1
|
Cebatoriene D, Vilkeviciute A, Gedvilaite-Vaicechauskiene G, Duseikaite M, Bruzaite A, Kriauciuniene L, Zaliuniene D, Liutkeviciene R. The Impact of ARMS2 (rs10490924), VEGFA (rs3024997), TNFRSF1B (rs1061622), TNFRSF1A (rs4149576), and IL1B1 (rs1143623) Polymorphisms and Serum Levels on Age-Related Macular Degeneration Development and Therapeutic Responses. Int J Mol Sci 2024; 25:9750. [PMID: 39273697 PMCID: PMC11396313 DOI: 10.3390/ijms25179750] [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: 07/02/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
Age-related macular degeneration (AMD) is a major global health problem as it is the leading cause of irreversible loss of central vision in the aging population. Anti-vascular endothelial growth factor (anti-VEGF) therapies are effective but do not respond optimally in all patients. This study investigates the genetic factors associated with susceptibility to AMD and response to treatment, focusing on key polymorphisms in the ARMS2 (rs10490924), IL1B1 (rs1143623), TNFRSF1B (rs1061622), TNFRSF1A (rs4149576), VEGFA (rs3024997), ARMS2, IL1B1, TNFRSF1B, TNFRSF1A, and VEGFA serum levels in AMD development and treatment efficacy. This study examined the associations of specific genetic polymorphisms and serum protein levels with exudative and early AMD and the response to anti-VEGF treatment. The AA genotype of VEGFA (rs3024997) was significantly associated with a 20-fold reduction in the odds of exudative AMD compared to the GG + GA genotypes. Conversely, the TT genotype of ARMS2 (rs10490924) was linked to a 4.2-fold increase in the odds of exudative AMD compared to GG + GT genotypes. In females, each T allele of ARMS2 increased the odds by 2.3-fold, while in males, the TT genotype was associated with a 5-fold increase. Lower serum IL1B levels were observed in the exudative AMD group compared to the controls. Early AMD patients had higher serum TNFRSF1B levels than controls, particularly those with the GG genotype of TNFRSF1B rs1061622. Exudative AMD patients with the CC genotype of TNFRSF1A rs4149576 had lower serum TNFRSF1A levels compared to the controls. Visual acuity (VA) analysis showed that non-responders had better baseline VA than responders but experienced decreased VA after treatment, whereas responders showed improvement. Central retinal thickness (CRT) reduced significantly in responders after treatment and was lower in responders compared to non-responders after treatment. The T allele of TNFRSF1B rs1061622 was associated with a better response to anti-VEGF treatment under both dominant and additive genetic models. These findings highlight significant genetic and biochemical markers associated with AMD and treatment response. This study found that the VEGFA rs3024997 AA genotype reduces the odds of exudative AMD, while the ARMS2 rs10490924 TT genotype increases it. Lower serum IL1B levels and variations in TNFRSF1B and TNFRSF1A levels were linked to AMD. The TNFRSF1B rs1061622 T allele was associated with better anti-VEGF treatment response. These markers could potentially guide risk assessment and personalized treatment for AMD.
Collapse
Affiliation(s)
- Dzastina Cebatoriene
- Medical Academy, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, LT-44307 Kaunas, Lithuania
| | - Alvita Vilkeviciute
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania
| | | | - Monika Duseikaite
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania
| | - Akvile Bruzaite
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania
| | - Loresa Kriauciuniene
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania
| | - Dalia Zaliuniene
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania
| | - Rasa Liutkeviciene
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania
| |
Collapse
|
2
|
Cebatoriene D, Vilkeviciute A, Gedvilaite G, Bruzaite A, Kriauciuniene L, Zaliuniene D, Liutkeviciene R. CFH (rs1061170, rs1410996), KDR (rs2071559, rs1870377) and KDR and CFH Serum Levels in AMD Development and Treatment Efficacy. Biomedicines 2024; 12:948. [PMID: 38790910 PMCID: PMC11117782 DOI: 10.3390/biomedicines12050948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Age-related macular degeneration (AMD) is a major global health problem as it is the leading cause of irreversible loss of central vision in the aging population. Av-vascular endothelial growth factor (anti-VEGF) therapies have been shown to be effective, but they do not respond optimally to all patients. OBJECTIVE This study investigates the genetic factors associated with susceptibility to AMD and response to treatment, focusing on key polymorphisms in the CFH (rs1061170, rs1410996) and KDR (rs2071559, rs1870377) genes and the association of CFH and KDR serum levels in patients with AMD. RESULTS A cohort of 255 patients with early AMD, 252 patients with exudative AMD, and 349 healthy controls underwent genotyping analysis, which revealed significant associations between CFH polymorphisms and the risk of exudative AMD. The CFH rs1061170 CC genotype was associated with an increased risk of early AMD (p = 0.046). For exudative AMD, the CFH rs1061170 TC + CC genotype increased odds (p < 0.001), while the rs1410996 GA + AA genotype decreased odds (p < 0.001). Haplotypes of CFH SNPs were associated with decreased odds of AMD. In terms of response to treatment, none of the SNPs were associated with the response to anti-VEGF treatment. We also found that both early and exudative AMD patients had lower CFH serum levels compared to the control group (p = 0.038 and p = 0.006, respectively). Exudative AMD patients with the CT genotype of CFH rs1061170 had lower CFH serum levels compared to the control group (p = 0.035). Exudative AMD patients with the GG genotype of CFH rs1410996 also had lower CFH serum levels compared to the control group (p = 0.021). CONCLUSIONS CFH polymorphisms influence susceptibility to AMD but do not correlate with a response to anti-VEGF therapy. Further research is imperative to fully evaluate the developmental significance, treatment efficacy, and predictive role in influencing susceptibility to anti-VEGF therapy for KDR and CFH.
Collapse
Affiliation(s)
- Dzastina Cebatoriene
- Medical Academy, Lithuanian University of Health Sciences, A. Mickeviciaus St. 9, LT-44307 Kaunas, Lithuania
| | - Alvita Vilkeviciute
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
| | - Greta Gedvilaite
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
| | - Akvile Bruzaite
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
| | - Loresa Kriauciuniene
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania;
| | - Dalia Zaliuniene
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania;
| | - Rasa Liutkeviciene
- Neuroscience Institute, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania; (A.V.); (G.G.); (A.B.); (L.K.); (R.L.)
- Department of Ophthalmology, Medical Academy, Lithuanian University of Health Sciences, Eiveniu St. 2, LT-50161 Kaunas, Lithuania;
| |
Collapse
|
3
|
Dueker ND, Pericak‐Vance MA. Analysis of Genetic Linkage Data for Mendelian Traits. ACTA ACUST UNITED AC 2014; 83:1.4.1-31. [DOI: 10.1002/0471142905.hg0104s83] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Nicole D. Dueker
- University of Miami Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami Florida
| | - Margaret A. Pericak‐Vance
- University of Miami Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami Florida
| |
Collapse
|
4
|
Urbanowicz RJ, Andrew AS, Karagas MR, Moore JH. Role of genetic heterogeneity and epistasis in bladder cancer susceptibility and outcome: a learning classifier system approach. J Am Med Inform Assoc 2013; 20:603-12. [PMID: 23444013 PMCID: PMC3721175 DOI: 10.1136/amiajnl-2012-001574] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Detecting complex patterns of association between genetic or environmental risk factors and disease risk has become an important target for epidemiological research. In particular, strategies that provide multifactor interactions or heterogeneous patterns of association can offer new insights into association studies for which traditional analytic tools have had limited success. MATERIALS AND METHODS To concurrently examine these phenomena, previous work has successfully considered the application of learning classifier systems (LCSs), a flexible class of evolutionary algorithms that distributes learned associations over a population of rules. Subsequent work dealt with the inherent problems of knowledge discovery and interpretation within these algorithms, allowing for the characterization of heterogeneous patterns of association. Whereas these previous advancements were evaluated using complex simulation studies, this study applied these collective works to a 'real-world' genetic epidemiology study of bladder cancer susceptibility. RESULTS AND DISCUSSION We replicated the identification of previously characterized factors that modify bladder cancer risk--namely, single nucleotide polymorphisms from a DNA repair gene, and smoking. Furthermore, we identified potentially heterogeneous groups of subjects characterized by distinct patterns of association. Cox proportional hazard models comparing clinical outcome variables between the cases of the two largest groups yielded a significant, meaningful difference in survival time in years (survivorship). A marginally significant difference in recurrence time was also noted. These results support the hypothesis that an LCS approach can offer greater insight into complex patterns of association. CONCLUSIONS This methodology appears to be well suited to the dissection of disease heterogeneity, a key component in the advancement of personalized medicine.
