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Kwong A, Zawistowski M, Fritsche LG, Zhan X, Bragg-Gresham J, Branham KE, Advani J, Othman M, Ratnapriya R, Teslovich TM, Stambolian D, Chew EY, Abecasis GR, Swaroop A. Whole genome sequencing of 4,787 individuals identifies gene-based rare variants in age-related macular degeneration. Hum Mol Genet 2024; 33:374-385. [PMID: 37934784 PMCID: PMC10840384 DOI: 10.1093/hmg/ddad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/12/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Genome-wide association studies have contributed extensively to the discovery of disease-associated common variants. However, the genetic contribution to complex traits is still largely difficult to interpret. We report a genome-wide association study of 2394 cases and 2393 controls for age-related macular degeneration (AMD) via whole-genome sequencing, with 46.9 million genetic variants. Our study reveals significant single-variant association signals at four loci and independent gene-based signals in CFH, C2, C3, and NRTN. Using data from the Exome Aggregation Consortium (ExAC) for a gene-based test, we demonstrate an enrichment of predicted rare loss-of-function variants in CFH, CFI, and an as-yet unreported gene in AMD, ORMDL2. Our method of using a large variant list without individual-level genotypes as an external reference provides a flexible and convenient approach to leverage the publicly available variant datasets to augment the search for rare variant associations, which can explain additional disease risk in AMD.
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Affiliation(s)
- Alan Kwong
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Lars G Fritsche
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Xiaowei Zhan
- Southwestern Medical Center, University of Texas, 5323 Harry Hines Blvd, Dallas, TX 75390, United States
| | - Jennifer Bragg-Gresham
- Kidney Epidemiology and Cost Center, Department of Internal Medicine-Nephrology, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, 1000 Wall St, Ann Arbor, MI 48105, United States
| | - Jayshree Advani
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
| | - Mohammad Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan Kellogg Eye Center, 1000 Wall St, Ann Arbor, MI 48105, United States
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
| | - Tanya M Teslovich
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, United States
| | - Dwight Stambolian
- Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania Medical School, 51 N. 39th Street, Philadelphia, PA 19104, United States
| | - Emily Y Chew
- Division of Epidemiology and Clinical Application, National Eye Institute, National Institutes of Health, 10 Center Drive Building 10-CRC, Bethesda, MD 20892, United States
| | - Gonçalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, United States
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Rd, Tarrytown, NY 10591, United States
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC 0610, Bethesda, MD 20892, United States
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2
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da Palma MM, Igelman AD, Ku C, Burr A, You JY, Place EM, Wang NK, Oh JK, Branham KE, Zhang X, Ahn J, Gorin MB, Lam BL, Ronquillo CC, Bernstein PS, Nagiel A, Huckfeldt R, Cabrera MT, Kelly JP, Bakall B, Iannaccone A, Hufnagel RB, Zein WM, Koenekoop RK, Birch DG, Yang P, Fahim AT, Pennesi ME. Characterization of the Spectrum of Ophthalmic Changes in Patients With Alagille Syndrome. Invest Ophthalmol Vis Sci 2021; 62:27. [PMID: 34185059 PMCID: PMC8254011 DOI: 10.1167/iovs.62.7.27] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Purpose The purpose of this study was to characterize the phenotypic spectrum of ophthalmic findings in patients with Alagille syndrome. Methods We conducted a retrospective, observational, multicenter, study on 46 eyes of 23 subjects with Alagille syndrome. We reviewed systemic and ophthalmologic data extracted from medical records, color fundus photography, fundus autofluorescence, optical coherence tomography, visual fields, electrophysiological assessments, and molecular genetic findings. Results Cardiovascular abnormalities were found in 83% of all cases (of those, 74% had cardiac murmur), whereas 61% had a positive history of hepatobiliary issues, and musculoskeletal anomalies were present in 61% of all patients. Dysmorphic facies were present in 16 patients, with a broad forehead being the most frequent feature. Ocular symptoms were found in 91%, with peripheral vision loss being the most frequent complaint. Median (range) Snellen visual acuity of all eyes was 20/25 (20/20 to hand motion [HM]). Anterior segment abnormalities were present in 74% of the patients; of those, posterior embryotoxon was the most frequent finding. Abnormalities of the optic disc were found in 52%, and peripheral retinal abnormalities were the most frequent ocular finding in this series, found in 96% of all patients. Fifteen JAG1 mutations were identified in 16 individuals; of those, 6 were novel. Conclusions This study reports a cohort of patients with Alagille syndrome in which peripheral chorioretinal changes were more frequent than posterior embryotoxon, the most frequent ocular finding according to a number of previous studies. We propose that these peripheral chorioretinal changes are a new hallmark to help diagnose this syndrome.
