1
|
Kim EE, Jang CS, Kim H, Han B. PASTRY: achieving balanced power for detecting risk and protective minor alleles in meta-analysis of association studies with overlapping subjects. BMC Bioinformatics 2024; 25:24. [PMID: 38216869 PMCID: PMC10790263 DOI: 10.1186/s12859-023-05627-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Meta-analysis is a statistical method that combines the results of multiple studies to increase statistical power. When multiple studies participating in a meta-analysis utilize the same public dataset as controls, the summary statistics from these studies become correlated. To solve this challenge, Lin and Sullivan proposed a method to provide an optimal test statistic adjusted for the correlation. This method quickly became the standard practice. However, we identified an unexpected power asymmetry phenomenon in this standard framework. This can lead to unbalanced power for detecting protective minor alleles and risk minor alleles. RESULTS We found that the power asymmetry of the current framework is mainly due to the errors in approximating the correlation term. We then developed a meta-analysis method based on an accurate correlation estimator, called PASTRY (A method to avoid Power ASymmeTRY). PASTRY outperformed the standard method on both simulated and real datasets in terms of the power symmetry. CONCLUSIONS Our findings suggest that PASTRY can help to alleviate the power asymmetry problem. PASTRY is available at https://github.com/hanlab-SNU/PASTRY .
Collapse
Affiliation(s)
- Emma E Kim
- Department of Chemistry, Seoul National University, Seoul, 03080, Korea
| | - Chloe Soohyun Jang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Hakin Kim
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 03080, Korea
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea.
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 03080, Korea.
| |
Collapse
|
2
|
Rivandi M, Martens JWM, Hollestelle A. Elucidating the Underlying Functional Mechanisms of Breast Cancer Susceptibility Through Post-GWAS Analyses. Front Genet 2018; 9:280. [PMID: 30116257 PMCID: PMC6082943 DOI: 10.3389/fgene.2018.00280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 170 single nucleotide polymorphisms (SNPs) associated with the susceptibility to breast cancer. Together, these SNPs explain 18% of the familial relative risk, which is estimated to be nearly half of the total familial breast cancer risk that is collectively explained by low-risk susceptibility alleles. An important aspect of this success has been the access to large sample sizes through collaborative efforts within the Breast Cancer Association Consortium (BCAC), but also collaborations between cancer association consortia. Despite these achievements, however, understanding of each variant's underlying mechanism and how these SNPs predispose women to breast cancer remains limited and represents a major challenge in the field, particularly since the vast majority of the GWAS-identified SNPs are located in non-coding regions of the genome and are merely tags for the causal variants. In recent years, fine-scale mapping studies followed by functional evaluation of putative causal variants have begun to elucidate the biological function of several GWAS-identified variants. In this review, we discuss the findings and lessons learned from these post-GWAS analyses of 22 risk loci. Identifying the true causal variants underlying breast cancer susceptibility and their function not only provides better estimates of the explained familial relative risk thereby improving polygenetic risk scores (PRSs), it also increases our understanding of the biological mechanisms responsible for causing susceptibility to breast cancer. This will facilitate the identification of further breast cancer risk alleles and the development of preventive medicine for those women at increased risk for developing the disease.
Collapse
Affiliation(s)
- Mahdi Rivandi
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands.,Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands.,Cancer Genomics Centre, Utrecht, Netherlands
| | | |
Collapse
|
3
|
Lin M, Zhang L, Hildebrandt MA, Huang M, Wu X, Ye Y. Common, germline genetic variations in the novel tumor suppressor BAP1 and risk of developing different types of cancer. Oncotarget 2017; 8:74936-74946. [PMID: 29088836 PMCID: PMC5650391 DOI: 10.18632/oncotarget.20465] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/26/2017] [Indexed: 01/09/2023] Open
Abstract
BRCA1 associated protein-1 (BAP1) is a novel tumor suppressor that has recently been shown to be somatically mutated in several cancers. The BAP1 gene also carries rare germline mutations in families with a high incidence of several types of cancers, such as mesothelioma, uveal melanoma, lung adenocarcinoma, melanocytic neoplasms, and renal cell carcinoma. To test the hypothesis that common, germline genetic variants in BAP1 may also contribute to the risk of developing different types of cancer, we genotyped germline single nucleotide polymorphisms (SNPs) for BAP1 in a large population of patients with cancer, including 2,340 with colorectal cancer, 1,436 with bladder cancer, 3,313 with lung cancer, 1,325 with renal cell carcinoma, and 1,162 with esophageal cancer. We identified significant association of rs11708581 (P = 0.0034) and rs390802 (P = 0.015) with risk of renal cell carcinoma and rs12163565 (P = 0.038) with risk of lung cancer. Expression quantitative trait loci analysis in renal cell carcinoma using publicly available data from TCGA showed that the proxy SNPs for rs11708581 and rs390802 were negatively associated with the expression level of BAP1. Our study indicate that common germline genetic variants of BAP1 play a role in mediating the risk of developing renal cell carcinoma and lung cancer.
Collapse
Affiliation(s)
- Moubin Lin
- Department of General Surgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Liren Zhang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|
4
|
Dungan JR, Qin X, Horne BD, Carlquist JF, Singh A, Hurdle M, Grass E, Haynes C, Gregory SG, Shah SH, Hauser ER, Kraus WE. Case-Only Survival Analysis Reveals Unique Effects of Genotype, Sex, and Coronary Disease Severity on Survivorship. PLoS One 2016; 11:e0154856. [PMID: 27187494 PMCID: PMC4871369 DOI: 10.1371/journal.pone.0154856] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/20/2016] [Indexed: 01/05/2023] Open
Abstract
Survival bias may unduly impact genetic association with complex diseases; gene-specific survival effects may further complicate such investigations. Coronary artery disease (CAD) is a complex phenotype for which little is understood about gene-specific survival effects; yet, such information can offer insight into refining genetic associations, improving replications, and can provide candidate genes for both mortality risk and improved survivorship in CAD. Building on our previous work, the purpose of this current study was to: evaluate LSAMP SNP-specific hazards for all-cause mortality post-catheterization in a larger cohort of our CAD cases; and, perform additional replication in an independent dataset. We examined two LSAMP SNPs—rs1462845 and rs6788787—using CAD case-only Cox proportional hazards regression for additive genetic effects, censored on time-to-all-cause mortality or last follow-up among Caucasian subjects from the Catheterization Genetics Study (CATHGEN; n = 2,224) and the Intermountain Heart Collaborative Study (IMHC; n = 3,008). Only after controlling for age, sex, body mass index, histories of smoking, type 2 diabetes, hyperlipidemia and hypertension (HR = 1.11, 95%CI = 1.01–1.22, p = 0.032), rs1462845 conferred significantly increased hazards of all-cause mortality among CAD cases. Even after controlling for multiple covariates, but in only the primary cohort, rs6788787 conferred significantly improved survival (HR = 0.80, 95% CI = 0.69–0.92, p = 0.002). Post-hoc analyses further stratifying by sex and disease severity revealed replicated effects for rs1462845: even after adjusting for aforementioned covariates and coronary interventional procedures, males with severe burden of CAD had significantly amplified hazards of death with the minor variant of rs1462845 in both cohorts (HR = 1.29, 95% CI = 1.08–1.55, p = 0.00456; replication HR = 1.25, 95% CI = 1.05–1.49, p = 0.013). Kaplan-Meier curves revealed unique cohort-specific genotype effects on survival. Additional analyses demonstrated that the homozygous risk genotype (‘A/A’) fully explained the increased hazard in both cohorts. None of the post-hoc analyses in control subjects were significant for any model. This suggests that genetic effects of rs1462845 on survival are unique to CAD presence. This represents formal, replicated evidence of genetic contribution of rs1462845 to increased risk for all-cause mortality; the contribution is unique to CAD case status and specific to males with severe burden of CAD.
