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Fibromyalgia is a rheumatic disorder whose main symptom is chronic generalized pain accompanied by a set of symptoms such as sleep disturbance, depression, and chronic fatigue, among others. Its pathophysiology is complex, of multifactorial origin, including the influence of genetic factors. It has been shown that individuals with fibromyalgia show a pattern of family aggregation and that the probability of an individual developing this condition is about 50% attributed to genetic factors. In this sense, the present article aims to carry out a narrative review of the literature on the genetic aspects of fibromyalgia in its development and severity of symptoms. To this end, searches were carried out in PubMed and Scopus databases, using specific descriptors: “fibromyalgia” and “polymorphism”. Polymorphisms that influence pain modulation, such as those that occur in genes of the monoaminergic pathway or of catecholamine metabolism, are frequently found in studies of association with fibromyalgia. However, other target genes have emerged, related to the pathways responsible for the mechanisms of the most diverse symptoms that can affect these patients, such as neuroplasticity, neurotransmission, inflammation, vascularization, oxidative stress, cell cycle, among others. La fibromialgia es un trastorno reumático cuyo principal síntoma es el dolor crónico generalizado acompañado de un conjunto de síntomas como alteración del sueño, depresión y fatiga crónica, entre otros. Su fisiopatología es compleja, de origen multifactorial, incluyendo la influencia de factores genéticos. Se ha demostrado que los individuos con fibromialgia muestran un patrón de agregación familiar y que la probabilidad de que un individuo desarrolle esta condición es de alrededor del 50% atribuida a factores genéticos. En este sentido, el presente artículo tiene como objetivo realizar una revisión narrativa de la literatura sobre los aspectos genéticos de la fibromialgia en su desarrollo y severidad de los síntomas. Para ello, se realizaron búsquedas en las bases de datos PubMed y Scopus, utilizando descriptores específicos: “fibromialgia” y “polimorfismo”. Los polimorfismos que influyen en la modulación del dolor, como los que ocurren en los genes de la vía monoaminérgica o del metabolismo de las catecolaminas, se encuentran con frecuencia en los estudios de asociación con la fibromialgia. Sin embargo, han surgido otros genes diana, relacionados con las vías responsables de los mecanismos de los más diversos síntomas que pueden afectar a estos pacientes, como la neuroplasticidad, la neurotransmisión, la inflamación, la vascularización, el estrés oxidativo, el ciclo celular, entre otros. A fibromialgia é uma desordem reumática que tem como principal sintoma a dor crônica generalizada acompanhada de um conjunto de sintomas como distúrbio do sono, depressão e fadiga crônica, entre outros. Sua fisiopatologia é complexa, de origem multifatorial, incluindo a influência de fatores genéticos. Já foi demonstrado que indivíduos com fibromialgia apresentam um padrão de agregação familiar e que a probabilidade de um indivíduo desenvolver essa condição é cerca de 50% atribuída a fatores genéticos. Neste sentido, o presente artigo tem por objetivo realizar uma revisão narrativa da literatura sobre os aspectos genéticos da fibromialgia em seu desenvolvimento e gravidade dos sintomas. Para tal foram feitas buscas nas bases de dados PubMed e Scopus, com a utilização de descritores específicos: “fibromyalgia” e “polymorphism”. Polimorfismos que influenciam na modulação da dor, como os que ocorrem em genes da via monoaminérgica ou do metabolismo das catecolaminas, são encontrados com frequência em estudos de associação com a fibromialgia. Porém, outros genes-alvo têm surgido, relacionados às vias responsáveis pelos mecanismos dos mais diversos sintomas que podem acometer esses pacientes, como neuroplasticidade, neurotransmissão, inflamação, vascularização, estresse oxidativo, ciclo celular, entre outros.

Purpose: Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin-Siris patients (ARID1BCSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods: Clinicians entered clinical data in an extensive webbased survey. Results: 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion: There are only minor differences between ARID1BID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features., We are grateful for the assistance of Pepijn Cox in setting up the website www.arid1bgene.com. This study has made use of data generated by the Human Disease Genes website series, www.humandiseasegenes.com. This work was financially supported by grants from the Netherlands Organisation for Health Research and Development (917-86-319 to B.B.A.d.V., 912-12-109 to B.B.A.d.V.)

