401
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Rare genomic deletions and duplications and their role in neurodevelopmental disorders. Curr Top Behav Neurosci 2011; 12:345-60. [PMID: 22241247 DOI: 10.1007/7854_2011_179] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Copy number variations (CNVs) are deletions and duplications of DNA sequences that vary in length from a few base pairs to several million. While these structural variations are often benign, they can disrupt vital biological functions and result in disease. CNVs have been identified as causal in a number of neurodevelopmental disorders (NDs), including but not limited to, autism, attention-deficit/hyperactivity disorder (ADHD), and schizophrenia. Here, we examine CNV research into these disorders, and discuss relevant methodological considerations. By identifying specific rare deletions and duplications, we may be better able to determine the etiology of neurodevelopmental disorders and identify appropriate treatments.
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402
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Abstract
The eating disorders anorexia nervosa (AN), bulimia nervosa (BN), binge eating disorder and allied diagnoses such as eating disorder not otherwise specified are common, complex psychiatric disorders with a significant genetic component. Aetiology is unknown, but both phenotypic characteristics and genetic factors appear to be shared across these disorders, and indeed patients often change between diagnostic categories. Molecular studies have attempted to define genetic risk factors for these disorders, including case-control and family-based candidate gene association studies and linkage analysis of multiply affected nuclear families. These have used both clinical diagnoses and eating disorder-related intermediate phenotypes such as drive-for-thinness or body dissatisfaction. Candidate gene studies have focussed on neurotransmitter and neurodevelopmental systems [e.g. serotonergic, opioid, cannabinoid and dopaminergic receptors, and brain-derived neurotrophic factor (BDNF)], appetite regulatory peptides and their receptors [leptin, ghrelin, agouti-related protein (AgRP), melanocortin receptors, neuropeptide Y], energy balance systems (e.g. uncoupling proteins), genes implicated in obesity (e.g. FTO) and sex hormone systems (e.g. oestrogen receptors), either identified on the basis of their function alone or as positional candidates from linkage analysis. Of these studies, linkage analysis implicates 1p33-36 for AN, 1q31.3 for quantitative behavioural traits related to anorexia and 10p14 for BN, as well as other behavioural phenotypes across both disorders. Candidate gene association has implicated BDNF, delta 1 opioid receptor (OPDR1) and AgRP. More recently, with the advent of genome-wide association studies (GWAS), analysis with microsatellite markers has implicated novel candidate loci for AN at 1q41 and 11q22, and further GWAS results are expected in the near future.
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Affiliation(s)
- Sietske G Helder
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, Denmark Hill, London, SE5 8AF, UK.
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403
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Novelli G, Predazzi IM, Mango R, Romeo F, Mehta JL. Role of genomics in cardiovascular medicine. World J Cardiol 2010; 2:428-36. [PMID: 21191544 PMCID: PMC3011138 DOI: 10.4330/wjc.v2.i12.428] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Revised: 10/25/2010] [Accepted: 11/01/2010] [Indexed: 02/06/2023] Open
Abstract
As all branches of science grow and new experimental techniques become readily accessible, our knowledge of medicine is likely to increase exponentially in the coming years. Recently developed technologies have revolutionized our analytical capacities, leading to vast knowledge of many genes or genomic regions involved in the pathogenesis of congenital heart diseases, which are often associated with other genetic syndromes, coronary artery disease and non-ischemic cardiomyopathies and channelopathies. The knowledge-base of the genesis of cardiovascular diseases is likely going to be further revolutionized in this new era of genomic medicine. Here, we review the advances that have been made over the last several years in this field and discuss different genetic mechanisms that have been shown to underlie a variety of cardiovascular diseases.
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Affiliation(s)
- Giuseppe Novelli
- Giuseppe Novelli, Irene M Predazzi, Department of Biopathology and Diagnostic Imaging, Section of Medical Genetics, School of Medicine, Tor Vergata University, Via Montpellier 1, 00133 Rome, Italy
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404
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Kurtz TW. Genome-wide association studies will unlock the genetic basis of hypertension.: con side of the argument. Hypertension 2010; 56:1021-5. [PMID: 21060005 DOI: 10.1161/hypertensionaha.110.156190] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past few years, it has been asserted that genome-wide association studies would open the door to identifying primary genetic mechanisms underlying a variety of common clinical disorders, including essential hypertension. Great hope was expressed that such research would ultimately lead to improved clinical outcomes by facilitating the discovery of novel targets for therapy and by spawning a new era of personalized medicine in which the results of genetic tests would be useful for guiding customized risk assessment and individual patient management. In this Controversies in Hypertension series, I contend that genome-wide association studies have failed, and will continue to fail, to unlock the genetic basis of essential hypertension and the research dollars being devoted to genome-wide association studies should be shifted to other strategies and technologies that may hold greater chance for advancing our understanding of the genetic factors that influence population variation in blood pressure and risk for hypertension.
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Affiliation(s)
- Theodore W Kurtz
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
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405
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Prakash SK, LeMaire SA, Guo DC, Russell L, Regalado ES, Golabbakhsh H, Johnson RJ, Safi HJ, Estrera AL, Coselli JS, Bray MS, Leal SM, Milewicz DM, Belmont JW. Rare copy number variants disrupt genes regulating vascular smooth muscle cell adhesion and contractility in sporadic thoracic aortic aneurysms and dissections. Am J Hum Genet 2010; 87:743-56. [PMID: 21092924 DOI: 10.1016/j.ajhg.2010.09.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 09/07/2010] [Accepted: 09/16/2010] [Indexed: 10/18/2022] Open
Abstract
Thoracic aortic aneurysms and dissections (TAAD) cause significant morbidity and mortality, but the genetic origins of TAAD remain largely unknown. In a genome-wide analysis of 418 sporadic TAAD cases, we identified 47 copy number variant (CNV) regions that were enriched in or unique to TAAD patients compared to population controls. Gene ontology, expression profiling, and network analysis showed that genes within TAAD CNVs regulate smooth muscle cell adhesion or contractility and interact with the smooth muscle-specific isoforms of α-actin and β-myosin, which are known to cause familial TAAD when altered. Enrichment of these gene functions in rare CNVs was replicated in independent cohorts with sporadic TAAD (STAAD, n = 387) and inherited TAAD (FTAAD, n = 88). The overall prevalence of rare CNVs (23%) was significantly increased in FTAAD compared with STAAD patients (Fisher's exact test, p = 0.03). Our findings suggest that rare CNVs disrupting smooth muscle adhesion or contraction contribute to both sporadic and familial disease.
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406
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Coassin S, Schweiger M, Kloss-Brandstätter A, Lamina C, Haun M, Erhart G, Paulweber B, Rahman Y, Olpin S, Wolinski H, Cornaciu I, Zechner R, Zimmermann R, Kronenberg F. Investigation and functional characterization of rare genetic variants in the adipose triglyceride lipase in a large healthy working population. PLoS Genet 2010; 6:e1001239. [PMID: 21170305 PMCID: PMC3000363 DOI: 10.1371/journal.pgen.1001239] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 11/04/2010] [Indexed: 12/14/2022] Open
Abstract
Recent studies demonstrated a strong influence of rare genetic variants on several lipid-related traits. However, their impact on free fatty acid (FFA) plasma concentrations, as well as the role of rare variants in a general population, has not yet been thoroughly addressed. The adipose triglyceride lipase (ATGL) is encoded by the PNPLA2 gene and catalyzes the rate-limiting step of lipolysis. It represents a prominent candidate gene affecting FFA concentrations. We therefore screened the full genomic region of ATGL for mutations in 1,473 randomly selected individuals from the SAPHIR (Salzburg Atherosclerosis Prevention program in subjects at High Individual Risk) Study using a combined Ecotilling and sequencing approach and functionally investigated all detected protein variants by in-vitro studies. We observed 55 novel mostly rare genetic variants in this general population sample. Biochemical evaluation of all non-synonymous variants demonstrated the presence of several mutated but mostly still functional ATGL alleles with largely varying residual lipolytic activity. About one-quarter (3 out of 13) of the investigated variants presented a marked decrease or total loss of catalytic function. Genetic association studies using both continuous and dichotomous approaches showed a shift towards lower plasma FFA concentrations for rare variant carriers and an accumulation of variants in the lower 10%-quantile of the FFA distribution. However, the generally rather small effects suggest either only a secondary role of rare ATGL variants on the FFA levels in the SAPHIR population or a recessive action of ATGL variants. In contrast to these rather small effects, we describe here also the first patient with “neutral lipid storage disease with myopathy” (NLSDM) with a point mutation in the catalytic dyad, but otherwise intact protein. The nature of the genetic variation underlying common traits is not yet completely understood. Recently, there has been a shift in the genetic research focus towards the elucidation of the influence of rare variants, which are thought to exert a strong impact on common traits. Circulating free fatty acids are immediate products of the triglyceride breakdown and represent a yet poorly addressed phenotype to study the impact of rare variants on lipolysis. Since ATGL (encoded by the PNPLA2 gene) controls the rate limiting step of lipolysis, we screened its whole gene region in 1,473 healthy individuals and found that 1 out of 13 individuals indeed carried at least one rare mutation. Biochemical investigations showed that, even in a healthy population, several missense variants lead to an impaired catalytic activity and 1 variant even produced a completely inactive protein. However, subsequent association studies revealed only small effects on the free fatty acids levels in the population. This suggests an only secondary role of rare ATGL variants on free fatty acids levels. More generally, we conclude that even in a healthy population pronounced allelic heterogeneity due to the presence of several rare variants may be common.