Collapse
Affiliation(s)
- Jennifer R. Dungan
- Duke University School of Nursing, Durham, NC, United States of America
- * E-mail:
| | - Xuejun Qin
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Benjamin D. Horne
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, United States of America
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States of America
| | - John F. Carlquist
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT, United States of America
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, United States of America
| | - Abanish Singh
- Behavioral Medicine Research Center, Duke University Medical Center, Durham, NC, United States of America
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Melissa Hurdle
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Elizabeth Grass
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Carol Haynes
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Simon G. Gregory
- Duke University Department of Medicine, Durham, NC, United States of America
| | - Svati H. Shah
- Duke University Department of Medicine, Durham, NC, United States of America
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Elizabeth R. Hauser
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States of America
| | - William E. Kraus
- Duke University Department of Medicine, Durham, NC, United States of America
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| |
Collapse
|
5
|
Abstract
Large population studies of immune system genes are essential for characterizing their role in diseases, including autoimmune conditions. Of key interest are a group of genes encoding the killer cell immunoglobulin-like receptors (KIRs), which have known and hypothesized roles in autoimmune diseases, resistance to viruses, reproductive conditions, and cancer. These genes are highly polymorphic, which makes typing expensive and time consuming. Consequently, despite their importance, KIRs have been little studied in large cohorts. Statistical imputation methods developed for other complex loci (e.g., human leukocyte antigen [HLA]) on the basis of SNP data provide an inexpensive high-throughput alternative to direct laboratory typing of these loci and have enabled important findings and insights for many diseases. We present KIR∗IMP, a method for imputation of KIR copy number. We show that KIR∗IMP is highly accurate and thus allows the study of KIRs in large cohorts and enables detailed investigation of the role of KIRs in human disease.
Collapse
|
6
|
Cutler DJ, Zwick ME, Okou DT, Prahalad S, Walters T, Guthery SL, Dubinsky M, Baldassano R, Crandall WV, Rosh J, Markowitz J, Stephens M, Kellermayer R, Pfefferkorn M, Heyman MB, LeLeiko N, Mack D, Moulton D, Kappelman MD, Kumar A, Prince J, Bose P, Mondal K, Ramachandran D, Bohnsack JF, Griffiths AM, Haberman Y, Essers J, Thompson SD, Aronow B, Keljo DJ, Hyams JS, Denson LA, Kugathasan S. Dissecting Allele Architecture of Early Onset IBD Using High-Density Genotyping. PLoS One 2015; 10:e0128074. [PMID: 26098103 PMCID: PMC4476779 DOI: 10.1371/journal.pone.0128074] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/23/2015] [Indexed: 01/15/2023] Open
Abstract
Background The inflammatory bowel diseases (IBD) are common, complex disorders in which genetic and environmental factors are believed to interact leading to chronic inflammatory responses against the gut microbiota. Earlier genetic studies performed in mostly adult population of European descent identified 163 loci affecting IBD risk, but most have relatively modest effect sizes, and altogether explain only ~20% of the genetic susceptibility. Pediatric onset represents about 25% of overall incident cases in IBD, characterized by distinct disease physiology, course and risks. The goal of this study is to compare the allelic architecture of early onset IBD with adult onset in population of European descent. Methods We performed a fine mapping association study of early onset IBD using high-density Immunochip genotyping on 1008 pediatric-onset IBD cases (801 Crohn’s disease; 121 ulcerative colitis and 86 IBD undetermined) and 1633 healthy controls. Of the 158 SNP genotypes obtained (out of the 163 identified in adult onset), this study replicated 4% (5 SNPs out of 136) of the SNPs identified in the Crohn’s disease (CD) cases and 0.8% (1 SNP out of 128) in the ulcerative colitis (UC) cases. Replicated SNPs implicated the well known NOD2 and IL23R. The point estimate for the odds ratio (ORs) for NOD2 was above and outside the confidence intervals reported in adult onset. A polygenic liability score weakly predicted the age of onset for a larger collection of CD cases (p< 0.03, R2= 0.007), but not for the smaller number of UC cases. Conclusions The allelic architecture of common susceptibility variants for early onset IBD is similar to that of adult onset. This immunochip genotyping study failed to identify additional common variants that may explain the distinct phenotype that characterize early onset IBD. A comprehensive dissection of genetic loci is necessary to further characterize the genetic architecture of early onset IBD.
Collapse
Affiliation(s)
- David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Michael E. Zwick
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - David T. Okou
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Sampath Prahalad
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | | | - Stephen L. Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Marla Dubinsky
- Icahn School of Medicine, Mount Sinai Hospital, New York, New York, United States of America
| | - Robert Baldassano
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | | | - Joel Rosh
- Goryeb Children’s Hospital, Morristown, New Jersey, United States of America
| | - James Markowitz
- Cohen Children’s Medical Center, New Hyde Park, New York, United States of America
| | - Michael Stephens
- Pediatric Gastroenterology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Richard Kellermayer
- Baylor College School of Medicine, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Marian Pfefferkorn
- Riley Children’s Hospital, Indiannapolis, Indianapolis, United States of America
| | - Melvin B. Heyman
- University of California, San Francisco, California, United States of America
| | - Neal LeLeiko
- Hasbro Children’s Hospital, Providence, Rhode Island, United States of America
| | - David Mack
- Children’s Hospital of Eastern Ontario, Ottawa, Canada
| | - Dedrick Moulton
- Vanderbilt Children’s Hospital, Nashville, Tennessee, United States of America
| | - Michael D. Kappelman
- University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Archana Kumar
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Jarod Prince
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Promita Bose
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Kajari Mondal
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Dhanya Ramachandran
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - John F. Bohnsack
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | | | - Yael Haberman
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jonah Essers
- Children’s Hospital of Boston, Boston, Massachusetts, United States of America
| | - Susan D. Thompson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Bruce Aronow
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - David J. Keljo
- Children Hospital of Pittsburgh, Pittsburg, Pennsylvania, United States of America
| | - Jeffrey S. Hyams
- Connecticut Children’s Medical Center, Hartford, Connecticut, United States of America
| | - Lee A. Denson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | | | - Subra Kugathasan
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
| |
Collapse
|
7
|
Barrett JH, Taylor JC, Bright C, Harland M, Dunning AM, Akslen LA, Andresen PA, Avril MF, Azizi E, Bianchi Scarrà G, Brossard M, Brown KM, Dębniak T, Elder DE, Friedman E, Ghiorzo P, Gillanders EM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Ingvar C, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Molven A, Novaković S, Olsson H, Puig S, Puig-Butille JA, van der Stoep N, van Doorn R, van Workum W, Goldstein AM, Kanetsky PA, Pharoah PDP, Demenais F, Hayward NK, Newton Bishop JA, Bishop DT, Iles MM. Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions. Int J Cancer 2015; 136:1351-60. [PMID: 25077817 PMCID: PMC4328144 DOI: 10.1002/ijc.29099] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/06/2014] [Indexed: 01/31/2023]
Abstract
At least 17 genomic regions are established as harboring melanoma susceptibility variants, in most instances with genome-wide levels of significance and replication in independent samples. Based on genome-wide single nucleotide polymorphism (SNP) data augmented by imputation to the 1,000 Genomes reference panel, we have fine mapped these regions in over 5,000 individuals with melanoma (mainly from the GenoMEL consortium) and over 7,000 ethnically matched controls. A penalized regression approach was used to discover those SNP markers that most parsimoniously explain the observed association in each genomic region. For the majority of the regions, the signal is best explained by a single SNP, which sometimes, as in the tyrosinase region, is a known functional variant. However in five regions the explanation is more complex. At the CDKN2A locus, for example, there is strong evidence that not only multiple SNPs but also multiple genes are involved. Our results illustrate the variability in the biology underlying genome-wide susceptibility loci and make steps toward accounting for some of the "missing heritability."
Collapse
Affiliation(s)
- Jennifer H Barrett
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
O'Rielly DD, Rahman P. Clinical genetic research 2: Genetic epidemiology of complex phenotypes. Methods Mol Biol 2015; 1281:349-67. [PMID: 25694321 DOI: 10.1007/978-1-4939-2428-8_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Genetic factors play a substantive role in the susceptibility to common diseases. Due to recent and rapid advancements in characterization of genetic variants and large-scale genotyping platforms, multiple genes and genetic variants have now been identified for common, complex diseases. The most efficient method for gene identification at present appears to be large-scale association-based studies, which integrate genetic and epidemiological principles. As the strategy for gene identification studies has shifted towards genetic association-based methods rather than traditional linkage analysis, epidemiological methods are increasingly being integrated into genetic investigations. Consequently, the disciplines of genetics and epidemiology, which historically have functioned separately, have been integrated into a discipline referred to as genetic epidemiology. In this chapter, we review methods for establishing the genetic burden of complex genetic disease, followed by methods for gene and/or genetic variant identification and when appropriate we highlight the epidemiological issues that guide these methods.