Background: tinnitus is a heterogeneous condition associated with audiological and/or mental disorders. Chronic, severe tinnitus is reported in 1% of the population and it shows a relevant heritability, according to twins, adoptees and familial aggregation studies. The genetic contribution to severe tinnitus is unknown since large genomic studies include individuals with self-reported tinnitus and large heterogeneity in the phenotype. The aim of this study was to identify genes for severe tinnitus in patients with extreme phenotype. Methods: for this extreme phenotype study, we used three different cohorts with European ancestry (Spanish with Meniere disease (MD), Swedes tinnitus and European generalized epilepsy). In addition, four independent control datasets were also used for comparisons. Whole-exome sequencing was performed for the MD and epilepsy cohorts and whole-genome sequencing was carried out in Swedes with tinnitus. Findings: we found an enrichment of rare missense variants in 24 synaptic genes in a Spanish cohort, the most significant being PRUNE2, AKAP9, SORBS1, ITGAX, ANK2, KIF20B and TSC2 (p < 2E 04), when they were compared with reference datasets. This burden was replicated for ANK2 gene in a Swedish cohort with 97 tinnitus individuals, and in a subset of 34 Swedish patients with severe tinnitus for ANK2, AKAP9 and TSC2 genes (p < 2E 02). However, these associations were not significant in a third cohort of 701 generalized epilepsy individuals without tinnitus. Gene ontology (GO) and gene-set enrichment analyses revealed several pathways and biological processes involved in severe tinnitus, including membrane trafficking and cytoskeletal protein binding in neurons. Interpretation: a burden of rare variants in ANK2, AKAP9 and TSC2 is associated with severe tinnitus. ANK2, encodes a cytoskeleton scaffolding protein that coordinates the assembly of several proteins, drives axonal branching and influences connectivity in neurons.

Exome sequencing has been commonly used to characterize rare diseases by selecting multiplex families or singletons with an extreme phenotype (EP) and searching for rare variants in coding regions. The EP strategy covers both extreme ends of a disease spectrum and it has been also used to investigate the contribution of rare variants to the heritability of complex clinical traits. We conducted a systematic review to find evidence supporting the use of EP strategies in the search for rare variants in genetic studies of complex diseases and highlight the contribution of rare variations to the genetic structure of polygenic conditions. After assessing the quality of the retrieved records, we selected 19 genetic studies considering EPs to demonstrate genetic association. All studies successfully identified several rare or de novo variants, and many novel candidate genes were also identified by selecting an EP. There is enough evidence to support that the EP approach for patients with an early onset of a disease can contribute to the identification of rare variants in candidate genes or pathways involved in complex diseases. EP patients may contribute to a better understanding of the underlying genetic architecture of common heterogeneous disorders such as tinnitus or age-related hearing loss. Yes

Non-alcoholic fatty liver disease (NAFLD) is a major cause of liver disease worldwide. Some genetic variants might be involved in the progression of this disease. The study hypothesized that individuals with the rs7359397 T allele have a higher risk of developing severe stages of NAFLD compared with non-carriers where dietary intake according to genotypes could have a key role on the pathogenesis of the disease. SH2B1 genetic variant was genotyped in 110 overweight/obese subjects with NAFLD. Imaging techniques, lipidomic analysis and blood liver biomarkers were performed. Body composition, general biochemical and dietary variables were also determined. The SH2B1 risk genotype was associated with higher HOMA-IR p = 0.001, and Fatty Liver Index (FLI) p = 0.032. Higher protein consumption (p = 0.028), less mono-unsaturated fatty acid and fiber intake (p = 0.045 and p = 0.049, respectively), was also referred to in risk allele genotype. Lipidomic analysis showed that T allele carriers presented a higher frequency of non-alcoholic steatohepatitis (NASH) (69.1% vs. 44.4%, p = 0.006). In the genotype risk group, adjusted logistic regression models indicated a higher risk of developing an advanced stage of NAFLD measured by FLI (OR 2.91) and ultrasonography (OR 4.15). Multinomial logistic regression models showed that risk allele carriers had higher liver fat accumulation risk (RRR 3.93) and an increased risk of NASH (RRR 7.88). Consequently, subjects carrying the T allele were associated with a higher risk of developing a severe stage of NAFLD. These results support the importance of considering genetic predisposition in combination with a healthy dietary pattern in the personalized evaluation and management of NAFLD.

