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Liu LS, Wang D, Tang R, Wang Q, Zheng L, Wei J, Li Y, He XF. Individual and combined effects of the GSTM1, GSTT1, and GSTP1 polymorphisms on type 2 diabetes mellitus risk: A systematic review and meta-analysis. Front Genet 2022; 13:959291. [PMID: 36419826 PMCID: PMC9676647 DOI: 10.3389/fgene.2022.959291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/14/2022] [Indexed: 10/13/2023] Open
Abstract
Backgrounds: Compared with previously published meta-analyses, this is the first study to investigate the combined effects of glutathione-S-transferase polymorphisms (GSTM1, GSTT1 and GSTP1 IIe105Val) and type 2 diabetes mellitus (T2DM) risk; moreover, the credibility of statistically significant associations was assessed; furthermore, many new original studies were published. Objectives: To determine the relationship between GSTM1, GSTT1, and GSTP1 polymorphisms with T2DM risk. Methods: PubMed, Embase, Wanfang, and China National Knowledge Infrastructure Databases were searched. We quantify the relationship using crude odds ratios and their 95% confidence intervals Moreover, the Venice criteria, false-positive report probability (FPRP), and Bayesian false discovery probability (BFDP) were used to validate the significance of the results. Results: Overall, significantly increased T2DM risk was found between individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on T2DM risk, but, combined effects of the GSTT1 and GSTP1 polymorphisms was not statistically significant. GSTT1 gene polymorphism significantly increases the risk of T2DM complications, while GSTM1 and GSTP1 polymorphisms had no statistical significance. The GSTM1 null genotype was linked to a particularly increased risk of T2DM in Caucasians; the GSTT1 null genotype was connected to a significantly higher risk of T2DM in Asians and Indians; and the GSTP1 IIe105Val polymorphism was related to a substantially increased T2DM risk in Indians. Moreover, the GSTM1 and GSTT1 double null genotype was associated with substantially increased T2DM risk in Caucasians and Indians; the combined effects of GSTM1 and GSTP1 polymorphisms was associated with higher T2DM risk in Caucasians. However, all significant results were false when the Venice criteria, FPRP, and BFDP test were used (any FPRP >0.2 and BFDP value >0.8). Conclusion: The current analysis strongly suggests that the individual and combined effects of GSTM1, GSTT1 and GSTP1 polymorphisms might not be connected with elevated T2DM risk.
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Affiliation(s)
| | - Di Wang
- Changzhi Medical College, Changzhi, Shanxi, China
| | - Ru Tang
- Changzhi Medical College, Changzhi, Shanxi, China
| | - Qi Wang
- Changzhi Medical College, Changzhi, Shanxi, China
| | - Lu Zheng
- Department of Endocrinology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Jian Wei
- Department of Endocrinology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Yan Li
- Department of Endocrinology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Xiao-feng He
- Department of Epidemiology, School of Public Health to Southern Medical University, Guangzhou, Guangdong, China
- Institute of Evidence-Based Medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
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2
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Hearing loss drug discovery and medicinal chemistry: Current status, challenges, and opportunities. PROGRESS IN MEDICINAL CHEMISTRY 2022; 61:1-91. [PMID: 35753714 DOI: 10.1016/bs.pmch.2022.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Hearing loss is a severe high unmet need condition affecting more than 1.5 billion people globally. There are no licensed medicines for the prevention, treatment or restoration of hearing. Prosthetic devices, such as hearing aids and cochlear implants, do not restore natural hearing and users struggle with speech in the presence of background noise. Hearing loss drug discovery is immature, and small molecule approaches include repurposing existing drugs, combination therapeutics, late-stage discovery optimisation of known chemotypes for identified molecular targets of interest, phenotypic tissue screening and high-throughput cell-based screening. Hearing loss drug discovery requires the integration of specialist therapeutic area biology and otology clinical expertise. Small molecule drug discovery projects in the global clinical portfolio for hearing loss are here collated and reviewed. An overview is provided of human hearing, inner ear anatomy, inner ear delivery, types of hearing loss and hearing measurement. Small molecule experimental drugs in clinical development for hearing loss are reviewed, including their underpinning biology, discovery strategy and activities, medicinal chemistry, calculated physicochemical properties, pharmacokinetics and clinical trial status. SwissADME BOILED-Egg permeability modelling is applied to the molecules reviewed, and these results are considered. Non-small molecule hearing loss assets in clinical development are briefly noted in this review. Future opportunities in hearing loss drug discovery for human genomics and targeted protein degradation are highlighted.
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3
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Molitoris BA, Sandoval RM, Yadav SPS, Wagner MC. Albumin Uptake and Processing by the Proximal Tubule: Physiologic, Pathologic and Therapeutic Implications. Physiol Rev 2022; 102:1625-1667. [PMID: 35378997 PMCID: PMC9255719 DOI: 10.1152/physrev.00014.2021] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
For nearly 50 years the proximal tubule (PT) has been known to reabsorb, process, and either catabolize or transcytose albumin from the glomerular filtrate. Innovative techniques and approaches have provided insights into these processes. Several genetic diseases, nonselective PT cell defects, chronic kidney disease (CKD), and acute PT injury lead to significant albuminuria, reaching nephrotic range. Albumin is also known to stimulate PT injury cascades. Thus, the mechanisms of albumin reabsorption, catabolism, and transcytosis are being reexamined with the use of techniques that allow for novel molecular and cellular discoveries. Megalin, a scavenger receptor, cubilin, amnionless, and Dab2 form a nonselective multireceptor complex that mediates albumin binding and uptake and directs proteins for lysosomal degradation after endocytosis. Albumin transcytosis is mediated by a pH-dependent binding affinity to the neonatal Fc receptor (FcRn) in the endosomal compartments. This reclamation pathway rescues albumin from urinary losses and cellular catabolism, extending its serum half-life. Albumin that has been altered by oxidation, glycation, or carbamylation or because of other bound ligands that do not bind to FcRn traffics to the lysosome. This molecular sorting mechanism reclaims physiological albumin and eliminates potentially toxic albumin. The clinical importance of PT albumin metabolism has also increased as albumin is now being used to bind therapeutic agents to extend their half-life and minimize filtration and kidney injury. The purpose of this review is to update and integrate evolving information regarding the reabsorption and processing of albumin by proximal tubule cells including discussion of genetic disorders and therapeutic considerations.
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Affiliation(s)
- Bruce A. Molitoris
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
- Dept.of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Ruben M. Sandoval
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Shiv Pratap S. Yadav
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Mark C. Wagner
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
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4
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Zhang WP, Yang C, Xu LJ, Wang W, Song L, He XF. Individual and combined effects of GSTM1, GSTT1, and GSTP1 polymorphisms on lung cancer risk: A meta-analysis and re-analysis of systematic meta-analyses. Medicine (Baltimore) 2021; 100:e26104. [PMID: 34190143 PMCID: PMC8257913 DOI: 10.1097/md.0000000000026104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 12/12/2020] [Indexed: 01/04/2023] Open
Abstract
Thirty-five previous meta-analyses have been reported on the individual glutathione S-transferase M1 (GSTM1) present/null, glutathione S-transferase T1 (GSTT1) present/null, and glutathione S-transferase P1 (GSTP1) IIe105Val polymorphisms with lung cancer (LC) risk. However, they did not appraise the credibility and explore the combined effects between the 3 genes and LC risk.We performed a meta-analysis and re-analysis of systematic previous meta-analyses to solve the above problems.Meta-analyses of Observational Studies in Epidemiology guidelines were used. Moreover, we employed false-positive report probability (FPRP), Bayesian false discovery probability (BFDP), and the Venice criteria to verify the credibility of current and previous meta-analyses.Significantly increased LC risk was considered as "highly credible" or "positive" for GSTM1 null genotype in Japanese (odds ratio (OR) = 1.30, 95% confidence interval (CI) = 1.17-1.44, I2 = 0.0%, statistical power = 0.997, FPRP = 0.008, BFDP = 0.037, and Venice criteria: AAB), for GSTT1 null genotype in Asians (OR = 1.23, 95% CI = 1.12-1.36, I2 = 49.1%, statistical power = 1.000, FPRP = 0.051, BFDP = 0.771, and Venice criteria: ABB), especially Chinese populations (OR = 1.31, 95% CI = 1.16-1.49, I2 = 48.9%, Statistical power = 0.980, FPRP = 0.039, BFDP = 0.673, and Venice criteria: ABB), and for GSTP1 IIe105Val polymorphism in Asians (Val vs IIe: OR = 1.28, 95% CI = 1.17-1.42, I2 = 30.3%, statistical power = 0.999, FPRP = 0.003, BFDP = 0.183, and Venice criteria: ABB). Significantly increased lung adenocarcinoma (AC) risk was also considered as "highly credible" or "positive" in Asians for the GSTM1 (OR = 1.35, 95% CI = 1.22-1.48, I2 = 25.5%, statistical power = 0.988, FPRP < 0.001, BFDP < 0.001, and Venice criteria: ABB) and GSTT1 (OR = 1.36, 95% CI = 1.17-1.58, I2 = 30.2%, statistical power = 0.900, FPRP = 0.061, BFDP = 0.727, and Venice criteria: ABB) null genotype.This study indicates that GSTM1 null genotype is associated with increased LC risk in Japanese and lung AC risk in Asians; GSTT1 null genotype is associated with increased LC risk in Chinese, and GSTP1 IIe105Val polymorphism is associated with increased LC risk in Asians.