Collapse
Affiliation(s)
- Ryan John Urbanowicz
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA.
| | | | | | | |
Collapse
|
5
|
Cheng Y, Huang L, Li X, Zhou P, Zeng W, Zhang C. Genetic and functional dissection of ARMS2 in age-related macular degeneration and polypoidal choroidal vasculopathy. PLoS One 2013; 8:e53665. [PMID: 23326481 PMCID: PMC3541181 DOI: 10.1371/journal.pone.0053665] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 12/03/2012] [Indexed: 12/18/2022] Open
Abstract
Age-related maculopathy susceptibility 2(ARMS2) was suggested to be associated with neovascular age-related macular degeneration (nAMD) and polypoidal choroidal vasculopathy (PCV) in multiple genetic studies in Caucasians and Japanese. To date, no biological properties have been attributed to the putative protein in nAMD and PCV. The complete genes of ARMS2 and HTRA1 including all exons and the promoter region were assessed using direct sequencing technology in 284 unrelated mainland northern Chinese individuals: 96 nAMD patients, 92 PCV patients and 96 controls. Significant associations with both nAMD and PCV were observed in 2 polymorphisms of ARMS2 and HTRA1 rs11200638, with different genotypic distributions between nAMD and PCV (p<0.001). After adjusting for rs11200638, ARMS2 rs10490924 remained significantly associated with nAMD and PCV (p<0.001). Then we overexpressed wild-type ARMS2 and ARMS2 A69S mutation (rs10490924) in RF/6A cells and RPE cells as in vitro study model. Cell proliferation, attachment, migration and tube formation were analyzed for the first time. Compare with wild-type ARMS2, A69S mutation resulted in a significant increase in proliferation and attachment but inhibited cell migration. Moreover, neither wild-type ARMS2 nor A69S mutation affected tube formation of RF/6A cells. There is a strong and consistent association of the ARMS2/HTRA1 locus with both nAMD and PCV, suggesting the two disorders share, at least partially, similar molecular mechanisms. Neither wild-type ARMS2 nor A69S mutation had direct association with neovascularisation in the pathogenesis of AMD.
Collapse
Affiliation(s)
- Yong Cheng
- Department of Ophthalmology, People’s Hospital, Peking University, Beijing, China
- Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, China
| | - LvZhen Huang
- Department of Ophthalmology, People’s Hospital, Peking University, Beijing, China
- Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, China
| | - Xiaoxin Li
- Department of Ophthalmology, People’s Hospital, Peking University, Beijing, China
- Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, China
| | - Peng Zhou
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Wotan Zeng
- Chinese National Human Genome Center, Beijing, China
| | - ChunFang Zhang
- Department of Clinical Epidemiology, People’s Hospital, Peking University, Beijing, China
| |
Collapse
|
6
|
Francis PJ. The influence of genetics on response to treatment with ranibizumab (Lucentis) for age-related macular degeneration: the Lucentis Genotype Study (an American Ophthalmological Society thesis). TRANSACTIONS OF THE AMERICAN OPHTHALMOLOGICAL SOCIETY 2011; 109:115-156. [PMID: 22253485 PMCID: PMC3259677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PURPOSE Age-related macular degeneration (AMD) has a complex etiology arising from genetic and environmental influences. This past decade have seen several genes associated with the disease. Variants in five genes have been confirmed to play a major role. The objective of this study was to evaluate whether genes influence treatment response to ranibizumab for neovascular AMD. The hypothesis was that an individual's genetic variation will determine treatment response. METHODS The study was a two-site prospective open-label observational study of patients newly diagnosed with exudative (neovascular) AMD receiving intravitreal ranibizumab therapy. Treatment-naïve patients were enrolled at presentation and received monthly "as needed" therapy. Clinical data was collected monthly and DNA extracted. Genotyping was performed using the Illumina (San Diego, California) 660-Quad single-nucleotide polymorphism (SNP) chip. Regression analyses were performed to identify SNPs associated with treatment-response end points. RESULTS Sixty-five patients were enrolled. No serious adverse events were recorded. The primary outcome measure was change in ETDRS visual acuity at 12 months. A SNP in the CFH gene was found to be associated with less improvement in visual acuity while receiving ranibizumab therapy. The C3 gene, among others, was associated with reduced thickening and improved retinal architecture. VEGFA, FLT1, and CFH were associated with requiring fewer ranibizumab injections over the 12-month study. CONCLUSIONS This study is one of the first prospective pharmacogenetic study of intravitreal ranibizumab. Although preliminary, the results identify a number of putative genetic variants, which will be further examined by replication and functional studies to elucidate the complete pharmacogenetic architecture of therapy for AMD.
Collapse
Affiliation(s)
- Peter James Francis
- Divisions of Retina and Ophthalmic Genetics, Casey Eye Institute, Oregon Health and Science University, Portland, OR, USA
| |
Collapse
|
7
|
Francis PJ, Klein ML. Update on the role of genetics in the onset of age-related macular degeneration. Clin Ophthalmol 2011; 5:1127-33. [PMID: 21887094 PMCID: PMC3162292 DOI: 10.2147/opth.s11627] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Indexed: 02/06/2023] Open
Abstract
Age-related macular degeneration (AMD), akin to other common age-related diseases, has a complex pathogenesis and arises from the interplay of genes, environmental factors, and personal characteristics. The past decade has seen very significant strides towards identification of those precise genetic variants associated with disease. That genes encoding proteins of the (alternative) complement pathway (CFH, C2, CFB, C3, CFI) are major players in etiology came as a surprise to many but has already lead to the development of therapies entering human clinical trials. Other genes replicated in many populations ARMS2, APOE, variants near TIMP3, and genes involved in lipid metabolism have also been implicated in disease pathogenesis. The genes discovered to date can be estimated to account for approximately 50% of the genetic variance of AMD and have been discovered by candidate gene approaches, pathway analysis, and latterly genome-wide association studies. Next generation sequencing modalities and meta-analysis techniques are being employed with the aim of identifying the remaining rarer but, perhaps, individually more significant sequence variations, linked to disease status. Complementary studies have also begun to utilize this genetic information to develop clinically useful algorithms to predict AMD risk and evaluate pharmacogenetics. In this article, contemporary commentary is provided on rapidly progressing efforts to elucidate the genetic pathogenesis of AMD as the field stands at the end of the first decade of the 21st century.
