Mapping of genes causing dyslexia susceptibility Clyde Francks Wellcome Trust Centre for Human Genetics University of Oxford Trinity 2001

Size: px

Start display at page:

Download "Mapping of genes causing dyslexia susceptibility Clyde Francks Wellcome Trust Centre for Human Genetics University of Oxford Trinity 2001"

Abraham Gaines
6 years ago
Views:

1 Mapping of genes causing dyslexia susceptibility Clyde Francks Wellcome Trust Centre for Human Genetics University of Oxford Trinity 2001

2 Thesis submitted for the degree of Doctor of Philosophy Mapping of genes causing dyslexia susceptibility Clyde Francks Wellcome Trust Centre for Human Genetics Faculty of Clinical Medicine St. Cross College University of Oxford Trinity 2001 Abstract Developmental dyslexia is defined as a specific impairment in reading ability that cannot be explained by deficits in intelligence, learning opportunity, motivation, or by any obvious neurological or sensory handicap. It is one of the most frequently diagnosed childhood disorders in developed countries. Dyslexia has a complex multifactorial aetiology which is poorly understood, although unidentified genetic factors are known to play an important role. The aim of this study was to identify chromosomal regions containing gene-variants contributing to dyslexia susceptibility, and to begin the fine-scale search of those regions for the functional polymorphisms involved. In view of the phenotypic and genetic complexity of dyslexia, sib-pair based quantitative linkage mapping methods were employed in the first two genome-wide screens for quantitative trait loci (QTLs) affecting reading disability, using 89 families from the UK and 119 families from Colorado. Four-hundred polymorphic microsatellite markers spanning the genome were genotyped for both samples to measure sibling genetic similarities at all loci. The quantitative linkage analysis then tested whether sibling genetic and phenotypic similarities were related at any loci. A simulation-based method was used to obtain unbiased estimates of the significance of linkage results. Three principle genetic loci affecting reading disability emerged from the screens. The chromosome 2p13-16 QTL was identified in the US sample (p= with a word recognition measure), and was concordant with the top locus identified by the only previous genome-wide dyslexia screen, which was performed using a single fourgeneration family. The 6p QTL (UK sample, p= with a nonword reading measure) had previously been identified by targeted studies of this locus using the UK and US samples, and also replicated by other studies. The previously unknown 18p11 QTL was found in both of the genome screen samples (UK sample, p= ; Colorado sample, p=0.0003; word recognition measures). All three loci showed linkage to multiple reading-related measures, and spanned intervals >20 centimorgans, each containing hundreds of genes. For greater positional resolution, the 6p and 2p loci were fine-mapped using microsatellite markers at 1cM spacings to extract as much linkage information as possible, and to perform preliminary family-based quantitative association analysis. However, both intervals remained >10cM. An additional sample of 83 UK families was analyzed at both loci, but linkage was not replicated for either locus. The exons of two candidate genes on 2p13-16 (SEMAW, OTX1) were screened for putative functional polymorphisms, but no polymorphisms were found in either gene that could substantially account for the linkage results. Many candidate genes remain to be tested at both loci. This study was an essential first step towards the identification of gene-variants predisposing to dyslexia, and included the first use of quantitative genome-wide genetic mapping methods for a human cognitive trait.

3 Associated publications Fisher SE*, Francks C*, Marlow AJ, MacPhie IL, Williams DF, Cardon LR, Ishikawa-Brush Y, Talcott JB, Richardson AJ, Gayan J, Olson RK, Pennington BF, Smith SD, DeFries JC, Stein JF, Monaco AP (Submitted). Genome-wide scans in independent samples reveal strong convergent evidence for a chromosome 18 quantitative-trait locus influencing developmental dyslexia. * These authors contributed equally to this work Francks C, Fisher SE, Smith SD, DeFries JC, Monaco AP (in preperation). Quantitative association analysis within the chromosome 2p12-16 dyslexia susceptibility region: Microsatellite markers and candidate genes SEMA4F and OTX1 Marlow AJ, Fisher SE, Richardson AJ, Francks C, Talcott JE, Monaco AP, Stein JS, Cardon LR (2001). Investigation of quantitative measures related to reading disability in a large sample of sib-pairs from the UK. Behaviour Genetics 31: Francks C, Fisher SE, Marlow AJ, Richardson AJ, Stein JF, Monaco AP. A siblingpair based approach for mapping genetic loci that influence quantitative measures of reading disability (2000). Prostaglandins, Leukotrienes and Essential Fatty Acids 63:27-31.