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Affiliation(s)
- Wen-Ping Zhang
- Department of Cardiothoracic Surgery, Heping Hospital Affiliated to Changzhi Medical College
| | - Chen Yang
- Teaching Reform Class of 2016 of the First Clinical College, Changzhi Medical College, Shanxi, Changzhi City
| | - Ling-Jun Xu
- Department of Pain Management, the First Affiliated Hospital, Jinan University, Guangzhou City
| | - Wei Wang
- Beijing Zhendong Guangming Pharmaceutical Research Institute Co Ltd, Beijing City
| | | | - Xiao-Feng He
- Department of Science and Education, Heping Hospital Affiliated to Changzhi Medical College, Shanxi, Changzhi City, PR China
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Tuna F, Doğanlar ZB, Özdemir H, Demirbag Kabayel D, Doğanlar O. Ehlers-Danlos syndrome-related genes and serum strontium, zinc, and lithium levels in generalized joint hypermobility: a case-control study. Connect Tissue Res 2021; 62:215-225. [PMID: 31594391 DOI: 10.1080/03008207.2019.1675648] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Aim of the study: Generalized joint hypermobility (GJH) is a common feature of almost all Ehlers-Danlos syndrome (EDS) types; however, its genetic basis remains unclear. Therefore, it is crucial to distinguish the genetic basis of GJH from other connective tissue disorders, including the different subtypes of EDS. The aim of this study was to determine the blood EDS-related gene expressions and serum element levels in GJH and reveal their predictive characteristics and correlations with the Beighton score. Materials and Methods: A total of 39 women aged 18-23 years with GJH and 38 age- and sex-matched controls were included in the study. Inductively coupled plasma mass spectrometry was used to analyze the serum levels of zinc (Zn), strontium (Sr), and lithium (Li). The relative expression levels of the EDS-related genes were determined using quantitative real-time polymerase chain reaction (PCR). Results: Our results showed that women with GJH possessed significantly lower Li and higher Zn and Sr levels than the controls. In addition, the gene expressions of TNXB and SLC39A13 were significantly higher, whereas those of COL1A1, COL1A2, COL5A1, FKBP14, and DSE were lower in the GJH group. Pearson correlation analyses revealed a strong negative correlation between the Beighton score and B4GALT7, FKBP14, COL1A1, and Li. However, a significant positive correlation was noted between the Beighton score and SLC39A13, TNXB, Zn, Sr, and B3GALT6. Conclusion: Our findings provide valuable basal levels for conducting gene function analysis of joint hypermobility-related connective tissue disorders.
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Affiliation(s)
- Filiz Tuna
- Department of Physical Medicine and Rehabilitation, Trakya University Faculty of Medicine , Edirne, Turkey
| | - Zeynep Banu Doğanlar
- Department of Medical Biology, Trakya Universtiy Faculty of Medicine , Edirne, Turkey
| | - Hande Özdemir
- Department of Physical Medicine and Rehabilitation, Trakya University Faculty of Medicine , Edirne, Turkey
| | - Derya Demirbag Kabayel
- Department of Physical Medicine and Rehabilitation, Trakya University Faculty of Medicine , Edirne, Turkey
| | - Oğuzhan Doğanlar
- Department of Medical Biology, Trakya Universtiy Faculty of Medicine , Edirne, Turkey
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6
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Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart defect, found in up to 2% of the population and associated with a 30% lifetime risk of complications. BAV is inherited as an autosomal dominant trait with incomplete penetrance and variable expressivity due to a complex genetic architecture that involves many interacting genes. In this review, we highlight the current state of knowledge about BAV genetics, principles and methods for BAV gene discovery, clinical applications of BAV genetics, and important future directions.
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7
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Cousins RPC. Medicines discovery for auditory disorders: Challenges for industry. THE JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 2019; 146:3652. [PMID: 31795652 DOI: 10.1121/1.5132706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Currently, no approved medicines are available for the prevention or treatment of hearing loss. Pharmaceutical industry productivity across all therapeutic indications has historically been disappointing, with a 90% chance of failure in delivering a marketed drug after entering clinical evaluation. To address these failings, initiatives have been applied in the three cornerstones of medicine discovery: target selection, clinical candidate selection, and clinical studies. These changes aimed to enable data-informed decisions on the translation of preclinical observations into a safe, clinically effective medicine by ensuring the best biological target is selected, the most appropriate chemical entity is advanced, and that the clinical studies enroll the correct patients. The specific underlying pathologies need to be known to allow appropriate patient selection, so improved diagnostics are required, as are methodologies for measuring in the inner ear target engagement, drug delivery and pharmacokinetics. The different therapeutic strategies of protecting hearing or preventing hearing loss versus restoring hearing are reviewed along with potential treatments for tinnitus. Examples of current investigational drugs are discussed to highlight key challenges in drug discovery and the learnings being applied to improve the probability of success of launching a marketed medicine.
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Affiliation(s)
- Rick P C Cousins
- University College London Ear Institute, University College London, London, WC1X 8EE, United Kingdom
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8
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Torres Cleuren YN, Ewe CK, Chipman KC, Mears ER, Wood CG, Al-Alami CEA, Alcorn MR, Turner TL, Joshi PM, Snell RG, Rothman JH. Extensive intraspecies cryptic variation in an ancient embryonic gene regulatory network. eLife 2019; 8:48220. [PMID: 31414984 PMCID: PMC6754231 DOI: 10.7554/elife.48220] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022] Open
Abstract
Innovations in metazoan development arise from evolutionary modification of gene regulatory networks (GRNs). We report widespread cryptic variation in the requirement for two key regulatory inputs, SKN-1/Nrf2 and MOM-2/Wnt, into the C. elegans endoderm GRN. While some natural isolates show a nearly absolute requirement for these two regulators, in others, most embryos differentiate endoderm in their absence. GWAS and analysis of recombinant inbred lines reveal multiple genetic regions underlying this broad phenotypic variation. We observe a reciprocal trend, in which genomic variants, or knockdown of endoderm regulatory genes, that result in a high SKN-1 requirement often show low MOM-2/Wnt requirement and vice-versa, suggesting that cryptic variation in the endoderm GRN may be tuned by opposing requirements for these two key regulatory inputs. These findings reveal that while the downstream components in the endoderm GRN are common across metazoan phylogeny, initiating regulatory inputs are remarkably plastic even within a single species.
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Affiliation(s)
- Yamila N Torres Cleuren
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Chee Kiang Ewe
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Kyle C Chipman
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Emily R Mears
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Cricket G Wood
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | | | - Melissa R Alcorn
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Thomas L Turner
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Pradeep M Joshi
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
| | - Russell G Snell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joel H Rothman
- Department of MCD Biology, University of California, Santa Barbara, Santa Barbara, United States.,School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, United States.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, United States
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9
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Elias SO, Sofola OA, Jaja SI. Epithelial sodium channel blockade and new β-ENaC polymorphisms among normotensive and hypertensive adult Nigerians. Clin Exp Hypertens 2018; 41:144-151. [PMID: 29580127 DOI: 10.1080/10641963.2018.1451538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We sought to determine the effect of amiloride on blood pressure (BP) and the presence of polymorphisms of the β-subunit of the epithelial sodium channel (ENaC) among normotensive (NT) and hypertensive (HT) Nigerians. Healthy volunteers-47 NT and 53 age-matched HT were recruited after giving informed consent. Subjects were salt-loaded with 200 mmol of NaCl daily for 5 days. Following a week washout period, salt-loading was repeated in addition to the administration of 5 mg amiloride daily for five days. Blood pressure, plasma and urine electrolytes were measured at baseline, after salt-loading and after salt-loading plus amiloride. PCR amplicons were sequenced for β-ENaC polymorphisms. Salt-loading led to a significant increase (p < 0.05) in SBP among NT and HT and in DBP (p < 0.001) only among HT. Amiloride reduced SBP and DBP to below baseline levels in NT (p < 0.05) and HT (p < 0.001) subjects. Five of the subjects had the β-T594M polymorphism, HT 3/53; NT 2/47 (p = 0.75). Four previously unreported β-ENaC mutations were recorded: E632V and E636V, respectively, among two HT subjects, D638Y in another HT and L628Q in one NT subject. We showed the presence of β-ENaC polymorphisms among our populace and the possible usefulness of amiloride as a single antihypertensive among Nigerians.