Collapse
Affiliation(s)
- Peter James Francis
- Macular Degeneration Center, Casey Eye Institute, Oregon Health and Science University, Portland, OR, USA
| | | |
Collapse
|
8
|
DeAngelis MM, Silveira AC, Carr EA, Kim IK. Genetics of age-related macular degeneration: current concepts, future directions. Semin Ophthalmol 2011; 26:77-93. [PMID: 21609220 PMCID: PMC4242505 DOI: 10.3109/08820538.2011.577129] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Age-related macular degeneration (AMD) is a progressive degenerative disease which leads to blindness, affecting the quality of life of millions of Americans. More than 1.75 million individuals in the United States are affected by the advanced form of AMD. The etiological pathway of AMD is not yet fully understood, but there is a clear genetic influence on disease risk. To date, the 1q32 (CFH) and 10q26 (PLEKHA1/ARMS2/HTRA1) loci are the most strongly associated with disease; however, the variation in these genomic regions alone is unable to predict disease development with high accuracy. Therefore, current genetic studies are aimed at identifying new genes associated with AMD and their modifiers, with the goal of discovering diagnostic or prognostic biomarkers. Moreover, these studies provide the foundation for further investigation into the pathophysiology of AMD by utilizing a systems-biology-based approach to elucidate underlying mechanistic pathways.
Collapse
Affiliation(s)
- Margaret M. DeAngelis
- Ocular Molecular Genetics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
- John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Alexandra C. Silveira
- Ocular Molecular Genetics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Elizabeth A. Carr
- John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
9
|
Spencer KL, Olson LM, Schnetz-Boutaud N, Gallins P, Wang G, Scott WK, Agarwal A, Jakobsdottir J, Conley Y, Weeks DE, Gorin MB, Pericak-Vance MA, Haines JL. Dissection of chromosome 16p12 linkage peak suggests a possible role for CACNG3 variants in age-related macular degeneration susceptibility. Invest Ophthalmol Vis Sci 2011; 52:1748-54. [PMID: 21169531 DOI: 10.1167/iovs.09-5112] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Age-related macular degeneration (AMD) is a complex disorder of the retina, characterized by drusen, geographic atrophy, and choroidal neovascularization. Cigarette smoking and the genetic variants CFH Y402H, ARMS2 A69S, CFB R32Q, and C3 R102G have been strongly and consistently associated with AMD. Multiple linkage studies have found evidence suggestive of another AMD locus on chromosome 16p12 but the gene responsible has yet to be identified. METHODS In the initial phase of the study, single-nucleotide polymorphisms (SNPs) across chromosome 16 were examined for linkage and/or association in 575 Caucasian individuals from 148 multiplex and 77 singleton families. Additional variants were tested in an independent dataset of unrelated cases and controls. According to these results, in combination with gene expression data and biological knowledge, five genes were selected for further study: CACNG3, HS3ST4, IL4R, Q7Z6F8, and ITGAM. RESULTS After genotyping additional tagging SNPs across each gene, the strongest evidence for linkage and association was found within CACNG3 (rs757200 nonparametric LOD* = 3.3, APL (association in the presence of linkage) P = 0.06, and rs2238498 MQLS (modified quasi-likelihood score) P = 0.006 in the families; rs2283550 P = 1.3 × 10(-6), and rs4787924 P = 0.002 in the case-control dataset). After adjusting for known AMD risk factors, rs2283550 remained strongly associated (P = 2.4 × 10(-4)). Furthermore, the association signal at rs4787924 was replicated in an independent dataset (P = 0.035) and in a joint analysis of all the data (P = 0.001). CONCLUSIONS These results suggest that CACNG3 is the best candidate for an AMD risk gene within the 16p12 linkage peak. More studies are needed to confirm this association and clarify the role of the gene in AMD pathogenesis.
Collapse
Affiliation(s)
- Kylee L Spencer
- Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Qin X, Hauser ER, Schmidt S. Ordered subset analysis for case-control studies. Genet Epidemiol 2010; 34:407-17. [PMID: 20568256 DOI: 10.1002/gepi.20489] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Genetic heterogeneity, which may manifest on a population level as different frequencies of a specific disease susceptibility allele in different subsets of patients, is a common problem for candidate gene and genome-wide association studies of complex human diseases. The ordered subset analysis (OSA) was originally developed as a method to reduce genetic heterogeneity in the context of family-based linkage studies. Here, we have extended a previously proposed method (OSACC) for applying the OSA methodology to case-control datasets. We have evaluated the type I error and power of different OSACC permutation tests with an extensive simulation study. Case-control datasets were generated under two different models by which continuous clinical or environmental covariates may influence the relationship between susceptibility genotypes and disease risk. Our results demonstrate that OSACC is more powerful under some disease models than the commonly used trend test and a previously proposed joint test of main genetic and gene-environment interaction effects. An additional unique benefit of OSACC is its ability to identify a more informative subset of cases that may be subjected to more detailed molecular analysis, such as DNA sequencing of selected genomic regions to detect functional variants in linkage disequilibrium with the associated polymorphism. The OSACC-identified covariate threshold may also improve the power of an additional dataset to replicate previously reported associations that may only be detectable in a fraction of the original and replication datasets. In summary, we have demonstrated that OSACC is a useful method for improving SNP association signals in genetically heterogeneous datasets.
Collapse
Affiliation(s)
- Xuejun Qin
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | | | |
Collapse
|
11
|
Bush WS, Haines J. Overview of linkage analysis in complex traits. CURRENT PROTOCOLS IN HUMAN GENETICS 2010; Chapter 1:Unit 1.9.1-18. [PMID: 20063263 DOI: 10.1002/0471142905.hg0109s64] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Linkage analysis is a well-established and powerful method for mapping disease genes. While linkage analysis has been most successful when applied to disorders with clear patterns of Mendelian inheritance, it can also be a useful technique for mapping susceptibility genes for common complex diseases. In this unit, we outline the key concepts of complex disease, and how linkage analysis for complex traits differs from simple Mendelian traits. Optimal genetic studies require careful study design, ascertainment strategy, and analysis methods. We describe how disease parameters such as prevalence, heritability estimates, and mode of inheritance should be considered before data is collected. Furthermore, we outline a general strategic approach for conducting linkage analysis of a complex disease, along with several design considerations that can optimize statistical power to detect disease loci and generally improve the quality of a study. Finally, we discuss the benefits and weaknesses of linkage analysis in contrast to genome-wide association studies.
Collapse
Affiliation(s)
- William S Bush
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | |
Collapse
|
12
|
Goto A, Akahori M, Okamoto H, Minami M, Terauchi N, Haruhata Y, Obazawa M, Noda T, Honda M, Mizota A, Tanaka M, Hayashi T, Tanito M, Ogata N, Iwata T. Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population. J Ocul Biol Dis Infor 2009; 2:164-175. [PMID: 20157352 PMCID: PMC2816809 DOI: 10.1007/s12177-009-9047-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2009] [Accepted: 11/06/2009] [Indexed: 11/29/2022] Open
Abstract
Age-related macular degeneration (AMD) is a common cause of blindness in the elderly. Caucasian patients are predominantly affected by the dry form of AMD, whereas Japanese patients have predominantly the wet form of AMD and/or polypoidal choroidal vasculopathy (PCV). Although genetic association in the 10q26 (ARMS2/HTRA1) region has been established in many ethnic groups for dry-type AMD, typical wet-type AMD, and PCV, the contribution of the 1q32 (CFH) region seem to differ among these groups. Here we show a single nucleotide polymorphism (SNP) in the ARMS2/HTRA1 locus is associated in the whole genome for Japanese typical wet-type AMD (rs10490924: \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$ p = 4.1 \times 10 ^{ - 4}$$\end{document}, OR = 4.16) and PCV (rs10490924: \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$ p = 3.7 \times 10 ^{ -8}$$\end{document}, OR = 2.72) followed by CFH (rs800292: \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$ p = 7.4 \times 10 ^{ -5}$$\end{document}, OR = 2.08; \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$ p = 2.6 \times {10^{ - 4}} $$\end{document}, OR = 2.00), which differs from previous studies in Caucasian populations. Moreover, a SNP (rs2241394) in complement component C3 gene showed significant association with PCV (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$ p = 2.5 \times {10^{ - 3}} $$\end{document}, OR = 3.47). We conclude that dry-type AMD, typical wet-type AMD, and PCV have both common and distinct genetic risks that become apparent when comparing Japanese versus Caucasian populations.
