Burden of genetic risk variants in multiple sclerosis families in the Netherlands

Contribution of common risk variants to multiple sclerosis in Orkney and Shetland

Orkney and Shetland, the population isolates that make up the Northern Isles of Scotland, are of particular interest to multiple sclerosis (MS) research. While MS prevalence is high in Scotland, Orkney has the highest global prevalence, higher than more northerly Shetland. Many hypotheses for the excess of MS cases in Orkney have been investigated, including vitamin D deficiency and homozygosity: neither was found to cause the high prevalence of MS. It is possible that this excess prevalence may be explained through unique genetics. We used polygenic risk scores (PRS) to look at the contribution of common risk variants to MS. Analyses were conducted using ORCADES (97/2118 cases/controls), VIKING (15/2000 cases/controls) and Generation Scotland (30/8708 cases/controls) data sets. However, no evidence of a difference in MS-associated common variant frequencies was found between the three control populations, aside from HLA-DRB1*15:01 tag SNP rs9271069. This SNP had a significantly higher risk allele frequency in Orkney (0.23, p value = 8 × 10-13) and Shetland (0.21, p value = 2.3 × 10-6) than mainland Scotland (0.17). This difference in frequency is estimated to account for 6 (95% CI 3, 8) out of 150 observed excess cases per 100,000 individuals in Shetland and 9 (95% CI 8, 11) of the observed 257 excess cases per 100,000 individuals in Orkney, compared with mainland Scotland. Common variants therefore appear to account for little of the excess burden of MS in the Northern Isles of Scotland.

EBNA-1 titer gradient in families with multiple sclerosis indicates a genetic contribution

OBJECTIVE

In multiplex MS families, we determined the humoral immune response to Epstein-Barr virus nuclear antigen 1 (EBNA-1)-specific immunoglobulin γ (IgG) titers in patients with MS, their healthy siblings, and biologically unrelated healthy spouses and investigated the role of specific genetic loci on the antiviral IgG titers.

METHODS

IgG levels against EBNA-1 and varicella zoster virus (VZV) as control were measured. HLA-DRB1*1501 and HLA-A*02 tagging single-nucleotide polymorphisms (SNPs) were genotyped. We assessed the associations between these SNPs and antiviral IgG titers.

RESULTS

OR for abundant EBNA-1 IgG was the highest in patients with MS and intermediate in their siblings compared with spouses. We confirmed that HLA-DRB1*1501 is associated with abundant EBNA-1 IgG. After stratification for HLA-DRB1*1501, the EBNA-1 IgG gradient was still significant in patients with MS and young siblings compared with spouses. HLA-A*02 was not explanatory for EBNA-1 IgG titer gradient. No associations for VZV IgG were found.

CONCLUSIONS

In families with MS, the EBNA-1 IgG gradient being the highest in patients with MS, intermediate in their siblings, and lowest in biologically unrelated spouses indicates a genetic contribution to EBNA-1 IgG levels that is only partially explained by HLA-DRB1*1501 carriership.

Inferring disease risk genes from sequencing data in multiplex pedigrees through sharing of rare variants

We previously demonstrated how sharing of rare variants (RVs) in distant affected relatives can be used to identify variants causing a complex and heterogeneous disease. This approach tested whether single RVs were shared by all sequenced affected family members. However, as with other study designs, joint analysis of several RVs (e.g., within genes) is sometimes required to obtain sufficient statistical power. Further, phenocopies can lead to false negatives for some causal RVs if complete sharing among affected is required. Here, we extend our methodology (Rare Variant Sharing, RVS) to address these issues. Specifically, we introduce gene-based analyses, a partial sharing test based on RV sharing probabilities for subsets of affected relatives and a haplotype-based RV definition. RVS also has the desirable feature of not requiring external estimates of variant frequency or control samples, provides functionality to assess and address violations of key assumptions, and is available as open source software for genome-wide analysis. Simulations including phenocopies, based on the families of an oral cleft study, revealed the partial and complete sharing versions of RVS achieved similar statistical power compared with alternative methods (RareIBD and the Gene-Based Segregation Test), and had superior power compared with the pedigree Variant Annotation, Analysis, and Search Tool (pVAAST) linkage statistic. In studies of multiplex cleft families, analysis of rare single nucleotide variants in the exome of 151 affected relatives from 54 families revealed no significant excess sharing in any one gene, but highlighted different patterns of sharing revealed by the complete and partial sharing tests.

Distinct HLA class I and II genotypes and haplotypes are associated with multiple sclerosis in Bahrain

Multiple sclerosis (MS) has become prevalent in the Arabian Gulf area with high incidence in Bahrain due to environmental influences and genetic susceptibilities, but there is a lack of study into human leukocyte antigen (HLA) types in patients with MS in Bahrain. The present study aimed to study the HLA types expressed in MS patients compared with in control subjects. Blood samples from 50 Bahraini patients with MS and 50 Bahraini control subjects' were subjected to HLA tissue typing by polymerase chain reaction using sequence-specific primers. In comparison with those in control subjects, the allele frequencies of HLA class-I antigens A2, A9, A19, B5, B35 and B40 were higher in MS patients. For class II antigens, the allele frequencies of DR3, DR4 and DR16 were higher in MS patients. The allele frequency of DR15 was lower in MS patients than in control subjects but the difference was not statistically significant (P=0.138). The higher prevalence of the HLA-ABDR allele was common among the female patients with MS, in relapse remission stage, in cases with higher expanded disability status scale scores and with disease duration between 4 and 9 years. Haplotype HLA-A2-B40-DR2 exhibited significantly higher frequency in MS patients compared with in control subjects (P=0.03). In conclusion, the results indicated different alleles associated with MS compared with previous reviews. The present study supports the importance of identifying genetic susceptibilities and targets for therapies in specific populations and individuals, to personalize disease management in terms of prediction, protective measures and treatment.

Linkage analysis and whole exome sequencing identify a novel candidate gene in a Dutch multiple sclerosis family

BACKGROUND

Multiple sclerosis (MS) is a complex disease resulting from the joint effect of many genes. It has been speculated that rare variants might explain part of the missing heritability of MS.

OBJECTIVE

To identify rare coding genetic variants by analyzing a large MS pedigree with 11 affected individuals in several generations.

METHODS

Genome-wide linkage screen and whole exome sequencing (WES) were performed to identify novel coding variants in the shared region(s) and in the known 110 MS risk loci. The candidate variants were then assessed in 591 MS patients and 3169 controls.

RESULTS

Suggestive evidence for linkage was obtained to 7q11.22-q11.23. In WES data, a rare missense variant p.R183C in FKBP6 was identified that segregated with the disease in this family. The minor allele frequency was higher in an independent cohort of MS patients than in healthy controls (1.27% vs 0.95%), but not significant (odds ratio (OR) = 1.33 (95% confidence interval (CI): 0.8-2.4), p = 0.31).

CONCLUSION

The rare missense variant in FKBP6 was identified in a large Dutch MS family segregating with the disease. This association to MS was not found in an independent MS cohort. Overall, genome-wide studies in larger cohorts are needed to adequately investigate the role of rare variants in MS risk.