A whole genome screen for linkage disequilibrium in multiple sclerosis performed in a continental Italian population

Genome-wide association study for mandibular prognathism using microsatellite and pooled DNA method

INTRODUCTION

The purpose of this study was to extend an association study from chromosome 1 to the whole genome (genome-wide association study) to find susceptibility loci of mandibular prognathism.

METHODS

Two hundred forty patients diagnosed with mandibular prognathism and 360 healthy controls of Japanese descent were recruited. The typing of microsatellites covering the whole genome was conducted using a pooled DNA method. Upon completion of the first and second screenings with pooled DNA, the positive microsatellite markers from both the first and second typings were retyped using individual-subject DNA samples to confirm the significance of allele frequency.

RESULTS

Six microsatellites (D1S0411i, D1S1358i, D3S0810i, D6S0827i, D7S0133i, and D15S0154i) showed differences between allele frequencies of the subjects and controls at P <0.001. D1S0411i, D1S1358i, D3S0810i, D6S0827i, D7S0133i, and D15S0154i were located on chromosomes 1p22.3, 1q32.2, 3q23, 6q23.2, 7q11.22, and 15q22.22, respectively. SSX2IP, PLXNA2, RASA2, TCF21, CALN1, and RORA were suggested as candidate genes.

CONCLUSIONS

The genome-wide association study using microsatellites suggested that 6 loci (1p22.3, 1q32.2, 3q23, 6q23.2, 7q11.22, and 15q22.22) were susceptibility regions of mandibular prognathism. The locus 1p22.3 was supported by a previous linkage analysis, and the other 5 were novel loci.

Tumor necrosis factor-alpha polymorphism and susceptibility to multiple sclerosis in the Iranian population

BACKGROUND

Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Tumor necrosis factor-α (TNF-α) microsatellite as a proinflammatory cytokine is believed to play an important role in the etiology of this disease.

OBJECTIVES

The aim of this study was to investigate the association of TNF-α microsatellite sequence variation in patients with MS and its risk factor in the southern Iranian population.

PATIENTS AND METHODS

This polymorphism was investigated in an Iranian population of 163 native southern people [81 patients with MS according to the poser criteria and 82 healthy controls (HC) with the same age, sex, social, ethnical and geographical features (Hormozgan and Fars provinces)]. All the controls were nonimmunological, neurological patients. All the cases and controls were chosen randomly and genotyped for polymorphism of TNF-α microsatellite.

RESULTS

The frequencies of TNF-α*11 (0.25, P < 0.005) and TNF-α*10 (P < 0.005) alleles increased in patients with MS compared with controls, showing a significant difference among the studied population.

CONCLUSIONS

The current study adds evidence to the association of TNF-α gene polymorphism and MS in this southern south Iranian population which is consistent with the genetic analysis of MS in Europeans (GAMES) project reports and these two alleles reported in this study may be one of the genetic risk factor for MS. Furthermore, this data can be used to build the Iranian gene bank for future studies.

Microsatellite genome-wide association study for mandibular prognathism

INTRODUCTION

Attempts have been made to identify susceptibility genes of mandibular prognathism by genome-wide linkage studies, but the results of susceptibility loci are inconsistent. There has been no genome-wide association study of mandibular prognathism. Our objective was to perform a genome-wide association study using 23,465 microsatellite markers to detect mandibular prognathism susceptibility regions.

METHODS

The study was based on the pooled DNA method, including 2 steps of screening on the whole genome and subsequent individual genotyping, with 240 experimental subjects and 360 control subjects from the Japanese population.

RESULTS

Two suggestive associations on chromosomes 1q32.2 (D1S1358i: P = 4.22 × 10(-4)) and 1p22.3 (D1S0411i: P = 6.66 × 10(-4)) were shown, and PLXNA2 and SSX2IP were suggested to be candidate genes; 1p22.3 flanked the region indicated by previous linkage analysis.

CONCLUSIONS

The results of the genome-wide association study showed that 2 loci (1q32.2 and 1p22.3) are likely to be susceptibility regions of mandibular prognathism: 1p32.2 is a novel locus, and identification of 1p22.3 supports the results of previous linkage analysis.

Assessment of chromosome 19 for genetic association in severe chronic periodontitis

BACKGROUND

A genome-association study is a powerful tool for analyzing small gene effects in complex diseases such as chronic periodontitis (CP), although the cost of analysis is prohibitive. We designed a study using the DNA pooling method, which could be a breakthrough in lowering such costs. This study was conducted to assess the genetic association in severe CP in a Japanese population.