Collapse
|
13
|
Silveira AC, Morrison MA, Ji F, Xu H, Reinecke JB, Adams SM, Arneberg TM, Janssian M, Lee JE, Yuan Y, Schaumberg DA, Kotoula MG, Tsironi EE, Tsiloulis AN, Chatzoulis DZ, Miller JW, Kim IK, Hageman GS, Farrer LA, Haider NB, DeAngelis MM. Convergence of linkage, gene expression and association data demonstrates the influence of the RAR-related orphan receptor alpha (RORA) gene on neovascular AMD: a systems biology based approach. Vision Res 2009; 50:698-715. [PMID: 19786043 DOI: 10.1016/j.visres.2009.09.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 09/04/2009] [Accepted: 09/18/2009] [Indexed: 12/28/2022]
Abstract
To identify novel genes and pathways associated with AMD, we performed microarray gene expression and linkage analysis which implicated the candidate gene, retinoic acid receptor-related orphan receptor alpha (RORA, 15q). Subsequent genotyping of 159 RORA single nucleotide polymorphisms (SNPs) in a family-based cohort, followed by replication in an unrelated case-control cohort, demonstrated that SNPs and haplotypes located in intron 1 were significantly associated with neovascular AMD risk in both cohorts. This is the first report demonstrating a possible role for RORA, a receptor for cholesterol, in the pathophysiology of AMD. Moreover, we found a significant interaction between RORA and the ARMS2/HTRA1 locus suggesting a novel pathway underlying AMD pathophysiology.
Collapse
Affiliation(s)
- Alexandra C Silveira
- Ocular Molecular Genetics Institute and Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Kenealy SJ, Herrel LA, Bradford Y, Schnetz-Boutaud N, Oksenberg JR, Hauser SL, Barcellos LF, Schmidt S, Gregory SG, Pericak-Vance MA, Haines JL. Examination of seven candidate regions for multiple sclerosis: strong evidence of linkage to chromosome 1q44. Genes Immun 2009; 7:73-6. [PMID: 16341055 DOI: 10.1038/sj.gene.6364275] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Multiple sclerosis (MS) is a debilitating neuroimmunological and neurodegenerative disease with a strong genetic component. Numerous studies have failed to consistently identify genes that confer disease susceptibility except for association with HLA-DR. Seven non-HLA regions (1q, 2q, 9q, 13q, 16q, 18p and 19q) identified in a recent genomic screen were investigated by genotyping approximately 20 single-nucleotide polymorphisms (SNPs) at approximately 1 Mb intervals. Non-parametric multipoint analyses identified a peak LOD* score of 2.99 for the 1q44 region and substantially narrowed the linkage peak to approximately 7 Mb. Ordered subset analyses (OSA) identified significant LOD score increases for 2q35 and 18p11 when ranking families by HLA-DR status and identified a significant LOD score increase in region 2q35 when ranking families by linkage to chromosome 1q44. 1q44 is particularly interesting because of linkage evidence for this region in studies of both rheumatoid arthritis and systemic lupus erythematosus.
Collapse
Affiliation(s)
- S J Kenealy
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232-0700, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Tam POS, Ng TK, Liu DTL, Chan WM, Chiang SWY, Chen LJ, DeWan A, Hoh J, Lam DSC, Pang CP. HTRA1 variants in exudative age-related macular degeneration and interactions with smoking and CFH. Invest Ophthalmol Vis Sci 2008; 49:2357-65. [PMID: 18316707 PMCID: PMC3215269 DOI: 10.1167/iovs.07-1520] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
PURPOSE Mapping the genes for age-related macular degeneration (AMD) had not been successful until recent genome-wide association studies revealed Tyr402His in CFH and rs11200638 in HTRA1 as AMD-related genetic variants. This study was conducted to identify other critical factors in HTRA1 that are associated with exudative AMD. METHODS The promoter, splice regions, and coding exons of HTRA1 were sequenced in 163 patients with exudative AMD and 183 sex- and age-matched control subjects. Also documented were the CFH genotype and smoking status. RESULTS Four significant SNPs were found in the promoter and the first exon of HTRA1: rs11200638 (-625G>A), rs2672598 (-487T>C), rs1049331 (102C>T, Ala34Ala), and rs2293870 (108G>T, Gly36Gly) with respective P = 1.7 x 10(-14), 3.0 x 10(-10), 3.7 x 10(-12), and 3.7 x 10(-12). Among them, rs11200638 is the most significant associated SNP with a high odds ratio (OR) of 7.6 (95% CI: 3.94-14.51). One risk haplotype block across the promoter and exon 1, ACCTT, significantly predisposes to AMD (P = 6.68 x 10(-14)). In both models, significant independent additive effects were identified with smoking and rs800292 (184G>A, Val62Ile) of CFH. Smoking and rs11200638 (HTRA1) combined caused a 15.7-fold increased risk, whereas combined rs800292 and rs11200638 caused a 23.3-fold increased risk. An extremely high population attributable risk (PAR) of 78% was also found. CONCLUSIONS A high impact of the additive effect of CFH and HTRA1 in the development of exudative AMD was shown. The HTRA1-smoking additive effect found in this study further suggests the importance of this environmental risk factor in AMD.
Collapse
Affiliation(s)
- Pancy O. S. Tam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tsz Kin Ng
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - David T. L. Liu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Man Chan
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Sylvia W. Y. Chiang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Andrew DeWan
- Department of Epidemiology and Public Health, Yale University, New Haven, Connecticut
| | - Josephine Hoh
- Department of Epidemiology and Public Health, Yale University, New Haven, Connecticut
| | - Dennis S. C. Lam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
16
|
Expression of recombinant protein encoded by LOC387715 in Escherichia coli. Protein Expr Purif 2007; 54:275-82. [PMID: 17485225 DOI: 10.1016/j.pep.2007.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 03/03/2007] [Accepted: 03/06/2007] [Indexed: 10/23/2022]
Abstract
LOC387715 is a hypothetical gene located on human chromosome 10q26.13 that is associated with the development of age-related macular degeneration (AMD). The native open reading frame (ORF) of LOC387715 cDNA - LOC387715(ORF), contains a large number of Escherichia coli (E. coli) rare codons (RC) including 5.6% and 15.0% Group-I and IIa translational problem causative (TPC) RCs, respectively, which forms 3 and 4 simple E. coli rare codon clusters (RCC) where RCs are spaced by 1 and 2 respective non-TPC codons and one complex E. coli RCC where RCs and RCCs are spaced by <5 non-TPC codons. We modified the entire 35 E. coli RCs (6, 16 and 13 Group I, IIa and IIb RCs, respectively) present in LOC387715(ORF) with their optimal or sub-optimal synonymous degenerate codons, and the resulted LOC387715(ORF)m was free from Shine-Dalgarno-like sequence (SDLS) and ribosome binding site complementary sequence (RBSCS). SDS-PAGE and Western blotting analysis demonstrated that LOC387715(ORF)m was capable of highly expressing the recombinant protein rLOC387715 in E. coli. Mass spectrometry analysis indicated that the bacterial expressed rLOC387715 contained the correct and expected amino acid (aa) sequence without aa misincorporation, aa missing or frame-shift. The results suggest that high and authentic expression of LOC387715 recombinant protein in E. coli was achieved by the synonymous modification of its native ORF cDNA sequence for all the 3 groups of bacterial RCs and the simultaneous elimination of SDLS and RBSCS sequences.