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Affiliation(s)
- Stefan Coassin
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Martina Schweiger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Anita Kloss-Brandstätter
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Claudia Lamina
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Margot Haun
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Gertraud Erhart
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Private Medical University Salzburg, Salzburg, Austria
| | - Yusof Rahman
- Department of Inherited Metabolic Diseases, Evelina Children Hospital, Guys and St. Thomas's National Health Service Foundation Trust, London, United Kingdom
| | - Simon Olpin
- Department of Clinical Chemistry, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Heimo Wolinski
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Irina Cornaciu
- Structural Biology Group, Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Robert Zimmermann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
- * E-mail:
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407
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Abstract
Meniere's disease remains a disorder of unknown origin despite the collective efforts to determine the pathogenesis, although experts have long recognized that disease development likely has some heritable component. Although genetic studies of Meniere's disease have been inconclusive, increasing knowledge of human genetic structure and mutation and investigative techniques have potential to further understanding of this disorder.
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Affiliation(s)
- Jeffrey T Vrabec
- Bobby R. Alford Department of Otolaryngology-Head and Neck Surgery Baylor College of Medicine, 6550 Fannin Street, SM1727, Houston, TX 77030, USA.
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408
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Affiliation(s)
- Jennifer Asimit
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom;
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409
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Bonilla C, Lefèvre JH, Winney B, Johnstone E, Tonks S, Colas C, Day T, Hutnik K, Boumertit A, Midgley R, Kerr D, Parc Y, Bodmer WF. Cyclin D1 rare variants in UK multiple adenoma and early-onset colorectal cancer patients. J Hum Genet 2010; 56:58-63. [PMID: 21107342 DOI: 10.1038/jhg.2010.144] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We examined the influence that rare variants and low-frequency polymorphisms in the cancer candidate gene CCND1 have on the development of multiple intestinal adenomas and the early onset of colorectal cancer. Individuals with <100 multiple polyps and patients with colorectal cancer diagnosed before 50 years of age were recruited in UK, and screened for sequence changes in the coding and regulatory regions of CCND1. A set of about 800 UK control individuals was genotyped for the variants discovered in the cases. Variants in the promoter, intron-exon boundaries and untranslated regions of the CCND1 gene had higher frequencies in cases than in controls. Five of these variants were typed in a set of French multiple adenoma and early-onset patients, who also showed higher allele frequencies than UK controls. When pooled together, variants with frequencies lower than 1% conferred an increased risk of disease that was significant in the multiple adenoma group (odds ratio (OR) 2.2; 95% confidence interval, 1.1-4.4; P = 0.03). Most variants had a putative functional effect when assessed in silico. We conclude that rare variants of CCND1 are risk factors for colorectal cancer, with considerably larger effects than common polymorphisms, and as such should be systematically evaluated in susceptibility studies.
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Affiliation(s)
- Carolina Bonilla
- Department of Clinical Pharmacology, University of Oxford, Headington, Oxford, UK
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410
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Ku CS, Naidoo N, Teo SM, Pawitan Y. Regions of homozygosity and their impact on complex diseases and traits. Hum Genet 2010; 129:1-15. [PMID: 21104274 DOI: 10.1007/s00439-010-0920-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 11/04/2010] [Indexed: 12/23/2022]
Abstract
Regions of homozygosity (ROHs) are more abundant in the human genome than previously thought. These regions are without heterozygosity, i.e. all the genetic variations within the regions have two identical alleles. At present there are no standardized criteria for defining the ROHs resulting in the different studies using their own criteria in the analysis of homozygosity. Compared to the era of genotyping microsatellite markers, the advent of high-density single nucleotide polymorphism genotyping arrays has provided an unparalleled opportunity to comprehensively detect these regions in the whole genome in different populations. Several studies have identified ROHs which were associated with complex phenotypes such as schizophrenia, late-onset of Alzheimer's disease and height. Collectively, these studies have conclusively shown the abundance of ROHs larger than 1 Mb in outbred populations. The homozygosity association approach holds great promise in identifying genetic susceptibility loci harboring recessive variants for complex diseases and traits.
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Affiliation(s)
- Chee Seng Ku
- Department of Epidemiology and Public Health, Centre for Molecular Epidemiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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411
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Li Y, Byrnes AE, Li M. To identify associations with rare variants, just WHaIT: Weighted haplotype and imputation-based tests. Am J Hum Genet 2010; 87:728-35. [PMID: 21055717 DOI: 10.1016/j.ajhg.2010.10.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/12/2010] [Accepted: 10/14/2010] [Indexed: 11/28/2022] Open
Abstract
Empirical evidences suggest that both common and rare variants contribute to complex disease etiology. Although the effects of common variants have been thoroughly assessed in recent genome-wide association studies (GWAS), our knowledge of the impact of rare variants on complex diseases remains limited. A number of methods have been proposed to test for rare variant association in sequencing-based studies, a study design that is becoming popular but is still not economically feasible. On the contrary, few (if any) methods exist to detect rare variants in GWAS data, the data we have collected on thousands of individuals. Here we propose two methods, a weighted haplotype-based approach and an imputation-based approach, to test for the effect of rare variants with GWAS data. Both methods can incorporate external sequencing data when available. We evaluated our methods and compared them with methods proposed in the sequencing setting through extensive simulations. Our methods clearly show enhanced statistical power over existing methods for a wide range of population-attributable risk, percentage of disease-contributing rare variants, and proportion of rare alleles working in different directions. We also applied our methods to the IFIH1 region for the type 1 diabetes GWAS data collected by the Wellcome Trust Case-Control Consortium. Our methods yield p values in the order of 10⁻³, whereas the most significant p value from the existing methods is greater than 0.17. We thus demonstrate that the evaluation of rare variants with GWAS data is possible, particularly when public sequencing data are incorporated.
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Affiliation(s)
- Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, 27599, USA.