Collapse
Affiliation(s)
- Darren D O'Rielly
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | | |
Collapse
|
9
|
Wen SH, Yeh JI. Cohen's h for detection of disease association with rare genetic variants. BMC Genomics 2014; 15:875. [PMID: 25294186 PMCID: PMC4198687 DOI: 10.1186/1471-2164-15-875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/03/2014] [Indexed: 11/16/2022] Open
Abstract
Background The power of the genome wide association studies starts to go down when the minor allele frequency (MAF) is below 0.05. Here, we proposed the use of Cohen’s h in detecting disease associated rare variants. The variance stabilizing effect based on the arcsine square root transformation of MAFs to generate Cohen’s h contributed to the statistical power for rare variants analysis. We re-analyzed published datasets, one microarray and one sequencing based, and used simulation to compare the performance of Cohen’s h with the risk difference (RD) and odds ratio (OR). Results The analysis showed that the type 1 error rate of Cohen’s h was as expected and Cohen’s h and RD were both less biased and had higher power than OR. The advantage of Cohen’s h was more obvious when MAF was less than 0.01. Conclusions Cohen’s h can increase the power to find genetic association of rare variants and diseases, especially when MAF is less than 0.01. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-875) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Jih-I Yeh
- Department of Molecular Biology and Human Genetics, Tzu-Chi University, 701, Sec 3, Chung-Yang Rd, Hualien 97004, Taiwan.
| |
Collapse
|
10
|
Chen Z, Craiu RV, Bull SB. A note on the efficiencies of sampling strategies in two-stage Bayesian regional fine mapping of a quantitative trait. Genet Epidemiol 2014; 38:599-609. [PMID: 25132153 DOI: 10.1002/gepi.21845] [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: 12/21/2013] [Revised: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 11/09/2022]
Abstract
In focused studies designed to follow up associations detected in a genome-wide association study (GWAS), investigators can proceed to fine-map a genomic region by targeted sequencing or dense genotyping of all variants in the region, aiming to identify a functional sequence variant. For the analysis of a quantitative trait, we consider a Bayesian approach to fine-mapping study design that incorporates stratification according to a promising GWAS tag SNP in the same region. Improved cost-efficiency can be achieved when the fine-mapping phase incorporates a two-stage design, with identification of a smaller set of more promising variants in a subsample taken in stage 1, followed by their evaluation in an independent stage 2 subsample. To avoid the potential negative impact of genetic model misspecification on inference we incorporate genetic model selection based on posterior probabilities for each competing model. Our simulation study shows that, compared to simple random sampling that ignores genetic information from GWAS, tag-SNP-based stratified sample allocation methods reduce the number of variants continuing to stage 2 and are more likely to promote the functional sequence variant into confirmation studies.
Collapse
Affiliation(s)
- Zhijian Chen
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | | |
Collapse
|
11
|
Smith S, Hay EH, Farhat N, Rekaya R. Genome wide association studies in presence of misclassified binary responses. BMC Genet 2013; 14:124. [PMID: 24369108 PMCID: PMC3879434 DOI: 10.1186/1471-2156-14-124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 12/17/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Misclassification has been shown to have a high prevalence in binary responses in both livestock and human populations. Leaving these errors uncorrected before analyses will have a negative impact on the overall goal of genome-wide association studies (GWAS) including reducing predictive power. A liability threshold model that contemplates misclassification was developed to assess the effects of mis-diagnostic errors on GWAS. Four simulated scenarios of case-control datasets were generated. Each dataset consisted of 2000 individuals and was analyzed with varying odds ratios of the influential SNPs and misclassification rates of 5% and 10%. RESULTS Analyses of binary responses subject to misclassification resulted in underestimation of influential SNPs and failed to estimate the true magnitude and direction of the effects. Once the misclassification algorithm was applied there was a 12% to 29% increase in accuracy, and a substantial reduction in bias. The proposed method was able to capture the majority of the most significant SNPs that were not identified in the analysis of the misclassified data. In fact, in one of the simulation scenarios, 33% of the influential SNPs were not identified using the misclassified data, compared with the analysis using the data without misclassification. However, using the proposed method, only 13% were not identified. Furthermore, the proposed method was able to identify with high probability a large portion of the truly misclassified observations. CONCLUSIONS The proposed model provides a statistical tool to correct or at least attenuate the negative effects of misclassified binary responses in GWAS. Across different levels of misclassification probability as well as odds ratios of significant SNPs, the model proved to be robust. In fact, SNP effects, and misclassification probability were accurately estimated and the truly misclassified observations were identified with high probabilities compared to non-misclassified responses. This study was limited to situations where the misclassification probability was assumed to be the same in cases and controls which is not always the case based on real human disease data. Thus, it is of interest to evaluate the performance of the proposed model in that situation which is the current focus of our research.
Collapse
Affiliation(s)
| | | | | | - Romdhane Rekaya
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA, USA.
| |
Collapse
|
12
|
Gusev A, Bhatia G, Zaitlen N, Vilhjalmsson BJ, Diogo D, Stahl EA, Gregersen PK, Worthington J, Klareskog L, Raychaudhuri S, Plenge RM, Pasaniuc B, Price AL. Quantifying missing heritability at known GWAS loci. PLoS Genet 2013; 9:e1003993. [PMID: 24385918 PMCID: PMC3873246 DOI: 10.1371/journal.pgen.1003993] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 10/16/2013] [Indexed: 12/02/2022] Open
Abstract
Recent work has shown that much of the missing heritability of complex traits can be resolved by estimates of heritability explained by all genotyped SNPs. However, it is currently unknown how much heritability is missing due to poor tagging or additional causal variants at known GWAS loci. Here, we use variance components to quantify the heritability explained by all SNPs at known GWAS loci in nine diseases from WTCCC1 and WTCCC2. After accounting for expectation, we observed all SNPs at known GWAS loci to explain more heritability than GWAS-associated SNPs on average (). For some diseases, this increase was individually significant: for Multiple Sclerosis (MS) () and for Crohn's Disease (CD) (); all analyses of autoimmune diseases excluded the well-studied MHC region. Additionally, we found that GWAS loci from other related traits also explained significant heritability. The union of all autoimmune disease loci explained more MS heritability than known MS SNPs () and more CD heritability than known CD SNPs (), with an analogous increase for all autoimmune diseases analyzed. We also observed significant increases in an analysis of Rheumatoid Arthritis (RA) samples typed on ImmunoChip, with more heritability from all SNPs at GWAS loci () and more heritability from all autoimmune disease loci () compared to known RA SNPs (including those identified in this cohort). Our methods adjust for LD between SNPs, which can bias standard estimates of heritability from SNPs even if all causal variants are typed. By comparing adjusted estimates, we hypothesize that the genome-wide distribution of causal variants is enriched for low-frequency alleles, but that causal variants at known GWAS loci are skewed towards common alleles. These findings have important ramifications for fine-mapping study design and our understanding of complex disease architecture. Heritable diseases have an unknown underlying “genetic architecture” that defines the distribution of effect-sizes for disease-causing mutations. Understanding this genetic architecture is an important first step in designing disease-mapping studies, and many theories have been developed on the nature of this distribution. Here, we evaluate the hypothesis that additional heritable variation lies at previously known associated loci but is not fully explained by the single most associated marker. We develop methods based on variance-components analysis to quantify this type of “local” heritability, demonstrating that standard strategies can be falsely inflated or deflated due to correlation between neighboring markers and propose a robust adjustment. In analysis of nine common diseases we find a significant average increase of local heritability, consistent with multiple common causal variants at an average locus. Intriguingly, for autoimmune diseases we also observe significant local heritability in loci not associated with the specific disease but with other autoimmune diseases, implying a highly correlated underlying disease architecture. These findings have important implications to the design of future studies and our general understanding of common disease.
