DOCSLIB.ORG

And a Deep Phenotype Association Study (Deepas) with Data from the Age‐Related Eye Disease Study 2 (Areds2)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
And a Deep Phenotype Association Study (Deepas) with Data from the Age‐Related Eye Disease Study 2 (Areds2) Identifying Genetic Pleiotropy through a Literature-wide Association Study (LitWAS) and a Phenotype Association Study (PheWAS) in the Age-related Eye Disease Study 2 (AREDS2) Item Type text; Electronic Thesis Authors Simmons, Michael Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the College of Medicine - Phoenix, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 26/09/2021 00:42:07 Link to Item http://hdl.handle.net/10150/623630 IDENTIFYING GENETIC PLEIOTROPY THROUGH A LITERATURE‐WIDE ASSOCIATION STUDY (LITWAS) AND A DEEP PHENOTYPE ASSOCIATION STUDY (DEEPAS) WITH DATA FROM THE AGE‐RELATED EYE DISEASE STUDY 2 (AREDS2) A thesis submitted to the University of Arizona College of Medicine – Phoenix in partial fulfillment of the requirements for the Degree of Doctor of Medicine Michael Simmons Class of 2017 Mentor: Zhiyong Lu, PhD Acknowledgements We acknowledge the contributions of Ayush Singhal PhD, Freekje VanAsten PhD, Tiarnan Keenan, FRCOphth, PhD, and Emily Chew MD in their support and indespensible contributions to this work. Particularly, Dr. Singhal designed the text mining algorithm and conducted the LitWAS, and Dr. VanAsten performed the principle work for execution of the DeePAS. This research was supported by the NIH Medical Research Scholars Program, a public‐private partnership supported jointly by the NIH and generous contributions to the Foundation for the NIH from the Doris Duke Charitable Foundation, the Howard Hughes Medical Institute, the American Association for Dental Research, the Colgate‐Palmolive Company, and other private donors. No funds from the Doris Duke Charitable Foundation were used to support research that used animals. Abstract Background/Significance: Genetic association studies simplify genotype‐phenotype relationship investigation by considering only the presence of a given polymorphism and the presence or absence of a given downstream phenotype. Although such associations do not indicate causation, collections of phenotypes sharing association with a single genetic polymorphism may provide valuable mechanistic insights. In this thesis we explore such genetic pleiotropy with Deep Phenotype Association Studies (DeePAS) using data from the Age‐Related Eye Study 2 (AREDS2). We also employ a novel text mining approach to extract pleiotropic associations from the published literature as a hypothesis generation mechanism. Research Question: Is it possible to identify pleiotropic genetic associations across multiple published abstracts and validate these in data from AREDS2? Methods: Data from the AREDS2 trial includes 123 phenotypes including AMD features, other ocular conditions, cognitive function and cardiovascular, neurological, gastrointestinal and endocrine disease. A previously validated relationship extraction algorithm was used to isolate descriptions of genetic associations with these phenotypes in MEDLINE abstracts. Results were filtered to exclude negated findings and normalize variant mentions. Genotype data was available for 1826 AREDS2 participants. A DeePAS was performed by evaluating the association between selected SNPs and all available phenotypes. Associations that remained significant after Bonferroni‐correction were replicated in AREDS. Results: LitWAS analysis identified 9372 SNPs with literature support for at least two distinct phenotypes, with an average of 3.1 phenotypes/SNP. PheWAS analyses revealed that two variants of the ARMS2‐HTRA1 locus at 10q26, rs10490924 and rs3750846, were significantly associated with sub‐retinal hemorrhage in AMD (rs3750846 OR 1.79 (1.41‐2.27), p=1.17*10‐7). This associated remained significant even in populations of participants with neovascular AMD. Furthermore, odds ratios for the development of sub‐retinal hemorrhage in the presence of the rs3750846 SNP were similar between incident and prevalent AREDS2 sub‐populations (OR: 1.94 vs 1.75). This association was also replicated in data from the AREDS trial. No literature‐defined pleiotropic associations tested remained significant after multiple‐testing correction. Conclusions: The rs3750846 variant of the ARMS2‐HTRA1 locus is associated with sub‐retinal hemorrhage. Automatic literature mining, when paired with clinical data, is a promising method for exploring genotype‐phenotype relationships. Table of Contents INTRODUCTION: ...................................................................................................................... 1 METHODS: ............................................................................................................................... 5 OVERVIEW ...................................................................................................................................... 5 AREDS2 STUDY DESIGN ................................................................................................................... 7 AREDS STUDY DESIGN ..................................................................................................................... 7 GENOTYPING ................................................................................................................................... 7 PHENOTYPE DEFINITIONS .................................................................................................................... 8 LITERATURE‐WIDE ASSOCIATION STUDY ................................................................................................ 