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412
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Wessel J, McDonald SM, Hinds DA, Stokowski RP, Javitz HS, Kennemer M, Krasnow R, Dirks W, Hardin J, Pitts SJ, Michel M, Jack L, Ballinger DG, McClure JB, Swan GE, Bergen AW. Resequencing of nicotinic acetylcholine receptor genes and association of common and rare variants with the Fagerström test for nicotine dependence. Neuropsychopharmacology 2010; 35:2392-402. [PMID: 20736995 PMCID: PMC3055324 DOI: 10.1038/npp.2010.120] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Common single-nucleotide polymorphisms (SNPs) at nicotinic acetylcholine receptor (nAChR) subunit genes have previously been associated with measures of nicotine dependence. We investigated the contribution of common SNPs and rare single-nucleotide variants (SNVs) in nAChR genes to Fagerström test for nicotine dependence (FTND) scores in treatment-seeking smokers. Exons of 10 genes were resequenced with next-generation sequencing technology in 448 European-American participants of a smoking cessation trial, and CHRNB2 and CHRNA4 were resequenced by Sanger technology to improve sequence coverage. A total of 214 SNP/SNVs were identified, of which 19.2% were excluded from analyses because of reduced completion rate, 73.9% had minor allele frequencies <5%, and 48.1% were novel relative to dbSNP build 129. We tested associations of 173 SNP/SNVs with the FTND score using data obtained from 430 individuals (18 were excluded because of reduced completion rate) using linear regression for common, the cohort allelic sum test and the weighted sum statistic for rare, and the multivariate distance matrix regression method for both common and rare SNP/SNVs. Association testing with common SNPs with adjustment for correlated tests within each gene identified a significant association with two CHRNB2 SNPs, eg, the minor allele of rs2072660 increased the mean FTND score by 0.6 Units (P=0.01). We observed a significant evidence for association with the FTND score of common and rare SNP/SNVs at CHRNA5 and CHRNB2, and of rare SNVs at CHRNA4. Both common and/or rare SNP/SNVs from multiple nAChR subunit genes are associated with the FTND score in this sample of treatment-seeking smokers.
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Affiliation(s)
- Jennifer Wessel
- Center for Health Sciences, SRI International, Menlo Park, CA, USA,Department of Public Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sarah M McDonald
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | | | | | - Harold S Javitz
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | | | - Ruth Krasnow
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | | | - Jill Hardin
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | | | - Martha Michel
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | - Lisa Jack
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | | | | | - Gary E Swan
- Center for Health Sciences, SRI International, Menlo Park, CA, USA
| | - Andrew W Bergen
- Center for Health Sciences, SRI International, Menlo Park, CA, USA,Molecular Genetics Program, Center for Health Sciences, SRI International, 333 Ravenswood Avenue, SRI International, Menlo Park, CA 94025, USA. Tel: +1 650 859 4618; Fax: +1 650 859 5099; E-mail:
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413
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Bansal V, Libiger O, Torkamani A, Schork NJ. Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet 2010; 11:773-85. [PMID: 20940738 PMCID: PMC3743540 DOI: 10.1038/nrg2867] [Citation(s) in RCA: 381] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The limitations of genome-wide association (GWA) studies that focus on the phenotypic influence of common genetic variants have motivated human geneticists to consider the contribution of rare variants to phenotypic expression. The increasing availability of high-throughput sequencing technologies has enabled studies of rare variants but these methods will not be sufficient for their success as appropriate analytical methods are also needed. We consider data analysis approaches to testing associations between a phenotype and collections of rare variants in a defined genomic region or set of regions. Ultimately, although a wide variety of analytical approaches exist, more work is needed to refine them and determine their properties and power in different contexts.
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Affiliation(s)
- Vikas Bansal
- The Scripps Translational Science Institute, 3344 North Torrey Pines Court, Suite 300, La Jolla, California 92037, USA
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414
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Li WF, Hou SX, Yu B, Jin D, Férec C, Chen JM. Genetics of osteoporosis: perspectives for personalized medicine. Per Med 2010; 7:655-668. [PMID: 29788568 DOI: 10.2217/pme.10.55] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Osteoporosis is the most common metabolic bone disorder worldwide. At least 15 genes (e.g., ESR1, LRP5, SOST, OPG, RANK and RANKL) have been confirmed as osteoporosis susceptibility genes, and another 30 have been highlighted as promising susceptibility genes. Notably, these genes are clustered in three biological pathways: the estrogen endocrine pathway, the Wnt/β-catenin signaling pathway and the RANK/RANKL/osteoprotegerin (OPG) pathway. In this article, using data pertaining to these three biological pathways as examples, we illustrate possible principles of personalized therapy for osteoporosis. In particular, we propose to use inhibitors (e.g., denosumab) of the RANK/RANKL/OPG signaling pathway to circumvent resistance to estrogen-replacement therapy: a novel idea resulting from the consideration of a mechanistic link between the estrogen endocrine pathway and the RANK/RANKL/OPG signaling pathway. In addition, we call for more attention to be focused on rare variants of major effects in future studies.
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Affiliation(s)
- Wen-Feng Li
- Department of Orthopaedics, The First Affiliated Hospital, General Hospital of the People’s Liberation Army, Beijing, China
| | - Shu-Xun Hou
- Department of Orthopaedics, The First Affiliated Hospital, General Hospital of the People’s Liberation Army, Beijing, China
| | - Bin Yu
- Department of Orthopaedic Trauma, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dan Jin
- Department of Orthopaedic Trauma, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale (INSERM), U613, Brest, France; INSERM, U613 and EFS – Bretagne, 46 rue Félix Le Dantec, 29218 Brest, France
- Etablissement Français du Sang (EFS) – Bretagne, Brest, France
- Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
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415
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Mort M, Evani US, Krishnan VG, Kamati KK, Baenziger PH, Bagchi A, Peters BJ, Sathyesh R, Li B, Sun Y, Xue B, Shah NH, Kann MG, Cooper DN, Radivojac P, Mooney SD. In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Hum Mutat 2010; 31:335-46. [PMID: 20052762 DOI: 10.1002/humu.21192] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An important challenge in translational bioinformatics is to understand how genetic variation gives rise to molecular changes at the protein level that can precipitate both monogenic and complex disease. To this end, we compiled datasets of human disease-associated amino acid substitutions (AAS) in the contexts of inherited monogenic disease, complex disease, functional polymorphisms with no known disease association, and somatic mutations in cancer, and compared them with respect to predicted functional sites in proteins. Using the sequence homology-based tool SIFT to estimate the proportion of deleterious AAS in each dataset, only complex disease AAS were found to be indistinguishable from neutral polymorphic AAS. Investigation of monogenic disease AAS predicted to be nondeleterious by SIFT were characterized by a significant enrichment for inherited AAS within solvent accessible residues, regions of intrinsic protein disorder, and an association with the loss or gain of various posttranslational modifications. Sites of structural and/or functional interest were therefore surmised to constitute useful additional features with which to identify the molecular disruptions caused by deleterious AAS. A range of bioinformatic tools, designed to predict structural and functional sites in protein sequences, were then employed to demonstrate that intrinsic biases exist in terms of the distribution of different types of human AAS with respect to specific structural, functional and pathological features. Our Web tool, designed to potentiate the functional profiling of novel AAS, has been made available at http://profile.mutdb.org/.
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Affiliation(s)
- Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
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416
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Johansen CT, Lanktree MB, Hegele RA. Translating genomic analyses into improved management of coronary artery disease. Future Cardiol 2010; 6:507-21. [PMID: 20608823 DOI: 10.2217/fca.10.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human genetic variation can modulate pathophysiologic processes that alter susceptibility to complex disease. Recent genomic analyses have sought to identify how common genetic variation alters susceptibility to coronary artery disease (CAD). From genome-wide association studies (GWAS), common genetic variants in several novel chromosomal loci have been associated with CAD. GWAS identified the 9p21 locus as the strongest independent genetic CAD risk factor, along with 11 additional loci that harbor common genetic variants associated with increased CAD risk. A thorough understanding of human genetic variation and genomic analyses will be crucial to understand how GWAS-identified loci increase susceptibility to CAD. This article outlines the relevance of genetic variation in the elucidation of novel CAD risk factors and the clinical utility of genetic variants in the management and treatment of CAD.