Collapse
Affiliation(s)
- Alexander Gusev
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail: (AG); (ALP)
| | - Gaurav Bhatia
- Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Harvard-Massachusetts Institute of Technology (MIT) Division of Health, Science and Technology, Cambridge, Massachusetts, United States of America
| | - Noah Zaitlen
- Department of Medicine Lung Biology Center, University of California San Francisco, San Francisco, California, United States of America
| | - Bjarni J. Vilhjalmsson
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Dorothée Diogo
- Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Eli A. Stahl
- Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Soumya Raychaudhuri
- Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Robert M. Plenge
- Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Alkes L. Price
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail: (AG); (ALP)
| |
Collapse
|
13
|
Cornejo-García JA, Liou LB, Blanca-López N, Doña I, Chen CH, Chou YC, Chuang HP, Wu JY, Chen YT, Plaza-Serón MDC, Mayorga C, Guéant-Rodríguez RM, Lin SC, Torres MJ, Campo P, Rondón C, Laguna JJ, Fernández J, Guéant JL, Canto G, Blanca M, Lee MTM. Genome-wide association study in NSAID-induced acute urticaria/angioedema in Spanish and Han Chinese populations. Pharmacogenomics 2013; 14:1857-69. [PMID: 24236485 DOI: 10.2217/pgs.13.166] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
AIM Acute urticaria/angioedema (AUA) induced by cross-intolerance to NSAIDs is the most frequent clinical entity in hypersensitivity reactions to drugs. In this work, we conducted a genome-wide association study in Spanish and Han Chinese patients suffering from NSAID-induced AUA. MATERIALS & METHODS A whole-genome scan was performed on a total of 232 cases (112 Spanish and 120 Han Chinese) with NSAID-induced AUA and 225 unrelated controls (124 Spanish and 101 Han Chinese). RESULTS Although no polymorphism reached genome-wide significance, we obtained suggestive associations for three clusters in the Spanish group (RIMS1, BICC1 and RAD51L 1) and one region in the Han Chinese population (ABI3BP). Five regions showed suggestive associations after meta-analysis: HLF, RAD51L1, COL24A1, GalNAc-T13 and FBXL7. A majority of these genes are related to Ca(2+), cAMP and/or P53 signaling pathways. CONCLUSION The associations described were different from those related to the metabolism of arachidonic acid and could provide new mechanisms underlying NSAID-induced AUA.
Collapse
|
14
|
Jostins L, Levine AP, Barrett JC. Using genetic prediction from known complex disease Loci to guide the design of next-generation sequencing experiments. PLoS One 2013; 8:e76328. [PMID: 24204614 PMCID: PMC3799779 DOI: 10.1371/journal.pone.0076328] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 08/27/2013] [Indexed: 12/14/2022] Open
Abstract
A central focus of complex disease genetics after genome-wide association studies (GWAS) is to identify low frequency and rare risk variants, which may account for an important fraction of disease heritability unexplained by GWAS. A profusion of studies using next-generation sequencing are seeking such risk alleles. We describe how already-known complex trait loci (largely from GWAS) can be used to guide the design of these new studies by selecting cases, controls, or families who are most likely to harbor undiscovered risk alleles. We show that genetic risk prediction can select unrelated cases from large cohorts who are enriched for unknown risk factors, or multiply-affected families that are more likely to harbor high-penetrance risk alleles. We derive the frequency of an undiscovered risk allele in selected cases and controls, and show how this relates to the variance explained by the risk score, the disease prevalence and the population frequency of the risk allele. We also describe a new method for informing the design of sequencing studies using genetic risk prediction in large partially-genotyped families using an extension of the Inside-Outside algorithm for inference on trees. We explore several study design scenarios using both simulated and real data, and show that in many cases genetic risk prediction can provide significant increases in power to detect low-frequency and rare risk alleles. The same approach can also be used to aid discovery of non-genetic risk factors, suggesting possible future utility of genetic risk prediction in conventional epidemiology. Software implementing the methods in this paper is available in the R package Mangrove.
Collapse
Affiliation(s)
- Luke Jostins
- Medical Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Trust Centre for Human Genetics, Univeristy of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Adam P. Levine
- Division of Medicine, University College London, London, United Kingdom
| | - Jeffrey C. Barrett
- Medical Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| |
Collapse
|
15
|
Liu CT, Monda KL, Taylor KC, Lange L, Demerath EW, Palmas W, Wojczynski MK, Ellis JC, Vitolins MZ, Liu S, Papanicolaou GJ, Irvin MR, Xue L, Griffin PJ, Nalls MA, Adeyemo A, Liu J, Li G, Ruiz-Narvaez EA, Chen WM, Chen F, Henderson BE, Millikan RC, Ambrosone CB, Strom SS, Guo X, Andrews JS, Sun YV, Mosley TH, Yanek LR, Shriner D, Haritunians T, Rotter JI, Speliotes EK, Smith M, Rosenberg L, Mychaleckyj J, Nayak U, Spruill I, Garvey WT, Pettaway C, Nyante S, Bandera EV, Britton AF, Zonderman AB, Rasmussen-Torvik LJ, Chen YDI, Ding J, Lohman K, Kritchevsky SB, Zhao W, Peyser PA, Kardia SLR, Kabagambe E, Broeckel U, Chen G, Zhou J, Wassertheil-Smoller S, Neuhouser ML, Rampersaud E, Psaty B, Kooperberg C, Manson JE, Kuller LH, Ochs-Balcom HM, Johnson KC, Sucheston L, Ordovas JM, Palmer JR, Haiman CA, McKnight B, Howard BV, Becker DM, Bielak LF, Liu Y, Allison MA, Grant SFA, Burke GL, Patel SR, Schreiner PJ, Borecki IB, Evans MK, Taylor H, Sale MM, Howard V, Carlson CS, Rotimi CN, Cushman M, Harris TB, Reiner AP, Cupples LA, North KE, Fox CS. Genome-wide association of body fat distribution in African ancestry populations suggests new loci. PLoS Genet 2013; 9:e1003681. [PMID: 23966867 PMCID: PMC3744443 DOI: 10.1371/journal.pgen.1003681] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 06/13/2013] [Indexed: 01/18/2023] Open
Abstract
Central obesity, measured by waist circumference (WC) or waist-hip ratio (WHR), is a marker of body fat distribution. Although obesity disproportionately affects minority populations, few studies have conducted genome-wide association study (GWAS) of fat distribution among those of predominantly African ancestry (AA). We performed GWAS of WC and WHR, adjusted and unadjusted for BMI, in up to 33,591 and 27,350 AA individuals, respectively. We identified loci associated with fat distribution in AA individuals using meta-analyses of GWA results for WC and WHR (stage 1). Overall, 25 SNPs with single genomic control (GC)-corrected p-values<5.0 × 10(-6) were followed-up (stage 2) in AA with WC and with WHR. Additionally, we interrogated genomic regions of previously identified European ancestry (EA) WHR loci among AA. In joint analysis of association results including both Stage 1 and 2 cohorts, 2 SNPs demonstrated association, rs2075064 at LHX2, p = 2.24×10(-8) for WC-adjusted-for-BMI, and rs6931262 at RREB1, p = 2.48×10(-8) for WHR-adjusted-for-BMI. However, neither signal was genome-wide significant after double GC-correction (LHX2: p = 6.5 × 10(-8); RREB1: p = 5.7 × 10(-8)). Six of fourteen previously reported loci for waist in EA populations were significant (p<0.05 divided by the number of independent SNPs within the region) in AA studied here (TBX15-WARS2, GRB14, ADAMTS9, LY86, RSPO3, ITPR2-SSPN). Further, we observed associations with metabolic traits: rs13389219 at GRB14 associated with HDL-cholesterol, triglycerides, and fasting insulin, and rs13060013 at ADAMTS9 with HDL-cholesterol and fasting insulin. Finally, we observed nominal evidence for sexual dimorphism, with stronger results in AA women at the GRB14 locus (p for interaction = 0.02). In conclusion, we identified two suggestive loci associated with fat distribution in AA populations in addition to confirming 6 loci previously identified in populations of EA. These findings reinforce the concept that there are fat distribution loci that are independent of generalized adiposity.