Behcet's disease (BD) is an immune-mediated vasculitis related to imbalances between the innate and adaptive immune response. Infectious agents or environmental factors may trigger the disease in genetically predisposed individuals. HLA-B51 is the genetic factor stronger associated with the disease, although the bases of this association remain elusive. NK cells have also been implicated in the etiopathogenesis of BD. A family of NK receptors, Killer-cell Immunoglobulin-like Receptor (KIR), with a very complex organization, is very important in the education and control of the NK cells by the union to their ligands, most of them, HLA class I molecules. This study aimed to investigate the contribution of certain KIR functional polymorphisms to the susceptibility to BD. A total of 466 BD patients and 444 healthy individuals were genotyped in HLA class I (A, B, and C). The set of KIR genes and the functional variants of KIR3DL1/DS1 and KIR2DS4 were also determined. Frequency of KIR3DL1*004 was lower in patients than in controls (0.15 vs. 0.20, P = 0.005, Pc = 0.015; OR = 0.70; 95% CI 0.54-0.90) in both B51 positive and negative individuals. KIR3DL1*004, which encodes a misfolded protein, is included in a common telomeric haplotype with only one functional KIR gene, KIR3DL2. Both, KIR3DL1 and KIR3DL2 sense pathogen-associated molecular patterns but they have different capacities to eliminate them. The education of the NK cells depending on the HLA, the balance of KIR3DL1/KIR3DL2 licensed NK cells and the different capacities of these receptors to eliminate pathogens could be involved in the etiopathogenesis of BD., This work was supported by Fondo de Investigaciones Sanitarias, Instituto de Salud Carlos III (ISCIII, 13/01118 and 16/01373), Fondos FEDER and Plan Andaluz de Investigacion (CTS-0197).

WOS: 000481590200024, PubMed ID: 31427717, Rett syndrome (RTT) is a severe neurological disorder usually caused by mutations in the MECP2 gene. Since the MECP2 gene is located on the X chromosome, X chromosome inactivation (XCI) could play a role in the wide range of phenotypic variation of RTT patients; however, classical methylation-based protocols to evaluate XCI could not determine whether the preferentially inactivated X chromosome carried the mutant or the wild-type allele. Therefore, we developed an allele-specific methylation-based assay to evaluate methylation at the loci of several recurrent MECP2 mutations. We analyzed the XCI patterns in the blood of 174 RTT patients, but we did not find a clear correlation between XCI and the clinical presentation. We also compared XCI in blood and brain cortex samples of two patients and found differences between XCI patterns in these tissues. However, RTT mainly being a neurological disease complicates the establishment of a correlation between the XCI in blood and the clinical presentation of the patients. Furthermore, we analyzed MECP2 transcript levels and found differences from the expected levels according to XCI. Many factors other than XCI could affect the RTT phenotype, which in combination could influence the clinical presentation of RTT patients to a greater extent than slight variations in the XCI pattern., Spanish Ministry of Health (Instituto de Salud Carlos III/FEDER) [PI15/01159]; Crowdfunding program PRECIPITA, from the Spanish Ministry of Health (Fundacion Espanola para la Ciencia y la Tecnologia); Catalan Association for Rett Syndrome; Fondobiorett; Mi Princesa Rett, We thank all patients and their families who contributed to this study. The work was supported by grants from the Spanish Ministry of Health (Instituto de Salud Carlos III/FEDER, PI15/01159); Crowdfunding program PRECIPITA, from the Spanish Ministry of Health (Fundacion Espanola para la Ciencia y la Tecnologia); the Catalan Association for Rett Syndrome; Fondobiorett and Mi Princesa Rett.