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Affiliation(s)
- Simiat O Elias
- Department of Physiology, Lagos State University College of Medicine, Lagos, Nigeria
| | - Olusoga A Sofola
- Department of Physiology, College of Medicine University of Lagos, Lagos, Nigeria
| | - Smith I Jaja
- Department of Physiology, College of Medicine University of Lagos, Lagos, Nigeria
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10
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Wiles BM, Llewellyn-Zaidi AM, Evans KM, O'Neill DG, Lewis TW. Large-scale survey to estimate the prevalence of disorders for 192 Kennel Club registered breeds. Canine Genet Epidemiol 2017; 4:8. [PMID: 28932406 PMCID: PMC5604186 DOI: 10.1186/s40575-017-0047-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/29/2017] [Indexed: 11/16/2022] Open
Abstract
Background Pedigree or purebred dogs are often stated to have high prevalence of disorders which are commonly assumed to be a consequence of inbreeding and selection for exaggerated features. However, few studies empirically report and rank the prevalence of disorders across breeds although such data are of critical importance in the prioritisation of multiple health concerns, and to provide a baseline against which to explore changes over time. This paper reports an owner survey that gathered disorder information on Kennel Club registered pedigree dogs, regardless of whether these disorders received veterinary care. This study aimed to determine the prevalence of disorders among pedigree dogs overall and, where possible, determine any variation among breeds. Results This study included morbidity data on 43,005 live dogs registered with the Kennel Club. Just under two thirds of live dogs had no reported diseases/conditions. The most prevalent diseases/conditions overall were lipoma (4.3%; 95% confidence interval 4.13-4.52%), skin (cutaneous) cyst (3.1%; 2.94-3.27%) and hypersensitivity (allergic) skin disorder (2.7%; 2.52-2.82%). For the most common disorders in the most represented breeds, 90 significant differences between the within breed prevalence and the overall prevalence are reported. Conclusion The results from this study have added vital epidemiological data on disorders in UK dogs. It is anticipated that these results will contribute to the forthcoming Breed Health & Conservation Plans, a Kennel Club initiative aiming to assist in the identification and prioritisation of breeding selection objectives for health and provide advice to breeders/owners regarding steps that may be taken to minimise the risk of the disease/disorders. Future breed-specific studies are recommended to report more precise prevalence estimates within more breeds. Electronic supplementary material The online version of this article (doi:10.1186/s40575-017-0047-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B M Wiles
- The Kennel Club, Clarges Street, London, W1J 8AB England, UK
| | - A M Llewellyn-Zaidi
- International Partnership for Dogs, 504547 Grey Rd 1, Georgia Bluffs, ON England, UK
| | - K M Evans
- The Kennel Club, Clarges Street, London, W1J 8AB England, UK.,School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD England, UK
| | - D G O'Neill
- Veterinary Epidemiology, Economics and Public Health, Royal Veterinary College, London, NW1 0TU UK
| | - T W Lewis
- The Kennel Club, Clarges Street, London, W1J 8AB England, UK.,School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD England, UK
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11
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Gall T, Valkanas E, Bello C, Markello T, Adams C, Bone WP, Brandt AJ, Brazill JM, Carmichael L, Davids M, Davis J, Diaz-Perez Z, Draper D, Elson J, Flynn ED, Godfrey R, Groden C, Hsieh CK, Fischer R, Golas GA, Guzman J, Huang Y, Kane MS, Lee E, Li C, Links AE, Maduro V, Malicdan MCV, Malik FS, Nehrebecky M, Park J, Pemberton P, Schaffer K, Simeonov D, Sincan M, Smedley D, Valivullah Z, Wahl C, Washington N, Wolfe LA, Xu K, Zhu Y, Gahl WA, Tifft CJ, Toro C, Adams DR, He M, Robinson PN, Haendel MA, Zhai RG, Boerkoel CF. Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience. Front Med (Lausanne) 2017; 4:62. [PMID: 28603714 PMCID: PMC5445140 DOI: 10.3389/fmed.2017.00062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/03/2017] [Indexed: 12/13/2022] Open
Abstract
Traditionally, the use of genomic information for personalized medical decisions relies on prior discovery and validation of genotype-phenotype associations. This approach constrains care for patients presenting with undescribed problems. The National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) hypothesized that defining disease as maladaptation to an ecological niche allows delineation of a logical framework to diagnose and evaluate such patients. Herein, we present the philosophical bases, methodologies, and processes implemented by the NIH UDP. The NIH UDP incorporated use of the Human Phenotype Ontology, developed a genomic alignment strategy cognizant of parental genotypes, pursued agnostic biochemical analyses, implemented functional validation, and established virtual villages of global experts. This systematic approach provided a foundation for the diagnostic or non-diagnostic answers provided to patients and serves as a paradigm for scalable translational research.
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Affiliation(s)
- Timothy Gall
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Elise Valkanas
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Christofer Bello
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Thomas Markello
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Christopher Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - William P. Bone
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Alexander J. Brandt
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Jennifer M. Brazill
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | | | - Mariska Davids
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Joie Davis
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Zoraida Diaz-Perez
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - David Draper
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | | | - Elise D. Flynn
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Rena Godfrey
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Catherine Groden
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | | | - Roxanne Fischer
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Gretchen A. Golas
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Jessica Guzman
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Yan Huang
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Megan S. Kane
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Elizabeth Lee
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Chong Li
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Amanda E. Links
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Valerie Maduro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - May Christine V. Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Fayeza S. Malik
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Michele Nehrebecky
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Joun Park
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Paul Pemberton
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Katherine Schaffer
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Dimitre Simeonov
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Murat Sincan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Damian Smedley
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Zaheer Valivullah
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Colleen Wahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Nicole Washington
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lynne A. Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Karen Xu
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Yi Zhu
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Cynthia J. Tifft
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Camillo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - David R. Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Miao He
- Palmieri Metabolic Disease Laboratory, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Melissa A. Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
| | - R. Grace Zhai
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Cornelius F. Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
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Su S, Zhang C, Zhang F, Li H, Yang X, Tang X. The association between leptin receptor gene polymorphisms and type 2 diabetes mellitus: A systematic review and meta-analysis. Diabetes Res Clin Pract 2016; 121:49-58. [PMID: 27657457 DOI: 10.1016/j.diabres.2016.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/30/2016] [Accepted: 08/19/2016] [Indexed: 01/23/2023]
Abstract
BACKGROUND Several case-control studies have demonstrated a relationship between leptin receptor (LEPR) gene polymorphism and type 2 diabetes mellitus (T2DM) risk, though the results have not always been consistent among diverse populations. This meta-analysis was designed to assess a more accurate association between LEPR polymorphism and T2DM. METHODS Eight electronic databases were consulted and researchers searched for Chinese and English peer-reviewed articles, published between 2000 and 2015, that referred to the association between LEPR polymorphism and T2DM. Pooled odds ratios (OR) with a 95% confidence interval (CI) were calculated in allele contrast, recessive, dominant and additive genetic models to assess this association. RESULTS Four repeatedly reviewed polymorphisms, taken from 22 studies on Arg109Lys, Asn656Lys, Gln223Arg and Pro1019Pro with 31,260 controls and 25,560 cases, were included in the meta-analysis model. The meta-result demonstrated that only the Pro1019Pro polymorphism was substantially associated with T2DM risk-G vs. A: OR with 95% CI 0.58 (0.43-0.79), Z=3.51, p=0.0005; GG vs. AG+AA: 0.57 (0.42-0.77), Z=3.66, p=0.0002; GG+AG vs. AA: 0.55 (0.37-0.81), Z=3.01, p=0.003; GG vs. AA: 0.51 (0.37-0.69), Z=4.24, p<0.001. CONCLUSIONS Our meta-analysis suggested a significant association between the LEPR Pro1019Pro polymorphism and T2DM risk. Thus, targeted healthcare should be strengthened with regard to this gene carrier in order to prevent T2DM.
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Affiliation(s)
- Shu Su
- Department of Epidemiology, School of Public Health and Management, Collaborative Innovation Center of Social Risks Governance in Health, Chongqing Medical University, Chongqing, China; School of Public Health and Preventive Medicine, Alfred Center, Monash University, Melbourne, Australia
| | - Chunhua Zhang
- Department of Epidemiology, School of Public Health and Management, Collaborative Innovation Center of Social Risks Governance in Health, Chongqing Medical University, Chongqing, China
| | - Fan Zhang
- Department of Epidemiology, School of Public Health and Management, Collaborative Innovation Center of Social Risks Governance in Health, Chongqing Medical University, Chongqing, China
| | - Hui Li
- Department of Epidemiology, School of Public Health and Management, Collaborative Innovation Center of Social Risks Governance in Health, Chongqing Medical University, Chongqing, China
| | - Xuewei Yang
- Department of Epidemiology, School of Public Health and Management, Collaborative Innovation Center of Social Risks Governance in Health, Chongqing Medical University, Chongqing, China
| | - Xiaojun Tang
- Department of Epidemiology, School of Public Health and Management, Collaborative Innovation Center of Social Risks Governance in Health, Chongqing Medical University, Chongqing, China.
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Li Z, Ding C, Gong X, Wang X, Cui T. Apolipoprotein E ε4 Allele was Associated With Nonlesional Mesial Temporal Lobe Epilepsy in Han Chinese Population. Medicine (Baltimore) 2016; 95:e2894. [PMID: 26945380 PMCID: PMC4782864 DOI: 10.1097/md.0000000000002894] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Apolipoprotein E (APOE) gene has been implicated as one of the genes susceptible to temporal lobe epilepsy (TLE), but the association is inconsistent. We carried out a study to investigate the association of APOEε4 allele with a subtype of TLE-nonlesional mesial temporal lobe epilepsy (NLMTLE) in Han Chinese people.T he study consisted of total 308 NLMTLE patients and 302 controls in Han Chinese. The APOE polymorphisms were genotyped using polymerase chain reaction (PCR) DNA sequencing. We compared the frequency of APOEε4 allele and carrying status between NLMTLE patients and control subjects to test for the association of APOEε4 allele with NLMTLE clinical status. Carrying status of APOEε4 allele was significantly associated with the risk of NLMTLE. No effect of APOEε4 allele was found on the age of onset, duration of epilepsy, or frequency of seizure. Moreover, there was no association between APOEε4 allele and hippocampal sclerosis (HS) or febrile convulsion (FC) history.O ur study provided an evidence that APOEε4 allele was a possible risk factor for NLMTLE, and further study with a larger sample is needed to warrant this finding.
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Affiliation(s)
- Zhimei Li
- From the Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, China National Clinical Research Center for Neurological Diseases (ZL, XG, TC); Department of Neurology, The 301 PLG General Hospital (CD); and Department of Sociology (XW), Peking University, Beijing, China
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Gonzalez GH, Tahsin T, Goodale BC, Greene AC, Greene CS. Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery. Brief Bioinform 2015; 17:33-42. [PMID: 26420781 PMCID: PMC4719073 DOI: 10.1093/bib/bbv087] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Indexed: 02/06/2023] Open
Abstract
Precision medicine will revolutionize the way we treat and prevent disease. A major barrier to the implementation of precision medicine that clinicians and translational scientists face is understanding the underlying mechanisms of disease. We are starting to address this challenge through automatic approaches for information extraction, representation and analysis. Recent advances in text and data mining have been applied to a broad spectrum of key biomedical questions in genomics, pharmacogenomics and other fields. We present an overview of the fundamental methods for text and data mining, as well as recent advances and emerging applications toward precision medicine.
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Bridging the gap between statistical and biological epistasis in Alzheimer's disease. BIOMED RESEARCH INTERNATIONAL 2015; 2015:870123. [PMID: 26075270 PMCID: PMC4449899 DOI: 10.1155/2015/870123] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/05/2015] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease affects millions of people worldwide and incidence is expected to rise as the population ages, but no effective therapies exist despite decades of research and more than 20 known disease markers. Research has shown that Alzheimer's disease's missing heritability remains extensive with an estimated 25% of phenotypic variance unexplained by known variants. The missing heritability may be explained by missing variants or by epistasis. Researchers often focus on individual loci rather than epistatic interactions, which is likely an oversimplification of the underlying biology since most phenotypes are affected by multiple genes. Focusing research efforts on epistasis will be critical to resolving Alzheimer's disease etiology, and a major key to identifying and properly interpreting key epistatic interactions will be bridging the gap between statistical and biological epistasis. This review covers the current state of epistasis research in Alzheimer's disease and how researchers can bridge the gap between statistical and biological epistasis to help resolve Alzheimer's disease etiology.