Collapse
|
17
|
|
18
|
Chamberlain M, Baird P, Dirani M, Guymer R. Unraveling a complex genetic disease: age-related macular degeneration. Surv Ophthalmol 2006; 51:576-86. [PMID: 17134647 DOI: 10.1016/j.survophthal.2006.08.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In most of the Western world, age-related macular degeneration (AMD) remains the largest single cause of severe visual impairment, and its prevalence continues to increase. It is considered to be a complex disease, in which multiple genes and environment play a role in pathogenesis. Several environmental insults are implicated with smoking, serum cholesterol, hypertension, sunlight exposure, and many other factors being variously associated with disease pathogenesis. Until recently, there have been relatively few breakthroughs to further our understanding of the genetics of AMD, despite remarkable progress in molecular genetic techniques over the last 20 years, and the fact that many rare inherited macular diseases have had their causative genes mapped. Development of new tools such as high-density single-nucleotide polymorphism chips and microarrays have changed the face of genetic research, but have yet to directly translate into improved clinical outcomes in ophthalmology. However with the recent finding of the Tyr402His polymorphism in the complement factor H gene being implicated in AMD, we are about to witness a new wave of research in this disease. Not only does the identification of a biologically plausible gene identify a new pathway, but it also identifies new biological mechanisms for disease, avenues to pursue treatment, and a better understanding of how the environment interacts with the genetic background to create disease. This article aims to review the process of gene discovery in complex disease, why the search for genes remains difficult, how to translate laboratory findings to a clinical setting, and how these findings will impact on disease treatment and public health issues.
Collapse
Affiliation(s)
- Matt Chamberlain
- Centre for Eye Research Australia, University of Melbourne, 32 Gisborne Street, East Melbourne, Australia 3002
| | | | | | | |
Collapse
|
19
|
Haddad S, Chen CA, Santangelo SL, Seddon JM. The Genetics of Age-Related Macular Degeneration: A Review of Progress to Date. Surv Ophthalmol 2006; 51:316-63. [PMID: 16818082 DOI: 10.1016/j.survophthal.2006.05.001] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Age-related macular degeneration (AMD) is the leading cause of vision loss and blindness among older adults in the USA and throughout the developed world. Etiological research suggests that AMD is a complex disease, caused by the actions and interactions of multiple genes and environmental factors. Familial aggregation studies, twin studies, and segregation analyses have provided strong evidence for the heritability of AMD, and linkage and association studies have been conducted to localize the disease-causing genes. Whole genome linkage scans have implicated nearly every chromosome in the human genome, with the most replicated signals residing on 1q25-31 and 10q26. Association studies have identified a major risk variant within the complement factor H gene (CFH), and recent reports suggest that PLEKHA1/LOC387715 and the BF/C2 regions may be major risk loci for AMD as well. Several other genes have had at least one positive association finding and deserve further exploration. Among these, apolipoprotein E (APOE) may be a minor risk locus. Additional genes will likely be identified, and future studies should explore the potential interactions of these genes with other genes as well as environmental factors.
Collapse
Affiliation(s)
- Stephen Haddad
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, 02114, USA
| | | | | | | |
Collapse
|
20
|
Gaffney PM, Langefeld CD, Graham RR, Ortmann WA, Williams AH, Rodine PR, Moser KL, Behrens TW. Fine-mapping chromosome 20 in 230 systemic lupus erythematosus sib pair and multiplex families: evidence for genetic epistasis with chromosome 16q12. Am J Hum Genet 2006; 78:747-758. [PMID: 16642431 PMCID: PMC1474034 DOI: 10.1086/503686] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Accepted: 02/07/2006] [Indexed: 11/04/2022] Open
Abstract
The presence of systemic lupus erythematosus (SLE) susceptibility genes on chromosome 20 is suggested by the observation of genetic linkage in several independent SLE family collections. To further localize the genetic effects, we typed 59 microsatellites in the two best regions, as defined by genome screens. Genotypes were analyzed for statistical linkage and/or association with SLE, by use of a combination of nonparametric linkage methods, family-based tests of association (transmission/disequilibrium and pedigree disequilibrium tests), and haplotype-sharing statistics (haplotype runs test), in a set of 230 SLE pedigrees. Maximal evidence for linkage to SLE was to 20p12 (LOD = 2.84) and 20q13.1 (LOD = 1.64) in the white pedigrees. Subsetting families on the basis of evidence for linkage to 16q12 significantly improved the LOD scores at both chromosome 20 locations (20p12 LOD = 5.06 and 20q13 LOD = 3.65), consistent with epistasis. We then typed 162 single-nucleotide polymorphism markers across a 1.3-Mb candidate region on 20q13.1 and identified several SNPs that demonstrated significant evidence for association. These data provide additional support for linkage and association to 20p12 and 20q13.1 in SLE and further refine the intervals of interest. These data further suggest the possibility of epistatic relationships among loci within the 20q12, 20q13, and 16q12 regions in SLE families.
Collapse
Affiliation(s)
- Patrick M Gaffney
- Department of Medicine, University of Minnesota School of Medicine, Minneapolis.
| | - Carl D Langefeld
- Department of Biostatistics, Wake Forest University School of Medicine, Winston-Salem, NC
| | | | - Ward A Ortmann
- Department of Medicine, University of Minnesota School of Medicine, Minneapolis
| | - Adrienne H Williams
- Department of Biostatistics, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Peter R Rodine
- Department of Medicine, University of Minnesota School of Medicine, Minneapolis
| | - Kathy L Moser
- Department of Medicine, University of Minnesota School of Medicine, Minneapolis
| | - Timothy W Behrens
- Department of Medicine, University of Minnesota School of Medicine, Minneapolis
| |
Collapse
|
21
|
Magnusson KP, Duan S, Sigurdsson H, Petursson H, Yang Z, Zhao Y, Bernstein PS, Ge J, Jonasson F, Stefansson E, Helgadottir G, Zabriskie NA, Jonsson T, Björnsson A, Thorlacius T, Jonsson PV, Thorleifsson G, Kong A, Stefansson H, Zhang K, Stefansson K, Gulcher JR. CFH Y402H confers similar risk of soft drusen and both forms of advanced AMD. PLoS Med 2006; 3:e5. [PMID: 16300415 PMCID: PMC1288033 DOI: 10.1371/journal.pmed.0030005] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Accepted: 09/27/2005] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Age-related macular degeneration (AMD) is the most common cause of irreversible visual impairment in the developed world. The two forms of advanced AMD, geographic atrophy and neovascular AMD, represent different pathological processes in the macula that lead to loss of central vision. Soft drusen, characterized by deposits in the macula without visual loss, are considered to be a precursor of advanced AMD. Recently, it has been proposed that a common missense variant, Y402H, in the Complement Factor H (CFH) gene increases the risk for advanced AMD. However, its impact on soft drusen, GA, or neovascular AMD--or the relationship between them--is unclear. METHODS AND FINDINGS We genotyped 581 Icelandic patients with advanced AMD (278 neovascular AMD, 203 GA, and 100 with mixed neovascular AMD/GA), and 435 with early AMD (of whom 220 had soft drusen). A second cohort of 431 US patients from Utah, 322 with advanced AMD (244 neovascular AMD and 78 GA) and 109 early-AMD cases with soft drusen, were analyzed. We confirmed that the CFH Y402H variant shows significant association to advanced AMD, with odds ratio of 2.39 in Icelandic patients (p = 5.9 x 10(-12)) and odds ratio of 2.14 in US patients from Utah (p = 2.0 x 10(-9)) with advanced AMD. Furthermore, we show that the Y402H variant confers similar risk of soft drusen and both forms of advanced AMD (GA or neovascular AMD). CONCLUSION Soft drusen occur prior to progression to advanced AMD and represent a histological feature shared by neovascular AMD and GA. Our results suggest that CFH is a major risk factor of soft drusen, and additional genetic factors and/or environmental factors may be required for progression to advanced AMD.