4 Acknowledgements For conceiving the dyslexia project, for nearly four years of laid back but effective supervision, and for giving me an exciting scientific opportunity, I thank my supervisor Anthony Monaco. For endless intricate discussions and debates, and for tireless and meticulous work in coordinating the genome screens, checking much of the genotype data and working closely with me on many aspects of the project, I thank Simon Fisher. Many thanks too to Angela Marlow, Lon Cardon, Stacey Cherny, Dan Weeks and Goncalo Abecasis for essential statistical and theoretical support, and to Laurence Macphie, Dianne Newbury, Yumiko Ishikawa-Brush, Joanne Smith, Phil Kelley, Helene Rees, Peter Field, Lorne Lonie and Chris Fletcher for helping with the genotyping/snp detection. Thanks too to all of our Oxford collaborators; John Stein, Alex Richardson, Joel Talcott, Kathleen Taylor, Janet Walter, Pam Southcott, Sue Fowler and Chris Clisby for the collection and testing of the UK families, and thanks to John DeFries, Shelley Smith, Richard Olson, Bruce Pennington and Javier Gayan for making the Colorado twin sample available. Raymond Allen, Tim Bardsley, David Smith and Slaven Suba provided essential computer support. All of the families who volunteered for the UK and Colorado studies deserve special thanks. The project was funded by the Wellcome Trust. Prof. Monaco is a Wellcome Trust Principal Research Fellow, and I was a Wellcome Trust Prize Student. For twenty-seven years of input, for a scientific outlook, and for peaceful weekends in Wales planting potatoes, I thank my parents John and Brigitta Francks, and I dedicate this work to them. Thanks too to Abbie; long may life remain so good. Clyde Francks, June Detail from MICHELANGELO; Last Judgement, , Fresco, Capella Sistina, Vatican.

5 Contents Page Introduction: Complex Traits Summary 1 Monogenic and complex traits 2 Genetic epidemiology 7 Twin and relative risk studies - is a trait genetic? 10 Defining traits 15 Trait definitions: qualitative or quantitative? 17 Introduction: Linkage and linkage disequilibrium Summary 21 Positional and functional approaches for gene identification 22 The Human Genome Project and the genome sequence 24 Polymorphic DNA markers and genetic identity 25 Linkage and linkage disequilibrium 28 Linkage analysis of complex traits 34 Quantitative linkage disequilibrium mapping of complex trait loci 40 Significance and power in genetic studies 41 Introduction: Dyslexia phenotype and previous genetic studies Summary 45 Defining dyslexia 46 Overview of reading 48 Language construction and cognitive components of reading 50 An unexpected problem learning to read 55 The search for a physiological deficit 57 Previous genetic studies of dyslexia 65 Introduction: The rationale for this study 75 Chapter 1: Materials and methods The family samples 78 Sample ascertainment details 79 Phenotypic measures - UK and UKWAVE2 samples 82 Phenotypic measures - US sample 85 Comparability of the UK+UKWAVE2 samples with the US sample 88 Microsatellite markers and genetic maps 90 Genomic DNA extraction 95 Microsatellite typing 96 In silico analysis of candidate genes 104 Polymorphism detection and characterisation within candidate genes 107 SNP typing by RFLP 111 Quantitative trait analysis 112 Quantitative linkage analysis 112 Quantitative association analysis 115 Linkage simulation 116 Chapter 2: Genome screens: Results and conclusions Summary 118 Analysis of quantitative measures; UK and US samples 119 Genome screens: Information content mapping 129 Linkage simulation in the UK and US samples 131 Genome screens: Linkage analysis results 140 Genome screens: Conclusions 164

6 Contents (continued) Page Chapter 3: Investigation of the 6p QTL Summary 176 Prior localization of the 6p locus 177 Regional characterisation 178 Fine linkage mapping of the 6p locus in the UK sample 180 Multipoint linkage simulation of 6p in the UK sample 188 Analysis of quantitative measures in the UKWAVE2 sample 191 Linkage mapping of 6p in the UKWAVE2 sample 193 Quantitative association analysis of 6p microsatellites 197 Conclusions 200 Chapter 4: Investigation of the 2p QTL Summary 205 Prior localization of the 2p locus 206 Fine linkage mapping of the 2p QTL 208 Quantitative association analysis of 2p microsatellites 212 Candidate gene studies on 2p in the US sample 215 Conclusions 225 Appendix 1: Linkage simulation notes 230 Appendix 2: Distributions of quantitative measures 233 Appendix 3: Reading ability in the general population 240 Bibliography 242

Independent genome-wide scans identify a chromosome 18 quantitative-trait locus influencing dyslexia theoret read

Independent genome-wide scans identify a chromosome 18 quantitative-trait locus influencing dyslexia Simon E. Fisher 1 *, Clyde Francks 1 *, Angela J. Marlow 1, I. Laurence MacPhie 1, Dianne F. Newbury