8 Gene‐variant‐disease relationship extraction ......................................................................... 9 Normalization of variant descriptions ..................................................................................... 9 Negation identification .......................................................................................................... 11 Overview: ........................................................................................................................... 11 Negation Corpus ................................................................................................................ 12 Negation phrase and term dictionaries: ............................................................................ 12 Prioritization of SNPs for inclusion in the PheWAS ................................................................ 13 PHENOTYPE ASSOCIATION STUDY ...................................................................................................... 14 RESULTS: ............................................................................................................................... 15 LITWAS ....................................................................................................................................... 15 Normalization of variant descriptions ................................................................................... 15 Negation identification .......................................................................................................... 17 LitWAS .................................................................................................................................... 19 PHEWAS ...................................................................................................................................... 23 Patient characteristics ........................................................................................................... 23 Abbreviations: L, lutein; Z, zeaxanthin; DHA, docosahexanoic acid; EPA, eicosapentaenoic acid ........................................................................................................................................ 24 PheWAS ................................................................................................................................. 25 FUTURE DIRECTIONS ............................................................................................................. 34 CONCLUSIONS ....................................................................................................................... 35 REFERENCES .......................................................................................................................... 36 List of Figures and Tables TABLES TABLE 1. COMMON ABBREVIATIONS ........................................................................................................ 4 TABLE 2. VARIANT NORMALIZATION EVALUATION .................................................................................... 16 TABLE 3. NEGATION IDENTIFICATION EVALUATION ................................................................................... 18 TABLE 4. LITERATURE‐WIDE ASSOCIATION STUDY RESULTS ......................................................................... 20 TABLE 5. LITERATURE‐MINED ASSOCIATIONS WITH THE ARMS2 VARIANT, RS1040924 .................................. 22 TABLE 6. AREDS2 BASELINE CHARACTERISTICS ....................................................................................... 24 TABLE 7. HTRA1‐ARMS2 (RS3750846) AND SUBRETINAL HEMORRHAGE IN AREDS2 ................................. 27 TABLE 8. ARMS2 (RS3750846) AND HEMORRHAGE CHARACTERISTIC OF AMD IN AREDS AND AREDS2 ....... 29 FIGURES FIGURE 1. STUDY OVERVIEW .................................................................................................................. 6 FIGURE
Load more

Recommended publications
  • Gene Interaction of CFH, ARMS2, and ARMS2&Sol;HTRA1 on the Risk Of
    Eye (2015) 29, 691–698 © 2015 Macmillan Publishers Limited All rights reserved 0950-222X/15 www.nature.com/eye 1,2,3,5 1,2,3,5 4,5 Gene–gene interaction L Huang , Q Meng , C Zhang , LABORATORY STUDY Y Sun1,2,3, Y Bai1,2,3,SLi1,2,3, X Deng1,2,3, of CFH, ARMS2, and B Wang1,2,3,WYu1,2,3, M Zhao1,2,3 and X Li1,2,3 ARMS2/HTRA1 on the risk of neovascular age-related macular degeneration and polypoidal choroidal vasculopathy in Chinese population Abstract rs1065489 did not show significant association with nAMD (P40.01), but was strongly Purpose To evaluate the association and associated with PCV in Chinese patients 1Department of interaction of five single-nucleotide (Po0.001). Ophthalmology, Peking polymorphisms (SNPs) in three genes (CFH, University People’s Conclusions In this study, we found that the ARMS2, and ARMS2/HTRA1) with Hospital, Beijing, China interaction of ARMS2 and ARMS2/HTRA1 is neovascular age-related macular degeneration significantly associated with nAMD, and the 2 (nAMD) and polypoidal choroidal Key Laboratory of Vision interaction of CFH and ARMS2 is pronounced vasculopathy (PCV) in Chinese population. Loss and Restoration, in PCV development in Chinese population. Ministry of Education, Methods A total of 300 nAMD and 300 PCV Eye 29, – Beijing, China patients and 301 normal subjects participated (2015) 691 698; doi:10.1038/eye.2015.32; published online 13 March 2015 in the present study. The allelic variants of 3Department of Abdominal rs800292, rs2274700, rs3750847, rs3793917, and Surgical Oncology, Cancer rs1065489 were determined by matrix-assisted Institute and Hospital, Introduction laser desorption/ionization time-of-flight mass Chinese Academy of Medical Sciences, Peking – Age-related macular degeneration (AMD) is the spectrometry (MALDI-TOF-MS).