Collapse
Affiliation(s)
- Kristinn P Magnusson
- 1DeCODE Genetics, Reykjavik, Iceland
- *To whom correspondence should be addressed. E-mail: (KPM), E-mail: (KZ), E-mail: (JRG)
| | - Shan Duan
- 2Department of Ophthalmology and Visual Science, Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
- 3 Program in Human Molecular Biology and Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- 4Zhongshan Ophthalmic Center, Sun Yat-Sen University, Gaung Zhou, China
| | - Haraldur Sigurdsson
- 5Department of Ophthalmology, National University Hospital, Reykjavik, Iceland
- 6Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Zhenglin Yang
- 2Department of Ophthalmology and Visual Science, Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
- 3 Program in Human Molecular Biology and Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- 7Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Yu Zhao
- 2Department of Ophthalmology and Visual Science, Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
- 3 Program in Human Molecular Biology and Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Paul S Bernstein
- 2Department of Ophthalmology and Visual Science, Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Jian Ge
- 4Zhongshan Ophthalmic Center, Sun Yat-Sen University, Gaung Zhou, China
| | - Fridbert Jonasson
- 5Department of Ophthalmology, National University Hospital, Reykjavik, Iceland
- 6Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Einar Stefansson
- 5Department of Ophthalmology, National University Hospital, Reykjavik, Iceland
- 6Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Gudleif Helgadottir
- 5Department of Ophthalmology, National University Hospital, Reykjavik, Iceland
| | - Norman A Zabriskie
- 2Department of Ophthalmology and Visual Science, Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
| | | | | | | | - Palmi V Jonsson
- 8Department of Geriatrics, National University Hospital, Reykjavik, Iceland
| | | | | | | | - Kang Zhang
- 2Department of Ophthalmology and Visual Science, Moran Eye Center, University of Utah, Salt Lake City, Utah, United States of America
- 3 Program in Human Molecular Biology and Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- *To whom correspondence should be addressed. E-mail: (KPM), E-mail: (KZ), E-mail: (JRG)
| | | | - Jeffrey R Gulcher
- 1DeCODE Genetics, Reykjavik, Iceland
- *To whom correspondence should be addressed. E-mail: (KPM), E-mail: (KZ), E-mail: (JRG)
| |
Collapse
|
22
|
Schmidt S, Schmidt MA, Qin X, Martin ER, Hauser ER. Linkage analysis with gene-environment interaction: model illustration and performance of ordered subset analysis. Genet Epidemiol 2006; 30:409-22. [PMID: 16671105 DOI: 10.1002/gepi.20152] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ordered subset analysis (OSA) method allows for the incorporation of covariates into the linkage analysis of a dichotomous disease phenotype in order to reduce genetic heterogeneity. Complex human diseases may involve gene-environment (G x E) interactions, which represent a special form of heterogeneity. Here, we present results of a simulation study to evaluate the performance of OSA when the disease-generating mechanism includes G x E interaction, in the absence of main effects of gene and environment. First, the complex simulation models are illustrated graphically. Second, we show that OSA is underpowered to detect small to moderate interaction effects, consistent with previous evaluations of other linkage analysis methods. When interaction effects are large enough to produce substantial marginal effects, standard linkage methods have sufficient power to detect significant baseline linkage evidence in the entire dataset. The power of OSA to improve upon a high baseline lod score is then strongly dependent on the underlying genetic model, especially the susceptibility allele frequency. If significant, OSA identifies family subsets that are more efficient for follow-up analysis than the entire dataset, in terms of the proportion of susceptible genotypes among generated marker genotypes. For example, when strong G x E interaction with RR(G x E) = 10 is operating in at least 70% of families in the dataset, OSA has at least 70% power to detect a subset of families with significantly greater linkage evidence, the majority of linked families are captured in the OSA subset, and the per-genotype efficiency in the subset is 20-30% greater than in the entire dataset.
Collapse
Affiliation(s)
- Silke Schmidt
- Center for Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA.
| | | | | | | | | |
Collapse
|
23
|
Rivera A, Fisher SA, Fritsche LG, Keilhauer CN, Lichtner P, Meitinger T, Weber BHF. Hypothetical LOC387715 is a second major susceptibility gene for age-related macular degeneration, contributing independently of complement factor H to disease risk. Hum Mol Genet 2005; 14:3227-36. [PMID: 16174643 DOI: 10.1093/hmg/ddi353] [Citation(s) in RCA: 517] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Age-related macular degeneration (AMD) is a multifactorial disease and a prevalent cause of visual impairment in developed countries. Risk factors include environmental components and genetic determinants. The complement factor H (CFH) has been the first major susceptibility gene for AMD identified within 1q32. Here, we focused on a second region of interest in 10q26 where a recent meta-analysis revealed strongest evidence for linkage to AMD at a genome-wide significance level. Within an interval of 22 Mb, we have analyzed 93 single nucleotide polymorphisms for allelic association with AMD in two independent case-control cohorts of German origin (AMD(combined) n=1166; controls(combined) n=945). Significant association was found across a 60 kb region of high linkage disequilibrium harboring two genes PLEKHA1 and hypothetical LOC387715. The strongest association (P=10(-34)) centered over a frequent coding polymorphism, Ala69Ser, at LOC387715, strongly implicating this gene in the pathogenesis of AMD. Besides abundant expression in placenta, we demonstrate weak expression of LOC387715 in the human retina. At present, however, there is no functional information on this gene, which appears to have evolved recently within the primate lineage. The joint contribution of the common risk allele at LOC387715, Ala69Ser, and at CFH, Tyr402His, was assessed in our case-control population, which suggests an additive model indicating an independent contribution of the two gene loci to disease risk. Our data show a disease odds ratio of 57.6 (95% CI: 37.2, 89.0) conferred by homozygosity for risk alleles at both CFH and LOC387715 when compared with the baseline non-risk genotype.
Collapse
Affiliation(s)
- Andrea Rivera
- Institute of Human Genetics, University of Regensburg, Germany
| | | | | | | | | | | | | |
Collapse
|
24
|
Schultz DW, Weleber RG, Lawrence G, Barral S, Majewski J, Acott TS, Klein ML. HEMICENTIN-1 (FIBULIN-6) and the 1q31 AMD locus in the context of complex disease: review and perspective. Ophthalmic Genet 2005; 26:101-5. [PMID: 16020313 DOI: 10.1080/13816810590968023] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Age-related macular degeneration (AMD) is the most common blinding disorder in the Western world. Similar to other common diseases in which age is a risk factor (e.g., type II diabetes or Alzheimer's disease), AMD is thought to have a complex etiology. Previously, a Gln5345Arg mutation in HEMICENTIN-1 was found to segregate with AMD in a large family. However, the population frequency of this allele is inconsistent with the large proportion of families shown by linkage studies to map near this gene at 1q31. This review summarizes current knowledge regarding the role of HEMICENTIN-1 in AMD, the results of association studies for the Gln5345Arg mutation, and the linkage evidence for an AMD locus on 1q31. The data can be reconciled through proposing both additional variants in HEMICENTIN-1 and a second genetic risk factor for AMD in the region.
