DOCSLIB.ORG

Towards the Identification of Causal Genes and Contributing

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

TOWARDS THE IDENTIFICATION OF CAUSAL GENES AND CONTRIBUTING MOLECULAR PROCESSES UNDERLYING STRABISMUS by Xin Ye B.Sc., The University of British Columbia, 2011 M.Sc., The University of British Columbia, 2014 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Medical Genetics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) May 2019 © Xin Ye, 2019 The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: Towards the identification of causal genes and contributing molecular processes underlying strabismus submitted by Xin Ye in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Medical Genetics Examining Committee: Wyeth Wasserman Supervisor Angela Brooks-Wilson Supervisory Committee Member Orson Moritz University Examiner Douglas Allan University Examiner Additional Supervisory Committee Members: Supervisory Committee Member Supervisory Committee Member ii Abstract Eye misalignment, or strabismus, has a frequency of up to 4% in a population, and is known to have both environmental and genetic causes. Genes associated with syndromic forms of strabismus (i.e. strabismus concurrent with multiple phenotypes) have emerged, but genes contributing to isolated strabismus remain to be discovered. Only one isolated strabismus locus, STBMS1 on chromosome 7, has been confirmed in more than one family, but the inheritance model of the locus is inconsistent between studied families and no specific causal variant has been reported. The large set of syndromes with strabismus suggests that within the visual system multiple perturbations of an underlying genetic network(s) can have the common output of disrupted eye alignment. Thus, I used a bioinformatic-driven approach to analyze curated genes associated with strabismus to provide insight into the biological mechanisms underlying strabismus, highlighting a link to the Ras-MAPK pathway. During the process, I noticed strabismus presenting within a large number of intellectual disability disorders. Therefore, I studied the co-occurrence of strabismus and other common phenotypes in a series of patients with intellectual disability, which confirmed a significant correlation between eye alignment and intellectual disability. Finally, I resumed efforts from my prior studies to identify the genetic cause in a seven-generation family with isolated strabismus inherited in an autosomal dominant manner. The likely casual gene disruption, altering a likely cis-regulatory region of the FOXG1gene, was identified through the incorporation of linkage analysis, next generation sequencing, and in-depth bioinformatic analyses. This thesis identifies potential roles for genes participating in the Ras-MAPK pathway, emphasizes the role of the central nervous system, and reveals FOXG1 as a causal gene candidate for isolated strabismus. iii Lay Summary Eye misalignment, or strabismus, can affect vision and self-image. Untreated strabismus can lead to blindness in extreme cases. Multiple surgeries may be needed to align the eyes, but the outcome may not be satisfying. Hippocrates observed that strabismus was often presented as a familial condition over 2400 years ago, implying a genetic cause of strabismus. However, we have little understanding of the genetics and mechanism(s) of strabismus today. I combined different methods to study the role of genetics in strabismus, including finding the gene likely causing strabismus in a large family with many afflicted. Strabismus is a complex condition that may involve mechanisms related to eyes, muscles and the brain. This study leads to new directions for research to unravel the causes of strabismus, and the improved understanding may lead to better prevention and treatment. iv Preface Chapter 1 is built upon a published review: Ye XC, Pegado V, Patel MS, Wasserman WW. Strabismus genetics across a spectrum of eye misalignment disorders. Clin Genet. 2014 Aug;86(2):103–11. A version of chapter 2 is published as: Ye XC, van der Lee R, Wasserman WW. Curation and bioinformatic analysis of strabismus genes supports functional heterogeneity and proposes candidate genes with connections to RASopathies. Gene. 2019. doi: 10.1016/j.gene.2019.02.020. WWW helped design the computational studies, reviewed and edited the manuscript, and acquired funding. RvdL reviewed/edited the manuscript and advised on the analyses. I designed and conducted the computational studies, collected and analyzed the data, wrote the manuscript, and made tables and figures. A version of chapter 3 is under review in Pediatric Neurology as: Ye XC, van der Lee R, Wasserman WW, CAUSES Study, Friedman JM, Lehman A. Strabismus in children with intellectual disability: part of a broader