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Affiliation(s)
- Mariana Matioli da Palma
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States.,Department of Ophthalmology and Visual Sciences, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Austin D Igelman
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Cristy Ku
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Amanda Burr
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Jia Yue You
- Departments of Ophthalmology, Human Genetics, and Pediatric Surgery, Montreal Children's Hospital, McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Emily M Place
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States
| | - Nan-Kai Wang
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, New York, New York, United States
| | - Jin Kyun Oh
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Irving Medical Center, New York, New York, United States.,State University of New York, Downstate Medical Center, Brooklyn, New York, United States
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | - Xinxin Zhang
- Duke Eye Center, Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, United States
| | - Jeeyun Ahn
- UCLA Stein Eye Institute, Division of Retinal Disorders and Ophthalmic Genetics, Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, California, United States.,Department of Ophthalmology, Seoul National University, College of Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Korea
| | - Michael B Gorin
- UCLA Stein Eye Institute, Division of Retinal Disorders and Ophthalmic Genetics, Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, California, United States.,Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, United States
| | - Byron L Lam
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Cecinio C Ronquillo
- John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States
| | - Paul S Bernstein
- John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States
| | - Aaron Nagiel
- The Vision Center, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, California, United States.,Roski Eye Institute, Department of Ophthalmology, University of Southern California, Los Angeles, California, United States
| | - Rachel Huckfeldt
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States
| | - Michelle T Cabrera
- Department of Ophthalmology, University of Washington, Seattle, Washington, United States.,Department of Ophthalmology, Seattle Children's Hospital, Seattle, Washington, United States
| | - John P Kelly
- Department of Ophthalmology, Seattle Children's Hospital, Seattle, Washington, United States
| | - Benjamin Bakall
- Department of Ophthalmology, University of Arizona College of Medicine, Phoenix, Arizon, United States
| | - Alessandro Iannaccone
- Duke Eye Center, Department of Ophthalmology, Duke University School of Medicine, Durham, North Carolina, United States
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert K Koenekoop
- Departments of Ophthalmology, Human Genetics, and Pediatric Surgery, Montreal Children's Hospital, McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - David G Birch
- Retina Foundation of the Southwest, Dallas, Texas, United States
| | - Paul Yang
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Abigail T Fahim
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
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3
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Thompson DA, Iannaccone A, Ali RR, Arshavsky VY, Audo I, Bainbridge JWB, Besirli CG, Birch DG, Branham KE, Cideciyan AV, Daiger SP, Dalkara D, Duncan JL, Fahim AT, Flannery JG, Gattegna R, Heckenlively JR, Heon E, Jayasundera KT, Khan NW, Klassen H, Leroy BP, Molday RS, Musch DC, Pennesi ME, Petersen-Jones SM, Pierce EA, Rao RC, Reh TA, Sahel JA, Sharon D, Sieving PA, Strettoi E, Yang P, Zacks DN. Advancing Clinical Trials for Inherited Retinal Diseases: Recommendations from the Second Monaciano Symposium. Transl Vis Sci Technol 2020; 9:2. [PMID: 32832209 PMCID: PMC7414644 DOI: 10.1167/tvst.9.7.2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 03/12/2020] [Indexed: 12/18/2022] Open
Abstract
Major advances in the study of inherited retinal diseases (IRDs) have placed efforts to develop treatments for these blinding conditions at the forefront of the emerging field of precision medicine. As a result, the growth of clinical trials for IRDs has increased rapidly over the past decade and is expected to further accelerate as more therapeutic possibilities emerge and qualified participants are identified. Although guided by established principles, these specialized trials, requiring analysis of novel outcome measures and endpoints in small patient populations, present multiple challenges relative to study design and ethical considerations. This position paper reviews recent accomplishments and existing challenges in clinical trials for IRDs and presents a set of recommendations aimed at rapidly advancing future progress. The goal is to stimulate discussions among researchers, funding agencies, industry, and policy makers that will further the design, conduct, and analysis of clinical trials needed to accelerate the approval of effective treatments for IRDs, while promoting advocacy and ensuring patient safety.
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Affiliation(s)
- Debra A Thompson
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alessandro Iannaccone
- Department of Ophthalmology, Duke Eye Center, Duke University Medical Center, Durham, NC, USA
| | - Robin R Ali
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA.,Institute of Ophthalmology, University College London, London, UK
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke Eye Center, Duke University Medical Center, Durham, NC, USA
| | - Isabelle Audo
- Sorbonne Université, Institut de la Vision, INSERM, CNRS, Paris, France.,CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France
| | | | - Cagri G Besirli
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Artur V Cideciyan
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven P Daiger
- Human Genetics Center, School of Public Health, University of Texas Health Science Center Houston, Houston, TX, USA
| | - Deniz Dalkara
- Sorbonne Université, Institut de la Vision, INSERM, CNRS, Paris, France
| | - Jacque L Duncan
- Department of Ophthalmology, University of California-San Francisco, San Francisco, CA, USA
| | - Abigail T Fahim
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John G Flannery
- Helen Wills Neuroscience Institute, University of California-Berkeley, Berkeley, CA, USA
| | | | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada
| | - K Thiran Jayasundera
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Naheed W Khan
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Henry Klassen
- Gavin Herbert Eye Institute, Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA
| | - Bart P Leroy
- Department of Ophthalmology and Center Medical Genetics, Ghent University Hospital and University, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert S Molday
- Department of Biochemistry/Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - David C Musch
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science Center, Portland, OR, USA
| | - Simon M Petersen-Jones
- Small Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, MI, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Rajesh C Rao
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Jose A Sahel
- Sorbonne Université, Institut de la Vision, INSERM, CNRS, Paris, France.,CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, Paris, France.,Fondation Ophtalmologique Rothschild, Paris, France.,Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paul A Sieving
- Department of Ophthalmology and Center for Ocular Regenerative Therapy, University of California-Davis School of Medicine, Sacramento, CA, USA.,National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Enrica Strettoi
- Institute of Neuroscience, National Research Council (CNR), Pisa, Italy
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science Center, Portland, OR, USA
| | - David N Zacks
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan Medical School, Ann Arbor, MI, USA
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4
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Jamshidi F, Place EM, Mehrotra S, Navarro-Gomez D, Maher M, Branham KE, Valkanas E, Cherry TJ, Lek M, MacArthur D, Pierce EA, Bujakowska KM. Contribution of noncoding pathogenic variants to RPGRIP1-mediated inherited retinal degeneration. Genet Med 2018; 21:694-704. [PMID: 30072743 PMCID: PMC6399075 DOI: 10.1038/s41436-018-0104-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/15/2018] [Indexed: 11/22/2022] Open
Abstract
Purpose: With the advent of gene therapies for inherited retinal degenerations (IRDs), genetic diagnostics will have an increasing role in clinical decision-making. Yet the genetic cause of disease cannot be identified using exon-based sequencing for a significant portion of patients. We hypothesized that non-coding mutations contribute significantly to the genetic causality of IRDs and evaluated patients with single coding mutations in RPGRIP1 to test this hypothesis. Methods: IRD families underwent targeted panel sequencing. Unsolved cases were explored by whole exome and genome sequencing looking for additional mutations. Candidate mutations were then validated by Sanger sequencing, quantitative PCR, and in vitro splicing assays in two cell lines analyzed through amplicon sequencing. Results: Among 1722 families, three had biallelic loss of function mutations in RPGRIP1 while seven had a single disruptive coding mutation. Whole exome and genome sequencing revealed potential non-coding mutations in these seven families. In six, the non-coding mutations were shown to lead to loss of function in vitro. Conclusion: Non-coding mutations were identified in 6 of 7 families with single coding mutations in RPGRIP1. The results suggest that non-coding mutations contribute significantly to the genetic causality of IRDs and RPGRIP1–mediated IRDs are more common than previously thought.
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Affiliation(s)
- Farzad Jamshidi
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily M Place
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Sudeep Mehrotra
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Mathew Maher
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Elise Valkanas
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Timothy J Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute and University of Washington, Department of Pediatrics, Seattle, Washington, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Boston, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA.
| | - Kinga M Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, USA.