    [Show full text]
  • Genetic Susceptibility to Age-Related Macular Degeneration: a Paradigm for Dissecting Complex Disease Traits
    Human Molecular Genetics, 2007, Vol. 16, Review Issue 2 R174–R182 doi:10.1093/hmg/ddm212 Genetic susceptibility to age-related macular degeneration: a paradigm for dissecting complex disease traits Anand Swaroop1,2,*, Kari EH Branham1, Wei Chen3 and Goncalo Abecasis3,* 1Departments of Ophthalmology and Visual Sciences, 2Department of Human Genetics and 3Department of Biostatistics, University of Michigan, Ann Arbor, MI 48105, USA Received July 20, 2007; Revised July 20, 2007; Accepted July 26, 2007 Age-related macular degeneration (AMD) is a progressive neurodegenerative disease, which affects quality of life for millions of elderly individuals worldwide. AMD is associated with a diverse spectrum of clinical phe- notypes, all of which include the death of photoreceptors in the central part of the human retina (called the macula). Tremendous progress has been made in identifying genetic susceptibility variants for AMD. Variants at chromosome 1q32 (in the region of CFH ) and 10q26 (LOC387715/ARMS2) account for a large part of the genetic risk to AMD and have been validated in numerous studies. In addition, susceptibility var- iants at other loci, several as yet unidentified, make substantial cumulative contribution to genetic risk for AMD; among these, multiple studies support the role of variants in APOE and C2/BF genes. Genome-wide association and re-sequencing projects, together with gene-environment interaction studies, are expected to further define the causal relationships that connect genetic variants to AMD pathogenesis and should assist in better design of prevention and intervention. INTRODUCTION studies of AMD illustrate both the promise and challenges of new gene-mapping approaches. Early-onset maculopathies, A vast majority of common diseases are complex and such as Stargardt’s disease, have long been known to have her- multi-factorial, resulting from the interplay of genetic com- editary basis.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 7,972,787 B2 Deangelis (45) Date of Patent: Jul
    US007972 787B2 (12) United States Patent (10) Patent No.: US 7,972,787 B2 Deangelis (45) Date of Patent: Jul. 5, 2011 (54) METHODS FOR DETECTINGAGE-RELATED WO WO-2006088950 8, 2006 MACULAR DEGENERATION WO WO-2006133295 A2 12/2006 WO WO-2007044897 A1 4/2007 WO WO-2008O13893 A2 1, 2008 (75) Inventor: Margaret M. Deangelis, Cambridge, WO WO-2008067551 A2 6, 2008 MA (US) WO WO-2008094,370 A2 8, 2008 WO WO-2008103299 A2 8, 2008 WO WO-2008110828 A1 9, 2008 (73) Assignee: Massachusetts Eye and Ear Infirmary, WO WO-2008103299 A3 12/2008 Boston, MA (US) OTHER PUBLICATIONS (*) Notice: Subject to any disclaimer, the term of this Hirschhornet al. Genetics in Medicine. Mar. 2002. vol. 4. No. 2, pp. patent is extended or adjusted under 35 45-61 U.S.C. 154(b) by 391 days. Yang et all. Science. 2006. 314: 992-993 and supplemental online content. (21) Appl. No.: 12/032,154 GeneCard for the HTRA1 gene available via url: <genecards.org/cgi bin/carddisp.pl?gene=Htral D, printed Jul. 20, 2010.* Lucentini et al. The Scientist (2004) vol. 18, p. 20.* (22) Filed: Feb. 15, 2008 Wacholder et al. J. Natl. Cancer Institute (2004) 96(6);434-442.* Ioannidis et al. Nature genetics (2001) 29:306-309.* (65) Prior Publication Data Halushka et al. Nature. Ju1 1999. 22: 239-247. “HtrA1: A novel TGFB antagonist.” Development (2003) 131:502. US 2008/O2O6263 A1 Aug. 28, 2008 Adams et al. “HTRA1 Genotypes Associated with Risk of Neovascular Age-related Macular Degeneration Independent of CFH Related U.S.
