María M. Abad-Grau

IL2RA/CD25 Gene Polymorphisms: Uneven Association with Multiple Sclerosis (MS) and Type 1 Diabetes (T1D)

Background IL-2 receptor (IL2R) alpha is the specific component of the high affinity IL2R system involved in the immune response and in the control of autoimmunity. Methods and Results Here we perform a replication and fine mapping of the IL2RA gene region analyzing 3 SNPs previously associated with multiple sclerosis (MS) and 5 SNPs associated with type 1 diabetes (T1D) in a collection of 798 MS patients and 927 matched Caucasian controls from the south of Spain. We observed association with MS in 6 of 8 SNPs. The rs1570538, at the 3′- UTR extreme of the gene, previously reported to have a weak association with MS, is replicated here (P = 0.032). The most associated T1D SNP (rs41295061) was not associated with MS in the present study. However, the rs35285258, belonging to another independent group of SNPs associated with T1D, showed the maximal association in this study but different risk allele. We replicated the association of only one (rs2104286) of the two IL2RA SNPs identified in the recently performed genome-wide association study of MS. Conclusions These findings confirm and extend the association of this gene with MS and reveal a genetic heterogeneity of the associated polymorphisms and risk alleles between MS and T1D suggesting different immunopathological roles of IL2RA in these two diseases.

Multiple Sclerosis Risk Variant HLA-DRB1*1501 Associates with High Expression of DRB1 Gene in Different Human Populations

The human leukocyte antigen (HLA) DRB1*1501 has been consistently associated with multiple sclerosis (MS) in nearly all populations tested. This points to a specific antigen presentation as the pathogenic mechanism though this does not fully explain the disease association. The identification of expression quantitative trait loci (eQTL) for genes in the HLA locus poses the question of the role of gene expression in MS susceptibility. We analyzed the eQTLs in the HLA region with respect to MS-associated HLA-variants obtained from genome-wide association studies (GWAS). We found that the Tag of DRB1*1501, rs3135388 A allele, correlated with high expression of DRB1, DRB5 and DQB1 genes in a Caucasian population. In quantitative terms, the MS-risk AA genotype carriers of rs3135388 were associated with 15.7-, 5.2- and 8.3-fold higher expression of DQB1, DRB5 and DRB1, respectively, than the non-risk GG carriers. The haplotype analysis of expression-associated variants in a Spanish MS cohort revealed that high expression of DRB1 and DQB1 alone did not contribute to the disease. However, in Caucasian, Asian and African American populations, the DRB1*1501 allele was always highly expressed. In other immune related diseases such as type 1 diabetes, inflammatory bowel disease, ulcerative colitis, asthma and IgA deficiency, the best GWAS-associated HLA SNPs were also eQTLs for different HLA Class II genes. Our data suggest that the DR/DQ expression levels, together with specific structural properties of alleles, seem to be the causal effect in MS and in other immunopathologies rather than specific antigen presentation alone.

Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis

Background and aim Several studies have highlighted the association of the 12q13.3–12q14.1 region with coeliac disease, type 1 diabetes, rheumatoid arthritis and multiple sclerosis (MS); however, the causal variants underlying diseases are still unclear. The authors sought to identify the functional variant of this region associated with MS. Methods Tag-single nucleotide polymorphism (SNP) analysis of the associated region encoding 15 genes was performed in 2876 MS patients and 2910 healthy Caucasian controls together with expression regulation analyses. Results rs6581155, which tagged 18 variants within a region where 9 genes map, was sufficient to model the association. This SNP was in total linkage disequilibrium (LD) with other polymorphisms that associated with the expression levels of FAM119B, AVIL, TSFM, TSPAN31 and CYP27B1 genes in different expression quantitative trait loci studies. Functional annotations from Encyclopedia of DNA Elements (ENCODE) showed that six out of these rs6581155-tagged-SNPs were located in regions with regulatory potential and only one of them, rs10877013, exhibited allele-dependent (ratio A/G=9.5-fold) and orientation-dependent (forward/reverse=2.7-fold) enhancer activity as determined by luciferase reporter assays. This enhancer is located in a region where a long-range chromatin interaction among the promoters and promoter-enhancer of several genes has been described, possibly affecting their expression simultaneously. Conclusions This study determines a functional variant which alters the enhancer activity of a regulatory element in the locus affecting the expression of several genes and explains the association of the 12q13.3–12q14.1 region with MS.