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5
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Sullivan LS, Bowne SJ, Koboldt DC, Cadena EL, Heckenlively JR, Branham KE, Wheaton DH, Jones KD, Ruiz RS, Pennesi ME, Yang P, Davis-Boozer D, Northrup H, Gurevich VV, Chen R, Xu M, Li Y, Birch DG, Daiger SP. A Novel Dominant Mutation in SAG, the Arrestin-1 Gene, Is a Common Cause of Retinitis Pigmentosa in Hispanic Families in the Southwestern United States. Invest Ophthalmol Vis Sci 2017; 58:2774-2784. [PMID: 28549094 PMCID: PMC5455168 DOI: 10.1167/iovs.16-21341] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Purpose To identify the causes of autosomal dominant retinitis pigmentosa (adRP) in a cohort of families without mutations in known adRP genes and consequently to characterize a novel dominant-acting missense mutation in SAG. Methods Patients underwent ophthalmologic testing and were screened for mutations using targeted-capture and whole-exome next-generation sequencing. Confirmation and additional screening were done by Sanger sequencing. Haplotypes segregating with the mutation were determined using short tandem repeat and single nucleotide variant polymorphisms. Genealogies were established by interviews of family members. Results Eight families in a cohort of 300 adRP families, and four additional families, were found to have a novel heterozygous mutation in the SAG gene, c.440G>T; p.Cys147Phe. Patients exhibited symptoms of retinitis pigmentosa and none showed symptoms characteristic of Oguchi disease. All families are of Hispanic descent and most were ascertained in Texas or California. A single haplotype including the SAG mutation was identified in all families. The mutation dramatically alters a conserved amino acid, is extremely rare in global databases, and was not found in 4000+ exomes from Hispanic controls. Molecular modeling based on the crystal structure of bovine arrestin-1 predicts protein misfolding/instability. Conclusions This is the first dominant-acting mutation identified in SAG, a founder mutation possibly originating in Mexico several centuries ago. The phenotype is clearly adRP and is distinct from the previously reported phenotypes of recessive null mutations, that is, Oguchi disease and recessive RP. The mutation accounts for 3% of the 300 families in the adRP Cohort and 36% of Hispanic families in this cohort.
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Affiliation(s)
- Lori S Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
| | - Sara J Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
| | | | - Elizabeth L Cadena
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States
| | - John R Heckenlively
- Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | - Kari E Branham
- Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | - Dianna H Wheaton
- Retina Foundation of the Southwest, Dallas, Texas, United States
| | - Kaylie D Jones
- Retina Foundation of the Southwest, Dallas, Texas, United States
| | - Richard S Ruiz
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - Paul Yang
- Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - David Davis-Boozer
- Casey Eye Institute, Oregon Health and Science University, Portland, Oregon, United States
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States
| | | | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Mingchu Xu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - David G Birch
- Retina Foundation of the Southwest, Dallas, Texas, United States
| | - Stephen P Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, Texas, United States 5Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States
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6
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Oliver VF, Jaffe AE, Song J, Wang G, Zhang P, Branham KE, Swaroop A, Eberhart CG, Zack DJ, Qian J, Merbs SL. Differential DNA methylation identified in the blood and retina of AMD patients. Epigenetics 2016; 10:698-707. [PMID: 26067391 DOI: 10.1080/15592294.2015.1060388] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Age-related macular degeneration (AMD) is a major cause of blindness in the western world. While genetic studies have linked both common and rare variants in genes involved in regulation of the complement system to increased risk of development of AMD, environmental factors, such as smoking and nutrition, can also significantly affect the risk of developing the disease and the rate of disease progression. Since epigenetics has been implicated in mediating, in part, the disease risk associated with some environmental factors, we investigated a possible epigenetic contribution to AMD. We performed genome-wide DNA methylation profiling of blood from AMD patients and controls. No differential methylation site reached genome-wide significance; however, when epigenetic changes in and around known GWAS-defined AMD risk loci were explored, we found small but significant DNA methylation differences in the blood of neovascular AMD patients near age-related maculopathy susceptibility 2 (ARMS2), a top-ranked GWAS locus preferentially associated with neovascular AMD. The methylation level of one of the CpG sites significantly correlated with the genotype of the risk SNP rs10490924, suggesting a possible epigenetic mechanism of risk. Integrating genome-wide DNA methylation analysis of retina samples with and without AMD together with blood samples, we further identified a consistent, replicable change in DNA methylation in the promoter region of protease serine 50 (PRSS50). These methylation changes may identify sites in novel genes that are susceptible to non-genetic factors known to contribute to AMD development and progression.
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Key Words
- AMD, Age-related macular degeneration
- AMD-MMAP, Michigan, Mayo
- AREDS, Age-Related Eye Disease Study
- AREDS, and Pennsylvania
- DNA methylation
- DNAm, DNA methylation
- GA, geographic atrophy
- GWAS, genome-wide association study
- KEC, Kellogg Eye Center
- LCLs, lymphoblastoid cell lines
- NV, choroidal neovascularization
- RPE, retinal pigment epithelium
- age-related macular degeneration
- genome-wide methylation
- meQTL, methylation quantitative trait loci
- methyl-QTL
- peripheral blood leukocytes
- retina
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Affiliation(s)
- Verity F Oliver
- a Department of Ophthalmology; Johns Hopkins University; School of Medicine ; Baltimore , MD USA
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7
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Thompson DA, Ali RR, Banin E, Branham KE, Flannery JG, Gamm DM, Hauswirth WW, Heckenlively JR, Iannaccone A, Jayasundera KT, Khan NW, Molday RS, Pennesi ME, Reh TA, Weleber RG, Zacks DN. Advancing therapeutic strategies for inherited retinal degeneration: recommendations from the Monaciano Symposium. Invest Ophthalmol Vis Sci 2015; 56:918-31. [PMID: 25667399 DOI: 10.1167/iovs.14-16049] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although rare in the general population, retinal dystrophies occupy a central position in current efforts to develop innovative therapies for blinding diseases. This status derives, in part, from the unique biology, accessibility, and function of the retina, as well as from the synergy between molecular discoveries and transformative advances in functional assessment and retinal imaging. The combination of these factors has fueled remarkable progress in the field, while at the same time creating complex challenges for organizing collective efforts aimed at advancing translational research. The present position paper outlines recent progress in gene therapy and cell therapy for this group of disorders, and presents a set of recommendations for addressing the challenges remaining for the coming decade. It is hoped that the formulation of these recommendations will stimulate discussions among researchers, funding agencies, industry, and policy makers that will accelerate the development of safe and effective treatments for retinal dystrophies and related diseases.