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Affiliation(s)
- Christopher T Johansen
- Blackburn Cardiovascular Genetics Laboratory, Robarts Research Institute, University of Western Ontario, London, ON N6A 5K8, Canada
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417
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George J, Motshwene PG, Wang H, Kubarenko AV, Rautanen A, Mills TC, Hill AVS, Gay NJ, Weber ANR. Two human MYD88 variants, S34Y and R98C, interfere with MyD88-IRAK4-myddosome assembly. J Biol Chem 2010; 286:1341-53. [PMID: 20966070 PMCID: PMC3020742 DOI: 10.1074/jbc.m110.159996] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Innate immune receptors detect microbial pathogens and subsequently activate adaptive immune responses to combat pathogen invasion. MyD88 is a key adaptor molecule in both Toll-like receptor (TLR) and IL-1 receptor superfamily signaling pathways. This is illustrated by the fact that human individuals carrying rare, naturally occurring MYD88 point mutations suffer from reoccurring life-threatening infections. Here we analyzed the functional properties of six reported non-synonymous single nucleotide polymorphisms of MYD88 in an in vitro cellular system. Two variants found in the MyD88 death domain, S34Y and R98C, showed severely reduced NF-κB activation due to reduced homo-oligomerization and IRAK4 interaction. Structural modeling highlights Ser-34 and Arg-98 as residues important for the assembly of the Myddosome, a death domain (DD) post-receptor complex involving the DD of MyD88, IRAK4, and IRAK2 or IRAK1. Using S34Y and R98C as functional probes, our data show that MyD88 homo-oligomerization and IRAK4 interaction is modulated by the MyD88 TIR and IRAK4 kinase domain, demonstrating the functional importance of non-DD regions not observed in a recent Myddosome crystal structure. The differential interference of S34Y and R98C with some (IL-1 receptor, TLR2, TLR4, TLR5, and TLR7) but not all (TLR9) MyD88-dependent signaling pathways also suggests that receptor specificities exist at the level of the Myddosome. Given their detrimental effect on signaling, it is not surprising that our epidemiological analysis in several case-control studies confirms that S34Y and R98C are rare variants that may drastically contribute to susceptibility to infection in only few individuals.
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Affiliation(s)
- Julie George
- Division Toll-like receptors and Cancer, German Cancer Research Centre DKFZ, Heidelberg, 69120 Germany
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418
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Panagiotou OA, Evangelou E, Ioannidis JPA. Genome-wide significant associations for variants with minor allele frequency of 5% or less--an overview: A HuGE review. Am J Epidemiol 2010; 172:869-89. [PMID: 20876667 DOI: 10.1093/aje/kwq234] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The authors survey uncommon variants (minor allele frequency, ≤5%) that have reached genome-wide significance (P ≤ 10⁻⁷) in genome-wide association study(ies) (GWAS). They examine the typical effect sizes of these associations; whether they have arisen in multiple GWAS on the same phenotype; and whether they pertain to genetic loci that have other variants discovered through GWAS, perceived biologic plausibility from the candidate gene era, or known mutations associated with related phenotypes. Forty-three associations with minor allele frequency of 5% or less and P ≤ 10⁻⁷ were studied, 12 of which involved nonsynonymous variants. Per-allele odds ratios ranged from 1.03 to 22.11. Thirty-two associations had P ≤ 10⁻⁸. Eight uncommon variants were identified in multiple GWAS. For 14 associations, also other common polymorphisms with genome-wide significance were identified in the same loci. Thirteen associations pertained to genetic loci considered to have biologic plausibility for association in the candidate gene era, and mutations with related phenotypic effects were identified for 11 associations. Twenty-five uncommon variants are common in at least 1 of the 4 different ancestry samples of the International HapMap Project. Although the number of uncommon variants with genome-wide significance is still limited, these data suggest a possible confluence of rare/uncommon and common genetic variation on the same genetic loci.
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Affiliation(s)
- Orestis A Panagiotou
- Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece
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419
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Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V. A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol 2010; 6:e1000954. [PMID: 20976246 PMCID: PMC2954823 DOI: 10.1371/journal.pcbi.1000954] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 09/08/2010] [Indexed: 11/19/2022] Open
Abstract
Genome wide association (GWA) studies, which test for association between common genetic markers and a disease phenotype, have shown varying degrees of success. While many factors could potentially confound GWA studies, we focus on the possibility that multiple, rare variants (RVs) may act in concert to influence disease etiology. Here, we describe an algorithm for RV analysis, RareCover. The algorithm combines a disparate collection of RVs with low effect and modest penetrance. Further, it does not require the rare variants be adjacent in location. Extensive simulations over a range of assumed penetrance and population attributable risk (PAR) values illustrate the power of our approach over other published methods, including the collapsing and weighted-collapsing strategies. To showcase the method, we apply RareCover to re-sequencing data from a cohort of 289 individuals at the extremes of Body Mass Index distribution (NCT00263042). Individual samples were re-sequenced at two genes, FAAH and MGLL, known to be involved in endocannabinoid metabolism (187Kbp for 148 obese and 150 controls). The RareCover analysis identifies exactly one significantly associated region in each gene, each about 5 Kbp in the upstream regulatory regions. The data suggests that the RVs help disrupt the expression of the two genes, leading to lowered metabolism of the corresponding cannabinoids. Overall, our results point to the power of including RVs in measuring genetic associations. We focus on the problem of detecting multiple rare variants (RVs) that act together to influence disease phenotypes. In considering this problem, we argue that the detection of causal rare variants must necessarily be different from typical single-marker analysis used for common variants and propose a novel algorithm, RareCover, to accomplish this analysis. RareCover combines a disparate collection of RVs, each with very low effect and modest penetrance. Extensive simulations over a range of values for penetrance and population attributable risk (PAR) illustrate the power of our approach over other published methods, including the collapsing and weighted-sum strategies. To showcase the method, we applied RareCover to data from 289 individuals at the extremes of Body Mass Index distribution (NCT00263042), sequenced around the FAAH and MGLL genes. RareCover analysis identified exactly one significantly associated region in each gene, each about 5Kbp in the upstream regulatory regions. The data suggests that the RVs help disrupt the expression of the two genes leading to lowered metabolism of the corresponding endocannabinoids previously linked with obesity. Overall, our results point to the power of including RVs in measuring genetic associations, and suggest that whole genome, DNA sequencing-based association studies investigating RV effects are feasible.
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Affiliation(s)
- Gaurav Bhatia
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.
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420
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Affiliation(s)
- Georg Winterer
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931 Cologne, Germany
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421
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Bloss CS, Schiabor KM, Schork NJ. Human behavioral informatics in genetic studies of neuropsychiatric disease: multivariate profile-based analysis. Brain Res Bull 2010; 83:177-88. [PMID: 20433907 PMCID: PMC2941546 DOI: 10.1016/j.brainresbull.2010.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 04/17/2010] [Accepted: 04/21/2010] [Indexed: 01/23/2023]
Abstract
While genome-wide association (GWA) studies have yielded notable findings with regard to the identification of risk variants in diseases such as obesity and diabetes, similar studies of schizophrenia - and neuropsychiatric diseases in general - have failed to produce strong findings. One, plausible explanation for this relates to phenotypic heterogeneity and what may be inherent imprecision associated with diagnostic categories in neuropsychiatric disorders. In this review we discuss a general approach to addressing the problem of heterogeneity that draws on concepts in behavioral informatics and the use of multivariable behavioral profiles in genetic studies of neuropsychiatric disease. The use of behavioral profiles as phenotypes eliminates the need for categorizing individuals with different 'subtypes' of a disease into one group and provides a way to investigate genetic susceptibility to different neuropsychiatric disorders that share similar clinical characteristics, such as schizophrenia and bipolar disorder. Further, behavioral profiles are a direct, quantitative representation of the emotional, personality, and neurocognitive functioning of the individuals being studied, and as such, the use of these profiles may provide increased statistical power to detect genetic associations and linkages. We describe and discuss four general data analysis approaches that can be used to analyze and integrate multivariate behavioral profile data and high-dimensional genomic data. Ultimately, we propose that behavioral profile-based phenotypes provide a meaningful alternative to the use of single measures, such as diagnostic category, in genetic association studies of neuropsychiatric disease.