motor control phenotype? AL helped design the study, reviewed and edited the manuscript. RvdL, WWW and JMF reviewed/edited the manuscript. I designed and conducted the study, collected and analyzed the data, wrote the manuscript and made tables and figures. CAUSES Study collected the data. v Chapter 4 is in preparation for publication as: Ye XC, Horton J, Lyons C, Pegado V, Ross C, Shyr C, Richmond P, Roslin N, Peterson A, Han X, Higginson M, Giaschi D, Gregory-Evans C, Patel M, Wasserman WW. Linkage analysis identifies an isolated strabismus locus at 14q12 overlapping the FOXG1 syndrome region. WWW and MP helped design the experiments, reviewed and edited the manuscript, and acquired funding. JH, VP, and CL performed ophthalmological exams. NR and AP performed the initial linkage analysis through the CARE4RARE network. MH extracted DNA from blood samples and prepared samples for WES and WGS. CR and XH designed and performed Sanger sequencing. CS and PR maintained and improved the WES and WGS pipelines and performed the analyses. DG was counselled for project development and helped develop the MRI protocol. CGE helped develop the project and provided experimental design support. I designed and conducted the experiments, worked with the family to build the pedigree, extracted DNA from saliva samples, performed the second round of linkage analysis with WGS data, performed WES and WGS analyses, analyzed and integrated relevant data for candidate prioritization, helped develop the MRI protocol, analyzed the data, wrote the manuscript and made tables and figures. Ethics statement: Approval for the study was obtained from University of British Columbia Children’s & Women’s Research Ethics Board (approval number CW10-0317/H10-03215). vi Table of Contents Abstract .................................................................................................................................... iii Lay Summary ........................................................................................................................... iv Preface ....................................................................................................................................... v Table of Contents .................................................................................................................... vii List of Figures ......................................................................................................................... xii List of Supplementary Material ............................................................................................ xiii List of Abbreviations ............................................................................................................. xiv Acknowledgements ................................................................................................................. xv Chapter 1: Introduction ........................................................................................................... 1 1.1 Overview ..................................................................................................................... 1 1.2 Introduction of strabismus ........................................................................................... 2 1.2.1 Classification ....................................................................................................... 2 1.2.2 Epidemiology ...................................................................................................... 2 1.2.3 Pathology............................................................................................................. 3 1.2.4 Animal models..................................................................................................... 4 1.3 Genes of strabismus ..................................................................................................... 5 1.3.1 Family and twin study .......................................................................................... 5 1.3.2 Linkage analysis .................................................................................................. 7 1.3.3 Genome-wide association studies ......................................................................... 8 1.3.4 Next generation sequencing ................................................................................. 9 1.4 Frontiers of strabismus research - genes implicated in strabismus .............................. 10 vii 1.4.1 Duane retraction syndrome ................................................................................ 10 1.4.2 Congenital fibrosis of the extraocular muscles ..................................................
Recommended publications
  • Clinical and Genetic Characteristics and Prenatal Diagnosis of Patients