Operations strategy and flexibility: modeling with Bayesian classifiers

Purpose – Information analysis tools enhance the possibilities of firm competition in terms of knowledge management. However, the generalization of decision support systems (DSS) is still far away from everyday use by managers and academicians. This paper aims to present a framework of analysis based on Bayesian networks (BN) whose accuracy is measured in order to assess scientific evidence.Design/methodology/approach – Different learning algorithms based on BN are applied to extract relevant information about the relationship between operations strategy and flexibility in a sample of engineering consulting firms. Feature selection algorithms automatically are able to improve the accuracy of these classifiers.Findings – Results show that the behaviors of the firms can be reduced to different rules that help in the decision‐making process about investments in technology and production resources.Originality/value – Contrasting with methods from the classic statistics, Bayesian classifiers are able to model ...

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

BackgroundOne of the challenges of the analysis of pooling-based genome wide association studies is to identify authentic associations among potentially thousands of false positive associations.ResultsWe present a hierarchical and modular approach to the analysis of genome wide genotype data that incorporates quality control, linkage disequilibrium, physical distance and gene ontology to identify authentic associations among those found by statistical association tests. The method is developed for the allelic association analysis of pooled DNA samples, but it can be easily generalized to the analysis of individually genotyped samples. We evaluate the approach using data sets from diverse genome wide association studies including fetal hemoglobin levels in sickle cell anemia and a sample of centenarians and show that the approach is highly reproducible and allows for discovery at different levels of synthesis.ConclusionResults from the integration of Bayesian tests and other machine learning techniques with linkage disequilibrium data suggest that we do not need to use too stringent thresholds to reduce the number of false positive associations. This method yields increased power even with relatively small samples. In fact, our evaluation shows that the method can reach almost 70% sensitivity with samples of only 100 subjects.

A functional variant that affects exon-skipping and protein expression of SP140 as genetic mechanism predisposing to multiple sclerosis

Several variants in strong linkage disequilibrium (LD) at the SP140 locus have been associated with multiple sclerosis (MS), Crohns disease (CD) and chronic lymphocytic leukemia (CLL). To determine the causal polymorphism, we have integrated high-density data sets of expression quantitative trait loci (eQTL), using GEUVADIS RNA sequences and 1000 Genomes genotypes, with MS-risk variants of the high-density Immunochip array performed by the International Multiple Sclerosis Genetic Consortium (IMSGC). The variants most associated with MS were also correlated with a decreased expression of the full-length RNA isoform of SP140 and an increase of an isoform lacking exon 7. By exon splicing assay, we have demonstrated that the rs28445040 variant was the causal factor for skipping of exon 7. Western blots of peripheral blood mononuclear cells from MS patients showed a significant allele-dependent reduction of the SP140 protein expression. To confirm the association of this functional variant with MS and to compare it with the best-associated variant previously reported by GWAS (rs10201872), a case-control study including 4384 MS patients and 3197 controls was performed. Both variants, in strong LD (r(2) = 0.93), were found similarly associated with MS [P-values, odds ratios: 1.9E-9, OR = 1.35 (1.22-1.49) and 4.9E-10, OR = 1.37 (1.24-1.51), respectively]. In conclusion, our data uncover the causal variant for the SP140 locus and the molecular mechanism associated with MS risk. In addition, this study and others previously reported strongly suggest that this functional variant may be shared with other immune-mediated diseases as CD and CLL.

Methodological Review: Evolution and challenges in the design of computational systems for triage assistance

Compared with expert systems for specific disease diagnosis, knowledge-based systems to assist decision making in triage usually try to cover a much wider domain but can use a smaller set of variables due to time restrictions, many of them subjective so that accurate models are difficult to build. In this paper, we first study criteria that most affect the performance of systems for triage assistance. Such criteria include whether principled approaches from machine learning can be used to increase accuracy and robustness and to represent uncertainty, whether data and model integration can be performed or whether temporal evolution can be modeled to implement retriage or represent medication responses. Following the most important criteria, we explore current systems and identify some missing features that, if added, may yield to more accurate triage systems.

