SNPs in Multi-Species Conserved Sequences (MCS) as useful markers in association studies: a practical approach

<p>Abstract</p> <p>Background</p> <p>Although genes play a key role in many complex diseases, the specific genes involved in most complex diseases remain largely unidentified. Their discovery will hinge on the identification of key sequence variants that are conclusively associated with disease. While much attention has been focused on variants in protein-coding DNA, variants in noncoding regions may also play many important roles in complex disease by altering gene regulation. Since the vast majority of noncoding genomic sequence is of unknown function, this increases the challenge of identifying "functional" variants that cause disease. However, evolutionary conservation can be used as a guide to indicate regions of noncoding or coding DNA that are likely to have biological function, and thus may be more likely to harbor SNP variants with functional consequences. To help bias marker selection in favor of such variants, we devised a process that prioritizes annotated SNPs for genotyping studies based on their location within Multi-species Conserved Sequences (MCSs) and used this process to select SNPs in a region of linkage to a complex disease. This allowed us to evaluate the utility of the chosen SNPs for further association studies. Previously, a region of chromosome 1q43 was linked to Multiple Sclerosis (MS) in a genome-wide screen. We chose annotated SNPs in the region based on location within MCSs (termed MCS-SNPs). We then obtained genotypes for 478 MCS-SNPs in 989 individuals from MS families.</p> <p>Results</p> <p>Analysis of our MCS-SNP genotypes from the 1q43 region and comparison to HapMap data confirmed that annotated SNPs in MCS regions are frequently polymorphic and show subtle signatures of selective pressure, consistent with previous reports of genome-wide variation in conserved regions. We also present an online tool that allows MCS data to be directly exported to the UCSC genome browser so that MCS-SNPs can be easily identified within genomic regions of interest.</p> <p>Conclusion</p> <p>Our results showed that MCS can easily be used to prioritize markers for follow-up and candidate gene association studies. We believe that this novel approach demonstrates a paradigm for expediting the search for genes contributing to complex diseases.</p

The genetic epidemiology of multiple sclerosis

Multiple sclerosis (MS) is a debilitating immunological and neurodegenerative disorder. Epidemiological studies have provided overwhelming evidence of complex genetic susceptibility to MS. However, with the exception of the human leukocyte antigen (HLA) locus, genetic studies have failed to consistently identify significant linkage or association with genes that modulate MS disease expression. Numerous functional candidate gene studies, linkage genomic screens, and locational candidate gene studies have been performed in an attempt to identify additional loci. However, these methods have demonstrated insufficient power to consistently identify genes or epigenetic factors for MS. More current approaches integrate information from a variety of sources (e.g. consistent linkage data, gene expression profiling, and functional characterization studies) and utilize high throughput methods (e.g. genotyping high density markers, utilizing pooling schemes and performing new statistical analyses) in an attempt to overcome power issues. The following article presents a review of MS genetics research and a brief overview of methods that are currently being developed and utilized for fine localization of MS loci, such as the method employed in the Genetic Analysis of Multiple sclerosis in EuropeanS (GAMES) study that is presented elsewhere in this journal. It is the hope of researchers that these methods will lead to the identification of susceptibility genes for MS that aid in elucidating pathogenic mechanisms and potential therapeutic strategies for this debilitating disease

Linkage analysis for age-related macular degeneration supports a gene on chromosome 10q26

Age-related macular degeneration (AMD) is a retinal degenerative disease that is the leading cause of blindness worldwide in individuals over the age of 60. Although the etiology of AMD remains largely unknown, numerous studies have suggested both genetic and environmental influences. A previous study of affected multiplex families identified four chromosomal regions that potentially harbor AMD susceptibility genes. The purpose of our study was to further investigate these regions with additional microsatellite marker coverage in our independent data set. We examined regions on chromosomes 1q, 9p, 10q, and 17q for genetic linkage in our 70 multiplex families (consisting of 133 affected sibpairs). Two point heterogeneity LOD score (HLOD) and nonparametric LOD score (MLS) analyses were performed for disease models defined by the most severe status in either eye. Conditional analyses were performed using apolipoprotein E (APOE) alleles as covariates in semiparametric LOD (LOD*) score calculations. Regions on chromosomes 1q, 9p, and 17q did not provide evidence of linkage in our data set. However, markers D10S1230 and D10S1656 on chromosome 10q26 generated maximum HLOD scores of 1.52 and 1.13, respectively. Marker D10S1230 also generated an MLS score of 1.56 in stage 4 and 5 individuals. Controlling for the potential effect of the APOE-epsilon4 allele did not substantially alter these scores. With the inclusion of this study, at least five AMD data sets provide support of genetic linkage to 10q26. Such consistency and confirmation of evidence strongly suggests that this region should be the subject of further detailed genomic efforts for the disease

Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis

Multiple sclerosis is a debilitating neuroimmunological and neurodegenerative disease affecting more than 400,000 individuals in the United States. Population and family-based studies have suggested that there is a strong genetic component. Numerous genomic linkage screens have identified regions of interest for MS loci. Our own second-generation genome-wide linkage study identified a handful of non-MHC regions with suggestive linkage. Several of these regions were further examined using single-nucleotide polymorphisms (SNPs) with average spacing between SNPs of approximately 1.0 Mb in a dataset of 173 multiplex families. The results of that study provided further evidence for the involvement of the chromosome 1q43 region. This region is of particular interest given linkage evidence in studies of other autoimmune and inflammatory diseases including rheumatoid arthritis and systemic lupus erythematosus. In this follow-up study, we saturated the region with ~700 SNPs (average spacing of 10kb per SNP) in search of disease associated variation within this region. We found preliminary evidence to suggest that common variation within the RGS7 locus may be involved in disease susceptibility

Functional candidate genes in age-related macular degeneration: significant association with VEGF

PURPOSE. Age-related macular degeneration (AMD) is a retinal degenerative disease that is the leading cause of blindness worldwide for individuals over the age of 60. Although the etiology of AMD remains largely unknown, numerous studies have suggested that both genes and environmental risk factors significantly influence the risk of developing AMD. Identification of the underlying genes has been difficult, with both genomic screen (locational) and candidate gene (functional) approaches being used. The present study tested candidate genes for association with AMD. [VLDLR]) were tested for genetic linkage and allelic association, using two independent datasets: a family-based association dataset including 162 families and an independent case-control dataset with 399 cases and 159 fully evaluated controls. RESULTS. Test results suggested that genetic variation in five of these genes (IL1A, CKB, A2M, MGST1, and DCP1) is unlikely to explain a significant fraction of the risk of developing AMD in this population. LRP6 showed evidence both for linkage (heterogeneity lod [HLOD] ϭ 1.14) in the family-based dataset and for association (P ϭ 0.004) in the case-control dataset. VEGF showed evidence of linkage (HLOD ϭ 1.32) and demonstrated significant independent allelic association in both the family-based (P ϭ 0.001) and case-control (P ϭ 0.02) datasets. METHODS. Eight genes (␣- VLDLR showed evidence of association in both the family based (P ϭ 0.03) and case-control (P ϭ 0 Complementing a genomic screening (e.g., locational) approach is the direct testing of candidate genes proposed because their putative functions are related to the known AMD pathology. One such set of genes consists of those already known to be responsible for Mendelian macular and retinal dystrophies that share common features with AMD. However, genes ELOVL4 (Stargardt disease), 20 bestrophin (Best disease), In contrast, the apolipoprotein E (APOE) gene, which is involved in lipid transport and distribution, has consistently demonstrated a protective effect for the APOE-⑀4 allele on disease risk in white AMD populations (Klaver CCW, et al. IOVS 1996;37:ARVO Abstract 1920). From th

Enhancing linkage analysis of complex disorders: an evaluation of high-density genotyping

To explore the potential value of recently developed high-density linkage mapping methods in the analysis of complex disease we have regenotyped five nuclear families first studied in the 1996 UK multiple sclerosis linkage genome screen, using Applied Biosystems high-density microsatellite linkage mapping set, the Illumina BeadArray linkage mapping panel (version 3) and the Affymetrix GeneChip Human Mapping 10K array. We found that genotyping success, information extraction and genotyping accuracy were improved with all systems. These improvements were particularly marked with the SNP-based methods (Illumina and Affymetrix), with little difference between these. The extent of additional information extracted is considerable, indicating that reanalysis of existing multiplex families using these newer systems would substantially increase power

A high-density screen for linkage in multiple sclerosis

To provide a definitive linkage map for multiple sclerosis, we have genotyped the Illumina BeadArray linkage mapping panel (version 4) in a data set of 730 multiplex families of Northern European descent. After the application of stringent quality thresholds, data from 4,506 markers in 2,692 individuals were included in the analysis. Multipoint nonparametric linkage analysis revealed highly significant linkage in the major histocompatibility complex (MHC) on chromosome 6p21 (maximum LOD score [MLS] 11.66) and suggestive linkage on chromosomes 17q23 (MLS 2.45) and 5q33 (MLS 2.18). This set of markers achieved a mean information extraction of 79.3% across the genome, with a Mendelian inconsistency rate of only 0.002%. Stratification based on carriage of the multiple sclerosis-associated DRB1*1501 allele failed to identify any other region of linkage with genomewide significance. However, ordered-subset analysis suggested that there may be an additional locus on chromosome 19p13 that acts independent of the main MHC locus. These data illustrate the substantial increase in power that can be achieved with use of the latest tools emerging from the Human Genome Project and indicate that future attempts to systematically identify susceptibility genes for multiple sclerosis will have to involve large sample sizes and an association-based methodology