    Clinical and Genetic Characteristics and Prenatal Diagnosis of Patients

    Lin et al. Orphanet J Rare Dis (2020) 15:317 https://doi.org/10.1186/s13023-020-01599-y RESEARCH Open Access Clinical and genetic characteristics and prenatal diagnosis of patients presented GDD/ID with rare monogenic causes Liling Lin1, Ying Zhang1, Hong Pan1, Jingmin Wang2, Yu Qi1 and Yinan Ma1* Abstract Background: Global developmental delay/intellectual disability (GDD/ID), used to be named as mental retardation (MR), is one of the most common phenotypes in neurogenetic diseases. In this study, we described the diagnostic courses, clinical and genetic characteristics and prenatal diagnosis of a cohort with patients presented GDD/ID with monogenic causes, from the perspective of a tertiary genetic counseling and prenatal diagnostic center. Method: We retrospectively analyzed the diagnostic courses, clinical characteristics, and genetic spectrum of patients presented GDD/ID with rare monogenic causes. We also conducted a follow-up study on prenatal diagnosis in these families. Pathogenicity of variants was interpreted by molecular geneticists and clinicians according to the guidelines of the American College of Medical Genetics and Genomics (ACMG). Results: Among 81 patients with GDD/ID caused by rare monogenic variants it often took 0.5–4.5 years and 2–8 referrals to obtain genetic diagnoses. Devlopmental delay typically occurred before 3 years of age, and patients usu- ally presented severe to profound GDD/ID. The most common co-existing conditions were epilepsy (58%), micro- cephaly (21%) and facial anomalies (17%). In total, 111 pathogenic variants were found in 62 diferent genes among the 81 pedigrees, and 56 variants were novel. The most common inheritance patterns in this outbred Chinese popula- tion were autosomal dominant (AD; 47%), following autosomal recessive (AR; 37%), and X-linked (XL; 16%).
  • Universidade Estadual De Campinas Faculdade De

    Universidade Estadual De Campinas Faculdade De

    1 UNIVERSIDADE ESTADUAL DE CAMPINAS FACULDADE DE CIÊNCIAS MÉDICAS ILÁRIA CRISTINA SGARDIOLI Investigação da Síndrome de deleção 22q11.2 utilizando diferentes estratégias para aplicação em saúde CAMPINAS 2018 ii Ilária Cristina Sgardioli Investigação da Síndrome de deleção 22q11.2 utilizando diferentes estratégias para aplicação em saúde Tese apresentada à Faculdade de Ciências Médicas da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do título de Doutora em Ciências, Área de Concentração Genética Médica. Orientadora: Profa. Dra. Vera Lúcia Gil da Silva Lopes Coorientador: Prof. Dr. Társis Antonio Paiva Vieira Este exemplar corresponde a versão final da Tese defendida pela aluna Ilária Cristina Sgardioli, orientada pela Profa. Dra. Vera Lúcia Gil-da-Silva Lopes. CAMPINAS 2018 iii Agência(s) de fomento e nº(s) de processo(s): Não se aplica. ORCID: https://orcid.org/0000-0002-7253-7830 Ficha catalográfica Universidade Estadual de Campinas Biblioteca da Faculdade de Ciências Médicas Maristella Soares dos Santos – CRB 8/8402 Sgardioli, Ilária Cristina, 1981- Sg16i Investigação da síndrome de deleção 22q11.2 utilizando diferentes estratégias para aplicação em saúde / Ilária Cristina Sgardioli. – Campinas, SP : [s.n.], 2018. Orientador: Vera Lúcia Gil da Silva Lopes. Coorientador: Társis Antonio Paiva Vieira. Tese (doutorado) – Universidade Estadual de Campinas, Faculdade de Ciências Médicas. 1. Síndrome da deleção 22q11.2. 2. Hibridização genômica comparativa. 3. Variações do número de cópias de DNA. 4.
  • Molecular Genetic Studies of Inherited Cystic Kidney Disease in Oman

