The University of Miami Udall center continues its focus on identifying genes important to causing Parkinson Disease (PD). As common variant polymorphisms (CV) have failed to explain a large amount of the genetic contribution to PD risk. Project one uses DNA capture technology and Next generation sequencing (NGS) to look for rare variants (RV) and mutations (M) in 500 patients and 500 controls. 809 genes from multiple data sources will be sequenced. Seventy of these genes are mitochondrial genes that will be used in Project 2. Subsequent genes containing potential RV will be sequenced in a second independent dataset of 500 patients and 500 controls, and aggregate analysis performed to see which RV are significantly associated with PD. It also uses a whole exome capture approach (180K exons) with NGS to identify M in six extended pedigree families with PD. Project 2 focuses on complex I of the mitochondria, using a new method called Mito-Seq to isolate mtDNA in brains of PD and controls for deletions, somatic mutations and heteroplasmy. We hypothesize that RV or de novo changes in nuclear encoded complex I genes are a risk factor for idiopathic PD directly, or through causing abnormal interaction between complex I's many components. The same brain tissue samples will be examined for protein modifications, and integrity of respiratory chain super-complexes using innovative proteomic and biochemical assays. Combining all data will allow for comparative studies of the pathology in PD brains. Project 3 examines the genetics of essential tremor (ET). To identify novel genes associated with ET, and study their potential influence on developing PD, we will 1) Identify novel ET loci by a genome wide linkage screen of the twelve largest ET kindreds;2) Genetically and physically map ET candidate gene regions using recombination breakpoint and haplotype analysis to refine the Minimal Candidate Regions (MCR);3) Identify positional candidate genes within each MCR and screen for causative disease mutations using NGS 4) Test confirmed ET genes in our full ET data set. The Center has four cores: Core A =administrative. Core B =clinical and neuropathology. Core C =statistical analysis and bioinformatics. Core D = education and training. PROJECT 1 Principal Investigator: Jeffery M. Vance Title: Discovery of Rare Variants and Mutations in Parkinson Disease Description (provided by applicant): Genetic studies have been a major tool fueling the tremendous growth in PD research over the last 10 years. Project 1 builds on our very successful work, 50 publications, 60 abstracts over the last funding period, examining the effect of common variants (CV) (polymorphisms) in PD. Table 1 shows the three primary types of genetic variations that contribute to disease risk. Genome wide association studies (GWAS) have focused on exploring the contribution of CV to disease susceptibility. While the traditional definition of CV is a minor allele frequency (MAF) >1% in the population, in practice, GWAS and association studies have only looked at CV with a MAF>5%. So we have defined CV for this proposal as those variants with MAF>5%. The individual contribution to disease risk (odds ratios) per CV is small. Therefore, it is the accumulation of CV associated with PD that affects the overall risk for PD in an individual. One of the first descriptions of rare variants (RV) came from (1) who suggested that """"""""subtle or unconventional mutations in cancer predisposition genes"""""""" may contribute to the increased risk of cancer observed in family members of cancer patients. Cohen et al (2) suggested that """"""""variants are likely to be rare individually;they may be sufficiently common in aggregate (in a gene) to contribute to variation in common traits in the population"""""""". RV can be considered genetic variations that often present with mildly deleterious effects on protein function. Their effect on gene and protein function is thought to lie between that of CV and those severely deleterious mutations (M). Recent estimates (3) suggest that 53% of de novo missense mutations fall within this RV category. This would be high enough to ensure their continued presence in the population, and would support their presence as a significant explanation for the genetic contributions of common disease. Indeed, Bodmer and Bonilla (4) in a recent review of RV suggest that 1/3 of the population attributable risk for complex disease may come from RV. Indeed, several examples of RV are already known in PD (5,6). Mutations are the rarest of DNA changes, and functionally cause PD by themselves. These are the changes that we refer to as Mendelian (autosomal recessive, autosomal dominant, or X-linked). Mutations are well known in PD as well (7). Identifying CV for association has been very successful. Six GWAS studies have now been reported for PD. However, only SNCA and MAPT have had highly significant association with PD across all of the studies. (8-13). Therefore, there is increasing realization that CV alone are not responsible for the genetic contribution to risk for PD and many other complex disorders. (14-17). This strongly suggests that the other categories of DNA variation in Table 1 must have a substantial contribution to PD. As RV can only be seen by sequencing (Table 1) it is only with the availability of an established target enrichment technology that captures specific DNA sequences for """"""""next-generation"""""""" sequencers (NGS), that we can search for RV/M on a large scale. Large versions of this same approach have lead to whole exome sequencing, i.e. providing sequence on 180,000 exons in each individual (18-20). We will use both of these approaches in this project. The resulting sequence data and RV/M from this project will be used by both Projects 1 and 2. For cost and efficiency, we have included the 70 mitochondrial genes of project 2 in the initial sequencing of project 1. However, follow-up on these genes will occur in project 2. In addition, genes identified by project 3 will be incorporated in subsequent DNA captures of project 1. The project will be administrated by Core A. and all individuals for sequencing will be obtained from Core B. The considerable statistical and bioinformatic analyses will be done in conjunction with Core C. Laboratory opportunities for Neurology residents and clinical experience for Project 1 laboratory personnel will be given through Cores B and D.
Showing the most recent 10 out of 45 publications