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Affiliation(s)
- Debra A Thompson
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Robin R Ali
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States Division of Molecular Therapy, University College London Institute of Ophthalmology, London, England, United Kingdom
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - John G Flannery
- Helen Wills Neuroscience Institute, University of California-Berkeley, Berkeley, California, United States
| | - David M Gamm
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States
| | - William W Hauswirth
- Department of Ophthalmology, University of Florida College of Medicine, Gainesville, Florida, United States
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Alessandro Iannaccone
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - K Thiran Jayasundera
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Naheed W Khan
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark E Pennesi
- Casey Eye Institute and the Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, United States
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, Seattle, Washington, United States
| | - Richard G Weleber
- Casey Eye Institute and the Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, United States Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, United States
| | - David N Zacks
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, Michigan, United States
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8
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Oliver VF, Franchina M, Jaffe AE, Branham KE, Othman M, Heckenlively JR, Swaroop A, Campochiaro B, Vote BJ, Craig JE, Saffery R, Mackey DA, Qian J, Zack DJ, Hewitt AW, Merbs SL. Hypomethylation of the IL17RC promoter in peripheral blood leukocytes is not a hallmark of age-related macular degeneration. Cell Rep 2014; 5:1527-35. [PMID: 24373284 DOI: 10.1016/j.celrep.2013.11.042] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/25/2013] [Accepted: 11/26/2013] [Indexed: 01/06/2023] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of visual impairment worldwide. Aberrant DNA methylation within the promoter of IL17RC in peripheral blood mononuclear cells has recently been reported in AMD. To validate this association, we examined DNA methylation of the IL17RC promoter in peripheral blood. First, we used Illumina Human Methylation450 Bead Arrays, a widely accepted platform for measuring global DNA methylation. Second, methylation status at multiple sites within the IL17RC promoter was determined by bisulfite pyrosequencing in two cohorts. Third, a methylation-sensitive quantitative PCR-based assay was performed on a subset of samples. In contrast to previous findings, we did not find evidence of differential methylation between AMD cases and age-matched controls. We conclude that hypomethylation within the IL17RC gene promoter in peripheral blood is not suitable for use as a clinical biomarker of AMD. This study highlights the need for considerable replication of epigenetic association studies prior to clinical application.
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Affiliation(s)
- Verity F Oliver
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
| | - Maria Franchina
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, WA 6009, Australia
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21287, USA
| | - Kari E Branham
- Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Mohammad Othman
- Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - John R Heckenlively
- Kellogg Eye Center, Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48105, USA
| | - Anand Swaroop
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Betsy Campochiaro
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
| | - Brendan J Vote
- Launceston Eye Institute, University of Tasmania, Launceston 7249, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA 5042, Australia
| | - Richard Saffery
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, WA 6009, Australia
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
| | - Donald J Zack
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA; Department of Molecular Biology and Genetics, Department of Neuroscience, and Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA; Institut de la Vision, Université Pierre et Marie Curie, Paris 75012, France
| | - Alex W Hewitt
- Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, WA 6009, Australia; Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia.
| | - Shannath L Merbs
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA.
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9
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Ratnapriya R, Zhan X, Fariss RN, Branham KE, Zipprer D, Chakarova CF, Sergeev YV, Campos MM, Othman M, Friedman JS, Maminishkis A, Waseem NH, Brooks M, Rajasimha HK, Edwards AO, Lotery A, Klein BE, Truitt BJ, Li B, Schaumberg DA, Morgan DJ, Morrison MA, Souied E, Tsironi EE, Grassmann F, Fishman GA, Silvestri G, Scholl HPN, Kim IK, Ramke J, Tuo J, Merriam JE, Merriam JC, Park KH, Olson LM, Farrer LA, Johnson MP, Peachey NS, Lathrop M, Baron RV, Igo RP, Klein R, Hagstrom SA, Kamatani Y, Martin TM, Jiang Y, Conley Y, Sahel JA, Zack DJ, Chan CC, Pericak-Vance MA, Jacobson SG, Gorin MB, Klein ML, Allikmets R, Iyengar SK, Weber BH, Haines JL, Léveillard T, Deangelis MM, Stambolian D, Weeks DE, Bhattacharya SS, Chew EY, Heckenlively JR, Abecasis GR, Swaroop A. Rare and common variants in extracellular matrix gene Fibrillin 2 (FBN2) are associated with macular degeneration. Hum Mol Genet 2014; 23:5827-37. [PMID: 24899048 DOI: 10.1093/hmg/ddu276] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Neurodegenerative diseases affecting the macula constitute a major cause of incurable vision loss and exhibit considerable clinical and genetic heterogeneity, from early-onset monogenic disease to multifactorial late-onset age-related macular degeneration (AMD). As part of our continued efforts to define genetic causes of macular degeneration, we performed whole exome sequencing in four individuals of a two-generation family with autosomal dominant maculopathy and identified a rare variant p.Glu1144Lys in Fibrillin 2 (FBN2), a glycoprotein of the elastin-rich extracellular matrix (ECM). Sanger sequencing validated the segregation of this variant in the complete pedigree, including two additional affected and one unaffected individual. Sequencing of 192 maculopathy patients revealed additional rare variants, predicted to disrupt FBN2 function. We then undertook additional studies to explore the relationship of FBN2 to macular disease. We show that FBN2 localizes to Bruch's membrane and its expression appears to be reduced in aging and AMD eyes, prompting us to examine its relationship with AMD. We detect suggestive association of a common FBN2 non-synonymous variant, rs154001 (p.Val965Ile) with AMD in 10 337 cases and 11 174 controls (OR = 1.10; P-value = 3.79 × 10(-5)). Thus, it appears that rare and common variants in a single gene--FBN2--can contribute to Mendelian and complex forms of macular degeneration. Our studies provide genetic evidence for a key role of elastin microfibers and Bruch's membrane in maintaining blood-retina homeostasis and establish the importance of studying orphan diseases for understanding more common clinical phenotypes.