RESUMEN: INTRODUCCIÓN: las epilepsias genéticas generalizadas (EGG) siguen patrones de herencia compleja. Este fenotipo es producto de la interacción de diferentes genes con factores ambientales. Los genes/loci más consistentemente asociados con este grupo de epilepsias son ECA1, ECA2-GABRG2, ECA3-CLCN2 (también conocido como JME6-CLCN2), JME1-EFHC1 y JME5-GABRA1. En Colombia poco se sabe sobre la contribución de las variantes genéticas en estos genes a la susceptibilidad para ser afectado por cualquiera de las formas de EGG. Nuestro propósito fue evaluar el papel de los cinco genes/loci más consistentemente asociados en otros estudios en un grupo de familias colombianas con EGG. MÉTODOS: se evaluaron dos marcadores para cada locus/gen. Los genotipos se obtuvieron mediante las técnicas de PCR-RFLP y ARMS-Tetraprimer. Los análisis estadísticos incluyeron pruebas de asociación alélica y haplotípica, además de pruebas de interacción gen-gen. RESULTADOS: se incluyeron 98 familias, de las cuales 51 fueron epilepsia de ausencias, mientras que 47 fueron epilepsia mioclónica juvenil. Se identificó una interacción significativa entre el alelo G del marcador rs4428455 (valor P=0,0008; gen GABRA1) y el alelo G de marcador rs719395 (valor P=0,002; gen EFHC1). CONCLUSIÓN: estos dos marcadores parecen incrementar el riesgo de EGG en población colombiana. Otros genes no analizados aquí podrían estudiarse con una muestra de mayor tamaño ABSTRACT: INTRODUCTION: Generalized genetic epilepsies (GGE) follow complex inheritance patterns. This phenotype is due to interaction of several genes with environmental factors. The genes/loci most consistently associated with this group of epilepsies are ECA1, ECA2-GABRG2, ECA3-CLCN2 (also known as JME6-CLCN2), JME1-EFHC1 and JME5-GABRA1. In Colombia, little is known about the contribution of gene variants to susceptibility to GGE forms. Our purpose was to evaluate the role of the five most consistently associated genes /loci in other studies, in Colombian families set with GGE. METHODS: Genotypes were obtained by means of PCR-RFLP and ARMS-Tetraprimer. Statistical analyses included both allelic and haplotypic association tests, in addition to gene-gene interaction tests. Two genetic markers were tested for each gene/locus. RESULTS: Ninety-eight families were included, from which 51 had absence epilepsy, and 47 had juvenile myoclonic epilepsy. A significant interaction was identified between allele G at marker rs4428455 (P-value= 0.0008; gene GABRA1) and allele G at marker rs719395 (P-value= 0.002; gene EFHC1). CONCLUSION: Our results suggest that these two markers are associated with GGE in the Colombian population. Other genes not analyzed could be tested using a larger sample size. COL0006723 COL0058784 COL0057491

RESUMEN Introducción. El lupus eritematoso sistémico es una enfermedad autoinmunitaria cuya gravedad varía según la raza, el sexo y la edad de aparición. Esta disparidad también se observa en los marcadores genéticos asociados con la enfermedad presentes en los genes PTPN22, VDR y TNF. La estratificación genética que presentan las diferentes poblaciones en el mundo puede influir en dicha variabilidad. Objetivo. Analizar la asociación de variantes genéticas de los genes PTPN22, VDR y TNF con nefritis lúpica en niños y su caracter de hereditarias en familias colombianas. Materiales y métodos. Se llevó a cabo un estudio basado en familias con 46 tríos (caso, padre y madre). Se hizo la genotipificación de las variantes rs2476601 de PTPN22, rs361525 y rs1800629 del TNF, y TaqI [rs731236], ApaI [rs7975232], BsmI [rs1544410] y FokI [rs2228570] del VDR, mediante reacción en cadena de la polimerasa cuantitativa (quantitative Polymerase Chain Reaction, qPCR). Se estimó el efecto de la transmisión del alelo de riesgo de padres a hijos y el desequilibrio de ligamiento de los loci VDR y TNF. Resultados. Se observó que el alelo A de rs2476601 en PTPN22 se distribuyó en 8,69 % (n=16) de los padres y en 19,5 % (n=18) de los casos, y que su transmisión de padres a hijos fue 17 veces mayor con relación al alelo G (p=0,028). Los polimorfismos de TNF y VDR no presentaron desequilibrio de transmisión. Las variantes TaqI, ApaI y BsmI del VDR presentaron desequilibrio de ligamiento. Conclusión. Estos hallazgos evidenciaron una asociación del polimorfismo rs2476601 de PTPN22 con la nefritis lúpica en niños, determinada por su transmisión en el grupo de familias estudiadas. ABSTRACT Introduction: Systemic lupus erythematosus is an autoimmune disease in which the severity varies according to race, sex and age of onset. This variation is also observed in the genetic markers associated with the disease, including PTPN22, VDR and TNF genes. The genetic stratification in different populations worldwide can influence the variability. Objective: To analyze the heritability of PTPN22, VDR and TNF genetic variants and their association with pediatric lupus nephritis in Colombian families. Materials and methods: We conducted a family-based study including 46 triads (case, father and mother). The variants rs2476601 of PTPN22; rs361525 and rs1800629 of TNF, and TaqI [rs731236], ApaI [rs7975232], BsmI [rs1544410] and FokI [rs2228570] of VDR were genotyped by qPCR. The effects of overtransmission of the risk allele from parents to children and linkage disequilibrium at the VDR and TNF loci were estimated. Results: We found that allele A of rs2476601 in PTPN22 was distributed among 8.69 % (n=16) of the parents and 19.5 % (n=18) of the cases; this allele was overtransmitted from parents to children 17 times more often than the G allele (p=0.028). TNF and VDR polymorphisms did not exhibit transmission disequilibrium. VDR TaqI, ApaI and BsmI variants exhibited linkage disequilibrium. Conclusion: These findings showed an association between the PTPN22 rs2476601 polymorphism and pediatric lupus nephritis due to its overtransmission in the group of families studied.