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Affiliation(s)
- Cinnamon S. Bloss
- Scripps Genomic Medicine, Scripps Translational Science Institute, Scripps Health
| | - Kelly M. Schiabor
- Scripps Genomic Medicine, Scripps Translational Science Institute, Scripps Health
| | - Nicholas J. Schork
- Scripps Genomic Medicine, Scripps Translational Science Institute, Scripps Health
- Department of Molecular and Experimental Medicine, The Scripps Research Institute
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422
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Fenstad MH, Johnson MP, Roten LT, Aas PA, Forsmo S, Klepper K, East CE, Abraham LJ, Blangero J, Brennecke SP, Austgulen R, Moses EK. Genetic and molecular functional characterization of variants within TNFSF13B, a positional candidate preeclampsia susceptibility gene on 13q. PLoS One 2010; 5:e12993. [PMID: 20927378 PMCID: PMC2947510 DOI: 10.1371/journal.pone.0012993] [Citation(s) in RCA: 15] [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: 06/17/2010] [Accepted: 09/03/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Preeclampsia is a serious pregnancy complication, demonstrating a complex pattern of inheritance. The elucidation of genetic liability to preeclampsia remains a major challenge in obstetric medicine. We have adopted a positional cloning approach to identify maternal genetic components, with linkages previously demonstrated to chromosomes 2q, 5q and 13q in an Australian/New Zealand familial cohort. The current study aimed to identify potential functional and structural variants in the positional candidate gene TNFSF13B under the 13q linkage peak and assess their association status with maternal preeclampsia genetic susceptibility. METHODOLOGY/PRINCIPAL FINDINGS The proximal promoter and coding regions of the positional candidate gene TNFSF13B residing within the 13q linkage region was sequenced using 48 proband or founder individuals from Australian/New Zealand families. Ten sequence variants (nine SNPs and one single base insertion) were identified and seven SNPs were successfully genotyped in the total Australian/New Zealand family cohort (74 families/480 individuals). Borderline association to preeclampsia (p = 0.0153) was observed for three rare SNPs (rs16972194, rs16972197 and rs56124946) in strong linkage disequilibrium with each other. Functional evaluation by electrophoretic mobility shift assays showed differential nuclear factor binding to the minor allele of the rs16972194 SNP, residing upstream of the translation start site, making this a putative functional variant. The observed genetic associations were not replicated in a Norwegian case/control cohort (The Nord-Trøndelag Health Study (HUNT2), 851 preeclamptic and 1,440 non-preeclamptic women). CONCLUSION/SIGNIFICANCE TNFSF13B has previously been suggested to contribute to the normal immunological adaption crucial for a successful pregnancy. Our observations support TNFSF13B as a potential novel preeclampsia susceptibility gene. We discuss a possible role for TNFSF13B in preeclampsia pathogenesis, and propose the rs16972194 variant as a candidate for further functional evaluation.
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Affiliation(s)
- Mona H. Fenstad
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matthew P. Johnson
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
| | - Linda T. Roten
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per A. Aas
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Siri Forsmo
- Department of Public Health and General Practice, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kjetil Klepper
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Christine E. East
- Department of Perinatal Medicine/Department of Obstetrics and Gynaecology, Royal Women's Hospital and University of Melbourne, Parkville, Australia
| | - Lawrence J. Abraham
- The School of Biomedical Biomolecular and Chemical Sciences, The University of Western Australia Crawley, Perth, Australia
| | - John Blangero
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
| | - Shaun P. Brennecke
- Department of Perinatal Medicine/Department of Obstetrics and Gynaecology, Royal Women's Hospital and University of Melbourne, Parkville, Australia
| | - Rigmor Austgulen
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Eric K. Moses
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
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423
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Cooper DN, Chen JM, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD. Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutat 2010; 31:631-55. [PMID: 20506564 DOI: 10.1002/humu.21260] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of reported germline mutations in human nuclear genes, either underlying or associated with inherited disease, has now exceeded 100,000 in more than 3,700 different genes. The availability of these data has both revolutionized the study of the morbid anatomy of the human genome and facilitated "personalized genomics." With approximately 300 new "inherited disease genes" (and approximately 10,000 new mutations) being identified annually, it is pertinent to ask how many "inherited disease genes" there are in the human genome, how many mutations reside within them, and where such lesions are likely to be located? To address these questions, it is necessary not only to reconsider how we define human genes but also to explore notions of gene "essentiality" and "dispensability."Answers to these questions are now emerging from recent novel insights into genome structure and function and through complete genome sequence information derived from multiple individual human genomes. However, a change in focus toward screening functional genomic elements as opposed to genes sensu stricto will be required if we are to capitalize fully on recent technical and conceptual advances and identify new types of disease-associated mutation within noncoding regions remote from the genes whose function they disrupt.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom.
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424
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Kubarenko AV, Ranjan S, Rautanen A, Mills TC, Wong S, Vannberg F, Neumaier M, Bekeredjian-Ding I, Hill AVS, Ahmad-Nejad P, Weber ANR. A naturally occurring variant in human TLR9, P99L, is associated with loss of CpG oligonucleotide responsiveness. J Biol Chem 2010; 285:36486-94. [PMID: 20843814 PMCID: PMC2978577 DOI: 10.1074/jbc.m110.117200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The innate immune system employs Toll-like receptors (TLRs) for the detection of invading microorganisms based on distinct molecular patterns. For example, TLR9 is activated by microbial DNA and also by short therapeutic CpG-containing oligonucleotides (CpG-ODN). TLR9 activation leads to the production of interferons and the priming of humoral adaptive immune responses. Unfortunately, the principles of ligand recognition by TLR9 are poorly understood, and genetic variants of TLR9, which may affect its function, have not been characterized systematically on the molecular level. We therefore sought to functionally characterize reported single nucleotide polymorphisms of TLR9 in the HEK293 model system. We discovered that two variants, P99L and M400I, are associated with altered receptor function regarding NF-κB activation and cytokine induction. Our investigations show that for the most functionally impaired variant, P99L, the ability to respond to physiological and therapeutic TLR9 ligands is severely compromised. However, CpG-ODN binding is normal. CpG-ODN recognition by TLR9 thus appears to involve two separate events, CpG-ODN binding and sensing. Our studies highlight Pro-99 as a residue important for the latter process. In genotyping studies, we confirmed that both M400I (rs41308230) and P99L (rs5743844) are relatively rare variants of TLR9. Our data add rs41308230 and rs5743844 to the list of functionally important TLR variants and warrant further research into their relevance for infectious disease susceptibility or responsiveness to CpG-ODN-based therapies.
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Affiliation(s)
- Andriy V Kubarenko
- Department of Toll-like Receptors and Cancer, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
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425
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Speicher MR, Geigl JB, Tomlinson IP. Effect of genome-wide association studies, direct-to-consumer genetic testing, and high-speed sequencing technologies on predictive genetic counselling for cancer risk. Lancet Oncol 2010; 11:890-8. [DOI: 10.1016/s1470-2045(09)70359-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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426
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Orozco G, Barrett JC, Zeggini E. Synthetic associations in the context of genome-wide association scan signals. Hum Mol Genet 2010; 19:R137-44. [PMID: 20805105 PMCID: PMC2953742 DOI: 10.1093/hmg/ddq368] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have successfully identified a large number of genetic variants associated with complex traits, but these only explain a small proportion of the total heritability. It has been recently proposed that rare variants can create 'synthetic association' signals in GWAS, by occurring more often in association with one of the alleles of a common tag single nucleotide polymorphism. While the ultimate evaluation of this hypothesis will require the completion of large-scale sequencing studies, it is informative to place it in the broader context of what is known about the genetic architecture of complex disease. In this review, we draw from empirical and theoretical data to summarize evidence showing that synthetic associations do not underlie many reported GWAS associations.