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O′Neill DG, Church DB, McGreevy PD, Thomson PC, Brodbelt DC. Prevalence of disorders recorded in dogs attending primary-care veterinary practices in England. PLoS One 2014; 9:e90501. [PMID: 24594665 PMCID: PMC3942437 DOI: 10.1371/journal.pone.0090501] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 02/03/2014] [Indexed: 01/17/2023] Open
Abstract
Purebred dog health is thought to be compromised by an increasing occurence of inherited diseases but inadequate prevalence data on common disorders have hampered efforts to prioritise health reforms. Analysis of primary veterinary practice clinical data has been proposed for reliable estimation of disorder prevalence in dogs. Electronic patient record (EPR) data were collected on 148,741 dogs attending 93 clinics across central and south-eastern England. Analysis in detail of a random sample of EPRs relating to 3,884 dogs from 89 clinics identified the most frequently recorded disorders as otitis externa (prevalence 10.2%, 95% CI: 9.1-11.3), periodontal disease (9.3%, 95% CI: 8.3-10.3) and anal sac impaction (7.1%, 95% CI: 6.1-8.1). Using syndromic classification, the most prevalent body location affected was the head-and-neck (32.8%, 95% CI: 30.7-34.9), the most prevalent organ system affected was the integument (36.3%, 95% CI: 33.9-38.6) and the most prevalent pathophysiologic process diagnosed was inflammation (32.1%, 95% CI: 29.8-34.3). Among the twenty most-frequently recorded disorders, purebred dogs had a significantly higher prevalence compared with crossbreds for three: otitis externa (P = 0.001), obesity (P = 0.006) and skin mass lesion (P = 0.033), and popular breeds differed significantly from each other in their prevalence for five: periodontal disease (P = 0.002), overgrown nails (P = 0.004), degenerative joint disease (P = 0.005), obesity (P = 0.001) and lipoma (P = 0.003). These results fill a crucial data gap in disorder prevalence information and assist with disorder prioritisation. The results suggest that, for maximal impact, breeding reforms should target commonly-diagnosed complex disorders that are amenable to genetic improvement and should place special focus on at-risk breeds. Future studies evaluating disorder severity and duration will augment the usefulness of the disorder prevalence information reported herein.
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Affiliation(s)
- Dan G. O′Neill
- Veterinary Epidemiology, Economics and Public Health, Royal Veterinary College, London, United Kingdom
| | - David B. Church
- Small Animal Medicine and Surgery Group, Royal Veterinary College, London, United Kingdom
| | - Paul D. McGreevy
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Peter C. Thomson
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Dave C. Brodbelt
- Veterinary Epidemiology, Economics and Public Health, Royal Veterinary College, London, United Kingdom
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Bernig T, Chanock SJ. Challenges of SNP genotyping and genetic variation: its future role in diagnosis and treatment of cancer. Expert Rev Mol Diagn 2014; 6:319-31. [PMID: 16706736 DOI: 10.1586/14737159.6.3.319] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Thorough annotation of common germline genetic variation in the human genome has generated a foundation for the investigation of the contribution of genetics to the etiology and pathogenesis of cancer. For many malignancies, it has become increasingly apparent that numerous alleles, with small-to-moderate effects, additively contribute to cancer susceptibility. The most common genetic variant in the genome, the single nucleotide polymorphism, is of special interest for the study of susceptibility to and protection from cancer. Similarly, intense effort has focused on genetic variants that can predict either response or toxicity to therapeutic interventions. This review discusses the challenges and prospects of genetic association studies in cancer research. On the basis of recent changes in genomics and high-throughput genotyping platforms, future genetic findings of association studies could impact clinical care and public health screening.
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Affiliation(s)
- Toralf Bernig
- National Cancer Institute, Section on Genomic Variation, Pediatric Oncology Branch, National Institutes of Health, Bethesda, MD 20892-4605, USA.
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Hicks C, Miele L, Koganti T, Vijayakumar S. Comprehensive assessment and network analysis of the emerging genetic susceptibility landscape of prostate cancer. Cancer Inform 2013; 12:175-91. [PMID: 24031161 PMCID: PMC3769142 DOI: 10.4137/cin.s12128] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Recent advances in high-throughput genotyping have made possible identification of genetic variants associated with increased risk of developing prostate cancer using genome-wide associations studies (GWAS). However, the broader context in which the identified genetic variants operate is poorly understood. Here we present a comprehensive assessment, network, and pathway analysis of the emerging genetic susceptibility landscape of prostate cancer. Methods We created a comprehensive catalog of genetic variants and associated genes by mining published reports and accompanying websites hosting supplementary data on GWAS. We then performed network and pathway analysis using single nucleotide polymorphism (SNP)-containing genes to identify gene regulatory networks and pathways enriched for genetic variants. Results We identified multiple gene networks and pathways enriched for genetic variants including IGF-1, androgen biosynthesis and androgen signaling pathways, and the molecular mechanisms of cancer. The results provide putative functional bridges between GWAS findings and gene regulatory networks and biological pathways.
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Affiliation(s)
- Chindo Hicks
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS. ; Department of Medicine, University of Mississippi Medical Center, Jackson, MS. ; Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS
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Arceo ME, Ernst CW, Lunney JK, Choi I, Raney NE, Huang T, Tuggle CK, Rowland RRR, Steibel JP. Characterizing differential individual response to porcine reproductive and respiratory syndrome virus infection through statistical and functional analysis of gene expression. Front Genet 2013; 3:321. [PMID: 23335940 PMCID: PMC3546301 DOI: 10.3389/fgene.2012.00321] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/23/2012] [Indexed: 12/20/2022] Open
Abstract
We evaluated differences in gene expression in pigs from the Porcine Reproductive and Respiratory Syndrome (PRRS) Host Genetics Consortium initiative showing a range of responses to PRRS virus infection. Pigs were allocated into four phenotypic groups according to their serum viral level and weight gain. RNA obtained from blood at 0, 4, 7, 11, 14, 28, and 42 days post-infection (DPI) was hybridized to the 70-mer 20K Pigoligoarray. We used a blocked reference design for the microarray experiment. This allowed us to account for individual biological variation in gene expression, and to assess baseline effects before infection (0 DPI). Additionally, this design has the flexibility of incorporating future data for differential expression analysis. We focused on evaluating transcripts showing significant interaction of weight gain and serum viral level. We identified 491 significant comparisons [false discovery rate (FDR) = 10%] across all DPI and phenotypic groups. We corroborated the overall trend in direction and level of expression (measured as fold change) at 4 DPI using qPCR (r = 0.91, p ≤ 0.0007). At 4 and 7 DPI, network and functional analyses were performed to assess if immune related gene sets were enriched for genes differentially expressed (DE) across four phenotypic groups. We identified cell death function as being significantly associated (FDR ≤ 5%) with several networks enriched for DE transcripts. We found the genes interferon-alpha 1(IFNA1), major histocompatibility complex, class II, DQ alpha 1 (SLA-DQA1), and major histocompatibility complex, class II, DR alpha (SLA-DRA) to be DE (p ≤ 0.05) between phenotypic groups. Finally, we performed a power analysis to estimate sample size and sampling time-points for future experiments. We concluded the best scenario for investigation of early response to PRRSV infection consists of sampling at 0, 4, and 7 DPI using about 30 pigs per phenotypic group.
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Affiliation(s)
- Maria E Arceo
- Department of Animal Science, Michigan State University East Lansing, MI, USA
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Cuypers KF, Loos RJF, Kvaløy K, Kulle B, Romundstad P, Holmen TL. Obesity-susceptibility loci and their influence on adiposity-related traits in transition from adolescence to adulthood--the HUNT study. PLoS One 2012; 7:e46912. [PMID: 23094032 PMCID: PMC3477114 DOI: 10.1371/journal.pone.0046912] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 09/06/2012] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Obesity-susceptibility loci have been related to adiposity traits in adults and may affect body fat estimates in adolescence. There are indications that different sets of obesity-susceptibility loci influence level of and change in obesity-related traits from adolescence to adulthood. OBJECTIVES To investigate whether previously reported obesity-susceptible loci in adults influence adiposity traits in adolescence and change in BMI and waist circumference (WC) from adolescence into young adulthood. We also examined whether physical activity modifies the effects of these genetic loci on adiposity-related traits. METHODS Nine obesity-susceptibility variants were genotyped in 1 643 adolescents (13-19 years old) from the HUNT study, Norway, who were followed-up into young adulthood. Lifestyle was assessed using questionnaires and anthropometric measurements were taken. The effects of genetic variants individually and combined in a genetic predisposition score (GPS) on obesity-related traits were studied cross-sectionally and longitudinally. A modifying effect of physical activity was tested. RESULTS The GPS was significantly associated to BMI (B: 0.046 SD/allele [0.020, 0.073], p = 0.001) in adolescence and in young adulthood (B: 0.041 SD/allele [0.015, 0.067], p = 0.002) as it was to waist circumference (WC). The GPS was not associated to change in BMI (p = 0.762) or WC (p = 0.726). We found no significant interaction effect between the GPS and physical activity. CONCLUSIONS Our observations suggest that obesity-susceptibility loci established in adults affect BMI and WC already in adolescence. However, an association with change in adiposity-related traits from adolescence to adulthood could not be verified for these loci. Neither could an attenuating effect of physical activity on the association between the obesity-susceptibility genes and body fat estimates be revealed.
