 5 (MAP5), Université Paris Descartes, Paris, France
| | - Paul Senghor
- Laboratoire de Parasitologie et de Mycologie, Département de Biologie et d'Explorations fonctionnelles, Faculté de Médecine, Université Cheikh Anta Diop, Dakar, Sénégal
| | - Florence Migot-Nabias
- UMR 216 - Mère et Enfant face aux infections tropicales, Institut de Recherche pour le Développement (IRD), Paris, France
- Laboratoire de parasitologie, Université Paris Descartes, Paris, France
| | - Oumar Gaye
- Laboratoire de Parasitologie et de Mycologie, Département de Biologie et d'Explorations fonctionnelles, Faculté de Médecine, Université Cheikh Anta Diop, Dakar, Sénégal
| | - André Garcia
- UMR 216 - Mère et Enfant face aux infections tropicales, Institut de Recherche pour le Développement (IRD), Paris, France
- Laboratoire de parasitologie, Université Paris Descartes, Paris, France
- * E-mail:
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Application of association mapping to understanding the genetic diversity of plant germplasm resources. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2010; 2008:574927. [PMID: 18551188 PMCID: PMC2423417 DOI: 10.1155/2008/574927] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 04/18/2008] [Indexed: 02/05/2023]
Abstract
Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a “powerful gene tagging” tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application.
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Wedenoja J, Tuulio-Henriksson A, Suvisaari J, Loukola A, Paunio T, Partonen T, Varilo T, Lönnqvist J, Peltonen L. Replication of association between working memory and Reelin, a potential modifier gene in schizophrenia. Biol Psychiatry 2010; 67:983-91. [PMID: 19922905 PMCID: PMC3083525 DOI: 10.1016/j.biopsych.2009.09.026] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 09/16/2009] [Accepted: 09/18/2009] [Indexed: 12/28/2022]
Abstract
BACKGROUND The challenges in gene identification for psychiatric disorders have awakened interest toward quantitative traits and endophenotypes that are potentially more closely related to the underlying biology and provide more power in the linkage and association analyses. Previously, we successfully replicated schizophrenia linkage on chromosome 7q21-32 in Finnish families and demonstrated that an intragenic short tandem repeat (STR) allele of the regional Reelin (RELN) gene is associated with multiple cognitive traits representing central cognitive functions regarded as valid endophenotypes for schizophrenia. METHODS Here, we used an extended sample of 290 Finnish families with schizophrenia and 375 control subjects in an association analysis between 96 SNPs and three STRs in RELN and diagnostic categories, clinical disorder features, as well as central cognitive functions impaired in schizophrenia. RESULTS We replicated the original association between RELN intragenic STR allele and working memory in individuals (n = 342) not overlapping with the previous study. This risk allele remained central in the whole study sample by being associated with impaired cognitive functioning and more severe positive and negative symptoms of schizophrenia (p = .0005-.00002). Additionally, multiple SNPs indicated association with the severity of positive symptoms of schizophrenia and together showed potential additive effect on the severity of the symptoms (p = .0000001). However, no significant associations with clinical diagnostic categories emerged. CONCLUSIONS The strongest effects on cognitive functions were detected among the affected individuals. We thus propose a particular role for RELN as a modifier gene of the pathogenesis of schizophrenia.