    [Show full text]
  • Population-Haplotype Models for Mapping and Tagging Structural Variation Using Whole Genome Sequencing
    Population-haplotype models for mapping and tagging structural variation using whole genome sequencing Eleni Loizidou Submitted in part fulfilment of the requirements for the degree of Doctor of Philosophy Section of Genomics of Common Disease Department of Medicine Imperial College London, 2018 1 Declaration of originality I hereby declare that the thesis submitted for a Doctor of Philosophy degree is based on my own work. Proper referencing is given to the organisations/cohorts I collaborated with during the project. 2 Copyright Declaration The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work 3 Abstract The scientific interest in copy number variation (CNV) is rapidly increasing, mainly due to the evidence of phenotypic effects and its contribution to disease susceptibility. Single nucleotide polymorphisms (SNPs) which are abundant in the human genome have been widely investigated in genome-wide association studies (GWAS). Despite the notable genomic effects both CNVs and SNPs have, the correlation between them has been relatively understudied. In the past decade, next generation sequencing (NGS) has been the leading high-throughput technology for investigating CNVs and offers mapping at a high-quality resolution. We created a map of NGS-defined CNVs tagged by SNPs using the 1000 Genomes Project phase 3 (1000G) sequencing data to examine patterns between the two types of variation in protein-coding genes.
    [Show full text]
  • Specific Correlation Between the Major Chromosome 10Q26 Haplotype Conferring Risk for Age-Related Macular Degeneration and the Expression of HTRA1
    Molecular Vision 2017; 23:318-333 <http://www.molvis.org/molvis/v23/318> © 2017 Molecular Vision Received 5 December 2016 | Accepted 12 June 2017 | Published 14 June 2017 Specific correlation between the major chromosome 10q26 haplotype conferring risk for age-related macular degeneration and the expression of HTRA1 Sha-Mei Liao,1 Wei Zheng,1 Jiang Zhu,2 Casey A. Lewis,1 Omar Delgado,1 Maura A. Crowley,1 Natasha M. Buchanan,1 Bruce D. Jaffee,1 Thaddeus P. Dryja1 1Department of Ophthalmology; NIBR Informatics, Novartis Institutes for Biomedical Research, Cambridge, MA; 2Scientific Data Analysis, NIBR Informatics, Novartis Institutes for Biomedical Research, Cambridge, MA Purpose: A region within chromosome 10q26 has a set of single nucleotide polymorphisms (SNPs) that define a haplo- type that confers high risk for age-related macular degeneration (AMD). We used a bioinformatics approach to search for genes in this region that may be responsible for risk for AMD by assessing levels of gene expression in individuals carrying different haplotypes and by searching for open chromatin regions in the retinal pigment epithelium (RPE) that might include one or more of the SNPs. Methods: We surveyed the PubMed and the 1000 Genomes databases to find all common (minor allele frequency > 0.01) SNPs in 10q26 strongly associated with AMD. We used the HaploReg and LDlink databases to find sets of SNPs with alleles in linkage disequilibrium and used the Genotype-Tissue Expression (GTEx) database to search for correlations between genotypes at individual SNPs and the relative level of expression of the genes. We also accessed Encyclopedia of DNA Elements (ENCODE) to find segments of open chromatin in the region with the AMD-associated SNPs.