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Affiliation(s)
- Gisela Orozco
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester, UK
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427
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The genetics of obsessive-compulsive disorder and Tourette syndrome: an epidemiological and pathway-based approach for gene discovery. J Am Acad Child Adolesc Psychiatry 2010; 49:810-9, 819.e1-2. [PMID: 20643314 DOI: 10.1016/j.jaac.2010.04.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 04/27/2010] [Accepted: 04/28/2010] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To provide a contemporary perspective on genetic discovery methods applied to obsessive-compulsive disorder (OCD) and Tourette syndrome (TS). METHOD A review of research trends in genetics research in OCD and TS is conducted, with emphasis on novel approaches. RESULTS Genome-wide association studies (GWAS) are now in progress in OCD and TS and will provide a platform for future discovery of common gene variants. Optimally, newer next-generation genome sequencing methods can also be used to detect larger effect genes (rare gene variants), taking advantage of pedigrees. Studies of gene networks or sets rather than individual genes will be required to elucidate biological etiology, as neural systems appear to act redundantly. Newer phenotyping strategies, such as symptom-based subtypes, cross-disorder latent class types, and intermediate phenotypes (endophenotypes) will need to be developed and tested to better align clinical and physiological measures with genetic architecture. CONCLUSION Although genetics research has made significant advances based on computational strength and bioinformatics advances, newer approaches to phenotyping and judicious study of gene etiological networks will be needed to uncover the genetic etiology of OCD and TS.
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428
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Cornelis MC, Nugent NR, Amstadter AB, Koenen KC. Genetics of post-traumatic stress disorder: review and recommendations for genome-wide association studies. Curr Psychiatry Rep 2010; 12:313-26. [PMID: 20549395 PMCID: PMC3108177 DOI: 10.1007/s11920-010-0126-6] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Post-traumatic stress disorder (PTSD) is a prevalent, disabling anxiety disorder that constitutes a major health care burden. Despite evidence supporting a genetic predisposition to PTSD, the precise genetic loci remain unclear. Herein we review the current state and limitations of genetic research on PTSD. Although recent years have seen an exponential increase in the number of studies examining the influence of candidate genes on PTSD diagnosis and symptomatology, most studies have been characterized by relatively low rates of PTSD, with apparent inconsistencies in gene associations linked to marked differences in methodology. We further discuss how current advances in the genetics field can be applied to studies of PTSD, emphasizing the need to adapt a genome-wide approach that facilitates discovery rather than hypothesis testing. Genome-wide association studies offer the best opportunity to identify novel "true" risk variants for the disorder that in turn has the potential to inform our understanding of PTSD etiology.
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Affiliation(s)
| | - Nicole R. Nugent
- Bradley/Hasbro Children’s Research Center of Rhode Island Hospital, Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
| | - Ananda B. Amstadter
- Department of Psychiatry, Medical University of South Carolina, Charleston, SC, USA
| | - Karestan C. Koenen
- Departments of Society, Human Development and Health and Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Kresge 613, Boston, MA 02115, USA
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429
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Abstract
PURPOSE OF REVIEW Elucidating the genetic background of Parkinson disease and essential tremor is crucial to understand the pathogenesis and improve diagnostic and therapeutic strategies. RECENT FINDINGS A number of approaches have been applied including familial and association studies, and studies of gene expression profiles to identify genes involved in susceptibility to Parkinson disease. These studies have nominated a number of candidate Parkinson disease genes and novel loci including Omi/HtrA2, GIGYF2, FGF20, PDXK, EIF4G1 and PARK16. A recent notable finding has been the confirmation for the role of heterozygous mutations in glucocerebrosidase (GBA) as risk factors for Parkinson disease. Finally, association studies have nominated genetic variation in the leucine-rich repeat and Ig containing 1 gene (LINGO1) as a risk for both Parkinson disease and essential tremor, providing the first genetic evidence of a link between the two conditions. SUMMARY Although undoubtedly genes remain to be identified, considerable progress has been achieved in the understanding of the genetic basis of Parkinson disease. This same effort is now required for essential tremor. The use of next-generation high-throughput sequencing and genotyping technologies will help pave the way for future insight leading to advances in diagnosis, prevention and cure.
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Affiliation(s)
- Christian Wider
- Division of Neurology, Department of Clinical Neuroscience, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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430
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Gandhi S, Wood NW. Genome-wide association studies: the key to unlocking neurodegeneration? Nat Neurosci 2010; 13:789-94. [PMID: 20581814 DOI: 10.1038/nn.2584] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The successful discovery of genes that cause rare monogenic disorders has dominated our understanding of the genetic basis of neurodegenerative disease. The emergence of robust genome-wide association methodologies promises to explain the genetic etiology of the common sporadic forms of complex diseases. In addition to revealing the genetic susceptibility of neurodegenerative disease, genome-wide association studies (GWASs) should also be an unbiased generator of molecules that are relevant in disease pathogenesis. Despite this exciting potential, GWAS results have varied in their consistency and their ability to deliver these aims. The largest challenge that faces neuroscientists is the interpretation of the results of GWASs and the translation of the genetic findings into functional mechanisms that are biologically important in disease pathogenesis and, ultimately, treatment design. We examine recent results from GWASs of Alzheimer's disease and Parkinson's disease and explore their use and limitations. We further reflect on how these results may expedite progress in understanding and influencing the molecular pathogenesis of neurodegeneration.
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Affiliation(s)
- Sonia Gandhi
- Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK
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431
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Lanktree MB, Hegele RA, Schork NJ, Spence JD. Extremes of unexplained variation as a phenotype: an efficient approach for genome-wide association studies of cardiovascular disease. ACTA ACUST UNITED AC 2010; 3:215-21. [PMID: 20407100 DOI: 10.1161/circgenetics.109.934505] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Matthew B Lanktree
- Department of Medicine, Robarts Research Institute, University of Western Ontario, London, Canada
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432
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Saus E, Soria V, Escaramís G, Vivarelli F, Crespo JM, Kagerbauer B, Menchón JM, Urretavizcaya M, Gratacòs M, Estivill X. Genetic variants and abnormal processing of pre-miR-182, a circadian clock modulator, in major depression patients with late insomnia. Hum Mol Genet 2010; 19:4017-25. [PMID: 20656788 DOI: 10.1093/hmg/ddq316] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Previous studies in mice have reported five different microRNAs (miRNAs; miR-219-1/132/183/96/182) to be modulators of the endogenous circadian clock and have presented experimental evidence for some of the genes involved in the molecular clock machinery as target sites. Moreover, disruption of circadian rhythms has long been implicated in the pathophysiology of major depression (MD). We investigated these miRNAs and some of their target sites at the sequence and functional levels as possible predisposing factors for susceptibility to MD and related chronobiological subphenotypes. Mutational screening was performed in a sample of 359 MD patients and 341 control individuals. We found a significant association between the T allele of the rs76481776 polymorphism in the pre-miR-182 and late insomnia in MD patients. Previous studies have reported an association between insomnia and CLOCK gene, a predicted miR-182 target site. A significant overexpression of miR-182 was detected by quantitative real-time polymerase chain reaction in cells transfected with the mutated form of the pre-miR-182 when compared with wild-type form. Moreover, a significant reduction in luciferase activity of plasmids with 3' UTR of ADCY6, CLOCK and DSIP genes was shown when transfecting cells with the mutated form of pre-miR-182 compared with cells that did not express miR-182. These data indicate that abnormal processing of pre-miR-182 in patients carrying the T allele of the rs76481776 polymorphism may contribute to the dysregulation of circadian rhythms in MD patients with insomnia, which could influence expression levels of the mature form of miR-182 and might increase downregulation in some of its target genes.
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Affiliation(s)
- Ester Saus
- Genes and Disease Program, Center for Genomic Regulation-UPF, and CIBER en Epidemiología y Salud Pública, Barcelona 08003, Catalonia, Spain
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433
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Mishmar D. The impact of darwinian evolution on medicine: the maternal side of the story. Rambam Maimonides Med J 2010; 1:e0010. [PMID: 23908782 PMCID: PMC3721657 DOI: 10.5041/rmmj.10010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Complex disorders are common in the human population and are caused by interplay between genetic and environmental factors. Therefore the quest for the genetic basis of such disorders has much similarity to deciphering the genetic basis of macro-evolutionary processes, such as speciation. Here I discuss conceptual connections between the principles underlying and processes occurring in disease and evolution. Special focus is given to the tremendous mitochondrial genetic variability in the population and within individuals and the impact of both types of variability on evolutionary processes and diseases.