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Affiliation(s)
- Juho Wedenoja
- Institute for Molecular Medicine Finland FIMM, University of Helsinki and National Institute for Health and Welfare, Helsinki, Finland
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Thornton T, McPeek MS. ROADTRIPS: case-control association testing with partially or completely unknown population and pedigree structure. Am J Hum Genet 2010; 86:172-84. [PMID: 20137780 DOI: 10.1016/j.ajhg.2010.01.001] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 01/06/2010] [Accepted: 01/10/2010] [Indexed: 12/01/2022] Open
Abstract
Genome-wide association studies are routinely conducted to identify genetic variants that influence complex disorders. It is well known that failure to properly account for population or pedigree structure can lead to spurious association as well as reduced power. We propose a method, ROADTRIPS, for case-control association testing in samples with partially or completely unknown population and pedigree structure. ROADTRIPS uses a covariance matrix estimated from genome-screen data to correct for unknown population and pedigree structure while maintaining high power by taking advantage of known pedigree information when it is available. ROADTRIPS can incorporate data on arbitrary combinations of related and unrelated individuals and is computationally feasible for the analysis of genetic studies with millions of markers. In simulations with related individuals and population structure, including admixture, we demonstrate that ROADTRIPS provides a substantial improvement over existing methods in terms of power and type 1 error. The ROADTRIPS method can be used across a variety of study designs, ranging from studies that have a combination of unrelated individuals and small pedigrees to studies of isolated founder populations with partially known or completely unknown pedigrees. We apply the method to analyze two data sets: a study of rheumatoid arthritis in small UK pedigrees, from Genetic Analysis Workshop 15, and data from the Collaborative Study of the Genetics of Alcoholism on alcohol dependence in a sample of moderate-size pedigrees of European descent, from Genetic Analysis Workshop 14. We detect genome-wide significant association, after Bonferroni correction, in both studies.
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Affiliation(s)
- Timothy Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
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Callegaro A, Lebrec JJP, Houwing-Duistermaat JJ. Testing for genetic association in the presence of linkage and gene-covariate interactions. Biom J 2010; 52:22-33. [PMID: 20166130 PMCID: PMC3410551 DOI: 10.1002/bimj.200900057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In order to study family-based association in the presence of linkage, we extend a generalized linear mixed model proposed for genetic linkage analysis (Lebrec and van Houwelingen (2007), Human Heredity 64, 5-15) by adding a genotypic effect to the mean. The corresponding score test is a weighted family-based association tests statistic, where the weight depends on the linkage effect and on other genetic and shared environmental effects. For testing of genetic association in the presence of gene-covariate interaction, we propose a linear regression method where the family-specific score statistic is regressed on family-specific covariates. Both statistics are straightforward to compute. Simulation results show that adjusting the weight for the within-family variance structure may be a powerful approach in the presence of environmental effects. The test statistic for genetic association in the presence of gene-covariate interaction improved the power for detecting association. For illustration, we analyze the rheumatoid arthritis data from GAW15. Adjusting for smoking and anti-cyclic citrullinated peptide increased the significance of the association with the DR locus.
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Affiliation(s)
- Andrea Callegaro
- Department of Medical Statistics and Bioinformatics, Leiden University MC, Leiden, The Netherlands.
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Brown BD, Nsengimana J, Barrett JH, Lawrence RA, Steiner L, Cheng S, Bishop DT, Samani NJ, Ball SG, Balmforth AJ, Hall AS. An evaluation of inflammatory gene polymorphisms in sibships discordant for premature coronary artery disease: the GRACE-IMMUNE study. BMC Med 2010; 8:5. [PMID: 20070880 PMCID: PMC2823655 DOI: 10.1186/1741-7015-8-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 01/13/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Inflammatory cytokines play a crucial role in coronary artery disease (CAD). We investigated the association between 48 coding and three non-coding single nucleotide polymorphisms (SNPs) from 35 inflammatory genes and the development of CAD, using a large discordant sibship collection (2699 individuals in 891 families). METHODS Family-based association tests (FBAT) and conditional logistic regression (CLR) were applied to single SNPs and haplotypes and, in CLR, traditional risk factors of CAD were adjusted for. RESULTS An association was observed between CAD and a common three-locus haplotype in the interleukin one (IL-1) cluster with P = 0.006 in all CAD cases, P = 0.01 in myocardial infarction (MI) cases and P = 0.0002 in young onset CAD cases (<50 years). The estimated odds ratio (OR) per copy of this haplotype is 1.21 (95% confidence interval [95CI] = 1.04 - 1.40) for CAD; 1.30 (95CI = 1.09 - 1.56) for MI and 1.50 (95CI = 1.22 - 1.86) for young onset CAD. When sex, smoking, hypertension and hypercholesterolaemia were adjusted for, the haplotype effect remained nominally significant (P = 0.05) in young onset CAD cases, more so (P = 0.002) when hypercholesterolaemia was excluded. As many as 82% of individuals affected by CAD had hypercholesterolaemia compared to only 29% of those unaffected, making the two phenotypes difficult to separate. CONCLUSION Despite the multiple hypotheses tested, the robustness of family design to population confoundings and the consistency with previous findings increase the likelihood of true association. Further investigation using larger data sets is needed in order for this to be confirmed. See the related commentary by Keavney: http://www.biomedcentral.com/1741-7015/8/6.