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Affiliation(s)
| | - Xiaowei Zhan
- Center for Statistical Genetics, Department of Biostatistics and
| | | | - Kari E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Zipprer
- Neurobiology Neurodegeneration and Repair Laboratory
| | - Christina F Chakarova
- Department of Genetics, UCL-Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK
| | | | | | - Mohammad Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | - Naushin H Waseem
- Department of Genetics, UCL-Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK
| | | | | | - Albert O Edwards
- Institute for Molecular Biology, University of Oregon and Oregon Retina, Eugene, OR 97401, USA
| | - Andrew Lotery
- Faculty of Medicine, Clinical and Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Barbara E Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and, Public Health, Madison, WI 53726, USA
| | - Barbara J Truitt
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Bingshan Li
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Debra A Schaumberg
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA, Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
| | - Denise J Morgan
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
| | - Margaux A Morrison
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
| | - Eric Souied
- Hôpital Intercommunal de Créteil, Hôpital Henri Mondor - Université Paris Est Créteil 94000, France
| | - Evangelia E Tsironi
- Department of Ophthalmology, University of Thessaly School of Medicine, Larissa, Greece
| | - Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Regensburg 93053, Germany
| | - Gerald A Fishman
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | - Hendrik P N Scholl
- Wilmer Eye Institute, Johns Hopkins University, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | - Ivana K Kim
- Retina Service and Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Jacqueline Ramke
- The Fred Hollows Foundation, Auckland, New Zealand, School of Social Sciences, University of New South Wales, Sydney, Australia
| | | | | | | | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul 463-707, Republic of Korea
| | - Lana M Olson
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Lindsay A Farrer
- Departments of Medicine (Section of Biomedical Genetics), Ophthalmology and Biostatistics, Neurology, Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA 02215, USA
| | | | - Neal S Peachey
- Cleveland Clinic Foundation, Cole Eye Institute, Cleveland, OH 44195, USA, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44195, USA
| | - Mark Lathrop
- Department of Genetics, Institut de la Vision - Inserm Université Pierre et Marie Curie UMR-S 968, Paris, France
| | | | - Robert P Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and, Public Health, Madison, WI 53726, USA
| | | | - Yoichiro Kamatani
- Department of Genetics, Institut de la Vision - Inserm Université Pierre et Marie Curie UMR-S 968, Paris, France
| | - Tammy M Martin
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Yingda Jiang
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yvette Conley
- Health Promotion and Development, School of Nursing, 440 Victoria Building, 3500 Victoria St, Pittsburgh, PA 15261, USA
| | - Jose-Alan Sahel
- Department of Genetics, Institut de la Vision - Inserm Université Pierre et Marie Curie UMR-S 968, Paris, France
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University, 600 N. Wolfe Street, Baltimore, MD 21287, USA
| | | | - Margaret A Pericak-Vance
- Bascom Palmer Eye Institute and Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33125, USA
| | - Samuel G Jacobson
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael B Gorin
- Department of Ophthalmology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael L Klein
- Macular Degeneration Center, Casey Eye Institute, Oregon Health and Science, University, Portland, OR 97201, USA
| | - Rando Allikmets
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Sudha K Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Bernhard H Weber
- Institute of Human Genetics, University of Regensburg, Regensburg 93053, Germany
| | - Jonathan L Haines
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Thierry Léveillard
- Department of Genetics, Institut de la Vision - Inserm Université Pierre et Marie Curie UMR-S 968, Paris, France
| | - Margaret M Deangelis
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT 84132, USA
| | - Dwight Stambolian
- Department of Ophthalmology, and Department of Genetics, University of Pennsylvania, Philadelphia, PA 9104, USA
| | - Daniel E Weeks
- Department of Human Genetics and Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Shomi S Bhattacharya
- Department of Genetics, UCL-Institute of Ophthalmology, Bath Street, London EC1V 9EL, UK
| | - Emily Y Chew
- Clinical Trials Branch, Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Anand Swaroop
- Neurobiology Neurodegeneration and Repair Laboratory,
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10
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Wang C, Zhan X, Bragg-Gresham J, Kang HM, Stambolian D, Chew EY, Branham KE, Heckenlively J, Fulton R, Wilson RK, Mardis ER, Lin X, Swaroop A, Zöllner S, Abecasis GR. Ancestry estimation and control of population stratification for sequence-based association studies. Nat Genet 2014; 46:409-15. [PMID: 24633160 DOI: 10.1038/ng.2924] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 02/21/2014] [Indexed: 12/15/2022]
Abstract
Estimating individual ancestry is important in genetic association studies where population structure leads to false positive signals, although assigning ancestry remains challenging with targeted sequence data. We propose a new method for the accurate estimation of individual genetic ancestry, based on direct analysis of off-target sequence reads, and implement our method in the publicly available LASER software. We validate the method using simulated and empirical data and show that the method can accurately infer worldwide continental ancestry when used with sequencing data sets with whole-genome shotgun coverage as low as 0.001×. For estimates of fine-scale ancestry within Europe, the method performs well with coverage of 0.1×. On an even finer scale, the method improves discrimination between exome-sequenced study participants originating from different provinces within Finland. Finally, we show that our method can be used to improve case-control matching in genetic association studies and to reduce the risk of spurious findings due to population structure.
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Affiliation(s)
- Chaolong Wang
- 1] Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA. [3]
| | - Xiaowei Zhan
- 1] Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA. [2]
| | - Jennifer Bragg-Gresham
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Hyun Min Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia, Pennsylvania, USA
| | - Emily Y Chew
- Division of Epidemiology and Clinical Research, National Eye Institute, Bethesda, Maryland, USA
| | - Kari E Branham
- Department of Ophthalmology, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, USA
| | - John Heckenlively
- Department of Ophthalmology, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, USA
| | | | - Robert Fulton
- Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard K Wilson
- Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Elaine R Mardis
- Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, Bethesda, Maryland, USA
| | - Sebastian Zöllner
- 1] Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA. [2] Department of Psychiatry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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11
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Maranhao B, Biswas P, Duncan JL, Branham KE, Silva GA, Naeem MA, Khan SN, Riazuddin S, Hejtmancik JF, Heckenlively JR, Riazuddin SA, Lee PL, Ayyagari R. exomeSuite: Whole exome sequence variant filtering tool for rapid identification of putative disease causing SNVs/indels. Genomics 2014; 103:169-76. [PMID: 24603341 DOI: 10.1016/j.ygeno.2014.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 02/19/2014] [Accepted: 02/24/2014] [Indexed: 12/30/2022]
Abstract
Exome and whole-genome analyses powered by next-generation sequencing (NGS) have become invaluable tools in identifying causal mutations responsible for Mendelian disorders. Given that individual exomes contain several thousand single nucleotide variants and insertions/deletions, it remains a challenge to analyze large numbers of variants from multiple exomes to identify causal alleles associated with inherited conditions. To this end, we have developed user-friendly software that analyzes variant calls from multiple individuals to facilitate identification of causal mutations. The software, termed exomeSuite, filters for putative causative variants of monogenic diseases inherited in one of three forms: dominant, recessive caused by a homozygous variant, or recessive caused by two compound heterozygous variants. In addition, exomeSuite can perform homozygosity mapping and analyze the variant data of multiple unrelated individuals. Here we demonstrate that filtering of variants with exomeSuite reduces datasets to a fraction of a percent of their original size. To the best of our knowledge this is the first freely available software developed to analyze variant data from multiple individuals that rapidly assimilates and filters large data sets based on pattern of inheritance.