Building chromosome-wide LD maps

SUMMARY BMapBuilder builds maps of pairwise linkage disequilibrium (LD) in either two or three dimensions. The optimized resolution allows for graphical display of LD for single nucleotide polymorphisms (SNPs) in a whole chromosome. AVAILABILITY The program is coded in Java, which runs on all relevant operating systems, including Windows, Mac and Unix/Linux, and is available from http://bios.ugr.es/BMapBuilder.

Variant alleles of the mannose binding lectin 2 gene (MBL2) confer heterozygote advantage within Crohn's families.

TO THE EDITOR: Mannose binding lectin (MBL) is a pattern recognition molecule of the innate immune system. Single nucleotide polymorphisms (SNPs) in the proximal promoter (L/H and X/Y), the 5¢UTR (P/Q) and SNPs in exon 1 at codons 52 (MBL2*D), 54 (MBL2*B), and 57 (MBL2*C) account for alterations in complement activation and decreased levels of MBL [1]. Researchers have reported the contribution of variant MBL alleles to disease susceptibility in infancy [2], spontaneous abortions, miscarriages and low weight newborns [3]. Other studies contemplated that the high frequency of these alleles is promoted by selective advantages providing protection against infections [4]. To evaluate the heterozygote advantage hypothesis in Crohn’s disease (CD), we analyzed individuals from 37 families. The cohort comprised 138 Caucasian individuals, among them 115 individuals were unaffected and 23 individuals had CD. Fifty-eight were parents (31 women, 27 men) and 65 were children (37 male and 28 female). Allelic variants of the MBL2 gene from individuals of families were determined by sequencing its promoter region and exon 1 [5]. Haplotype frequencies were estimated and a robust transmission disequilibrium test (rTDT) was performed to compare transmission of each of the two alleles of six SNPs [6]. Since there was no association of MBL haplotypes with CD, the promoter variants were ignored and all MBL variant alleles were pooled, i.e. SNPs in exon 1 as O haplotype and normal MBL2 allele as A haplotype. The segregation pattern was inferred across A/A, A/O and for O/O haplotypes. A Fisher’s exact test on these patterns was performed to validate whether all allelic combinations (A/A, A/O and O/O) contribute to CD. MBL2 genotype frequencies do not differ significantly between individuals affected and unaffected by Crohn’s disease (p = 0.928). The rTDT analysis revealed no significant preferential transmission of the alleles and haplotypes of the SNPs (Table I). Validation of all allelic combinations (A/A, A/O and O/O) remained insignificant (p = 0.195). In addition, neither the wild type (A/A, A/O) nor the mutant (O/O) contributed to disease (p = 0.324) (Table II). In accordance with other studies in Caucasians, HYPA and LXPA remained the most prominent haplotypes followed by LYPB, HYPD and LYQA [7]. Since no significant preferential transmission of the alleles or the haplotypes of the SNPs across generations was inferred, this led us to theorize the unknown advantage of these MBL2 variants and evaluate whether they confer any vital advantage on carrier generation. None of the observed frequencies of variants deviated from the expected. Studies have proposed that the complexity of signatures of possible

INCREASING POWER BY USING HAPLOTYPE SIMILARITY IN A MULTIMARKER TRANSMISSION/DISEQUILIBRIUM TEST

It is already known that power in multimarker transmission/disequilibrium tests may improve with the number of markers as some associations may require several markers to be captured. However, a mechanism such as haplotype grouping must be used to avoid incremental complexity with the number of markers. 2G, a state-of-the-art transmission/disequilibrium test, implements this mechanism to its maximum extent by grouping haplotypes into only two groups, high and low-risk haplotypes, so that the test has only one degree of freedom regardless of the number of markers. The test checks whether those haplotypes more often transmitted from parents to offspring are truly high-risk haplotypes. In this paper we use haplotype similarity as prior knowledge to classify haplotypes as high or low risk ones and start with those haplotypes in which the prior will have lower impact i.e. those with the largest differences between transmission and non-transmission counts. If their counts are very different, the prior knowledge has little effect and haplotypes are classified as low or high risk as 2G does. We show a substantial gain in power achieved by this approach, in both simulation and real data sets.