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Affiliation(s)
- Benjamin D Brown
- Leeds Institute of Genetics, Health and Therapeutics (LIGHT), University of Leeds, UK
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Alter A, de Léséleuc L, Van Thuc N, Thai VH, Huong NT, Ba NN, Cardoso CC, Grant AV, Abel L, Moraes MO, Alcaïs A, Schurr E. Genetic and functional analysis of common MRC1 exon 7 polymorphisms in leprosy susceptibility. Hum Genet 2009; 127:337-48. [PMID: 20035344 DOI: 10.1007/s00439-009-0775-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 12/04/2009] [Indexed: 10/20/2022]
Abstract
The chromosomal region 10p13 has been linked to paucibacillary leprosy in two independent studies. The MRC1 gene, encoding the human mannose receptor (MR), is located in the 10p13 region and non-synonymous SNPs in exon 7 of the gene have been suggested as leprosy susceptibility factors. We determined that G396S is the only non-synonymous exon 7-encoded polymorphism in 396 unrelated Vietnamese subjects. This SNP was genotyped in 490 simplex and 90 multiplex leprosy families comprising 704 patients (47% paucibacillary; 53% multibacillary). We observed significant under-transmission of the serine allele of the G396S polymorphism with leprosy per se (P = 0.036) and multibacillary leprosy (P = 0.034). In a sample of 384 Brazilian leprosy cases (51% paucibacillary; 49% multibacillary) and 399 healthy controls, we observed significant association of the glycine allele of the G396S polymorphism with leprosy per se (P = 0.016) and multibacillary leprosy (P = 0.023). In addition, we observed a significant association of exon 7 encoded amino acid haplotypes with leprosy per se (P = 0.012) and multibacillary leprosy (P = 0.004). Next, we tested HEK293 cells over-expressing MR constructs (293-MR) with three exon 7 haplotypes of MRC1 for their ability to bind and internalize ovalbumin and zymosan, two classical MR ligands. No difference in uptake was measured between the variants. In addition, 293-MR failed to bind and internalize viable Mycobacterium leprae and BCG. We propose that the MR-M. leprae interaction is modulated by an accessory host molecule of unknown identity.
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Affiliation(s)
- Andrea Alter
- Department of Medicine, McGill Centre for the Study of Host Resistance, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
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Sun X, Feng T, Song Y, Elston RC, Zhu X. Comparison of a unified analysis approach for family and unrelated samples with the transmission-disequilibrium test to study associations of hypertension in the Framingham Heart Study. BMC Proc 2009; 3 Suppl 7:S22. [PMID: 20018012 PMCID: PMC2795919 DOI: 10.1186/1753-6561-3-s7-s22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Population stratification is one of the major causes of spurious associations in association studies. A unified association approach based on principal-component analysis can overcome the effect of population stratification, as well as make use of both family and unrelated samples combined to increase power (family-case-control, or FamCC). In this study, we compared FamCC and the transmission-disequilibrium test (TDT) using data on hypertension, systolic blood pressure, and diastolic blood pressure in the Framingham Heart Study. Our study indicated FamCC has reasonable type I error for both the unrelated sample and the family sample for all three traits. For these three traits, we found results from FamCC were inconsistent with those from the TDT. We discuss the reasons for this inconsistency. After correcting for multiple tests, we did not detect any significant single-nucleotide polymorphisms by either FamCC or the TDT.