    Molecular Genetic Studies of Inherited Cystic Kidney Disease in Oman

    Molecular Genetic Studies of Inherited Cystic Kidney Disease in Oman Intisar Hamed Al Alawi A Thesis Submitted For the Degree of Doctor of Philosophy Institute of Genetic Medicine Newcastle University January 2020 Abstract Inherited kidney diseases are fundamental causes of chronic kidney disease (CKD) and end stage kidney disease (ESKD); accounting for approximately 20% of all CKD cases and up to 10% of adults and over 70% of children reaching ESKD. Oman is the second largest country in the South East of Arabian Peninsula. Omani population is characterized by large family size, presence of tribal and geographical settlements and higher rates of consanguineous marriages, which facilitate the study of autosomal recessive disorders. Rare genetic disorders create considerable burden on healthcare system in Oman and are major causes of congenital abnormalities and perinatal deaths in hospitals. The prevalence of inherited kidney disease was estimated to be high, but there is a lack for a comprehensive data. Therefore, this study aimed to evaluate the magnitude of inherited kidney disease in this population and identify the molecular genetic causes of inherited cystic kidney diseases in Omani patients. First, I performed a population-based retrospective analysis of ESKD patients commencing RRT from 2001 to 2015 using the national renal replacement therapy (RRT) registry and evaluated the epidemiological and etiological causes of ESKD with focused attention on inherited kidney diseases. Second, I designed a targeted gene panel (49 genes) and used massive parallel sequencing technologies for the molecular genetic diagnosis of cystic kidney disease in 53 patients. An overall molecular genetic diagnostic yield of 75% was achieved; with 46% of detected causative variants were novel genetic findings.
  • Novel Gene Discovery in Primary Ciliary Dyskinesia

    Novel Gene Discovery in Primary Ciliary Dyskinesia

    Novel Gene Discovery in Primary Ciliary Dyskinesia Mahmoud Raafat Fassad Genetics and Genomic Medicine Programme Great Ormond Street Institute of Child Health University College London A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy University College London 1 Declaration I, Mahmoud Raafat Fassad, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 Abstract Primary Ciliary Dyskinesia (PCD) is one of the ‘ciliopathies’, genetic disorders affecting either cilia structure or function. PCD is a rare recessive disease caused by defective motile cilia. Affected individuals manifest with neonatal respiratory distress, chronic wet cough, upper respiratory tract problems, progressive lung disease resulting in bronchiectasis, laterality problems including heart defects and adult infertility. Early diagnosis and management are essential for better respiratory disease prognosis. PCD is a highly genetically heterogeneous disorder with causal mutations identified in 36 genes that account for the disease in about 70% of PCD cases, suggesting that additional genes remain to be discovered. Targeted next generation sequencing was used for genetic screening of a cohort of patients with confirmed or suggestive PCD diagnosis. The use of multi-gene panel sequencing yielded a high diagnostic output (> 70%) with mutations identified in known PCD genes. Over half of these mutations were novel alleles, expanding the mutation spectrum in PCD genes. The inclusion of patients from various ethnic backgrounds revealed a striking impact of ethnicity on the composition of disease alleles uncovering a significant genetic stratification of PCD in different populations.
  • Opportunities and Challenges for Molecular Understanding of Ciliopathies–The 100,000 Genomes Project

    Opportunities and Challenges for Molecular Understanding of Ciliopathies–The 100,000 Genomes Project

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Queen Mary Research Online REVIEW published: 11 March 2019 doi: 10.3389/fgene.2019.00127 Opportunities and Challenges for Molecular Understanding of Ciliopathies–The 100,000 Genomes Project Gabrielle Wheway 1†, Genomics England Research Consortium and Hannah M. Mitchison 2* 1 Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom, 2 Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, United Kingdom Cilia are highly specialized cellular organelles that serve multiple functions in human development and health. Their central importance in the body is demonstrated by the occurrence of a diverse range of developmental disorders that arise from defects of cilia structure and function, caused by a range of different inherited mutations found in more Edited by: than 150 different genes. Genetic analysis has rapidly advanced our understanding of Carlo Iomini, the cell biological basis of ciliopathies over the past two decades, with more recent Icahn School of Medicine at Mount technological advances in genomics rapidly accelerating this progress. The 100,000 Sinai, United States Genomes Project was launched in 2012 in the UK to improve diagnosis and future Reviewed by: John Andrew Sayer, care for individuals affected by rare diseases like ciliopathies, through whole genome Newcastle University, United Kingdom sequencing (WGS). In this review we discuss the potential promise and medical impact Theodora Katsila, of WGS for ciliopathies and report on current progress of the 100,000 Genomes Project, University of Patras, Greece *Correspondence: reviewing the medical, technical and ethical challenges and opportunities that new, large Hannah M.
  • Multilocus Disease-Causing Genomic Variations for Mendelian Disorders: Role of Systematic Phenotyping and Implications on Genetic Counselling