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Affiliation(s)
- Dan Mishmar
- Department of Life Sciences and the National Institute of Biotechnology (NIBN), Ben-Gurion University of the Negev, Beer Sheva, Israel
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434
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Garner C. A statistical method for scanning the genome for regions with rare disease alleles. Genet Epidemiol 2010; 34:386-95. [DOI: 10.1002/gepi.20483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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435
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Inflammatory genetic markers of prostate cancer risk. Cancers (Basel) 2010; 2:1198-220. [PMID: 24281113 PMCID: PMC3835126 DOI: 10.3390/cancers2021198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 05/24/2010] [Accepted: 06/01/2010] [Indexed: 01/14/2023] Open
Abstract
Prostate cancer is the most common cancer in Western society males, with incidence rates predicted to rise with global aging. Etiology of prostate cancer is however poorly understood, while current diagnostic tools can be invasive (digital rectal exam or biopsy) and/or lack specificity for the disease (prostate-specific antigen (PSA) testing). Substantial histological, epidemiological and molecular genetic evidence indicates that inflammation is important in prostate cancer pathogenesis. In this review, we summarize the current status of inflammatory genetic markers influencing susceptibility to prostate cancer. The focus will be on inflammatory cytokines regulating T-helper cell and chemokine homeostasis, together with the Toll-like receptors as key players in the host innate immune system. Although association studies indicating a genetic basis for prostate cancer are presently limited mainly due to lack of replication, larger and more ethnically and clinically defined study populations may help elucidate the true contribution of inflammatory gene variants to prostate cancer risk.
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436
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Mirabello L, Berndt SI, Seratti GF, Burdett L, Yeager M, Chowdhury S, Teshome K, Uzoka A, Douglass C, Hayes RB, Hoover RN, Savage SA. Genetic variation at chromosome 8q24 in osteosarcoma cases and controls. Carcinogenesis 2010; 31:1400-4. [PMID: 20530236 DOI: 10.1093/carcin/bgq117] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Osteosarcoma is a primary bone malignancy that typically occurs during the pubertal growth spurt. Only a few small association studies have evaluated common germ line variation in individuals with osteosarcoma. The 8q24 chromosomal region contains several loci that are associated with risk of many different cancers. We conducted an association study of common single-nucleotide polymorphisms (SNPs) across 8q24 to explore the role this region may play in osteosarcoma risk. We genotyped 214 tag SNPs in 99 osteosarcoma cases and 1430 controls (65 controls from a hospital-based case-control study and 1365 controls from a population-based study). Additive, dominant and recessive genetic models were evaluated using unconditional logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Analyses of nine SNPs previously associated with cancer did not show strong statistically significant associations. Of the remaining 205 SNPs, 7 were statistically significant (P </= 0.05) in one or more genetic models; the most significant association was observed for the additive effect of the minor allele at rs896324 (OR 1.75, 95% CI 1.13-2.69, P = 0.01). This study suggests that several SNPs in 8q24 may be associated with osteosarcoma, but the susceptibility observed was modest. Future large studies of osteosarcoma genetic risk factors are warranted to improve our understanding of the genetic contribution to this cancer of adolescents and young adults.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20892, USA
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437
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Evolution and disease converge in the mitochondrion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1099-104. [DOI: 10.1016/j.bbabio.2010.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 12/31/2009] [Accepted: 01/07/2010] [Indexed: 11/18/2022]
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438
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Carvajal-Carmona LG. Challenges in the identification and use of rare disease-associated predisposition variants. Curr Opin Genet Dev 2010; 20:277-81. [DOI: 10.1016/j.gde.2010.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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439
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Cirulli ET, Goldstein DB. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 2010; 11:415-25. [PMID: 20479773 DOI: 10.1038/nrg2779] [Citation(s) in RCA: 821] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although genome-wide association (GWA) studies for common variants have thus far succeeded in explaining only a modest fraction of the genetic components of human common diseases, recent advances in next-generation sequencing technologies could rapidly facilitate substantial progress. This outcome is expected if much of the missing genetic control is due to gene variants that are too rare to be picked up by GWA studies and have relatively large effects on risk. Here, we evaluate the evidence for an important role of rare gene variants of major effect in common diseases and outline discovery strategies for their identification.
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Affiliation(s)
- Elizabeth T Cirulli
- Center for Human Genome Variation, Duke University Medical School, Durham, North Carolina 27708, USA
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440
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Turic D, Swanson J, Sonuga-Barke E. DRD4 and DAT1 in ADHD: Functional neurobiology to pharmacogenetics. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2010; 3:61-78. [PMID: 23226043 PMCID: PMC3513209 DOI: 10.2147/pgpm.s6800] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Indexed: 12/26/2022]
Abstract
Attention deficit/hyperactivity disorder (ADHD) is a common and potentially very impairing neuropsychiatric disorder of childhood. Statistical genetic studies of twins have shown ADHD to be highly heritable, with the combination of genes and gene by environment interactions accounting for around 80% of phenotypic variance. The initial molecular genetic studies where candidates were selected because of the efficacy of dopaminergic compounds in the treatment of ADHD were remarkably successful and provided strong evidence for the role of DRD4 and DAT1 variants in the pathogenesis of ADHD. However, the recent application of non-candidate gene strategies (eg, genome-wide association scans) has failed to identify additional genes with substantial genetic main effects, and the effects for DRD4 and DAT1 have not been replicated. This is the usual pattern observed for most other physical and mental disorders evaluated with current state-of-the-art methods. In this paper we discuss future strategies for genetic studies in ADHD, highlighting both the pitfalls and possible solutions relating to candidate gene studies, genome-wide studies, defining the phenotype, and statistical approaches.
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Affiliation(s)
- Darko Turic
- Institute for Disorders of Impulse and Attention, School of Psychology, University of Southampton, UK
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441
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Ku CS, Loy EY, Salim A, Pawitan Y, Chia KS. The discovery of human genetic variations and their use as disease markers: past, present and future. J Hum Genet 2010; 55:403-15. [DOI: 10.1038/jhg.2010.55] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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442
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Wang K, Dickson SP, Stolle CA, Krantz ID, Goldstein DB, Hakonarson H. Interpretation of association signals and identification of causal variants from genome-wide association studies. Am J Hum Genet 2010; 86:730-42. [PMID: 20434130 DOI: 10.1016/j.ajhg.2010.04.003] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 02/19/2010] [Accepted: 04/05/2010] [Indexed: 12/21/2022] Open
Abstract
GWAS have been successful in identifying disease susceptibility loci, but it remains a challenge to pinpoint the causal variants in subsequent fine-mapping studies. A conventional fine-mapping effort starts by sequencing dozens of randomly selected samples at susceptibility loci to discover candidate variants, which are then placed on custom arrays or used in imputation algorithms to find the causal variants. We propose that one or several rare or low-frequency causal variants can hitchhike the same common tag SNP, so causal variants may not be easily unveiled by conventional efforts. Here, we first demonstrate that the true effect size and proportion of variance explained by a collection of rare causal variants can be underestimated by a common tag SNP, thereby accounting for some of the "missing heritability" in GWAS. We then describe a case-selection approach based on phasing long-range haplotypes and sequencing cases predicted to harbor causal variants. We compare this approach with conventional strategies on a simulated data set, and we demonstrate its advantages when multiple causal variants are present. We also evaluate this approach in a GWAS on hearing loss, where the most common causal variant has a minor allele frequency (MAF) of 1.3% in the general population and 8.2% in 329 cases. With our case-selection approach, it is present in 88% of the 32 selected cases (MAF = 66%), so sequencing a subset of these cases can readily reveal the causal allele. Our results suggest that thinking beyond common variants is essential in interpreting GWAS signals and identifying causal variants.