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Affiliation(s)
- B Maranhao
- Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - P Biswas
- Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA.
| | - J L Duncan
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA.
| | - K E Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - G A Silva
- Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Neurosciences Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - M A Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - S N Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - S Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - J F Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Institutes of Health, Bethesda, MD 20892, USA.
| | - J R Heckenlively
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - S A Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan; The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - P L Lee
- Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA.
| | - R Ayyagari
- Department of Ophthalmology, University of California, San Diego, UC Jacobs Retina Center, 9415 Campus Point Drive, La Jolla, CA 92037-0946, USA.
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12
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Bowne SJ, Sullivan LS, Avery CE, Sasser EM, Roorda A, Duncan JL, Wheaton DH, Birch DG, Branham KE, Heckenlively JR, Sieving PA, Daiger SP. Mutations in the small nuclear riboprotein 200 kDa gene (SNRNP200) cause 1.6% of autosomal dominant retinitis pigmentosa. Mol Vis 2013; 19:2407-17. [PMID: 24319334 PMCID: PMC3850977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/22/2013] [Indexed: 12/02/2022] Open
Abstract
PURPOSE The purpose of this project was to determine the spectrum and frequency of mutations in the small nuclear riboprotein 200 kDa gene (SNRNP200) that cause autosomal dominant retinitis pigmentosa (adRP). METHODS A well-characterized adRP cohort of 251 families was tested for mutations in the exons and intron/exon junctions of SNRNP200 using fluorescent dideoxy sequencing. An additional 21 adRP families from the eyeGENE® Network were tested for possible mutations. Bioinformatic and segregation analysis was performed on novel variants. RESULTS SNRNP200 mutations were identified in seven of the families tested. Two previously reported mutations, p.Arg681Cys and p.Ser1087Leu, were found in two families each. One family had the previously reported p.Arg681His mutation. Two novel SNRNP200 variants, p.Pro682Ser and p.Ala542Val, were also identified in one family each. Bioinformatic and segregation analyses suggested that these novel variants are likely to be pathogenic. Clinical examination of patients with SNRNP200 mutations showed a wide range of clinical symptoms and severity, including one instance of non-penetrance. CONCLUSIONS Mutations in SNRNP200 caused 1.6% of disease in our adRP cohort. Pathogenic mutations were found primarily in exons 16 and 25, but the novel p.Ala542Val mutation in exon 13 suggests that variation in other genetic regions is also responsible for causing dominant disease. SNRNP200 mutations were associated with a wide range of clinical symptoms similar to those of individuals with other splice-factor gene mutations.
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Affiliation(s)
- Sara J. Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
| | - Lori S. Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
| | - Cheryl E. Avery
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
| | - Elizabeth M. Sasser
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
| | - Austin Roorda
- School of Optometry and Vision Sciences Graduate Group, University of California, Berkeley, CA
| | - Jacque L. Duncan
- Department of Ophthalmology, University of California, San Francisco, CA
| | | | | | | | | | - Paul A. Sieving
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Stephen P. Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center Houston, TX
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13
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Wang F, Wang H, Tuan HF, Nguyen DH, Sun V, Keser V, Bowne SJ, Sullivan LS, Luo H, Zhao L, Wang X, Zaneveld JE, Salvo JS, Siddiqui S, Mao L, Wheaton DK, Birch DG, Branham KE, Heckenlively JR, Wen C, Flagg K, Ferreyra H, Pei J, Khan A, Ren H, Wang K, Lopez I, Qamar R, Zenteno JC, Ayala-Ramirez R, Buentello-Volante B, Fu Q, Simpson DA, Li Y, Sui R, Silvestri G, Daiger SP, Koenekoop RK, Zhang K, Chen R. Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. Hum Genet 2013; 133:331-45. [PMID: 24154662 DOI: 10.1007/s00439-013-1381-5] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
Retinitis pigmentosa (RP) is a devastating form of retinal degeneration, with significant social and professional consequences. Molecular genetic information is invaluable for an accurate clinical diagnosis of RP due to its high genetic and clinical heterogeneity. Using a gene capture panel that covers 163 of the currently known retinal disease genes, including 48 RP genes, we performed a comprehensive molecular screening in a collection of 123 RP unsettled probands from a wide variety of ethnic backgrounds, including 113 unrelated simplex and 10 autosomal recessive RP (arRP) cases. As a result, 61 mutations were identified in 45 probands, including 38 novel pathogenic alleles. Interestingly, we observed that phenotype and genotype were not in full agreement in 21 probands. Among them, eight probands were clinically reassessed, resulting in refinement of clinical diagnoses for six of these patients. Finally, recessive mutations in CLN3 were identified in five retinal degeneration patients, including four RP probands and one cone-rod dystrophy patient, suggesting that CLN3 is a novel non-syndromic retinal disease gene. Collectively, our results underscore that, due to the high molecular and clinical heterogeneity of RP, comprehensive screening of all retinal disease genes is effective in identifying novel pathogenic mutations and provides an opportunity to discover new genotype-phenotype correlations. Information gained from this genetic screening will directly aid in patient diagnosis, prognosis, and treatment, as well as allowing appropriate family planning and counseling.