    [Show full text]
  • Cell-Deposited Matrix Improves Retinal Pigment Epithelium Survival on Aged Submacular Human Bruch’S Membrane
    Retinal Cell Biology Cell-Deposited Matrix Improves Retinal Pigment Epithelium Survival on Aged Submacular Human Bruch’s Membrane Ilene K. Sugino,1 Vamsi K. Gullapalli,1 Qian Sun,1 Jianqiu Wang,1 Celia F. Nunes,1 Noounanong Cheewatrakoolpong,1 Adam C. Johnson,1 Benjamin C. Degner,1 Jianyuan Hua,1 Tong Liu,2 Wei Chen,2 Hong Li,2 and Marco A. Zarbin1 PURPOSE. To determine whether resurfacing submacular human most, as cell survival is the worst on submacular Bruch’s Bruch’s membrane with a cell-deposited extracellular matrix membrane in these eyes. (Invest Ophthalmol Vis Sci. 2011;52: (ECM) improves retinal pigment epithelial (RPE) survival. 1345–1358) DOI:10.1167/iovs.10-6112 METHODS. Bovine corneal endothelial (BCE) cells were seeded onto the inner collagenous layer of submacular Bruch’s mem- brane explants of human donor eyes to allow ECM deposition. here is no fully effective therapy for the late complications of age-related macular degeneration (AMD), the leading Control explants from fellow eyes were cultured in medium T cause of blindness in the United States. The prevalence of only. The deposited ECM was exposed by removing BCE. Fetal AMD-associated choroidal new vessels (CNVs) and/or geo- RPE cells were then cultured on these explants for 1, 14, or 21 graphic atrophy (GA) in the U.S. population 40 years and older days. The explants were analyzed quantitatively by light micros- is estimated to be 1.47%, with 1.75 million citizens having copy and scanning electron microscopy. Surviving RPE cells from advanced AMD, approximately 100,000 of whom are African explants cultured for 21 days were harvested to compare bestro- American.1 The prevalence of AMD increases dramatically with phin and RPE65 mRNA expression.
    [Show full text]
  • And Non-Risk-Associated Variants at the 10Q26 AMD Locus Influence ARMS2 Mrna Expression but Exclude Pathogenic Effects Due to Protein Deficiency
    Human Molecular Genetics, 2011, Vol. 20, No. 7 1387–1399 doi:10.1093/hmg/ddr020 Advance Access published on January 20, 2011 Risk- and non-risk-associated variants at the 10q26 AMD locus influence ARMS2 mRNA expression but exclude pathogenic effects due to protein deficiency Ulrike Friedrich1, Connie A. Myers2, Lars G. Fritsche1, Andrea Milenkovich1, Armin Wolf3, Joseph C. Corbo 2 and Bernhard H.F. Weber1,∗ 1Institute of Human Genetics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany, 2Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA and 3Department of Ophthalmology, Ludwig-Maximilians University, Mathildenstrasse 8, 80336 Munich, Germany Received December 11, 2010; Revised and Accepted January 13, 2011 Fifteen variants in 10q26 are in strong linkage disequilibrium and are associated with an increased risk for age-related macular degeneration (AMD), a frequent cause of blindness in developed countries. These var- iants tag a single-risk haplotype encompassing the genes ARMS2 (age-related maculopathy susceptibility 2) and part of HTRA1 (HtrA serine peptidase 1). To define the true AMD susceptibility gene in 10q26, several studies have focused on the influence of risk alleles on the expression of ARMS2 and/or HTRA1,butthe results have been inconsistent. By heterologous expression of genomic ARMS2 variants, we now show that ARMS2 mRNA levels transcribed from the risk haplotype are significantly reduced compared with non-risk mRNA isoforms. Analyzing variant ARMS2 constructs, this effect could specifically be assigned to the known insertion/deletion polymorphism (c.(∗)372_815del443ins54) in the 3′-untranslated region of ARMS2.