    Multilocus Disease-Causing Genomic Variations for Mendelian Disorders: Role of Systematic Phenotyping and Implications on Genetic Counselling

    www.nature.com/ejhg ARTICLE OPEN Multilocus disease-causing genomic variations for Mendelian disorders: role of systematic phenotyping and implications on genetic counselling Dhanya Lakshmi Narayanan 1, Divya Udyawar1, Parneet Kaur1, Suvasini Sharma2, Narayanaswamy Suresh2, Sheela Nampoothiri 3, 1 1 1 1 1 1 Michelle C. do Rosario , Puneeth H. Somashekar , Lakshmi Priya Rao , Neethukrishna Kausthubham✉ , Purvi Majethia , Shruti Pande , Y. Ramesh Bhat4, Aroor Shrikiran4, Stephanie Bielas5, Katta Mohan Girisha 1 and Anju Shukla 1 © The Author(s) 2021 Multilocus disease-causing genomic variations (MGVs) and multiple genetic diagnoses (MGDs) are increasingly being recognised in individuals and families with Mendelian disorders. This can be mainly attributed to the widespread use of genomic tests for the evaluation of these disorders. We conducted a retrospective study of families evaluated over the last 6 years at our centre to identify families with MGVs and MGDs. MGVs were observed in fourteen families. We observed five different consequences: (i) individuals with MGVs presenting as blended phenotypes (ii) individuals with MGVs presenting with distinct phenotypes (iii) individuals with MGVs with age-dependent penetrance (iv) individuals with MGVs with one phenotype obscured by another more predominant phenotype (v) two distinct phenotypes in different individuals in families with MGVs. Consanguinity was present in eight (8/14, 57.1%) of them. Thirteen families had two Mendelian disorders and one had three Mendelian disorders. The risk of recurrence of one or more conditions in these families ranged from 25% to 75%. Our findings underline the importance of the role of a clinical geneticist in systematic phenotyping, challenges in genetic counselling and risk estimation in families with MGVs and MGDs, especially in highly inbred populations.
  • Signatures of Adaptive Evolution in Platyrrhine Primate Genomes 5 6 Hazel Byrne*, Timothy H

    Signatures of Adaptive Evolution in Platyrrhine Primate Genomes 5 6 Hazel Byrne*, Timothy H

    1 2 Supplementary Materials for 3 4 Signatures of adaptive evolution in platyrrhine primate genomes 5 6 Hazel Byrne*, Timothy H. Webster, Sarah F. Brosnan, Patrícia Izar, Jessica W. Lynch 7 *Corresponding author. Email [email protected] 8 9 10 This PDF file includes: 11 Section 1: Extended methods & results: Robust capuchin reference genome 12 Section 2: Extended methods & results: Signatures of selection in platyrrhine genomes 13 Section 3: Extended results: Robust capuchins (Sapajus; H1) positive selection results 14 Section 4: Extended results: Gracile capuchins (Cebus; H2) positive selection results 15 Section 5: Extended results: Ancestral Cebinae (H3) positive selection results 16 Section 6: Extended results: Across-capuchins (H3a) positive selection results 17 Section 7: Extended results: Ancestral Cebidae (H4) positive selection results 18 Section 8: Extended results: Squirrel monkeys (Saimiri; H5) positive selection results 19 Figs. S1 to S3 20 Tables S1–S3, S5–S7, S10, and S23 21 References (94 to 172) 22 23 Other Supplementary Materials for this manuscript include the following: 24 Tables S4, S8, S9, S11–S22, and S24–S44 1 25 1) Extended methods & results: Robust capuchin reference genome 26 1.1 Genome assembly: versions and accessions 27 The version of the genome assembly used in this study, Sape_Mango_1.0, was uploaded to a 28 Zenodo repository (see data availability). An assembly (Sape_Mango_1.1) with minor 29 modifications including the removal of two short scaffolds and the addition of the mitochondrial 30 genome assembly was uploaded to NCBI under the accession JAGHVQ. The BioProject and 31 BioSample NCBI accessions for this project and sample (Mango) are PRJNA717806 and 32 SAMN18511585.
  • 2.04.107 Carrier Screening for Genetic Diseases Original Policy Date: February 1, 2017 Effective Date: January 1, 2020 Section: 2.0 Medicine Page: Page 1 of 24