Collapse
Affiliation(s)
- Dennis W Schultz
- Macular Degeneration Center, Casey Eye Institute, Oregon Health & Science University, 3375 SW Terwilliger Boulevard, Portland, OR 97239-4197, U.S.A.
| | | | | | | | | | | | | |
Collapse
|
25
|
Jakobsdottir J, Conley YP, Weeks DE, Mah TS, Ferrell RE, Gorin MB. Susceptibility genes for age-related maculopathy on chromosome 10q26. Am J Hum Genet 2005; 77:389-407. [PMID: 16080115 PMCID: PMC1226205 DOI: 10.1086/444437] [Citation(s) in RCA: 396] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Accepted: 06/29/2005] [Indexed: 11/03/2022] Open
Abstract
On the basis of genomewide linkage studies of families affected with age-related maculopathy (ARM), we previously identified a significant linkage peak on 10q26, which has been independently replicated by several groups. We performed a focused SNP genotyping study of our families and an additional control cohort. We identified a strong association signal overlying three genes, PLEKHA1, LOC387715, and PRSS11. All nonsynonymous SNPs in this critical region were genotyped, yielding a highly significant association (P < .00001) between PLEKHA1/LOC387715 and ARM. Although it is difficult to determine statistically which of these two genes is most important, SNPs in PLEKHA1 are more likely to account for the linkage signal in this region than are SNPs in LOC387715; thus, this gene and its alleles are implicated as an important risk factor for ARM. We also found weaker evidence supporting the possible involvement of the GRK5/RGS10 locus in ARM. These associations appear to be independent of the association of ARM with the Y402H allele of complement factor H, which has previously been reported as a major susceptibility factor for ARM. The combination of our analyses strongly implicates PLEKHA1/LOC387715 as primarily responsible for the evidence of linkage of ARM to the 10q26 locus and as a major contributor to ARM susceptibility. The association of either a single or a double copy of the high-risk allele within the PLEKHA1/LOC387715 locus accounts for an odds ratio of 5.0 (95% confidence interval 3.2-7.9) for ARM and a population attributable risk as high as 57%.
Collapse
Affiliation(s)
- Johanna Jakobsdottir
- Departments of Biostatistics and Human Genetics, Graduate School of Public Health, Department of Health Promotion and Development, School of Nursing, and UPMC Eye Center, Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh
| | - Yvette P. Conley
- Departments of Biostatistics and Human Genetics, Graduate School of Public Health, Department of Health Promotion and Development, School of Nursing, and UPMC Eye Center, Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh
| | - Daniel E. Weeks
- Departments of Biostatistics and Human Genetics, Graduate School of Public Health, Department of Health Promotion and Development, School of Nursing, and UPMC Eye Center, Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh
| | - Tammy S. Mah
- Departments of Biostatistics and Human Genetics, Graduate School of Public Health, Department of Health Promotion and Development, School of Nursing, and UPMC Eye Center, Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh
| | - Robert E. Ferrell
- Departments of Biostatistics and Human Genetics, Graduate School of Public Health, Department of Health Promotion and Development, School of Nursing, and UPMC Eye Center, Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh
| | - Michael B. Gorin
- Departments of Biostatistics and Human Genetics, Graduate School of Public Health, Department of Health Promotion and Development, School of Nursing, and UPMC Eye Center, Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh
| |
Collapse
|
26
|
Allingham RR, Wiggs JL, Hauser ER, Larocque-Abramson KR, Santiago-Turla C, Broomer B, Del Bono EA, Graham FL, Haines JL, Pericak-Vance MA, Hauser MA. Early adult-onset POAG linked to 15q11-13 using ordered subset analysis. Invest Ophthalmol Vis Sci 2005; 46:2002-5. [PMID: 15914615 PMCID: PMC1389566 DOI: 10.1167/iovs.04-1477] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Primary open-angle glaucoma (POAG) is a complex inherited disorder. It has been demonstrated in other complex disorders that phenotypic heterogeneity may be the result of genetic heterogeneity and that stratification analysis can be used to increase the power of detection. Ordered subset analysis (OSA) is a recently described method that utilizes the variability of phenotypic traits to determine underlying genetic heterogeneity. METHODS Eighty-six multiplex families with POAG were clinically ascertained for genetic analysis. Age at diagnosis (AAD) was used as a surrogate for age of onset in affected family members. Nine genetic markers within the 15q11-13 interval on chromosome 15 were used for OSA analysis. RESULTS An 11-cM linkage interval with a peak LOD score of 3.24 centered at the GABRB3 locus (P = 0.013 by permutation test) was identified in a subset of 15 families, which represents 17% of the total dataset (15/86 families). The mean AAD for the affected OSA families was 44.1 +/- 9.1 years (SD). The mean AAD for the complementary group was 61.3 +/- 10.4 years. African-American and white families were well represented in the OSA subset. CONCLUSIONS Linkage was identified for POAG to an 11-cM region on chromosome 15, designated GLC1I. This result provides further evidence that AAD and other phenotypic traits can be used as stratification variables to identify genes in complex disorders such as POAG and suggests that the 15q11-13 locus is one of the largest genetic contributors to POAG identified to date.
Collapse
Affiliation(s)
- R Rand Allingham
- Duke University Eye Center and the Department of Ophthalmology, Duke University Medical Center, Durham, NC 27710, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Gorin MB. The coming of age for age-related macular degeneration genetics. Ophthalmic Genet 2005; 26:57-9. [PMID: 16020307 DOI: 10.1080/13816810590969914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
28
|
Zareparsi S, Branham KEH, Li M, Shah S, Klein RJ, Ott J, Hoh J, Abecasis GR, Swaroop A. Strong association of the Y402H variant in complement factor H at 1q32 with susceptibility to age-related macular degeneration. Am J Hum Genet 2005; 77:149-53. [PMID: 15895326 PMCID: PMC1226187 DOI: 10.1086/431426] [Citation(s) in RCA: 250] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 04/27/2005] [Indexed: 11/03/2022] Open
Abstract
Using a large sample of cases and controls from a single center, we show that a T-->C substitution in exon 9 (Y402H) of the complement factor H gene is strongly associated with susceptibility to age-related macular degeneration, the most common cause of blindness in the elderly. Frequency of the C allele was 0.61 in cases, versus 0.34 in age-matched controls (P<1x10(-24)). Genotype frequencies also differ markedly between cases and controls (chi2=112.68 [2 degrees of freedom]; P<1x10(-24)). A multiplicative model fits the data well, and we estimate the population frequency of the high-risk C allele to be 0.39 (95% confidence interval 0.36-0.42) and the genotype relative risk to be 2.44 (95% confidence interval 2.08-2.83) for TC heterozygotes and 5.93 (95% confidence interval 4.33-8.02) for CC homozygotes.