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Affiliation(s)
- Feng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
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Neveling K, Collin RW, Gilissen C, van Huet RA, Visser L, Kwint MP, Gijsen SJ, Zonneveld MN, Wieskamp N, de Ligt J, Siemiatkowska AM, Hoefsloot LH, Buckley MF, Kellner U, Branham KE, den Hollander AI, Hoischen A, Hoyng C, Klevering BJ, van den Born LI, Veltman JA, Cremers FP, Scheffer H. Next Generation Genetic Testing for Retinitis Pigmentosa. Hum Mutat 2013. [DOI: 10.1002/humu.22357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Fritsche LG, Chen W, Schu M, Yaspan BL, Yu Y, Thorleifsson G, Zack DJ, Arakawa S, Cipriani V, Ripke S, Igo RP, Buitendijk GHS, Sim X, Weeks DE, Guymer RH, Merriam JE, Francis PJ, Hannum G, Agarwal A, Armbrecht AM, Audo I, Aung T, Barile GR, Benchaboune M, Bird AC, Bishop PN, Branham KE, Brooks M, Brucker AJ, Cade WH, Cain MS, Campochiaro PA, Chan CC, Cheng CY, Chew EY, Chin KA, Chowers I, Clayton DG, Cojocaru R, Conley YP, Cornes BK, Daly MJ, Dhillon B, Edwards AO, Evangelou E, Fagerness J, Ferreyra HA, Friedman JS, Geirsdottir A, George RJ, Gieger C, Gupta N, Hagstrom SA, Harding SP, Haritoglou C, Heckenlively JR, Holz FG, Hughes G, Ioannidis JPA, Ishibashi T, Joseph P, Jun G, Kamatani Y, Katsanis N, N Keilhauer C, Khan JC, Kim IK, Kiyohara Y, Klein BEK, Klein R, Kovach JL, Kozak I, Lee CJ, Lee KE, Lichtner P, Lotery AJ, Meitinger T, Mitchell P, Mohand-Saïd S, Moore AT, Morgan DJ, Morrison MA, Myers CE, Naj AC, Nakamura Y, Okada Y, Orlin A, Ortube MC, Othman MI, Pappas C, Park KH, Pauer GJT, Peachey NS, Poch O, Priya RR, Reynolds R, Richardson AJ, Ripp R, Rudolph G, Ryu E, Sahel JA, Schaumberg DA, Scholl HPN, Schwartz SG, Scott WK, Shahid H, Sigurdsson H, Silvestri G, Sivakumaran TA, Smith RT, Sobrin L, Souied EH, Stambolian DE, Stefansson H, Sturgill-Short GM, Takahashi A, Tosakulwong N, Truitt BJ, Tsironi EE, Uitterlinden AG, van Duijn CM, Vijaya L, Vingerling JR, Vithana EN, Webster AR, Wichmann HE, Winkler TW, Wong TY, Wright AF, Zelenika D, Zhang M, Zhao L, Zhang K, Klein ML, Hageman GS, Lathrop GM, Stefansson K, Allikmets R, Baird PN, Gorin MB, Wang JJ, Klaver CCW, Seddon JM, Pericak-Vance MA, Iyengar SK, Yates JRW, Swaroop A, Weber BHF, Kubo M, Deangelis MM, Léveillard T, Thorsteinsdottir U, Haines JL, Farrer LA, Heid IM, Abecasis GR. Seven new loci associated with age-related macular degeneration. Nat Genet 2013; 45:433-9, 439e1-2. [PMID: 23455636 PMCID: PMC3739472 DOI: 10.1038/ng.2578] [Citation(s) in RCA: 573] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 02/07/2012] [Indexed: 12/11/2022]
Abstract
Age-related macular degeneration (AMD) is a common cause of blindness in older individuals. To accelerate the understanding of AMD biology and help design new therapies, we executed a collaborative genome-wide association study, including >17,100 advanced AMD cases and >60,000 controls of European and Asian ancestry. We identified 19 loci associated at P < 5 × 10(-8). These loci show enrichment for genes involved in the regulation of complement activity, lipid metabolism, extracellular matrix remodeling and angiogenesis. Our results include seven loci with associations reaching P < 5 × 10(-8) for the first time, near the genes COL8A1-FILIP1L, IER3-DDR1, SLC16A8, TGFBR1, RAD51B, ADAMTS9 and B3GALTL. A genetic risk score combining SNP genotypes from all loci showed similar ability to distinguish cases and controls in all samples examined. Our findings provide new directions for biological, genetic and therapeutic studies of AMD.
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Affiliation(s)
- Lars G Fritsche
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
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Churchill JD, Bowne SJ, Sullivan LS, Lewis RA, Wheaton DK, Birch DG, Branham KE, Heckenlively JR, Daiger SP. Mutations in the X-linked retinitis pigmentosa genes RPGR and RP2 found in 8.5% of families with a provisional diagnosis of autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 2013; 54:1411-6. [PMID: 23372056 DOI: 10.1167/iovs.12-11541] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE We determined the fraction of families in a well-characterized cohort with a provisional diagnosis of autosomal dominant retinitis pigmentosa (adRP) that have disease-causing mutations in the X-linked retinitis pigmentosa GTPase regulator (RPGR) gene or the retinitis pigmentosa 2 (RP2) gene. METHODS Families with a provisional clinical diagnosis of adRP, and a pedigree consistent with adRP but no male-to-male transmission were selected from a cohort of 258 families, and tested for mutations in the RPGR and RP2 genes with di-deoxy sequencing. To facilitate testing of RPGR in "adRP" families that had no male members available for testing, the repetitive and purine-rich ORF15 of RPGR was subcloned and sequenced in heterozygous female subjects from 16 unrelated families. RESULTS Direct sequencing of RPGR and RP2 allowed for identification of a disease-causing mutation in 21 families. Of these "adRP" families 19 had RPGR mutations, and two had RP2 mutations. Subcloning and sequencing of ORF15 of RPGR in female subjects identified one additional RPGR mutation. Of the 22 mutations identified, 15 have been reported previously. CONCLUSIONS These data show that 8.5% (22 in 258) of families thought to have adRP truly have X-linked retinitis pigmentosa (XLRP). These results have substantive implications for calculation of recurrence risk, genetic counseling, and potential treatment options, and illustrate the importance of screening families with a provisional diagnosis of autosomal inheritance and no male-to-male transmission for mutations in X-linked genes. Mutations in RPGR are one of the most common causes of all forms of retinitis pigmentosa.