    [Show full text]
  • Molecular Pathology of Age-Related Macular Degeneration
    Progress in Retinal and Eye Research 28 (2009) 1–18 Contents lists available at ScienceDirect Progress in Retinal and Eye Research journal homepage: www.elsevier.com/locate/prer Molecular pathology of age-related macular degeneration Xiaoyan Ding a,b,1, Mrinali Patel a,c,1, Chi-Chao Chan a,* a Immunopathology Section, Laboratory of Immunology, National Eye Institute, 10 Center Drive, 10/10N103, Bethesda, MD 20892-1857, USA b Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, PR China c Howard Hughes Medical Institute, Chevy Chase, MD, USA abstract Keywords: Age-related macular degeneration (AMD) is a leading cause of irreversible blindness in the world. Age-related macular degeneration Although the etiology and pathogenesis of AMD remain largely unclear, a complex interaction of genetic Inflammation and environmental factors is thought to exist. AMD pathology is characterized by degeneration involving Single nucleotide polymorphism the retinal photoreceptors, retinal pigment epithelium, and Bruch’s membrane, as well as, in some cases, Genetics alterations in choroidal capillaries. Recent research on the genetic and molecular underpinnings of AMD Retinal pigment epithelium Retinal photoreceptors brings to light several basic molecular pathways and pathophysiological processes that might mediate Drusen AMD risk, progression, and/or response to therapy. This review summarizes, in detail, the molecular Vascular endothelial growth factor pathological findings in both humans and animal models, including genetic variations in CFH, CX3CR1, Bruch’s membrane and ARMS2/HtrA1, as well as the role of numerous molecules implicated in inflammation, apoptosis, Molecular pathology cholesterol trafficking, angiogenesis, and oxidative stress. Published by Elsevier Ltd. Contents 1. Introduction . ........................................................2 1.1.
    [Show full text]
  • ARMS2 Gene Age-Related Maculopathy Susceptibility 2
    ARMS2 gene age-related maculopathy susceptibility 2 Normal Function The ARMS2 gene provides instructions for making a protein whose function is unknown. Studies suggest that the ARMS2 protein is found primarily in the placenta and in the specialized light-sensing tissue in the back of the eye (the retina). However, it is unclear what role, if any, the protein plays in early development or normal vision. Health Conditions Related to Genetic Changes Age-related macular degeneration The ARMS2 gene is located on the long (q) arm of chromosome 10 in a region known as 10q26. This region has been strongly associated with the risk of developing age- related macular degeneration, a common cause of vision loss in older adults. Researchers have identified several variations (polymorphisms) in and near the ARMS2 gene that may explain the association between the 10q26 region and age-related macular degeneration. The best-studied of these variations, known as rs10490924, alters a single protein building block (amino acid) in the ARMS2 protein. Another common variation, a complex change that deletes a segment of the ARMS2 gene and inserts new genetic material, may also contribute to disease risk. It is unclear how polymorphisms in the ARMS2 gene might be related to age-related macular degeneration. In the 10q26 region, the ARMS2 gene is located next to a gene called HTRA1; changes in this gene have also been studied as a risk factor for the disease. Because the two genes are so close together, it is difficult to tell whether changes in one gene or the other, or possibly changes in both genes, account for the increased disease risk.
    [Show full text]
  • Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss
    cells Review Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss 1, 1, 1 1,2,3 1 Gayle B. Collin y, Navdeep Gogna y, Bo Chang , Nattaya Damkham , Jai Pinkney , Lillian F. Hyde 1, Lisa Stone 1 , Jürgen K. Naggert 1 , Patsy M. Nishina 1,* and Mark P. Krebs 1,* 1 The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; [email protected] (G.B.C.); [email protected] (N.G.); [email protected] (B.C.); [email protected] (N.D.); [email protected] (J.P.); [email protected] (L.F.H.); [email protected] (L.S.); [email protected] (J.K.N.) 2 Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand 3 Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand * Correspondence: [email protected] (P.M.N.); [email protected] (M.P.K.); Tel.: +1-207-2886-383 (P.M.N.); +1-207-2886-000 (M.P.K.) These authors contributed equally to this work. y Received: 29 February 2020; Accepted: 7 April 2020; Published: 10 April 2020 Abstract: Inherited retinal degeneration (RD) leads to the impairment or loss of vision in millions of individuals worldwide, most frequently due to the loss of photoreceptor (PR) cells. Animal models, particularly the laboratory mouse, have been used to understand the pathogenic mechanisms that underlie PR cell loss and to explore therapies that may prevent, delay, or reverse RD. Here, we reviewed entries in the Mouse Genome Informatics and PubMed databases to compile a comprehensive list of monogenic mouse models in which PR cell loss is demonstrated.