Collapse
Affiliation(s)
- Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Keri L. Monda
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kira C. Taylor
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Epidemiology and Population Health, University of Louisville, Louisville, Kentucky, United States of America
| | - Leslie Lange
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ellen W. Demerath
- University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Walter Palmas
- Department of Medicine, Columbia University, New York, New York, United States of America
| | - Mary K. Wojczynski
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jaclyn C. Ellis
- Department of Genetics, UNC School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Mara Z. Vitolins
- Department of Epidemiology & Prevention, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Simin Liu
- Departments of Epidemiology, Medicine, and Obstetrics and Gynecology and Center for Metabolic Disease Prevention, Los Angeles, California, United States of America
| | - George J. Papanicolaou
- Division of Cardiovascular Sciences, Prevention and Population Sciences Program, National Heart, Lung, & Blood Institute, Bethesda, Maryland, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, UAB, Birmingham, Alabama, United States of America
| | - Luting Xue
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Paula J. Griffin
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Michael A. Nalls
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Jiankang Liu
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Guo Li
- University of Washington, Seattle, Washington, United States of America
| | - Edward A. Ruiz-Narvaez
- Slone Epidemiology Center, Boston University, Boston, Massachusetts, United States of America
| | - Wei-Min Chen
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Fang Chen
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Robert C. Millikan
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Sara S. Strom
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Xiuqing Guo
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jeanette S. Andrews
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Yan V. Sun
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas H. Mosley
- Division of Geriatrics, Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Talin Haritunians
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | | | - Megan Smith
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Lynn Rosenberg
- Slone Epidemiology Center, Boston University, Boston, Massachusetts, United States of America
| | - Josyf Mychaleckyj
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Uma Nayak
- Center for Public Health and Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ida Spruill
- Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - W. Timothy Garvey
- Department of Epidemiology, UAB School of Public Health, Birmingham, Alabama, United States of America
| | - Curtis Pettaway
- Department of Urology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Sarah Nyante
- Department of Epidemiology, Gillings School of Global Public Health, and Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Elisa V. Bandera
- The Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America
| | - Angela F. Britton
- Laboratory of Neurogenetics, National Institute of Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan B. Zonderman
- Laboratory of Personality and Cognition, National Institute on Aging, National Institutes of Health, NIH Biomedical Center, Baltimore, Maryland, United States of America
| | - Laura J. Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Yii-Der Ida Chen
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Jingzhong Ding
- Department of Internal Medicine/Geriatrics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Kurt Lohman
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Stephen B. Kritchevsky
- Department of Internal Medicine/Geriatrics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Wei Zhao
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Patricia A. Peyser
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Edmond Kabagambe
- Department of Epidemiology, UAB, Birmingham, Alabama, United States of America
| | - Ulrich Broeckel
- Department of Pediatrics, Medicine and Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Marian L. Neuhouser
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Evadnie Rampersaud
- Miami Institute for Human Genomics, Miami, Florida, United States of America
- John T. McDonald Department of Human Genetics, University of Miami, Miami, Florida, United States of America
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services and Group Health Research Institute, Group Health Cooperative, Seattle, Washington, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lewis H. Kuller
- Department of Epidemiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Heather M. Ochs-Balcom
- Department of Social and Preventive Medicine, University at Buffalo, Buffalo, New York, United States of America
| | - Karen C. Johnson
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Lara Sucheston
- Department of Biostatistics, University of Buffalo School of Public Health and Health Professions, New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York, United States of America
| | - Jose M. Ordovas
- Tufts University, Boston, Massachusetts, United States of America
| | - Julie R. Palmer
- Slone Epidemiology Center, Boston University, Boston, Massachusetts, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Barbara V. Howard
- MedStar Health Research Institute and Georgetown University, Hyattsville, Maryland, United States of America
| | - Diane M. Becker
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Lawrence F. Bielak
- Department of Epidemiolgy, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Matthew A. Allison
- University of California at San Diego Department of Preventive Medicine, La Jolla, California, United States of America
| | - Struan F. A. Grant
- Division of Human Genetics, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, United States of America
| | - Gregory L. Burke
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Sanjay R. Patel
- Division of Sleep Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Pamela J. Schreiner
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ingrid B. Borecki
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michele K. Evans
- Health Disparities Research Section, Clinical Research Branch, National Institute on Aging, National Institutes of Health, NIH Biomedical Center, Baltimore, Maryland, United States of America
| | - Herman Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Michele M. Sale
- Center for Public Genomics, Department of Biochemistry and Molecular Genetics and Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Virginia Howard
- Department of Epidemiology, UAB School of Public Health, Birmingham, Alabama, United States of America
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Mary Cushman
- Department of Medicine, University of Vermont, Colchester, Vermont, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, NIA, Bethesda, Maryland, United States of America
| | - Alexander P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- NHLBI's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Caroline S. Fox
- NHLBI's Framingham Heart Study, Framingham, Massachusetts, United States of America
- NHLBI's Center for Population Studies, Framingham, Massachusetts, United States of America
- Division of Endocrinology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
16
|
Abstract
Genome-wide association studies (GWASs) have been heralded as a major advance in biomedical discovery, having identified ~2,000 robust associations with complex diseases since 2005. Despite this success, they have met considerable scepticism regarding their clinical applicability; this scepticism arises from such aspects as the modest effect sizes of associated variants and their unclear functional consequences. There are, however, promising examples of GWAS findings that will or that may soon be translated into clinical care. These examples include variants identified through GWASs that provide strongly predictive or prognostic information or that have important pharmacological implications; these examples may illustrate promising approaches to wider clinical application.
Collapse
|
17
|
Imputation-based meta-analysis of severe malaria in three African populations. PLoS Genet 2013; 9:e1003509. [PMID: 23717212 PMCID: PMC3662650 DOI: 10.1371/journal.pgen.1003509] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 03/28/2013] [Indexed: 01/15/2023] Open
Abstract
Combining data from genome-wide association studies (GWAS) conducted at different locations, using genotype imputation and fixed-effects meta-analysis, has been a powerful approach for dissecting complex disease genetics in populations of European ancestry. Here we investigate the feasibility of applying the same approach in Africa, where genetic diversity, both within and between populations, is far more extensive. We analyse genome-wide data from approximately 5,000 individuals with severe malaria and 7,000 population controls from three different locations in Africa. Our results show that the standard approach is well powered to detect known malaria susceptibility loci when sample sizes are large, and that modern methods for association analysis can control the potential confounding effects of population structure. We show that pattern of association around the haemoglobin S allele differs substantially across populations due to differences in haplotype structure. Motivated by these observations we consider new approaches to association analysis that might prove valuable for multicentre GWAS in Africa: we relax the assumptions of SNP-based fixed effect analysis; we apply Bayesian approaches to allow for heterogeneity in the effect of an allele on risk across studies; and we introduce a region-based test to allow for heterogeneity in the location of causal alleles.
Collapse
|
18
|
Magné J, Aminoff A, Perman Sundelin J, Mannila MN, Gustafsson P, Hultenby K, Wernerson A, Bauer G, Listenberger L, Neville MJ, Karpe F, Borén J, Ehrenborg E. The minor allele of the missense polymorphism Ser251Pro in perilipin 2 (PLIN2) disrupts an α-helix, affects lipolysis, and is associated with reduced plasma triglyceride concentration in humans. FASEB J 2013; 27:3090-9. [PMID: 23603836 DOI: 10.1096/fj.13-228759] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Perilipin 2 (PLIN2) is the most abundant lipid droplet (LD)-associated protein in nonadipose tissue, and its expression correlates with intracellular lipid accumulation. Here we identified a missense polymorphism, Ser251Pro, that has major effect on protein structure and function, along with an influence on human plasma triglyceride concentration. The evolutionarily conserved Ser251Pro polymorphism was identified with the ClustalW program. Structure modeling using 3D-JigSaw and the Chimera package revealed that the Pro251 allele disrupts a predicted α-helix in PLIN2. Analyses of macrophages from individuals carrying Ser251Pro variants and human embryonic kidney 293 (HEK293) cells stably transfected with either of the alleles demonstrated that the Pro251 variant causes increased lipid accumulation and decreased lipolysis. Analysis of LD size distribution in stably transfected cells showed that the minor Pro251 allele resulted in an increased number of small LDs per cell and increased perilipin 3 protein expression levels as compared with cells carrying the major Ser251 allele. Genotyping of 2113 individuals indicated that the Pro251 variant is associated with decreased plasma triglyceride and very low-density lipoprotein concentrations. Altogether, these data provide the first evidence of a polymorphism in PLIN2 that affects PLIN2 function and may influence the development of metabolic and cardiovascular diseases.