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Affiliation(s)
- Koenraad Frans Cuypers
- HUNT Research Center, Levanger, Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
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Abstract
Summary Background Several studies have reported that HLA-DRB1 may be correlated with pemphigus vulgaris (PV), but most have been based on small samples and the results remain inconsistent and unclear. Objectives To investigate the correlation between DRB1 and PV by a meta-analysis of case–control/nonfamily studies. Methods PubMed, Wiley Online Library, ScienceDirect, Google Scholar, Cochrane Library, Chinese National Knowledge Infrastructure and Wanfang databases were searched for studies including: (i) ‘pemphigus’; and (ii) ‘human leukocyte antigen’, ‘HLA’, ‘major histocompatibility complex’, ‘MHC’ or ‘DRB1’. Eighteen selected studies were used in meta-analyses to evaluate DRB1 alleles and phenotypes by calculating the respective odds ratios (ORs) and 95% confidence intervals (CIs). Stratified meta-analyses and meta-regression analysis were also conducted. Results The frequencies of three genotypes (allele and phenotype, respectively) were significantly increased in PV: DRB1*04 [P-value for comparability (Pc) < 0·00001, OR 3·61, 95% CI 2·28–5·71; Pc = 0·0002, OR 4·14, 95% CI 1·98–8·65], DRB1*08 (Pc = 0·03, OR 2·25, 95% CI 1·07–4·70; Pc = 0·0003, OR 2·46, 95% CI 1·51–4·01) and DRB1*14 (Pc < 0·00001, OR 6·47, 95% CI 4·52–9·26; Pc < 0·00001, OR 9·68, 95% CI 4·47–20·98). Three others (allele and phenotype, respectively) were significantly decreased in PV: DRB1*03 (Pc < 0·00001, OR 0·28, 95% CI 0·19–0·41; Pc = 0·0001, OR 0·25, 95% CI 0·12–0·51), DRB1*07 (Pc = 0·004, OR 0·45, 95% CI 0·26–0·78; Pc = 0·0002, OR 0·27, 95% CI 0·14–0·54) and DRB1*15 (Pc = 0·001, OR 0·35, 95% CI 0·18–0·66; Pc = 0·002, OR 0·32, 95% CI 0·16–0·65). Ethnicity partially explained the heterogeneity of DRB1*07, DRB1*08 and DRB1*14 phenotypes. Conclusions Our findings suggest that DRB1*04, DRB1*08 and DRB1*14 are statistically significant susceptibility factors for PV. Conversely, DRB1*03, DRB1*07 and DRB1*15 may be negatively associated with PV. Specific HLA-DRB1 types may influence the susceptibility or resistance to PV, which needs further investigations.
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Affiliation(s)
- L Yan
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Baiyun District, Guangzhou, Guangdong Province, 510515, China
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Li A, Meyre D. Challenges in reproducibility of genetic association studies: lessons learned from the obesity field. Int J Obes (Lond) 2012; 37:559-67. [DOI: 10.1038/ijo.2012.82] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Abstract
Recent advances in Molecular Biology and improvements in microarray and sequencing technologies have led biologists toward high-throughput genomic studies. These studies aim at finding associations between genetic markers and a phenotype and involve conducting many statistical tests on these markers. Such Please confirm the changes in the sentence "Such a wide..." a wide investigation of the genome not only renders genomic studies quite attractive but also lead to a major shortcoming. That is, among the markers detected as associated with the phenotype, a nonnegligible proportion is not in reality (false-positives) and also true associations can be missed (false-negatives). A main cause of these spurious associations is due to the multiple-testing problem, inherent to conducting numerous statistical tests. Several approaches exist to work around this issue. These multiple-testing adjustments aim at defining new statistical confidence measures that are controlled to guarantee that the outcomes of the tests are pertinent.The most natural correction was introduced by Bonferroni and aims at controlling the family-wise error-rate (FWER) that is the probability of having at least one false-positive. Another approach is based on the false-discovery-rate (FDR) and considers the proportion of significant results that are expected to be false-positives. Finally, the local-FDR focuses on the actual probability for a marker of being associated or not with the phenotype. These strategies are widely used but one has to be careful about when and how to apply them. We propose in this chapter a discussion on the multiple-testing issue and on the main approaches to take it into account. We aim at providing a theoretical and intuitive definition of these concepts along with practical advises to guide researchers in choosing the more appropriate multiple-testing procedure corresponding to the purposes of their studies.
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Bouaziz M, Ambroise C, Guedj M. Accounting for population stratification in practice: a comparison of the main strategies dedicated to genome-wide association studies. PLoS One 2011; 6:e28845. [PMID: 22216125 PMCID: PMC3244428 DOI: 10.1371/journal.pone.0028845] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 11/16/2011] [Indexed: 01/06/2023] Open
Abstract
Genome-Wide Association Studies are powerful tools to detect genetic variants associated with diseases. Their results have, however, been questioned, in part because of the bias induced by population stratification. This is a consequence of systematic differences in allele frequencies due to the difference in sample ancestries that can lead to both false positive or false negative findings. Many strategies are available to account for stratification but their performances differ, for instance according to the type of population structure, the disease susceptibility locus minor allele frequency, the degree of sampling imbalanced, or the sample size. We focus on the type of population structure and propose a comparison of the most commonly used methods to deal with stratification that are the Genomic Control, Principal Component based methods such as implemented in Eigenstrat, adjusted Regressions and Meta-Analyses strategies. Our assessment of the methods is based on a large simulation study, involving several scenarios corresponding to many types of population structures. We focused on both false positive rate and power to determine which methods perform the best. Our analysis showed that if there is no population structure, none of the tests led to a bias nor decreased the power except for the Meta-Analyses. When the population is stratified, adjusted Logistic Regressions and Eigenstrat are the best solutions to account for stratification even though only the Logistic Regressions are able to constantly maintain correct false positive rates. This study provides more details about these methods. Their advantages and limitations in different stratification scenarios are highlighted in order to propose practical guidelines to account for population stratification in Genome-Wide Association Studies.
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Madsen AM, Hodge SE, Ottman R. Causal models for investigating complex disease: I. A primer. Hum Hered 2011; 72:54-62. [PMID: 21912138 DOI: 10.1159/000330779] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Accepted: 07/11/2011] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND/AIMS To illustrate the utility of causal models for research in genetic epidemiology and statistical genetics. Causal models are increasingly applied in risk factor epidemiology, economics, and health policy, but seldom used in statistical genetics or genetic epidemiology. Unlike the statistical models usually used in genetic epidemiology, causal models are explicitly formulated in terms of cause and effect relationships occurring at the individual level. METHODS We describe two causal models, the sufficient component cause model and the potential outcomes model, and show how key concepts in genetic epidemiology, including penetrance, phenocopies, genetic heterogeneity, etiologic heterogeneity, gene-gene interaction, and gene-environment interaction, can be framed in terms of these causal models. We also illustrate how potential outcomes models can provide insight into the potential for confounding and bias in the measurement of causal effects in genetic studies. RESULTS Our analysis illustrates how causal models can elucidate the relationships among underlying causal mechanisms and measures obtained from statistical analysis of observed data. CONCLUSION Causal models can enhance research aimed at identifying causal genes.
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Affiliation(s)
- Ann M Madsen
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
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Rosenfeld G, Bressler B. Mycobacterium avium paratuberculosis and the etiology of Crohn's disease: a review of the controversy from the clinician's perspective. CANADIAN JOURNAL OF GASTROENTEROLOGY = JOURNAL CANADIEN DE GASTROENTEROLOGIE 2010; 24:619-24. [PMID: 21037992 PMCID: PMC2975476 DOI: 10.1155/2010/698362] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 02/11/2010] [Indexed: 11/18/2022]
Abstract
Mycobacterium avium paratuberculosis (MAP) is an obligate intracellular organism that has frequently been associated with Crohn's disease (CD). Because CD is a chronic inflammatory condition, many researchers have speculated that an infectious agent must be the cause of CD. MAP has often been proposed to be one such agent; however, despite considerable research, the evidence remains inconclusive. Higher levels of MAP have been found in the tissues and blood of CD patients than in controls, forming the foundation for much of the research into the role of MAP in CD and the primary argument in support of a causative role for MAP in CD. MAP is a slow-growing and fastidious organism that is difficult to grow in culture and, therefore, challenging to detect in patients. As a result, there has been variability in the results of studies attempting to detect the presence of MAP in CD patients, and considerable controversy over whether this organism has a causative role in the etiology of CD. Two main hypotheses exist with respect to the role of MAP in CD. The first is that MAP is a principal cause of CD, while the second is that MAP is more prevalent because of the immune dysfunction seen in CD but does not play a causative role. Clinicians are often faced with questions regarding the role of this organism and the need to treat it. The present article attempts to provide an overview of the controversy including the nature of the mycobacterium, the difficulty in detecting it, the use of antimycobacterial agents to treat it and the effect of immunosuppressive agents - all from a clinician's perspective. Although the role of MAP in CD remains controversial and an area of considerable research, it is currently only of academic interest because there is no clinically useful test to identify the presence of the organism, and no evidence to support the use of antibiotics to eradicate it for the treatment of CD.
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Affiliation(s)
- Greg Rosenfeld
- Department of Medicine, University of British Columbia, Vancouver, British Columbia.
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van der Zwaluw CS, Engels RCME, Vermulst AA, Franke B, Buitelaar J, Verkes RJ, Scholte RHJ. Interaction between dopamine D2 receptor genotype and parental rule-setting in adolescent alcohol use: evidence for a gene-parenting interaction. Mol Psychiatry 2010; 15:727-35. [PMID: 19238152 DOI: 10.1038/mp.2009.4] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Association studies investigating the link between the dopamine D2 receptor gene (DRD2) and alcohol (mis)use have shown inconsistent results. This may be due to lack of attention for environmental factors. High levels of parental rule-setting are associated with lower levels of adolescent alcohol use and delay of initiation of drinking. We tested whether DRD2 TaqI A (rs1800497) genotype interacts with alcohol-specific parenting practices in predicting the uptake of regular adolescent alcohol use. Non-regular drinkers were selected from a Dutch, nationwide sample of 428 adolescents (mean age 13.4 years at baseline) and participated in a prospective, community-based study with three annual waves. Parental rule-setting was directly and inversely related to adolescent alcohol use over time. For DRD2 genotype no significant main effect was found. DRD2 genotype interacted with parental rule-setting on adolescent alcohol use over time: adolescents, with parents highly permissive toward alcohol consumption and carrying a genotype with the DRD2 A1 (rs1800497T) allele, used significantly more alcohol over time than adolescents without these characteristics. The DRD2 genotype may pose an increased risk for alcohol use and abuse, depending on the presence of environmental risk factors, such as alcohol-specific parenting.