    2.04.107 Carrier Screening for Genetic Diseases Original Policy Date: February 1, 2017 Effective Date: January 1, 2020 Section: 2.0 Medicine Page: Page 1 of 24

    Medical Policy 2.04.107 Carrier Screening for Genetic Diseases Original Policy Date: February 1, 2017 Effective Date: January 1, 2020 Section: 2.0 Medicine Page: Page 1 of 24 Policy Statement Carrier screening (related to pregnancy or planned pregnancy) for genetic diseases in biological parents may be considered medically necessary when one or more of the following criteria is met: • One or both individuals have a first- or second-degree relative who is affected (see Policy Guidelines section*) • One individual is known to be a carrier • One or both individuals are members of a population known to have a carrier rate that exceeds a threshold considered appropriate for testing for a particular condition (see Policy Guidelines 1 section) AND all of the following criteria are met: • The natural history of the disease is well understood and there is a reasonable likelihood that the disease is one with high morbidity in the homozygous or compound heterozygous state • Alternative biochemical or other clinical tests to definitively diagnose carrier status are not available, or, if available, provide an indeterminate result or are individually less efficacious than genetic testing • The genetic test has adequate clinical validity to guide clinical decision making and residual risk is understood (see Policy Guidelines 2 section) • An association of the marker with the disorder has been established All targeted screening not meeting any of the above criteria is considered not medically necessary. Limited genetic panels (i.e., code 81443, see Coding in the Policy Guidelines section) that include testing for Spinal Muscular Atrophy (SMN1 gene) and Cystic Fibrosis (CFTR gene) may be considered medically necessary as an alternative to testing of individual genes for all women who are pregnant or are considering pregnancy.
  • Clinician-Centric Diagnosis of Rare Genetic Diseases: Performance of a Gene Pertinence Metric in Decision Support for Clinicians Michael M

    Clinician-Centric Diagnosis of Rare Genetic Diseases: Performance of a Gene Pertinence Metric in Decision Support for Clinicians Michael M

    Segal et al. Orphanet Journal of Rare Diseases (2020) 15:191 https://doi.org/10.1186/s13023-020-01461-1 RESEARCH Open Access Clinician-centric diagnosis of rare genetic diseases: performance of a gene pertinence metric in decision support for clinicians Michael M. Segal1* , Renee George2,3, Peter Waltman4,5, Ayman W. El-Hattab6, Kiely N. James2,3, Valentina Stanley2,3 and Joseph Gleeson2,3 Abstract Background: In diagnosis of rare genetic diseases we face a decision as to the degree to which the sequencing lab offers one or more diagnoses based on clinical input provided by the clinician, or the clinician reaches a diagnosis based on the complete set of variants provided by the lab. We tested a software approach to assist the clinician in making the diagnosis based on clinical findings and an annotated genomic variant table, using cases already solved using less automated processes. Results: For the 81 cases studied (involving 216 individuals), 70 had genetic abnormalities with phenotypes previously described in the literature, and 11 were not described in the literature at the time of analysis (“discovery genes”). These included cases beyond a trio, including ones with different variants in the same gene. In 100% of cases the abnormality was recognized. Of the 70, the abnormality was ranked #1 in 94% of cases, with an average rank 1.1 for all cases. Large CNVs could be analyzed in an integrated analysis, performed in 24 of the cases. The process is rapid enough to allow for periodic reanalysis of unsolved cases. Conclusions: A clinician-friendly environment for clinical correlation can be provided to clinicians who are best positioned to have the clinical information needed for this interpretation.