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Affiliation(s)
- Jennifer D Churchill
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
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Neveling K, Collin RWJ, Gilissen C, van Huet RAC, Visser L, Kwint MP, Gijsen SJ, Zonneveld MN, Wieskamp N, de Ligt J, Siemiatkowska AM, Hoefsloot LH, Buckley MF, Kellner U, Branham KE, den Hollander AI, Hoischen A, Hoyng C, Klevering BJ, van den Born LI, Veltman JA, Cremers FPM, Scheffer H. Next-generation genetic testing for retinitis pigmentosa. Hum Mutat 2012; 33:963-72. [PMID: 22334370 PMCID: PMC3490376 DOI: 10.1002/humu.22045] [Citation(s) in RCA: 213] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 01/18/2012] [Indexed: 01/07/2023]
Abstract
Molecular diagnostics for patients with retinitis pigmentosa (RP) has been hampered by extreme genetic and clinical heterogeneity, with 52 causative genes known to date. Here, we developed a comprehensive next-generation sequencing (NGS) approach for the clinical molecular diagnostics of RP. All known inherited retinal disease genes (n = 111) were captured and simultaneously analyzed using NGS in 100 RP patients without a molecular diagnosis. A systematic data analysis pipeline was developed and validated to prioritize and predict the pathogenicity of all genetic variants identified in each patient, which enabled us to reduce the number of potential pathogenic variants from approximately 1,200 to zero to nine per patient. Subsequent segregation analysis and in silico predictions of pathogenicity resulted in a molecular diagnosis in 36 RP patients, comprising 27 recessive, six dominant, and three X-linked cases. Intriguingly, De novo mutations were present in at least three out of 28 isolated cases with causative mutations. This study demonstrates the enormous potential and clinical utility of NGS in molecular diagnosis of genetically heterogeneous diseases such as RP. De novo dominant mutations appear to play a significant role in patients with isolated RP, having major implications for genetic counselling.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Friedman JS, Ray JW, Waseem N, Johnson K, Brooks MJ, Hugosson T, Breuer D, Branham KE, Krauth DS, Bowne SJ, Sullivan LS, Ponjavic V, Gränse L, Khanna R, Trager EH, Gieser LM, Hughbanks-Wheaton D, Cojocaru RI, Ghiasvand NM, Chakarova CF, Abrahamson M, Göring HH, Webster AR, Birch DG, Abecasis GR, Fann Y, Bhattacharya SS, Daiger SP, Heckenlively JR, Andréasson S, Swaroop A. Mutations in a BTB-Kelch protein, KLHL7, cause autosomal-dominant retinitis pigmentosa. Am J Hum Genet 2009; 84:792-800. [PMID: 19520207 DOI: 10.1016/j.ajhg.2009.05.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 05/19/2009] [Accepted: 05/20/2009] [Indexed: 01/08/2023] Open
Abstract
Retinitis pigmentosa (RP) refers to a genetically heterogeneous group of progressive neurodegenerative diseases that result in dysfunction and/or death of rod and cone photoreceptors in the retina. So far, 18 genes have been identified for autosomal-dominant (ad) RP. Here, we describe an adRP locus (RP42) at chromosome 7p15 through linkage analysis in a six-generation Scandinavian family and identify a disease-causing mutation, c.449G-->A (p.S150N), in exon 6 of the KLHL7 gene. Mutation screening of KLHL7 in 502 retinopathy probands has revealed three different missense mutations in six independent families. KLHL7 is widely expressed, including expression in rod photoreceptors, and encodes a 75 kDa protein of the BTB-Kelch subfamily within the BTB superfamily. BTB-Kelch proteins have been implicated in ubiquitination through Cullin E3 ligases. Notably, all three putative disease-causing KLHL7 mutations are within a conserved BACK domain; homology modeling suggests that mutant amino acid side chains can potentially fill the cleft between two helices, thereby affecting the ubiquitination complexes. Mutations in an identical region of another BTB-Kelch protein, gigaxonin, have previously been associated with giant axonal neuropathy. Our studies suggest an additional role of the ubiquitin-proteasome protein-degradation pathway in maintaining neuronal health and in disease.
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Abstract
10-Formyl-7,8-dihydrofolic acid (10-HCO-H2folate) was prepared by controlled air oxidation of 10-formyl-5,6,7,8-tetrahydrofolic acid (10-HCO-H4folate). The UV spectra of the 10-HCO-H2folate preparation has lambda max. 234, 333 nm and lambda min. 301 nm at pH 7.4, and lambda max. 257, 328 nm and lambda min. 229, 307 nm at pH 1. 1H-NMR spectroscopy of 10-HCO-H2folate (in 2H2O; 300 MHz) suggested a pure compound and gave resonances for one formyl group proton, two protons on C-7 and C-9, and no evidence for a C-6 proton, which is consistent with the structure proposed. The spectral properties indicated that the 10-HCO-H2folate preparation is not appreciably contaminated with 10-HCO-H4folate, 5,10-methenyltetrahydrofolic acid (5,10-CH = H4folate) or 10-formylfolic acid (10-HCO-folate). The above data establish that the 10-HCO-H2folate prepared here is authentic. In contrast, a folate with a UV spectrum having lambda max. 272 nm and lambda min. 256 nm at pH 7, which was prepared by 2,6-dichloro-indophenol oxidation of 10-HCO-H4folate and reported to be 97% pure [Baram, Chabner, Drake, Fitzhugh, Sholar and Allegra (1988) J. Biol. Chem. 263, 7105-7111], is apparently not 10-HCO-H2folate. 10-HCO-H2folate is utilized by Jurkat-cell (human T-cell leukaemia) and chicken liver aminoimidazolecarboxamide ribonucleotide transformylase (AICAR T'ase; EC 2.1.2.3) in the presence of excess 5-amino-imidazole-4-carboxamide ribotide (AICAR) resulting in the appearance of approximately 1 mol of H2folate product for each mol of AICAR formylated. The present 10-HCO-H2folate preparation had a kinetic advantage over 10-HCO-H4folate resulting from a difference of approx. 5-fold in K(m) values when both folates were used as cofactors for Jurkat-cell and rat bone marrow AICAR T'ase. No substantial kinetic advantage was observed using chicken liver AICAR T'ase. 10-HCO-H2folate had little or no activity with Jurkat-cell or chicken liver glycinamide ribonucleotide transformylase (GAR T'ase, EC 2.1.2.2). The existence in vivo of 10-HCO-H2folate is suggested in mammals by several reports of detectable amounts of radiolabelled 10-HCO-folate in bile and urine after administration of radiolabelled folic acid.
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Affiliation(s)
- J E Baggott
- Department of Nutrition Sciences, University of Alabama, Birmingham 35294, USA
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Abstract
Angiotensin-converting enzyme from human lung was purified to apparent homogeneity using a five-step purification procedure consisting of ammonium sulfate precipitation, ion-exchange chromatography on DEAE Sephadex A-50, gel permeation on Sephadex G-200, chromatofocusing on a polybuffer exchange (PBE 94) column and high-performance liquid chromatographic gel permeation on a Bio-Sil TSK-250 column. This procedure gave an approximately 700-fold purification with a 20% yield compared to a 550-fold purification and a 1% yield with an affinity chromatography-based procedure. The 20-fold greater yield of the five-step procedure offers a major advantage for preparative use in the structural characterization of angiotensin-converting enzyme.
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Affiliation(s)
- Q C Meng
- Department of Cell Biology and Medicine, University of Alabama, Birmingham 35294
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