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Affiliation(s)
- C S van der Zwaluw
- Behavioral Science Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Abstract
Pediatric heart disease comprises many forms of cardiovascular disease in the young including cardiovascular malformations (CVM), cardiomyopathies, vasculopathies, e.g., Marfan syndrome, and cardiac arrhythmias. CVM are an important component of pediatric heart disease and constitute a major portion of clinically significant birth defects. In the past decade, the complementary nature of genetic, developmental, and biochemical approaches have contributed to extraordinary advances in understanding the origins of pediatric heart disease. Results of the studies of the cardiac transcription factor, NKX2.5, illustrate these accomplishments and at the same time provide a forecast of the nature of future genetic studies to better understand the origins of pediatric heart disease.
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Grant SF, Petri M, Bradfield JP, Kim CE, Santa E, Annaiah K, Frackelton EC, Glessner JT, Otieno FG, Shaner JL, Smith RM, Eckert AW, Chiavacci RM, Imielinski M, Sullivan KE, Hakonarson H. Association of the BANK 1 R61H variant with systemic lupus erythematosus in Americans of European and African ancestry. APPLICATION OF CLINICAL GENETICS 2009; 2:1-5. [PMID: 23776345 PMCID: PMC3681036 DOI: 10.2147/tacg.s4089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Recently an association was demonstrated between the single nucleotide polymorphism (SNP), rs10516487, within the B-cell gene BANK1 and systemic lupus erythematosus (SLE) as a consequence of a genome wide association study of this disease in European and Argentinean populations. In a bid for replication, we examined the effects of the R61H non-synonymous variant with respect to SLE in our genotyped American cohorts of European and African ancestry. Utilizing data from our ongoing genome-wide association study in our cohort of 178 Caucasian SLE cases and 1808 Caucasian population-based controls plus 148 African American (AA) SLE cases and 1894 AA population-based controls we investigated the association of the previously described non-synonymous SNP at the BANK1 locus with the disease in the two ethnicities separately. Using a Fisher’s exact test, the minor allele frequency (MAF) of rs10516487 in the Caucasian cases was 22.6% while it was 31.2% in Caucasian controls, yielding a protective odds ratio (OR) of 0.64 (95% CI 0.49-0.85; one-sided p = 7.07 × 10−4). Furthermore, the MAF of rs10516487 in the AA cases was 18.7% while it was 23.3% in AA controls, yielding a protective OR of 0.75 (95% CI 0.55–1.034; one-sided p = 0.039). The OR of the BANK1 variant in our study cohorts is highly comparable with that reported previously in a South American/European SLE case-control cohort (OR = 0.72). As such, R61H in the BANK1 gene confers a similar magnitude of SLE protection, not only in European Americans, but also in African Americans.
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Affiliation(s)
- Struan Fa Grant
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA, USA ; Department of Pediatrics and Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA ; Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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Chen EYH, Wong GHY, Hui CLM, Tang JYM, Chiu CPY, Lam MML, Sham PC. Phenotyping psychosis: room for neurocomputational and content-dependent cognitive endophenotypes? Cogn Neuropsychiatry 2009; 14:451-72. [PMID: 19634039 DOI: 10.1080/13546800902965695] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The endophenotype research strategy aims at reducing complex clinical phenomena to reveal a more tractable mapping to underlying genes. Cognitive dysfunctions have been widely pursued as target endophenotype in schizophrenia. We critically discuss the promise and limitations of this approach. METHODS Relevant theoretical and empirical issues on genes and behaviour, neurocognitive structure and psychopathology were selectively reviewed and discussed. RESULTS Some important inherent limitations of the current cognitive endophenotype approach were identified. These include reliance on (1) classic neuropsychology; (2) deficit measures; and (3) a general information processing approach with the use of content-independent, neutral stimuli. As a result, many current cognitive endophenotypes are likely to overlap and converge with general cognitive impairments, which may be shared with other disorders. CONCLUSIONS We propose three novel directions for further psychosis endophenotype research: (1) in addition to such content-independent computational processes, which operate in a similar way regardless of the stimuli, it is important to consider the potential roles of "content-dependent endophenotypes", which operate on different stimuli in consistently different manners. Advances in cognitive studies suggest there may be evolutionarily important aspects of cognition which are content-dependent. We propose that both content-independent and content-dependent processes should be addressed in psychosis research. (2) In line with the emphasis on content, close attention should be paid to the study of "psychopathological endophenotypes" in addition to cognitive endophenotypes. (3) "Neurocomputational endophenotypes" may be defined by parsing cognitive processes into "subsystems" with specific computational processing algorithms and considering key computational parameters suggested from these models. These potential "neurocomputational endophenotypes" (such as neuronal noise, synaptic learning algorithms) are potentially intermediate variables located between the levels of cognition and neurobiology.
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Affiliation(s)
- Eric Y H Chen
- Department of Psychiatry, University of Hong Kong, Hong Kong.
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Epistasis and its implications for personal genetics. Am J Hum Genet 2009; 85:309-20. [PMID: 19733727 DOI: 10.1016/j.ajhg.2009.08.006] [Citation(s) in RCA: 240] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 07/31/2009] [Accepted: 08/10/2009] [Indexed: 12/22/2022] Open
Abstract
The widespread availability of high-throughput genotyping technology has opened the door to the era of personal genetics, which brings to consumers the promise of using genetic variations to predict individual susceptibility to common diseases. Despite easy access to commercial personal genetics services, our knowledge of the genetic architecture of common diseases is still very limited and has not yet fulfilled the promise of accurately predicting most people at risk. This is partly because of the complexity of the mapping relationship between genotype and phenotype that is a consequence of epistasis (gene-gene interaction) and other phenomena such as gene-environment interaction and locus heterogeneity. Unfortunately, these aspects of genetic architecture have not been addressed in most of the genetic association studies that provide the knowledge base for interpreting large-scale genetic association results. We provide here an introductory review of how epistasis can affect human health and disease and how it can be detected in population-based studies. We provide some thoughts on the implications of epistasis for personal genetics and some recommendations for improving personal genetics in light of this complexity.
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Benson DW. Compound heterozygous SCN5A mutations: Does the sum of the parts equal the whole? Heart Rhythm 2009; 6:1176-7. [DOI: 10.1016/j.hrthm.2009.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Indexed: 10/20/2022]
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Szoeke C, Sills GJ, Kwan P, Petrovski S, Newton M, Hitiris N, Baum L, Berkovic SF, Brodie MJ, Sheffield LJ, O’Brien TJ. Multidrug-resistant genotype (ABCB1) and seizure recurrence in newly treated epilepsy: Data from international pharmacogenetic cohorts. Epilepsia 2009; 50:1689-96. [DOI: 10.1111/j.1528-1167.2009.02059.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Arnold PD, Macmaster FP, Richter MA, Hanna GL, Sicard T, Burroughs E, Mirza Y, Easter PC, Rose M, Kennedy JL, Rosenberg DR. Glutamate receptor gene (GRIN2B) associated with reduced anterior cingulate glutamatergic concentration in pediatric obsessive-compulsive disorder. Psychiatry Res 2009; 172:136-9. [PMID: 19324536 PMCID: PMC2670773 DOI: 10.1016/j.pscychresns.2009.02.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 02/12/2009] [Accepted: 02/19/2009] [Indexed: 12/16/2022]
Abstract
In this preliminary study, 16 psychotropic-naïve pediatric patients with obsessive-compulsive disorder (OCD) were studied using magnetic resonance spectroscopy (MRS) and genotyped for six candidate polymorphisms in two glutamate system genes. A significant association was identified between the rs1019385 polymorphism of the glutamate receptor, ionotropic, N-methyl-d-aspartate 2B (GRIN2B) and decreased anterior cingulate cortex (ACC) glutamatergic concentration (Glx) but not with occipital Glx. These results suggest that GRIN2B may be associated with Glx in the ACC, a region consistently implicated in OCD.
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Affiliation(s)
- Paul Daniel Arnold
- Program in Genetics and Genomic Biology, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8.
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Greenbaum D, Gerstein M. Social networking and personal genomics: suggestions for optimizing the interaction. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2009; 9:15-19. [PMID: 19998104 DOI: 10.1080/15265160902894039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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Grant SF, Li M, Bradfield JP, Kim CE, Annaiah K, Santa E, Glessner JT, Casalunovo T, Frackelton EC, Otieno FG, Shaner JL, Smith RM, Eckert AW, Imielinski M, Chiavacci RM, Berkowitz RI, Hakonarson H. Association of HMGA2 Gene Variation with Height in Specific Pediatric Age Categories. GENOMICS INSIGHTS 2008. [DOI: 10.4137/gei.s944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Background Recently an association was demonstrated between the single nucleotide polymorphism (SNP), rs1042725, within the HMGA2 locus and height as a consequence of a genome wide association (GWA) study of this trait in adults; this observation was also reported in children aged 7–11 years old. Objective We examined in our Caucasian childhood cohort the effects of two strong surrogates for this SNP at this locus with height, rs8756 and rs7968902, with respect to the same pediatric age category but also in children grouped separately as younger and older. Methods Utilizing data from an ongoing GWA study in our cohort of 2,619 Caucasian children with measurements for height, we investigated the association of the previously reported variation at the HMGA2 locus with this height treated as a quantitative trait (age and sex corrected) in childhood in the 2–6 (n = 706), 7–11 (n = 617) and 12–18 (n = 1293) years old categories. Results The minor alleles of rs8756 and rs7968902 respectively (strong surrogates for rs1042725 i.e. r 2 = 0.873 and 0.761 in the CEU HapMap respectively) were significantly associated with height in the 7–11 years old age group ( P = 3.53 × 10–3 and 2.82 × 10–4, respectively) However in the 2–6 and 12–18 years old age groups, no association was observed. Conclusions We observe a strong association with height in same age group of 7–11 years old as has been previously reported. However, in the under 7s and the over 11s, no such association was observed.