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Affiliation(s)
- Xiangqing Sun
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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Chen MH, Van Eerdewegh P, Vincent QB, Alcais A, Abel L, Dupuis J. Evaluation of approaches to identify associated SNPs that explain the linkage evidence in nuclear families with affected siblings. Hum Hered 2009; 69:104-19. [PMID: 19996608 DOI: 10.1159/000264448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Accepted: 07/22/2009] [Indexed: 11/19/2022] Open
Abstract
Linkage analysis is often followed by association mapping to localize disease variants. In this paper, we evaluate approaches to determine how much of the observed linkage evidence, namely the identity-by-descent (IBD) sharing at the linkage peak, is explained by associated SNPs. We study several methods: Homozygote Sharing Tests (HST), Genotype Identity-by-Descent Sharing Test (GIST), and a permutation approach. We also propose a new approach, HSTMLB, combining HST and the Maximum Likelihood Binomial (MLB) linkage statistic. These methods can identify SNPs partially explaining the linkage peak, but only HST and HSTMLB can identify SNPs that do not fully explain the linkage evidence and be applied to multiple-SNPs. We contrast these methods with the association tests implemented in the software LAMP. In our simulations, GIST is more powerful at finding SNPs that partially explain the linkage peak, while HST and HSTMLB are equally powerful at identifying SNPs that do not fully explain the linkage peak. When applied to the North American Rheumatoid Arthritis Consortium data, HST and HSTMLB identify marker pairs that may fully explain the linkage peak on chromosome 6. In conclusion, HST and HSTMLB provide simple and flexible tools to identify SNPs that explain the IBD sharing at the linkage peak.
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Affiliation(s)
- Ming-Huei Chen
- Department of Neurology and Framingham Heart Study, Boston University, Boston, Mass., USA.
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Weissglas-Volkov D, Plaisier CL, Huertas-Vazquez A, Cruz-Bautista I, Riaño-Barros D, Herrera-Hernandez M, Riba L, Cantor RM, Sinsheimer JS, Aguilar-Salinas CA, Tusie-Luna T, Pajukanta P. Identification of two common variants contributing to serum apolipoprotein B levels in Mexicans. Arterioscler Thromb Vasc Biol 2009; 30:353-9. [PMID: 19965785 DOI: 10.1161/atvbaha.109.196402] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND AND PURPOSE Although the Mexican population has a high predisposition to dyslipidemias and premature coronary artery disease, this population is underinvestigated for the genetic factors conferring the high susceptibility. This study attempted to determine these genetic factors. METHODS AND RESULTS First, we investigated apolipoprotein B (apoB) levels in Mexican extended families with familial combined hyperlipidemia using a two-step testing strategy. In the screening step, we screened 5721 single-nucleotide polymorphisms (SNPs) for linkage signals with apoB. In the test step, we analyzed the 130 SNPs residing in regions of suggestive linkage signals for association with apoB. We identified significant associations with two SNPs (ie, rs1424032 [P=6.07x10(-6)] and rs1349411 [P=2.72x10(-4)]) that surpassed the significance level for the number of tests performed in the test step (P<3.84x10(-4)). Second, these SNPs were tested for replication in Mexican hyperlipidemic case-control samples. The same risk alleles as in the families with familial combined hyperlipidemia were significantly associated (P<0.05) with apoB in the case-control samples. The rs1349411 resides near the apoB messenger RNA editing enzyme (APOBEC1) involved in the processing of APOB messenger RNA in the small intestine. The rs1424032 resides in a highly conserved noncoding region predicted to function as a regulatory element. CONCLUSIONS We identified two novel variants, rs1349411 and rs1424032, for serum apoB levels in Mexicans.