Collapse
Affiliation(s)
- Sepideh Zareparsi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Schmidt M, Hauser ER, Martin ER, Schmidt S. Extension of the SIMLA package for generating pedigrees with complex inheritance patterns: environmental covariates, gene-gene and gene-environment interaction. Stat Appl Genet Mol Biol 2005; 4:Article15. [PMID: 16646832 PMCID: PMC1403827 DOI: 10.2202/1544-6115.1133] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We have previously distributed a software package, SIMLA (SIMulation of Linkage and Association), which can be used to generate disease phenotype and marker genotype data in three-generational pedigrees of user-specified structure. To our knowledge, SIMLA is the only publicly available program that can simulate variable levels of both linkage (recombination) and linkage disequilibrium (LD) between marker and disease loci in general pedigrees. While the previous SIMLA version provided flexibility in choosing many parameters relevant for linkage and association mapping of complex human diseases, it did not allow for the segregation of more than one disease locus in a given pedigree and did not incorporate environmental covariates possibly interacting with disease susceptibility genes. Here, we present an extension of the simulation algorithm characterized by a much more general penetrance function, which allows for the joint action of up to two genes and up to two environmental covariates in the simulated pedigrees, with all possible multiplicative interaction effects between them. This makes the program even more useful for comparing the performance of different linkage and association analysis methods applied to complex human phenotypes. SIMLA can assist investigators in planning and designing a variety of linkage and association studies, and can help interpret results of real data analyses by comparing them to results obtained under a user-controlled data generation mechanism.A free download of the SIMLA package is available at http://wwwchg.duhs.duke.edu/software.
Collapse
Affiliation(s)
- Mike Schmidt
- Center for Human Genetics, Duke University Medical Center,
| | | | - Eden R. Martin
- Center for Human Genetics, Duke University Medical Center,
| | - Silke Schmidt
- Center for Human Genetics, Duke University Medical Center,
| |
Collapse
|
30
|
Zareparsi S, Buraczynska M, Branham KEH, Shah S, Eng D, Li M, Pawar H, Yashar BM, Moroi SE, Lichter PR, Petty HR, Richards JE, Abecasis GR, Elner VM, Swaroop A. Toll-like receptor 4 variant D299G is associated with susceptibility to age-related macular degeneration. Hum Mol Genet 2005; 14:1449-55. [PMID: 15829498 DOI: 10.1093/hmg/ddi154] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Age-related macular degeneration (AMD) is a genetically heterogeneous disease that leads to progressive and irreversible vision loss among the elderly. Inflammation, oxidative damage, cholesterol metabolism and/or impaired function of retinal pigment epithelium (RPE) have been implicated in AMD pathogenesis. We examined toll-like receptor 4 (TLR4) as a candidate gene for AMD susceptibility because: (i) the TLR4 gene is located on chromosome 9q32-33, a region exhibiting evidence of linkage to AMD in three independent reports; (ii) the TLR4-D299G variant is associated with reduced risk of atherosclerosis, a chronic inflammatory disease with subendothelial accumulation; (iii) the TLR4 is not only a key mediator of proinflammatory signaling pathways but also linked to regulation of cholesterol efflux and (iv) the TLR4 participates in phagocytosis of photoreceptor outer segments by the RPE. We examined D299G and T399I variants of TLR4 in a sample of 667 unrelated AMD patients and 439 unrelated controls, all of Caucasian ancestry. Multiple logistic regression demonstrated an increased risk of AMD in carriers of the G allele at TLR4 residue 299 (odds ratio=2.65, P=0.025), but lack of an independent effect by T399I variant. TLR4-D299G showed an additive effect on AMD risk (odds ratio=4.13, P=0.002) with allelic variants of apolipoprotein E (APOE) and ATP-binding cassette transporter-1 (ABCA1), two genes involved in cholesterol efflux. Interestingly, the effect of TLR4, APOE and ABCA1 variants on AMD susceptibility was opposite to that of association with atherosclerosis risk. Our data provide evidence of a link between multiple diverse mechanisms underlying AMD pathogenesis.
Collapse
Affiliation(s)
- Sepideh Zareparsi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Thornton-Wells TA, Moore JH, Haines JL. Genetics, statistics and human disease: analytical retooling for complexity. Trends Genet 2005; 20:640-7. [PMID: 15522460 DOI: 10.1016/j.tig.2004.09.007] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Molecular biologists and geneticists alike now acknowledge that most common human diseases with a genetic component are likely to have complex etiologies. Yet despite this belief, many statistical geneticists continue applying, in slightly new and different ways, methodologies that were developed to dissect much simpler etiologies. In this article, we characterize, with examples, the various factors that can complicate genetic analysis and demonstrate their shared features and how they affect genetic analysis. We describe a variety of approaches that are currently available, revealing methodological gaps and suggesting new directions for method development. Finally, we propose a comprehensive two-step approach to analysis that systemically addresses the different genetic factors that are likely to underlie complex diseases.
Collapse
Affiliation(s)
- Tricia A Thornton-Wells
- Neuroscience Graduate Program, Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37240, USA
| | | | | |
Collapse
|
32
|
McCauley JL, Li C, Jiang L, Olson LM, Crockett G, Gainer K, Folstein SE, Haines JL, Sutcliffe JS. Genome-wide and Ordered-Subset linkage analyses provide support for autism loci on 17q and 19p with evidence of phenotypic and interlocus genetic correlates. BMC MEDICAL GENETICS 2005; 6:1. [PMID: 15647115 PMCID: PMC546213 DOI: 10.1186/1471-2350-6-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2004] [Accepted: 01/12/2005] [Indexed: 11/10/2022]
Abstract
BACKGROUND Autism is a neurobehavioral spectrum of phenotypes characterized by deficits in the development of language and social relationships and patterns of repetitive, rigid and compulsive behaviors. Twin and family studies point to a significant genetic etiology, and several groups have performed genomic linkage screens to identify susceptibility loci. METHODS We performed a genome-wide linkage screen in 158 combined Tufts, Vanderbilt and AGRE (Autism Genetics Research Exchange) multiplex autism families using parametric and nonparametric methods with a categorical autism diagnosis to identify loci of main effect. Hypothesizing interdependence of genetic risk factors prompted us to perform exploratory studies applying the Ordered-Subset Analysis (OSA) approach using LOD scores as the trait covariate for ranking families. We employed OSA to test for interlocus correlations between loci with LOD scores > or =1.5, and empirically determined significance of linkage in optimal OSA subsets using permutation testing. Exploring phenotypic correlates as the basis for linkage increases involved comparison of mean scores for quantitative trait-based subsets of autism between optimal subsets and the remaining families. RESULTS A genome-wide screen for autism loci identified the best evidence for linkage to 17q11.2 and 19p13, with maximum multipoint heterogeneity LOD scores of 2.9 and 2.6, respectively. Suggestive linkage (LOD scores > or =1.5) at other loci included 3p, 6q, 7q, 12p, and 16p. OSA revealed positive correlations of linkage between the 19p locus and 17q, between 19p and 6q, and between 7q and 5p. While potential phenotypic correlates for these findings were not identified for the chromosome 7/5 combination, differences indicating more rapid achievement of "developmental milestones" was apparent in the chromosome 19 OSA-defined subsets for 17q and 6q. OSA was used to test the hypothesis that 19p linkage involved more rapid achievement of these milestones and it revealed significantly increased LOD* scores at 19p13. CONCLUSIONS Our results further support 19p13 as harboring an autism susceptibility locus, confirm other linkage findings at 17q11.2, and demonstrate the need to analyze more discreet trait-based subsets of complex phenotypes to improve ability to detect genetic effects.
Collapse
Affiliation(s)
- Jacob L McCauley
- Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Chun Li
- Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
- Biostatistics, Vanderbilt University, Nashville, TN, USA
| | - Lan Jiang
- Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Lana M Olson
- Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Genea Crockett
- Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Kimberly Gainer
- Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Susan E Folstein
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Jonathan L Haines
- Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
| | - James S Sutcliffe
- Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, USA
| |
Collapse
|