METHODS

We adopted a DNA pooling method by genotyping 454 densely spaced microsatellite (MS) markers in chromosome 19 as a pilot study, with the possibility of future use in a whole-genome study. This can reduce the high cost and technical burden, which is generally unavoidable in a genomic association study. Pooled DNA samples from 300 case subjects, 300 control subjects, and 200 systemically healthy subjects were screened by genotyping MS markers. The case-control association in the candidate region was analyzed by individual typing of MS and single nucleotide polymorphisms (SNPs).

RESULTS

The single MS marker allele 17 of 1902G31 was isolated in association with severe CP (P = 0.0012 for 2 x 2; P <0.046 for 2 x m, where m refers to the number of polymorphic alleles observed in a population). No other SNP or MS polymorphism hypothesized to affect biologic functions in the critical region was found in the linkage disequilibrium block analysis.

CONCLUSIONS

We efficiently isolated the susceptible locus for severe CP in chromosome 19 and identified a useful marker to evaluate the risk for disease. This approach can be applied to a whole-genome study in severe CP.

Multiple sclerosis genetics

Multiple sclerosis (MS) clusters with the so-called complex genetic diseases, a group of common disorders characterized by modest disease risk heritability and multifaceted gene-environment interactions. The major histocompatibility complex (MHC) is the only genomic region consistently associated with MS, and susceptible MHC haplotypes have been identified. Although the MHC does not account for all genetic contribution to MS, the other genetic contributors have been elusive. Microarray gene-expression studies, which also have not identified a major MS locus, have, however, been promising in elucidating some of the possible pathways involved in the disease. Yet, microarray studies thus far have been unable to separate the genetic causes of MS from the expression consequences of MS. The use of new methodologies and technologies to refine the phenotype, such as brain spectroscopy, PET and functional magnetic resonance imaging combined with novel computational tools and a better understanding of the human genome architecture, may help resolve the genetic causes of MS.

HLA‐DRB1*1501, ‐DQB1*0301, ‐DQB1*0302, ‐DQB1*0602, and ‐DQB1*0603 Alleles are Associated With More Severe Disease Outcome on Mri in Patients With Multiple Sclerosis

The most important confirmed genetic factor of susceptibility to multiple sclerosis (MS) has been identified in the HLA class II region. The hypothesis that several genes, including HLA class II, may influence the prognosis of patients with MS has been proposed. In a recent study, using low intermediate resolution typing, we found that some HLA alleles may predict disease severity as assessed by magnetic resonance imaging (MRI) measures. The aim of this study was to examine the relationship between high-resolution typing of HLA alleles and disease severity as measured by brain MRI quantitative markers of demyelinating and destructive pathology in patients with MS. In 41 MS patients (27 relapsing-remitting, 7 secondary progressive, and 7 primary progressive), we performed high-resolution typing of alleles HLA-DRB1*04, -DQB1*03, -DRB1*15, -DQB1*06, and of haplotypes -DRB1*04-DQB1*03 and -DRB1*15-DQB1*06. These alleles and haplotypes were associated with higher susceptibility to MS in a recently published case-control study conducted in the Friuli-Venezia-Giulia region, Italy. Of 41 included patients, 13 were men and 28 were women. Mean age was 43.3 (SD 11.4) years, mean disease duration 10.3 (SD 7.8) years, and mean EDSS 2.3. DNA extraction and genomic typing were obtained with the sequence-specific primers method using primer pairs that amplified the HLA alleles. All patients underwent a 1.5-T MRI examination of the brain. Disease severity was assessed by clinical measures [Expanded Disability Status Scale (EDSS)] and MRI measures. T2- and T1-lesion volumes (LVs) and brain atrophy measures [fractions of brain parenchyma (BPF), gray matter (GMF), and white matter (WMF)] were calculated. We used general linear model analysis (GML), controlled for age, disease duration, and treatment status, to compare the MRI measures according to allele and haplotype status. The following significant results were found: HLA-DRB1*1501 positive patients had significantly lower GMF (0.493 vs 0.526, p < 0.001), lower BPF (0.784 vs 0.815, p = 0.018), and higher T1-LV (2.8 vs 0.7ml, p = 0.036); -DQB1*0301 positive patients had significantly higher T2-LV (34.1 vs 0.7 ml, p = 0.041), and showed a trend for lower BPF (0.790 vs 0.846, p = 0.064); -DQB1*0302 positive patients had significantly lower T1-LV (2.4 vs 0.9 ml, p = 0.016); and -DQB1*0602 positive patients had significantly lower GMF (0.492 vs 0.521, p = 0.007) and lower BPF (0.781 vs 0.811, p = 0.023). No differences were found in the indices of MRI disease severity according to HLA haplotype associations. Both in correlation and in regression analyses, we observed significant associations between HLA-DRB1*1501 and lower GMF and BPF and higher T1-LV, between -DQB1*0301 and higher T2-LV and disease duration, between -DQB1*0302 and lower GMF and higher T1- and T2-LV, between -DQB1*0602 and lower GMF and BPF, and between -DQB1*0603 and higher T1-LV and EDSS. High-resolution HLA genotyping analysis revealed a robust relationship between alleles HLA-DRB1*1501, -DQB1*0301, -DQB1*0302, -DQB1*0602, and -DQB1*0603, and more severe damage on inflammatory and neurodegenerative MRI measures.