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Affiliation(s)
- Struan F.A. Grant
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
- Department of Pediatrics and Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
- Department of Pediatrics University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania 19104, U.S.A
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Cecilia E. Kim
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Kiran Annaiah
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Erin Santa
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Joseph T. Glessner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Tracy Casalunovo
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Edward C Frackelton
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - F. George Otieno
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Julie L. Shaner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Ryan M. Smith
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Andrew W. Eckert
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Marcin Imielinski
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Rosetta M. Chiavacci
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
| | - Robert I. Berkowitz
- Behavioral Health Center and Department of Child and Adolescent Psychiatry, The Children's Hospital of Philadelphia, Philadelphia PA 19104, U.S.A
- Center for Weight and Eating Disorders, Department of Psychiatry, University of Pennsylvania, Philadelphia PA 19104, U.S.A
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
- Department of Pediatrics and Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, U.S.A
- Department of Pediatrics University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania 19104, U.S.A
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Grant SFA, Baldassano RN, Hakonarson H. Classification of genetic profiles of Crohn's disease: a focus on the ATG16L1 gene. Expert Rev Mol Diagn 2008; 8:199-207. [PMID: 18366306 DOI: 10.1586/14737159.8.2.199] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inflammatory bowel disease constitutes two related clinical entities, Crohn's disease (CD) and ulcerative colitis (UC), both of which have increased in prevalence over the last decade. Family and twin studies have strongly indicated that genetic factors play a large role in an individual's risk of developing inflammatory bowel disease. Despite this, it has proven difficult to isolate disease genes that confer susceptibility to this disease using classical candidate gene and linkage approaches, with the notable exception of the isolation of the caspase recruitment domain family, member 15 (CARD15) gene. However, over the last 2 years, genome-wide association (GWA) studies have become feasible, where modern high-throughput single nucleotide polymorphism (SNP) genotyping technologies can be applied to large and comprehensively phenotyped patient cohorts. Such approaches have enabled scientists to robustly associate specific variants with many complex diseases, including age-related macular degeneration, Type 2 diabetes, breast cancer and asthma. In the inflammatory bowel disease field, positive associations with CD and UC coming from GWA studies have been reported for an ever increasing number of genes. The most consistently and strongly associated variants have been in the CARD15, the interleukin 23 receptor (IL23R) and autophagy-related 16-like 1 (ATG16L1) genes. With respect to ATG16L1, the G allele of SNP rs2241880 has been shown in multiple association studies to confer strong risk for CD, although its association with UC remains more debatable. This SNP is in fact a common coding variant, specifically a threonine-to-alanine substitution at amino acid position 300 of the ATG16L1 protein (T300A), and appears to account for all of the disease risk conferred by this locus. This review addresses recent advances in GWA studies of inflammatory bowel disease, with specific focus on the growing evidence of the ATG16L1 gene's role in CD and how its protein product operating within the autophagic pathway makes autophagy an attractive therapeutic target for this debilitating disorder.
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Affiliation(s)
- Struan F A Grant
- The Center for Applied Genomics and Division of Human Genetics, The Abramson Research Center of the Joseph Stokes Jr Research Institute, Department of Pediatrics, The Children's Hospital of Philadelphia, PA 19104-4318, USA.
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Yesupriya A, Evangelou E, Kavvoura FK, Patsopoulos NA, Clyne M, Walsh MC, Lin BK, Yu W, Gwinn M, Ioannidis JPA, Khoury MJ. Reporting of human genome epidemiology (HuGE) association studies: an empirical assessment. BMC Med Res Methodol 2008; 8:31. [PMID: 18492284 PMCID: PMC2413261 DOI: 10.1186/1471-2288-8-31] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Accepted: 05/20/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several thousand human genome epidemiology association studies are published every year investigating the relationship between common genetic variants and diverse phenotypes. Transparent reporting of study methods and results allows readers to better assess the validity of study findings. Here, we document reporting practices of human genome epidemiology studies. METHODS Articles were randomly selected from a continuously updated database of human genome epidemiology association studies to be representative of genetic epidemiology literature. The main analysis evaluated 315 articles published in 2001-2003. For a comparative update, we evaluated 28 more recent articles published in 2006, focusing on issues that were poorly reported in 2001-2003. RESULTS During both time periods, most studies comprised relatively small study populations and examined one or more genetic variants within a single gene. Articles were inconsistent in reporting the data needed to assess selection bias and the methods used to minimize misclassification (of the genotype, outcome, and environmental exposure) or to identify population stratification. Statistical power, the use of unrelated study participants, and the use of replicate samples were reported more often in articles published during 2006 when compared with the earlier sample. CONCLUSION We conclude that many items needed to assess error and bias in human genome epidemiology association studies are not consistently reported. Although some improvements were seen over time, reporting guidelines and online supplemental material may help enhance the transparency of this literature.
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Affiliation(s)
- Ajay Yesupriya
- National Office of Public Health Genomics, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, USA
| | - Evangelos Evangelou
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina, School of Medicine, Ioannina, Greece
| | - Fotini K Kavvoura
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina, School of Medicine, Ioannina, Greece
| | - Nikolaos A Patsopoulos
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina, School of Medicine, Ioannina, Greece
| | - Melinda Clyne
- National Office of Public Health Genomics, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, USA
| | - Matthew C Walsh
- Department of Population Health Sciences, University of Wisconsin, Madison, USA
| | - Bruce K Lin
- Office of the Medical Director, March of Dimes Birth Defects Foundation, White Plains, USA
| | - Wei Yu
- National Office of Public Health Genomics, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, USA
| | - Marta Gwinn
- National Office of Public Health Genomics, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, USA
| | - John PA Ioannidis
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, University of Ioannina, School of Medicine, Ioannina, Greece
| | - Muin J Khoury
- National Office of Public Health Genomics, Coordinating Center for Health Promotion, Centers for Disease Control and Prevention, Atlanta, USA
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Grant SFA, Li M, Bradfield JP, Kim CE, Annaiah K, Santa E, Glessner JT, Casalunovo T, Frackelton EC, Otieno FG, Shaner JL, Smith RM, Imielinski M, Eckert AW, Chiavacci RM, Berkowitz RI, Hakonarson H. Association analysis of the FTO gene with obesity in children of Caucasian and African ancestry reveals a common tagging SNP. PLoS One 2008; 3:e1746. [PMID: 18335027 PMCID: PMC2262153 DOI: 10.1371/journal.pone.0001746] [Citation(s) in RCA: 166] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Accepted: 02/08/2008] [Indexed: 01/23/2023] Open
Abstract
Recently an association was demonstrated between the single nucleotide polymorphism (SNP), rs9939609, within the FTO locus and obesity as a consequence of a genome wide association (GWA) study of type 2 diabetes in adults. We examined the effects of two perfect surrogates for this SNP plus 11 other SNPs at this locus with respect to our childhood obesity cohort, consisting of both Caucasians and African Americans (AA). Utilizing data from our ongoing GWA study in our cohort of 418 Caucasian obese children (BMI>or=95th percentile), 2,270 Caucasian controls (BMI<95th percentile), 578 AA obese children and 1,424 AA controls, we investigated the association of the previously reported variation at the FTO locus with the childhood form of this disease in both ethnicities. The minor allele frequencies (MAF) of rs8050136 and rs3751812 (perfect surrogates for rs9939609 i.e. both r(2) = 1) in the Caucasian cases were 0.448 and 0.443 respectively while they were 0.391 and 0.386 in Caucasian controls respectively, yielding for both an odds ratio (OR) of 1.27 (95% CI 1.08-1.47; P = 0.0022). Furthermore, the MAFs of rs8050136 and rs3751812 in the AA cases were 0.449 and 0.115 respectively while they were 0.436 and 0.090 in AA controls respectively, yielding an OR of 1.05 (95% CI 0.91-1.21; P = 0.49) and of 1.31 (95% CI 1.050-1.643; P = 0.017) respectively. Investigating all 13 SNPs present on the Illumina HumanHap550 BeadChip in this region of linkage disequilibrium, rs3751812 was the only SNP conferring significant risk in AA. We have therefore replicated and refined the association in an AA cohort and distilled a tag-SNP, rs3751812, which captures the ancestral origin of the actual mutation. As such, variants in the FTO gene confer a similar magnitude of risk of obesity to children as to their adult counterparts and appear to have a global impact.
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Affiliation(s)
- Struan F. A. Grant
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Cecilia E. Kim
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Kiran Annaiah
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Erin Santa
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Joseph T. Glessner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Tracy Casalunovo
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Edward C. Frackelton
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - F. George Otieno
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Julie L. Shaner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Ryan M. Smith
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Marcin Imielinski
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Andrew W. Eckert
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Rosetta M. Chiavacci
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Robert I. Berkowitz
- Weight and Eating Disorders Program, Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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Smith JA, Arnett DK, Kelly RJ, Ordovas JM, Sun YV, Hopkins PN, Hixson JE, Straka RJ, Peacock JM, Kardia SLR. The genetic architecture of fasting plasma triglyceride response to fenofibrate treatment. Eur J Hum Genet 2008; 16:603-13. [PMID: 18212815 DOI: 10.1038/sj.ejhg.5202003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Metabolic response to the triglyceride (TG)-lowering drug, fenofibrate, is shaped by interactions between genetic and environmental factors, yet knowledge regarding the genetic determinants of this response is primarily limited to single-gene effects. Since very low-density lipoprotein (VLDL) is the central carrier of fasting TG, identifying factors that affect both total TG and VLDL-TG response to fenofibrate is critical for predicting individual fenofibrate response. As part of the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study, 688 individuals from 161 families were genotyped for 91 single-nucleotide polymorphisms (SNPs) in 25 genes known to be involved in lipoprotein metabolism. Using generalized estimating equations to control for family structure, we performed linear modeling to investigate whether single SNPs, single covariates, SNP-SNP interactions, and/or SNP-covariate interactions had a significant association with the change in total fasting TG and fasting VLDL-TG after 3 weeks of fenofibrate treatment. A 10-iteration fourfold cross-validation procedure was used to validate significant associations and quantify their predictive abilities. More than one-third of the significant, cross-validated SNP-SNP interactions predicting each outcome involved just five SNPs, showing that these SNPs are of key importance to fenofibrate response. Multiple variable models constructed using the top-ranked SNP--covariate interactions explained 11.9% more variation in the change in TG and 7.8% more variation in the change in VLDL than baseline TG alone. These results yield insight into the complex biology of fenofibrate response, which can be used to target fenofibrate therapy to individuals who are most likely to benefit from the drug.