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Affiliation(s)
- Daphna Weissglas-Volkov
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, Calif 90095-7088, USA
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Shugart YY, Wang Y, Samuels JF, Grados MA, Greenberg BD, Knowles JA, McCracken JT, Rauch SL, Murphy DL, Rasmussen SA, Cullen B, Hoehn-Saric R, Pinto A, Fyer AJ, Piacentini J, Pauls DL, Bienvenu OJ, Riddle MA, Liang KY, Nestadt G. A family-based association study of the glutamate transporter gene SLC1A1 in obsessive-compulsive disorder in 378 families. Am J Med Genet B Neuropsychiatr Genet 2009; 150B:886-92. [PMID: 19152386 DOI: 10.1002/ajmg.b.30914] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
SLC1A encodes the neuronal and epithelial glutamate transporter and was previously tested as a candidate for obsessive-compulsive disorder (OCD) by several research groups. Recently, three independent research groups reported significant association findings between OCD and several genetic variants in SLC1A1. This study reports the results from a family-based association study, which examined the association between 13 single nucleotide polymorphisms (SNPs) within or in proximity to the SLC1A1 gene. Although we did not replicate association findings for those significant SNPs reported by previous studies, our study indicated a strong association signal with the SNP RS301443 (P-value = 0.000067; Bonferroni corrected P-value = 0.0167) under a dominant model, with an estimated odds ratio of 3.5 (confidence interval: 2.66-4.50). Further, we conducted single SNP analysis after stratifying the full data set by the gender status of affected in each family. The P-value for RS301443 in families with the male affected was 0.00027, and the P-value in families with female affected was 0.076. The fact that we identified a signal which was not previously reported by the other research groups may be due to differences in study designs and sample ascertainment. However, it is also possible that this significant SNP may be part of a regulator for SLC1A1, given that it is roughly 7.5 kb away from the boundary of the SLC1A1 gene. However, this potential finding needs to be validated biologically. Further functional studies in this region are planned by this research group.
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Affiliation(s)
- Y Y Shugart
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21044, USA.
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Chen WM, Manichaikul A, Rich SS. A generalized family-based association test for dichotomous traits. Am J Hum Genet 2009; 85:364-76. [PMID: 19732865 DOI: 10.1016/j.ajhg.2009.08.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2009] [Revised: 06/09/2009] [Accepted: 08/11/2009] [Indexed: 12/11/2022] Open
Abstract
Recent advances in genotyping technology make it possible to utilize large-scale association analysis for disease-gene mapping. Powerful and robust family-based association methods are crucial for successful gene mapping. We propose a family-based association method, the generalized disequilibrium test (GDT), in which the genotype differences of all discordant relative pairs are utilized in assessing association within a family. The improvement of the GDT over existing methods is threefold: (1) information beyond first-degree relatives is incorporated efficiently, yielding substantial gains in power in comparison to existing tests; (2) the GDT statistic is implemented via a robust technique that does not rely on large sample theory, resulting in further power gains, especially at high levels of significance; and (3) covariates and weights based on family size are incorporated. Advantages of the GDT over existing methods are demonstrated by extensive computer simulations and by application to recently published large-scale genome-wide linkage data from the Type 1 Diabetes Genetics Consortium (T1DGC). In our simulations, the GDT consistently outperforms other tests for a common disease and frequently outperforms other tests for a rare disease; the power improvement is > 13% in 6 out of 8 extended pedigree scenarios. All of the six strongest associations identified by the GDT have been reported by other studies, whereas only three or four of these associations can be identified by existing methods. For the T1D association at gene UBASH3A, the GDT resulted in a genome-wide significance (p = 4.3 x 10(-6)), much stronger than the published significance (p = 10(-4)).
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Affiliation(s)
- Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.
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