Sex ratio of multiple sclerosis in Canada: a longitudinal study

BACKGROUND

Incidence of multiple sclerosis is thought to be increasing, but this notion has been difficult to substantiate. In a longitudinal population-based dataset of patients with multiple sclerosis obtained over more than three decades, we did not show a difference in time to diagnosis by sex. We reasoned that if a sex-specific change in incidence was occurring, the female to male sex ratio would serve as a surrogate of incidence change.

METHODS

Since environmental risk factors seem to act early in life, we calculated sex ratios by birth year in 27 074 Canadian patients with multiple sclerosis identified as part of a longitudinal population-based dataset.

FINDINGS

The female to male sex ratio by year of birth has been increasing for at least 50 years and now exceeds 3.2:1 in Canada. Year of birth was a significant predictor for sex ratio (p<0.0001, chi(2)=124.4; rank correlation r=0.84).

INTERPRETATION

The substantial increase in the female to male sex ratio in Canada seems to result from a disproportional increase in incidence of multiple sclerosis in women. This rapid change must have environmental origins even if it is associated with a gene-environment interaction, and implies that a large proportion of multiple sclerosis cases may be preventable in situ. Although the reasons why incidence of the disease is increasing are unknown, there are major implications for health-care provision because lifetime costs of multiple sclerosis exceed pound1 million per case in the UK.

Linkage disequilibrium screening for multiple sclerosis implicates JAG1 and POU2AF1 as susceptibility genes in Europeans

By combining all the data available from the Genetic Analysis of Multiple sclerosis in EuropeanS (GAMES) project, we have been able to identify 17 microsatellite markers showing consistent evidence for apparent association. As might be expected five of these markers map within the Major Histocompatibility Complex (MHC) and are in LD with HLA-DRB1. Individual genotyping of the 12 non-MHC markers confirmed association for three of them--D11S1986, D19S552 and D20S894. Association mapping across the candidate genes implicated by these markers in 937 UK trio families revealed modestly associated haplotypes in JAG1 (p=0.019) on chromosome 20p12.2 and POU2AF1 (p=0.003) on chromosome 11q23.1.

Mapping gene activity in complex disorders: Integration of expression and genomic scans for multiple sclerosis

Genetic predisposition contributes to the pathogenesis of most common diseases. Genetic studies have been extremely successful in the identification of genes responsible for a number of Mendelian disorders. However, with a few exceptions, genes predisposing to diseases with complex inheritance remain unknown despite multiple efforts. In this article we collected detailed information for all genome-wide genetic screens performed to date in multiple sclerosis (MS) and in its animal model experimental autoimmune encephalomyelitis (EAE), and integrated these results with those from all high throughput gene expression studies in humans and mice. We analyzed a total of 55 studies. We found that differentially expressed genes (DEG) are not uniformly distributed in the genome, but rather appear in clusters. Furthermore, these clusters significantly differ from the known heterogeneous organization characteristic of eukaryotic gene distributions. We also identified regions of susceptibility that overlapped with clusters of DEG leading to the prioritization of candidate genes. Integration of genomic and transcriptional information is a powerful tool to dissect genetic susceptibility in complex multifactorial disorders like MS.