Collapse
Affiliation(s)
- Joëlle Magné
- Atherosclerosis Research Unit, Department of Medicine, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Wu Y, Waite LL, Jackson AU, Sheu WHH, Buyske S, Absher D, Arnett DK, Boerwinkle E, Bonnycastle LL, Carty CL, Cheng I, Cochran B, Croteau-Chonka DC, Dumitrescu L, Eaton CB, Franceschini N, Guo X, Henderson BE, Hindorff LA, Kim E, Kinnunen L, Komulainen P, Lee WJ, Le Marchand L, Lin Y, Lindström J, Lingaas-Holmen O, Mitchell SL, Narisu N, Robinson JG, Schumacher F, Stančáková A, Sundvall J, Sung YJ, Swift AJ, Wang WC, Wilkens L, Wilsgaard T, Young AM, Adair LS, Ballantyne CM, Bůžková P, Chakravarti A, Collins FS, Duggan D, Feranil AB, Ho LT, Hung YJ, Hunt SC, Hveem K, Juang JMJ, Kesäniemi AY, Kuusisto J, Laakso M, Lakka TA, Lee IT, Leppert MF, Matise TC, Moilanen L, Njølstad I, Peters U, Quertermous T, Rauramaa R, Rotter JI, Saramies J, Tuomilehto J, Uusitupa M, Wang TD, Boehnke M, Haiman CA, Chen YDI, Kooperberg C, Assimes TL, Crawford DC, Hsiung CA, North KE, Mohlke KL. Trans-ethnic fine-mapping of lipid loci identifies population-specific signals and allelic heterogeneity that increases the trait variance explained. PLoS Genet 2013; 9:e1003379. [PMID: 23555291 PMCID: PMC3605054 DOI: 10.1371/journal.pgen.1003379] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 01/19/2013] [Indexed: 12/03/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified ∼100 loci associated with blood lipid levels, but much of the trait heritability remains unexplained, and at most loci the identities of the trait-influencing variants remain unknown. We conducted a trans-ethnic fine-mapping study at 18, 22, and 18 GWAS loci on the Metabochip for their association with triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C), respectively, in individuals of African American (n = 6,832), East Asian (n = 9,449), and European (n = 10,829) ancestry. We aimed to identify the variants with strongest association at each locus, identify additional and population-specific signals, refine association signals, and assess the relative significance of previously described functional variants. Among the 58 loci, 33 exhibited evidence of association at P<1×10−4 in at least one ancestry group. Sequential conditional analyses revealed that ten, nine, and four loci in African Americans, Europeans, and East Asians, respectively, exhibited two or more signals. At these loci, accounting for all signals led to a 1.3- to 1.8-fold increase in the explained phenotypic variance compared to the strongest signals. Distinct signals across ancestry groups were identified at PCSK9 and APOA5. Trans-ethnic analyses narrowed the signals to smaller sets of variants at GCKR, PPP1R3B, ABO, LCAT, and ABCA1. Of 27 variants reported previously to have functional effects, 74% exhibited the strongest association at the respective signal. In conclusion, trans-ethnic high-density genotyping and analysis confirm the presence of allelic heterogeneity, allow the identification of population-specific variants, and limit the number of candidate SNPs for functional studies. Lipid traits are heritable, but many of the DNA variants that influence lipid levels remain unknown. In a genomic region, more than one variant may affect gene expression or function, and the frequencies of these variants can differ across populations. Genotyping densely spaced variants in individuals with different ancestries may increase the chance of identifying variants that affect gene expression or function. We analyzed high-density genotyped variants for association with TG, HDL-C, and LDL-C in African Americans, East Asians, and Europeans. At several genomic regions, we provide evidence that two or more variants can influence lipid traits; across loci, these additional signals increase the proportion of trait variation that can be explained by genes. At some association signals shared across populations, combining data from individuals of different ancestries narrowed the set of likely functional variants. At PCSK9 and APOA5, the data suggest that different variants influence trait levels in different populations. Variants previously reported to alter gene expression or function frequently exhibited the strongest association at those signals. The multiple signals and population-specific characteristics of the loci described here may be shared by genetic loci for other complex traits.
Collapse
Affiliation(s)
- Ying Wu
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lindsay L. Waite
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Anne U. Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Wayne H-H. Sheu
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- College of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Steven Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Donna K. Arnett
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Eric Boerwinkle
- The Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lori L. Bonnycastle
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cara L. Carty
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Iona Cheng
- University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Barbara Cochran
- The Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Damien C. Croteau-Chonka
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Logan Dumitrescu
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Charles B. Eaton
- Departments of Family Medicine and Epidemiology, Alpert Medical School, Brown University, Providence, Rhode Island, United States of America
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Xiuqing Guo
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Lucia A. Hindorff
- Office of Population Genomics, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eric Kim
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Leena Kinnunen
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | | | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Loic Le Marchand
- University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Yi Lin
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jaana Lindström
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Oddgeir Lingaas-Holmen
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway
| | - Sabrina L. Mitchell
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Narisu Narisu
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Fred Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Alena Stančáková
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Jouko Sundvall
- National Institute for Health and Welfare, Disease Risk Unit, Helsinki, Finland
| | - Yun-Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Amy J. Swift
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Wen-Chang Wang
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Lynne Wilkens
- University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Tom Wilsgaard
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Alicia M. Young
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Linda S. Adair
- Department of Nutrition, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | | | - Petra Bůžková
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Francis S. Collins
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Alan B. Feranil
- Office of Population Studies Foundation, University of San Carlos, Cebu, Philippines
| | - Low-Tone Ho
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Internal Medicine and Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yi-Jen Hung
- Division of Endocrinology and Metabolism, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Steven C. Hunt
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway
| | - Jyh-Ming J. Juang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Antero Y. Kesäniemi
- Institute of Clinical Medicine, Department of Medicine, University of Oulu and Clinical Research Center, Oulu University Hospital, Oulu, Finland
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Timo A. Lakka
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - I-Te Lee
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Mark F. Leppert
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Tara C. Matise
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Leena Moilanen
- Department of Medicine, Kuopio University Hospital, Kuopio, Finland
- Pirkanmaa Hospital District, Tampere, Finland
| | - Inger Njølstad
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Ulrike Peters
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Thomas Quertermous
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Rainer Rauramaa
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | | | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- South Ostrobothnia Central Hospital, Seinäjoki, Finland
- Red RECAVA Grupo RD06/0014/0015, Hospital Universitario La Paz, Madrid, Spain
- Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
| | - Matti Uusitupa
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Research Unit, Kuopio University Hospital, Kuopio, Finland
| | - Tzung-Dau Wang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Yii-Der I. Chen
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Charles Kooperberg
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Themistocles L. Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Dana C. Crawford
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Chao A. Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
20
|
Baxter AG, Jordan MA. From markers to molecular mechanisms: type 1 diabetes in the post-GWAS era. Rev Diabet Stud 2012; 9:201-23. [PMID: 23804261 DOI: 10.1900/rds.2012.9.201] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
By the year 2000, a draft of the human genome sequence was completed. Millions of single-nucleotide polymorphisms (SNPs) had been deposited into public databases, and high throughput technologies were under development for SNP genotyping. At that time, it was predicted that large case control association studies would provide far better resolution and power than genome-wide linkage studies. Type 1 diabetes was one of the first phenotypes to be examined by genome-wide association studies (GWAS), and to date over 50 genomic regions have been associated with the disease. In general, the great majority of these loci individually contribute a relatively small degree of risk, and most loci lie outside of coding sequences. The identification of molecular mechanisms from these genomic data therefore remains a significant challenge. Here, we summarize genetic candidate, linkage, and association studies of type 1 diabetes and discuss a potential strategy to identify mechanisms of disease from genomic data.
Collapse
Affiliation(s)
- Alan G Baxter
- Comparative Genomics Centre, Molecular Sciences Building 21, James Cook University, Townsville QLD 4811, Australia.
| | | |
Collapse
|
21
|
Gao C, Devarajan K, Zhou Y, Slater CM, Daly MB, Chen X. Identifying breast cancer risk loci by global differential allele-specific expression (DASE) analysis in mammary epithelial transcriptome. BMC Genomics 2012; 13:570. [PMID: 23107584 PMCID: PMC3532379 DOI: 10.1186/1471-2164-13-570] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/24/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The significant mortality associated with breast cancer (BCa) suggests a need to improve current research strategies to identify new genes that predispose women to breast cancer. Differential allele-specific expression (DASE) has been shown to contribute to phenotypic variables in humans and recently to the pathogenesis of cancer. We previously reported that nonsense-mediated mRNA decay (NMD) could lead to DASE of BRCA1/2, which is associated with elevated susceptibility to breast cancer. In addition to truncation mutations, multiple genetic and epigenetic factors can contribute to DASE, and we propose that DASE is a functional index for cis-acting regulatory variants and pathogenic mutations, and that global analysis of DASE in breast cancer precursor tissues can be used to identify novel causative alleles for breast cancer susceptibility. RESULTS To test our hypothesis, we employed the Illumina(®) Omni1-Quad BeadChip in paired genomic DNA (gDNA) and double-stranded cDNA (ds-cDNA) samples prepared from eight BCa patient-derived normal mammary epithelial lines (HMEC). We filtered original array data according to heterozygous genotype calls and calculated DASE values using the Log ratio of cDNA allele intensity, which was normalized to the corresponding gDNA. We developed two statistical methods, SNP- and gene-based approaches, which allowed us to identify a list of 60 candidate DASE loci (DASE ≥ 2.00, P ≤ 0.01, FDR ≤ 0.05) by both methods. Ingenuity Pathway Analysis of DASE loci revealed one major breast cancer-relevant interaction network, which includes two known cancer causative genes, ZNF331 (DASE = 2.31, P = 0.0018, FDR = 0.040) and USP6 (DASE = 4.80, P = 0.0013, FDR = 0.013), and a breast cancer causative gene, DMBT1 (DASE=2.03, P = 0.0017, FDR = 0.014). Sequence analysis of a 5' RACE product of DMBT1 demonstrated that rs2981745, a putative breast cancer risk locus, appears to be one of the causal variants leading to DASE in DMBT1. CONCLUSIONS Our study demonstrated for the first time that global DASE analysis is a powerful new approach to identify breast cancer risk allele(s).