    [Show full text]
  • Identification of Candidate Protective Variants for Common Diseases and Evaluation of Their Protective Potential Joe M
    Butler et al. BMC Genomics (2017) 18:575 DOI 10.1186/s12864-017-3964-3 RESEARCHARTICLE Open Access Identification of candidate protective variants for common diseases and evaluation of their protective potential Joe M. Butler1, Neil Hall2, Niro Narendran3, Yit C. Yang3 and Luminita Paraoan1* Abstract Background: Human polymorphisms with derived alleles that are protective against disease may provide powerful translational opportunities. Here we report a method to identify such candidate polymorphisms and apply it to common non-synonymous SNPs (nsSNPs) associated with common diseases. Our study also sought to establish which of the identified protective nsSNPs show evidence of positive selection, taking this as indirect evidence that the protective variant has a beneficial effect on phenotype. Further, we performed an analysis to quantify the predicted effect of each protective variant on protein function/structure. Results: An initial analysis of eight SNPs previously identified as associated with age-related macular degeneration (AMD), revealed that two of them have a derived allele that is protective against developing the disease. One is in the complement component 2 gene (C2; E318D) and the other is in the complement factor B gene (CFB; R32Q). Then, combining genomewide ancestral allele information with known common disease-associated nsSNPs from the GWAS catalog, we found 32 additional SNPs which have a derived allele that is disease protective. Out of the total 34 identified candidate protective variants (CPVs), we found that 30 show stronger evidence of positive selection than the protective variant in lipoprotein lipase (LPL; S447X), which has already been translated into gene therapy. Furthermore, 11 of these CPVs have a higher probability of affecting protein structure than the lipoprotein lipase protective variant (LPL; S447X).
    [Show full text]
  • Analysis of Six Genetic Risk Factors Highly Associated with AMD in the Region Surrounding ARMS2 and HTRA1 on Chromosome 10, Region Q26
    Retina Analysis of Six Genetic Risk Factors Highly Associated with AMD in the Region Surrounding ARMS2 and HTRA1 on Chromosome 10, Region q26 Dexter Hadley,1,2,3 Anton Orlin,1,3 Gary Brown,4,5 Alexander J. Brucker,1 Allen C. Ho,4,5 Carl D. Regillo,4,5 Larry A. Donoso,6 Lifeng Tian,1,2 Brian Kaderli,1,2 and Dwight Stambolian1,2 PURPOSE. To determine the relationship of six genetic variants dently confirm, for the first time, an association with AMD and (rs10490924, rs3750848, del443ins54, rs3793917, rs11200638, the indel (del443ins54) polymorphism in a Caucasian popula- and rs932275) localized to the ARMS2-HTRA1 region of chro- tion. Two major haplotypes that are associated with AMD and mosome 10, region q26, as risk factors for age-related macular many minor novel haplotypes were identified. The novel hap- degeneration (AMD), to define the haplotype structure of these lotypes, identified from 36 cases and controls with discordant six loci, and to confirm their genetic association with the alleles spanning the ARMS2–HTRA1 region provide unique disease. opportunities to gauge the relative phenotypic contributions of METHODS. Caucasian patients (n ϭ 482) were stratified into each of these genetic risk factors. With the identification of categories based on AREDS (Age-Related Eye Disease Study) more discordant patients in the future, it may be possible to grading criteria (groups 0 and 1 served as the control, groups resolve the ongoing controversy as to which of the risk alleles 3 and 4 contained subjects with AMD, and group 2 was ex- and genes (ARMS2 vs.
    [Show full text]