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443
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Oberbauer AM, Belanger JM, Grossman DI, Regan KR, Famula TR. Genome-wide linkage scan for loci associated with epilepsy in Belgian shepherd dogs. BMC Genet 2010; 11:35. [PMID: 20441595 PMCID: PMC2877138 DOI: 10.1186/1471-2156-11-35] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 05/04/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Idiopathic epilepsy in the Belgian shepherd dog is known to have a substantial genetic component. The objective of this study was to identify genomic regions associated with the expression of generalized seizures in the Belgian Tervuren and Sheepdog. RESULTS DNA from 366 dogs, of which 74 were classified as epileptic, representing two extended families were subjected to a genome-wide linkage scan using 410 microsatellite markers yielding informative coverage averaging 5.95 +/- 0.21 Mb. Though previous studies based on pedigree analyses proposed a major gene of influence, the present study demonstrated the trait to be highly polygenic. Studies of complex disorders in humans indicate that a liberal composite evaluation of genetic linkage is needed to identify underlying quantitative trait loci (QTLs). Four chromosomes yielded tentative linkage based upon LOD scores in excess of 1.0. Possible QTLs within these regions were supported also by analyses of multipoint linkage, allele frequency, TDT, and transmission of haplotype blocks. CONCLUSIONS Taken together the data tentatively indicate six QTLs, three on CFA 2, and one on each of CFA 6, 12, and 37, that support fine mapping for mutations associated with epilepsy in the Belgian shepherd. The study also underscores the complexity of genomic linkage studies for polygenic disorders.
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Affiliation(s)
- Anita M Oberbauer
- Department of Animal Science, University of California, Davis, CA, USA.
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444
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Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, Boehnke M. Genome-wide association studies in diverse populations. Nat Rev Genet 2010; 11:356-66. [PMID: 20395969 PMCID: PMC3079573 DOI: 10.1038/nrg2760] [Citation(s) in RCA: 414] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genome-wide association (GWA) studies have identified a large number of SNPs associated with disease phenotypes. As most GWA studies have been performed in populations of European descent, this Review examines the issues involved in extending the consideration of GWA studies to diverse worldwide populations. Although challenges exist with issues such as imputation, admixture and replication, investigation of a greater diversity of populations could make substantial contributions to the goal of mapping the genetic determinants of complex diseases for the human population as a whole.
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Affiliation(s)
- Noah A Rosenberg
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.
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445
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Han F, Pan W. A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered 2010; 70:42-54. [PMID: 20413981 PMCID: PMC2912645 DOI: 10.1159/000288704] [Citation(s) in RCA: 241] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 02/05/2010] [Indexed: 12/14/2022] Open
Abstract
Since associations between complex diseases and common variants are typically weak, and approaches to genotyping rare variants (e.g. by next-generation resequencing) multiply, there is an urgent demand to develop powerful association tests that are able to detect disease associations with both common and rare variants. In this article we present such a test. It is based on data-adaptive modifications to a so-called Sum test originally proposed for common variants, which aims to strike a balance between utilizing information on multiple markers in linkage disequilibrium and reducing the cost of large degrees of freedom or of multiple testing adjustment. When applied to multiple common or rare variants in a candidate region, the proposed test is easy to use with 1 degree of freedom and without the need for multiple testing adjustment. We show that the proposed test has high power across a wide range of scenarios with either common or rare variants, or both. In particular, in some situations the proposed test performs better than several commonly used methods.
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Affiliation(s)
| | - Wei Pan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minn., USA
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446
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Vercelli D. Genetics and biology of asthma 2010: La' ci darem la mano... J Allergy Clin Immunol 2010; 125:347-8. [PMID: 20159243 DOI: 10.1016/j.jaci.2009.12.976] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 12/18/2009] [Indexed: 12/18/2022]
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447
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Abstract
It is now 5 years since the first genome-wide association studies (GWAS), published in 2005, identified a common risk allele with large effect size for age-related macular degeneration in a small sample set. Following this exciting finding, researchers have become optimistic about the prospect of the genome-wide association approach. However, most of the risk alleles identified in the subsequent GWAS for various complex diseases are common with small effect sizes (odds ratio <1.5). So far, more than 450 GWAS have been published and the associations of greater than 2000 single nucleotide polymorphisms (SNPs) or genetic loci were reported. The aim of this review paper is to give an overview of the evolving field of GWAS, discuss the progress that has been made by GWAS and some of the interesting findings, and summarize what we have learned over the past 5 years about the genetic basis of human complex diseases. This review will focus on GWAS of SNPs association for complex diseases but not studies of copy number variations.
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448
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Möller M, Hoal EG. Current findings, challenges and novel approaches in human genetic susceptibility to tuberculosis. Tuberculosis (Edinb) 2010; 90:71-83. [PMID: 20206579 DOI: 10.1016/j.tube.2010.02.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 02/03/2010] [Indexed: 12/22/2022]
Abstract
The evidence for a human genetic component in susceptibility to tuberculosis (TB) is incontrovertible. Quite apart from studies of rare disease events illustrating the importance of key genes in humans and animals, TB at the population level is also influenced by the genetics of the host. Heritability of disease concordance and immune responses to mycobacterial antigens has been clearly shown, and ranges up to 71%. Linkage studies, designed to identify major susceptibility genes in a disease, have produced a number of candidate loci but few, except for regions on chromosome 5p15, 20p and 20q, have been replicated. The region on 5p15 regulates the intensity of the response to the tuberculin skin test, and another locus on 11p14 appears to control resistance to the bacterium. In addition, numerous genes and pathways have been implicated in candidate gene association studies, with validation of polymorphisms in IFNG, NRAMP1, and NOS2A and equivocal results for IL10, CCL2, DC-SIGN, P2RX7, VDR, TLR2, TLR9 and SP110. Other more recently researched candidate genes such as TNFRSF1B remain to be validated, preferably in meta-analyses. New approaches have provided early evidence for the importance of gene-gene interactions in regulating resistance to disease, and also the prospect that applying host genetics in the field of vaccinomics could lead to a more targeted approach in designing interventions to aid the human immune system in combating mycobacteria. Genome-wide association studies and admixture mapping are approaches that remain to be applied to TB, and it is not clear, as is the case with other complex diseases, how much of the heritability of the TB susceptibility phenotype will be determined by multiple genes of small effect versus rare variants with disproportionately large effects.
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Affiliation(s)
- Marlo Möller
- Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology and the DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, P.O. Box 19063, Stellenbosch University, Tygerberg 7505, South Africa
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449
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Mir KU. Sequencing genomes: from individuals to populations. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2010; 8:367-78. [PMID: 19808932 DOI: 10.1093/bfgp/elp040] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The whole genome sequences of Jim Watson and Craig Venter are early examples of personalized genomics, which promises to change how we approach healthcare in the future. Before personal sequencing can have practical medical benefits, however, and before it should be advocated for implementation at the population-scale, there needs to be a better understanding of which genetic variants influence which traits and how their effects are modified by epigenetic factors. Nonetheless, for forging links between DNA sequence and phenotype, efforts to sequence the genomes of individuals need to continue; this includes sequencing sub-populations for association studies which analyse the difference in sequence between disease affected and unaffected individuals. Such studies can only be applied on a large enough scale to be effective if the massive strides in sequencing technology that have recently occurred also continue.
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Affiliation(s)
- Kalim U Mir
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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450
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Kiltie AE. Common predisposition alleles for moderately common cancers: bladder cancer. Curr Opin Genet Dev 2010; 20:218-24. [PMID: 20153630 DOI: 10.1016/j.gde.2010.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 01/20/2010] [Indexed: 11/30/2022]
Abstract
Bladder cancer is the 5th commonest cancer and two major risk factors are smoking and occupational chemical exposure. There is also evidence of a genetic component to its aetiology. Candidate gene studies have mostly focused on genes involved in adduct metabolism and DNA repair, including a recent consortium-based meta-analysis. Recently, two genome-wide association studies in bladder cancer have been published and a third is awaited with interest. These first two studies have identified three SNPs of genome-wide significance, two located within the 8q24 'gene desert'. These SNPs are positioned near or within loci of genes potentially implicated in cancer predisposition, namely MYC, TP63 and PSCA, although the functional significance of this is as yet unclear.
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Affiliation(s)
- Anne E Kiltie
- Gray Institute for Radiation Oncology and Biology, Old Road Campus Research Building, Headington, Oxford, United Kingdom.
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