Collapse
Affiliation(s)
- Chuan Gao
- Cancer Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | | | | | | | | | | |
Collapse
|
22
|
Chang D, Keinan A. Predicting signatures of "synthetic associations" and "natural associations" from empirical patterns of human genetic variation. PLoS Comput Biol 2012; 8:e1002600. [PMID: 22792059 PMCID: PMC3390358 DOI: 10.1371/journal.pcbi.1002600] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 05/23/2012] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association studies (GWAS) have in recent years discovered thousands of associated markers for hundreds of phenotypes. However, associated loci often only explain a relatively small fraction of heritability and the link between association and causality has yet to be uncovered for most loci. Rare causal variants have been suggested as one scenario that may partially explain these shortcomings. Specifically, Dickson et al. recently reported simulations of rare causal variants that lead to association signals of common, tag single nucleotide polymorphisms, dubbed "synthetic associations". However, an open question is what practical implications synthetic associations have for GWAS. Here, we explore the signatures exhibited by such "synthetic associations" and their implications based on patterns of genetic variation observed in human populations, thus accounting for human evolutionary history -a force disregarded in previous simulation studies. This is made possible by human population genetic data from HapMap 3 consisting of both resequencing and array-based genotyping data for the same set of individuals from multiple populations. We report that synthetic associations tend to be further away from the underlying risk alleles compared to "natural associations" (i.e. associations due to underlying common causal variants), but to a much lesser extent than previously predicted, with both the age and the effect size of the risk allele playing a part in this phenomenon. We find that while a synthetic association has a lower probability of capturing causal variants within its linkage disequilibrium block, sequencing around the associated variant need not extend substantially to have a high probability of capturing at least one causal variant. We also show that the minor allele frequency of synthetic associations is lower than of natural associations for most, but not all, loci that we explored. Finally, we find the variance in associated allele frequency to be a potential indicator of synthetic associations.
Collapse
Affiliation(s)
- Diana Chang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, United States of America
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| |
Collapse
|
23
|
Abstract
PURPOSE OF REVIEW To discuss the basis of 'missing heritability', which has emerged as an enigma in the post-genome-wide association studies (GWAS) era. RECENT FINDINGS Alleles identified through GWAS account for a relatively small fraction of heritability of the complex phenotypes. Accordingly, a significant part of heritability of the complex traits remains unaccounted for ('missing heritability'). Recent findings offer several explanations, including overestimation of heritability of the complex traits and underestimation of the effects of alleles identified through GWAS. In addition, yet-to-be identified common as well as rare alleles might in part explain the 'missing heritability'. Moreover, gene-gene (epistasis) and gene-environmental interactions might explain another fraction of heritability of complex traits. Moreover, transgenerational epigenetic changes, regulated in part by microRNAs, might also contribute to the 'missing heritability'. SUMMARY The new findings suggest a multifarious nature of the 'missing heritability'. The findings de-emphasize the focus on delineating the basis of 'missing heritability' and shift the focus to elucidation of the molecular mechanisms by which genomic and genetic factors govern the pathogenesis of the complex phenotypes.
Collapse
|
24
|
Sampson JN, Jacobs K, Wang Z, Yeager M, Chanock S, Chatterjee N. A two-platform design for next generation genome-wide association studies. Genet Epidemiol 2012; 36:400-8. [PMID: 22508365 DOI: 10.1002/gepi.21634] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/16/2012] [Accepted: 03/01/2012] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies (GWAS) have been successful in their search for common genetic variants associated with complex traits and diseases. With new advances in array technologies together with available genetic reference sets, the next generation of GWAS will extend the search for associations with uncommon SNPs (1% ≤ MAF ≤ 10%). Two possible approaches are genotyping all participants, a prohibitively expensive option for large GWAS, or using a combination of genotyping and imputation. Here, we consider a two platform method that genotypes all participants on a standard genotyping array, designed to identify common variants, and then supplements that data by genotyping only a small proportion of the participants on a platform that has higher coverage for uncommon SNPs. This subset of the study population is then included as part of the imputation reference set. To demonstrate the use of this two-platform design, we evaluate its potential efficiency using a newly available dataset containing 756 individuals genotyped on both the Illumina Human OmniExpress and Omni2.5 Quad. Although genotyping all individuals on the denser array would be ideal, we find that genotyping only 100 individuals on this array, in combination with imputation, leads to only a modest loss of power for detecting associations. However, the loss of power due to imputation can be more substantial if the relative risks for rare variants are significantly larger than those previously observed for common variants.
Collapse
Affiliation(s)
- Joshua N Sampson
- Biostatistics Branch, DCEG, National Cancer Institute, Rockville, Maryland 20852, USA.
| | | | | | | | | | | |
Collapse
|
25
|
Abstract
The individual human genome and epigenome are being defined at unprecedented resolution by current advances in sequencing technologies with important implications for human disease. This review uses examples relevant to clinical practice to illustrate the functional consequences of genetic and epigenetic variation. The insights gained from genome-wide association studies are described together with current efforts to understand the role of rare variants in common disease, set in the context of recent successes in Mendelian traits through the application of whole exome sequencing. The application of functional genomics to interrogate the genome and epigenome, build up an integrated picture of the regulatory genomic landscape and inform disease association studies is discussed, together with the role of expression quantitative trait mapping and analysis of allele-specific gene expression.
Collapse
Affiliation(s)
- J C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| |
Collapse
|
26
|
Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat Genet 2012; 44:483-9. [PMID: 22446960 DOI: 10.1038/ng.2232] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 03/01/2012] [Indexed: 12/15/2022]
Abstract
The genetic architectures of common, complex diseases are largely uncharacterized. We modeled the genetic architecture underlying genome-wide association study (GWAS) data for rheumatoid arthritis and developed a new method using polygenic risk-score analyses to infer the total liability-scale variance explained by associated GWAS SNPs. Using this method, we estimated that, together, thousands of SNPs from rheumatoid arthritis GWAS explain an additional 20% of disease risk (excluding known associated loci). We further tested this method on datasets for three additional diseases and obtained comparable estimates for celiac disease (43% excluding the major histocompatibility complex), myocardial infarction and coronary artery disease (48%) and type 2 diabetes (49%). Our results are consistent with simulated genetic models in which hundreds of associated loci harbor common causal variants and a smaller number of loci harbor multiple rare causal variants. These analyses suggest that GWAS will continue to be highly productive for the discovery of additional susceptibility loci for common diseases.
Collapse
|
27
|
Trynka G, Hunt KA, Bockett NA, Romanos J, Mistry V, Szperl A, Bakker SF, Bardella MT, Bhaw-Rosun L, Castillejo G, de la Concha EG, de Almeida RC, Dias KRM, van Diemen CC, Dubois PCA, Duerr RH, Edkins S, Franke L, Fransen K, Gutierrez J, Heap GAR, Hrdlickova B, Hunt S, Plaza Izurieta L, Izzo V, Joosten LAB, Langford C, Mazzilli MC, Mein CA, Midah V, Mitrovic M, Mora B, Morelli M, Nutland S, Núñez C, Onengut-Gumuscu S, Pearce K, Platteel M, Polanco I, Potter S, Ribes-Koninckx C, Ricaño-Ponce I, Rich SS, Rybak A, Santiago JL, Senapati S, Sood A, Szajewska H, Troncone R, Varadé J, Wallace C, Wolters VM, Zhernakova A, Thelma BK, Cukrowska B, Urcelay E, Bilbao JR, Mearin ML, Barisani D, Barrett JC, Plagnol V, Deloukas P, Wijmenga C, van Heel DA. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet 2011; 43:1193-201. [PMID: 22057235 PMCID: PMC3242065 DOI: 10.1038/ng.998] [Citation(s) in RCA: 574] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 10/05/2011] [Indexed: 12/13/2022]
Abstract
Using variants from the 1000 Genomes Project pilot European CEU dataset and data from additional resequencing studies, we densely genotyped 183 non-HLA risk loci previously associated with immune-mediated diseases in 12,041 individuals with celiac disease (cases) and 12,228 controls. We identified 13 new celiac disease risk loci reaching genome-wide significance, bringing the number of known loci (including the HLA locus) to 40. We found multiple independent association signals at over one-third of these loci, a finding that is attributable to a combination of common, low-frequency and rare genetic variants. Compared to previously available data such as those from HapMap3, our dense genotyping in a large sample collection provided a higher resolution of the pattern of linkage disequilibrium and suggested localization of many signals to finer scale regions. In particular, 29 of the 54 fine-mapped signals seemed to be localized to single genes and, in some instances, to gene regulatory elements. Altogether, we define the complex genetic architecture of the risk regions of and refine the risk signals for celiac disease, providing the next step toward uncovering the causal mechanisms of the disease.