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Affiliation(s)
- Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109-2029, USA.
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Abstract
Definition of the phenotype is crucial in designing any genetic study, especially an association study, intended to detect the disease predisposing genes. In this chapter, we review the different types of phenotypes such as discrete or continuous and discuss the issues impacting on the phenotype definition related to study design, specifically, the impact of diagnostic error (misclassification) in case-control studies and measurement error in continuous traits. We show that the power of a study depends heavily on the phenotype measured and that misclassification or measurement error can dramatically reduce the power. We also suggest some possible responses to these challenges.
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Affiliation(s)
- Mary K Wojczynski
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Grant SFA, Hakonarson H. Recent development in pharmacogenomics: from candidate genes to genome-wide association studies. Expert Rev Mol Diagn 2007; 7:371-93. [PMID: 17620046 DOI: 10.1586/14737159.7.4.371] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genetic diversity, most notably through single nucleotide polymorphisms and copy-number variation, together with specific environmental exposures, contributes to both disease susceptibility and drug response variability. It has proved difficult to isolate disease genes that confer susceptibility to complex disorders, and as a consequence, even fewer genetic variants that influence clinical drug responsiveness have been uncovered. As such, the candidate gene approach has largely failed to deliver and, although the family-based linkage approach has certain theoretical advantages in dealing with common/complex disorders, progress has been slower than was hoped. More recently, genome-wide association studies have gained increasing popularity, as they enable scientists to robustly associate specific variants with the predisposition for complex disease, such as age-related macular degeneration, Type 2 diabetes, inflammatory bowel disease, obesity, autism and leukemia. This relatively new methodology has stirred new hope for the mapping of genes that regulate drug response related to these conditions. Collectively, these studies support the notion that modern high-throughput single nucleotide polymorphism genotyping technologies, when applied to large and comprehensively phenotyped patient cohorts, will readily reveal the most clinically relevant disease-modifying and drug response genes. This review addresses both recent advances in the genotyping field and highlights from genome-wide association studies, which have conclusively uncovered variants that underlie disease susceptibility and/or variability in drug response in common disorders.
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Affiliation(s)
- Struan F A Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, PA 19104-4318, USA.
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Hersh CP, Raby BA, Soto-Quirós ME, Murphy AJ, Avila L, Lasky-Su J, Sylvia JS, Klanderman BJ, Lange C, Weiss ST, Celedón JC. Comprehensive testing of positionally cloned asthma genes in two populations. Am J Respir Crit Care Med 2007; 176:849-57. [PMID: 17702965 PMCID: PMC2048676 DOI: 10.1164/rccm.200704-592oc] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 08/07/2007] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Replication of gene-disease associations has become a requirement in complex trait genetics. OBJECTIVES In studies of childhood asthma from two different ethnic groups, we attempted to replicate associations with five potential asthma susceptibility genes previously identified by positional cloning. METHODS We analyzed two family-based samples ascertained through an asthmatic proband: 497 European-American children from the Childhood Asthma Management Program and 439 Hispanic children from the Central Valley of Costa Rica. We genotyped 98 linkage disequilibrium-tagging single-nucleotide polymorphisms (SNPs) in five genes: ADAM33, DPP10, GPR154 (HUGO name: NPSR1), HLA-G, and the PHF11 locus (includes genes SETDB2 and RCBTB1). SNPs were tested for association with asthma and two intermediate phenotypes: airway hyperresponsiveness and total serum immunoglobulin E levels. MEASUREMENTS AND MAIN RESULTS Despite differing ancestries, linkage disequilibrium patterns were similar in both cohorts. Of the five evaluated genes, SNP-level replication was found only for GPR154 (NPSR1). In this gene, three SNPs were associated with asthma in both cohorts, although the opposite alleles were associated in either study. Weak evidence for locus-level replication with asthma was found in the PHF11 locus, although there was no overlap in the associated SNP across the two cohorts. No consistent associations were observed for the three other genes. CONCLUSIONS These results provide some further support for the role of genetic variation in GPR154 (NPSR1) and PHF11 in asthma susceptibility and also highlight the challenges of replicating genetic associations in complex traits such as asthma, even for genes identified by linkage analysis.
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Affiliation(s)
- Craig P Hersh
- Channing Laboratory and Center for Genomic Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.
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Fontana P, Hulot JS, De Moerloose P, Gaussem P. Influence of CYP2C19 and CYP3A4 gene polymorphisms on clopidogrel responsiveness in healthy subjects. J Thromb Haemost 2007; 5:2153-5. [PMID: 17697139 DOI: 10.1111/j.1538-7836.2007.02722.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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UZOIGWE J, KHAITSA M, GIBBS P. Epidemiological evidence for Mycobacterium avium subspecies paratuberculosis as a cause of Crohn's disease. Epidemiol Infect 2007; 135:1057-68. [PMID: 17445316 PMCID: PMC2870686 DOI: 10.1017/s0950268807008448] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2007] [Indexed: 11/07/2022] Open
Abstract
Mycobacterium avium subspecies paratuberculosis is the causative agent of Johne's disease, a chronic enteritis in ruminants including cattle, sheep, goats, and farmed deer. Recently, this bacterium has received an increasingly wide interest because of a rapidly growing body of scientific evidence which suggests that human infection with this microorganism may be causing some, and possibly all, cases of Crohn's disease. Recent studies have shown that a high percentage of people with Crohn's disease are infected with M. avium subsp. paratuberculosis; whether the association of this bacterium and Crohn's disease is causal or coincidental is not known. Crohn's disease is a gastrointestinal disease in humans with similar histopathological findings to those observed in the paucibacillary form of Johne's disease in cattle. The search for risk factors in Crohn's disease has been frustrating. However, epidemiologists have gathered enough information that points to an association between M. avium subsp. paratuberculosis and Crohn's disease. This paper reviews epidemiological models of disease causation, the major philosophical doctrines about causation, the established epidemiological criteria for causation, and the currently known epidemiological evidence of M. avium subsp. paratuberculosis as a possible cause of Crohn's disease.
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Affiliation(s)
- J. C. UZOIGWE
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, ND, USA
| | - M. L. KHAITSA
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND, USA
| | - P. S. GIBBS
- Department of Veterinary and Microbiological Sciences, North Dakota State University, Fargo, ND, USA
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Ioannidis JPA, Boffetta P, Little J, O'Brien TR, Uitterlinden AG, Vineis P, Balding DJ, Chokkalingam A, Dolan SM, Flanders WD, Higgins JPT, McCarthy MI, McDermott DH, Page GP, Rebbeck TR, Seminara D, Khoury MJ. Assessment of cumulative evidence on genetic associations: interim guidelines. Int J Epidemiol 2007; 37:120-32. [PMID: 17898028 DOI: 10.1093/ije/dym159] [Citation(s) in RCA: 442] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Established guidelines for causal inference in epidemiological studies may be inappropriate for genetic associations. A consensus process was used to develop guidance criteria for assessing cumulative epidemiologic evidence in genetic associations. A proposed semi-quantitative index assigns three levels for the amount of evidence, extent of replication, and protection from bias, and also generates a composite assessment of 'strong', 'moderate' or 'weak' epidemiological credibility. In addition, we discuss how additional input and guidance can be derived from biological data. Future empirical research and consensus development are needed to develop an integrated model for combining epidemiological and biological evidence in the rapidly evolving field of investigation of genetic factors.
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Affiliation(s)
- John P A Ioannidis
- Clinical and Molecular Epidemiology Unit, University of Ioannina School of Medicine, Ioannina 45110, Greece.
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Lucarini N, Verrotti A, Napolioni V, Bosco G, Curatolo P. Genetic polymorphisms and idiopathic generalized epilepsies. Pediatr Neurol 2007; 37:157-64. [PMID: 17765802 DOI: 10.1016/j.pediatrneurol.2007.06.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 03/14/2007] [Accepted: 06/01/2007] [Indexed: 10/22/2022]
Abstract
In recent years, progress in understanding the genetic basis of idiopathic generalized epilepsies has proven challenging because of their complex inheritance patterns and genetic heterogeneity. Genetic polymorphisms offer a convenient avenue for a better understanding of the genetic basis of idiopathic generalized epilepsy by providing evidence for the involvement of a given gene in these disorders, and by clarifying its pathogenetic mechanisms. Many of these genes encode for some important central nervous system ion channels (KCNJ10, KCNJ3, KCNQ2/KCNQ3, CLCN2, GABRG2, GABRA1, SCN1B, and SCN1A), while many others encode for ubiquitary enzymes that play crucial roles in various metabolic pathways (HP, ACP1, ME2, LGI4, OPRM1, GRIK1, BRD2, EFHC1, and EFHC2). We review the main genetic polymorphisms reported in idiopathic generalized epilepsy, and discusses their possible functional significance in the pathogenesis of seizures.
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Affiliation(s)
- Nazzareno Lucarini
- Department of Molecular, Cellular, and Animal Biology, University of Camerino, Camerino, Italy.
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