Collapse
Affiliation(s)
- Gosia Trynka
- Genetics Department, University Medical Center and University of Groningen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Dudbridge F, Fletcher O, Walker K, Johnson N, Orr N, Dos Santos Silva I, Peto J. Estimating causal effects of genetic risk variants for breast cancer using marker data from bilateral and familial cases. Cancer Epidemiol Biomarkers Prev 2011; 21:262-72. [PMID: 22028405 DOI: 10.1158/1055-9965.epi-11-0719] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Cases with a family history are enriched for genetic risk variants, and the power of association studies can be improved by selecting cases with a family history of disease. However, in recent genome-wide association scans utilizing familial sampling, the excess relative risk for familial cases is less than predicted when compared with unselected cases. This can be explained by incomplete linkage disequilibrium between the tested marker and the underlying causal variant. METHODS We show that the allele frequency and effect size of the underlying causal variant can be estimated by combining marker data from studies that ascertain cases based on different family histories. This allows us to learn about the genetic architecture of a complex trait, without having identified any causal variants. We consider several validated common marker alleles for breast cancer, using our own study of high risk, predominantly bilateral cases, cases preferentially selected to have at least two affected first- or second-degree relatives, and published estimates of relative risk from standard case-control studies. RESULTS To obtain realistic estimates and to accommodate some prior beliefs, we use Bayesian estimation to infer that the causal variants are probably common, with minor allele frequency >5%, and have small effects, with relative risk around 1.2. CONCLUSION These results strongly support the common disease common variant hypothesis for these specific loci associated with breast cancer. IMPACT Our results agree with recent assertions that synthetic associations of rare variants are unlikely to account for most associations seen in genome-wide studies.
Collapse
Affiliation(s)
- Frank Dudbridge
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom.
| | | | | | | | | | | | | |
Collapse
|
29
|
Fine mapping of five loci associated with low-density lipoprotein cholesterol detects variants that double the explained heritability. PLoS Genet 2011; 7:e1002198. [PMID: 21829380 PMCID: PMC3145627 DOI: 10.1371/journal.pgen.1002198] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 06/07/2011] [Indexed: 12/23/2022] Open
Abstract
Complex trait genome-wide association studies (GWAS) provide an efficient strategy for evaluating large numbers of common variants in large numbers of individuals and for identifying trait-associated variants. Nevertheless, GWAS often leave much of the trait heritability unexplained. We hypothesized that some of this unexplained heritability might be due to common and rare variants that reside in GWAS identified loci but lack appropriate proxies in modern genotyping arrays. To assess this hypothesis, we re-examined 7 genes (APOE, APOC1, APOC2, SORT1, LDLR, APOB, and PCSK9) in 5 loci associated with low-density lipoprotein cholesterol (LDL-C) in multiple GWAS. For each gene, we first catalogued genetic variation by re-sequencing 256 Sardinian individuals with extreme LDL-C values. Next, we genotyped variants identified by us and by the 1000 Genomes Project (totaling 3,277 SNPs) in 5,524 volunteers. We found that in one locus (PCSK9) the GWAS signal could be explained by a previously described low-frequency variant and that in three loci (PCSK9, APOE, and LDLR) there were additional variants independently associated with LDL-C, including a novel and rare LDLR variant that seems specific to Sardinians. Overall, this more detailed assessment of SNP variation in these loci increased estimates of the heritability of LDL-C accounted for by these genes from 3.1% to 6.5%. All association signals and the heritability estimates were successfully confirmed in a sample of ∼10,000 Finnish and Norwegian individuals. Our results thus suggest that focusing on variants accessible via GWAS can lead to clear underestimates of the trait heritability explained by a set of loci. Further, our results suggest that, as prelude to large-scale sequencing efforts, targeted re-sequencing efforts paired with large-scale genotyping will increase estimates of complex trait heritability explained by known loci. Despite the striking success of genome-wide association studies in identifying genetic loci associated with common complex traits and diseases, much of the heritable risk for these traits and diseases remains unexplained. A higher resolution investigation of the genome through sequencing studies is expected to clarify the sources of this missing heritability. As a preview of what we might learn in these more detailed assessments of genetic variation, we used sequencing to identify potentially interesting variants in seven genes associated with low-density lipoprotein cholesterol (LDL-C) in 256 Sardinian individuals with extreme LDL-C levels, followed by large scale genotyping in 5,524 individuals, to examine newly discovered and previously described variants. We found that a combination of common and rare variants in these loci contributes to variation in LDL-C levels, and also that the initial estimate of the heritability explained by these loci doubled. Importantly, our results include a Sardinian-specific rare variant, highlighting the need for sequencing studies in isolated populations. Our results provide insights about what extensive whole-genome sequencing efforts are likely to reveal for the understanding of the genetic architecture of complex traits.
Collapse
|
30
|
Yang C, Zhou X, Wan X, Yang Q, Xue H, Yu W. Identifying disease-associated SNP clusters via contiguous outlier detection. ACTA ACUST UNITED AC 2011; 27:2578-85. [PMID: 21784794 DOI: 10.1093/bioinformatics/btr424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MOTIVATION Although genome-wide association studies (GWAS) have identified many disease-susceptibility single-nucleotide polymorphisms (SNPs), these findings can only explain a small portion of genetic contributions to complex diseases, which is known as the missing heritability. A possible explanation is that genetic variants with small effects have not been detected. The chance is < 8 that a causal SNP will be directly genotyped. The effects of its neighboring SNPs may be too weak to be detected due to the effect decay caused by imperfect linkage disequilibrium. Moreover, it is still challenging to detect a causal SNP with a small effect even if it has been directly genotyped. RESULTS In order to increase the statistical power when detecting disease-associated SNPs with relatively small effects, we propose a method using neighborhood information. Since the disease-associated SNPs account for only a small fraction of the entire SNP set, we formulate this problem as Contiguous Outlier DEtection (CODE), which is a discrete optimization problem. In our formulation, we cast the disease-associated SNPs as outliers and further impose a spatial continuity constraint for outlier detection. We show that this optimization can be solved exactly using graph cuts. We also employ the stability selection strategy to control the false positive results caused by imperfect parameter tuning. We demonstrate its advantage in simulations and real experiments. In particular, the newly identified SNP clusters are replicable in two independent datasets. AVAILABILITY The software is available at: http://bioinformatics.ust.hk/CODE.zip. CONTACT eeyu@ust.hk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Can Yang
- Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | | | | | | | | | | |
Collapse
|
31
|
Abstract
Asthma and allergy are common conditions with complex etiologies involving both genetic and environmental contributions. Recent genome-wide association studies (GWAS) and meta-analyses of GWAS have begun to shed light on both common and distinct pathways that contribute to asthma and allergic diseases. Associations with variation in genes encoding the epithelial cell-derived cytokines, interleukin-33 (IL-33) and thymic stromal lymphopoietin (TSLP), and the IL1RL1 gene encoding the IL-33 receptor, ST2, highlight the central roles for innate immune response pathways that promote the activation and differentiation of T-helper 2 cells in the pathogenesis of both asthma and allergic diseases. In contrast, variation at the 17q21 asthma locus, encoding the ORMDL3 and GSDML genes, is specifically associated with risk for childhood onset asthma. These and other genetic findings are providing a list of well-validated asthma and allergy susceptibility genes that are expanding our understanding of the common and unique biological pathways that are dysregulated in these related conditions. Ongoing studies will continue to broaden our understanding of asthma and allergy and unravel the mechanisms for the development of these complex traits.
Collapse
Affiliation(s)
- Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.
| | | |
Collapse
|