Introducción. El lupus eritematoso sistémico es una enfermedad autoinmune cuya gravedad varía según la raza, género y edad de aparición. Esta disparidad también se observa en los marcadores genéticos asociados con la enfermedad presentes en los genes PTPN22, VDR y TNF. La estratificación genética que presentan las diferentes poblaciones en el mundo puede estar influyendo dicha variabilidad. Objetivo. Analizar la asociación y heredabilidad de variantes genéticas de los genes PTPN22, VDR y TNF con nefritis lúpica pediátrica (NLp) en familias colombianas. Materiales y métodos. Se realizó un estudio basado en familias con 46 tríos (caso/padre y madre). Se genotipificaron las variantes rs2476601 de PTPN22; rs361525 y rs1800629 de TNF; TaqI [rs731236], ApaI [rs7975232], BsmI [rs1544410] y FokI [rs2228570] de VDR mediante qPCR. Se estimó el efecto de la sobretransmisión del alelo de riesgo de padres a hijos y el desequilibrio de ligamiento de los loci VDR y TNF. Resultados. Se observó que el alelo A de rs2476601 en PTPN22 se distribuyó en el 8,69 % [n=16] de los padres mientras que en los casos es de 19,5 % [n=18] al igual que es sobretransmitido de padres a hijos 17 veces más con relación al alelo G (p=0,028). Los polimorfismos de TNF y VDR no se mostraron en desequilibrio de transmisión. Las variantes TaqI, ApaI y BsmI del VDR se mostraron en desequilibrio de ligamiento. Conclusión. Estos hallazgos muestran una asociación del polimorfismo rs2476601 de PTPN22 con NLp debido a su sobretransmisión en el grupo de familias estudiadas. Introduction: Systemic lupus erythematosus is an autoimmune disease with severity that varies according to race, gender and age of onset. This variation is also observed in genetic markers associated with the disease, present in the PTPN22, VDR, and TNF genes. It is possible that the genetic stratification observed in different populations in the world can be influencing this variability. Objective: To analyze the association and heritability of PTPN22, VDR and TNF gene variants with pediatric lupus nephritis (PLN) in Colombian families. Materials and methods: a study based on 46 trios (Case / parents) was performed. Genotyping by qPCR of variants of rs2476601 in PTPN22; rs361525 and rs1800629 in TNF; TaqI [rs731236], ApaI [rs7975232] BsmI [rs1544410] and FokI [rs2228570] in VDR was performed. The effect of the risk of allele over-transmission through families and linkage disequilibrium of VDR and TNF loci was estimated. Results: We observed that the A allele of rs2476601 in PTPN22 was distributed in 8.69% [n = 16] parents, and increased to 19.5% [n = 18] in cases. Over-transmission of this allele was also observed from parents to offspring 17 times relative to the G allele (p = 0.028). TNF and VDR polymorphisms were not overtransmitted. SNPs TaqI, ApaI y BsmI in VDR showed linkage disequilibrium. Conclusion: These findings seem to demonstrate an association of rs2476601 in PTPN22 with PLN due to its overtransmission in the group of families studied.

Sunitinib is the currently standard treatment for metastatic renal cell carcinoma (mRCC). Multiple candidate predictive biomarkers for sunitinib response have been evaluated but none of them has been implemented in the clinic yet. The aim of this study was to analyze single nucleotide polymorphisms (SNPs) in genes linked to mode of action of sunitinib and immune response as biomarkers for mRCC. This is a multicenter, prospective and observational study involving 20 hospitals. Seventy-five mRCC patients treated with sunitinib as first line were used to assess the impact of 63 SNPs in 31 candidate genes on clinical outcome. rs2243250 (IL4) and rs5275 (PTGS2) were found to be significantly associated with shorter cancer-specific survival (CSS). Moreover, allele C (rs5275) was associated with higher PTGS2 expression level confirming its functional role. Combination of rs5275 and rs7651265 or rs2243250 for progression free survival (PFS) or CSS, respectively, was a more valuable predictive biomarker remaining significant after correction for multiple testing. It is the first time that association of rs5275 with survival in mRCC patients is described. Two-SNP models containing this functional variant may serve as more predictive biomarkers for sunitinib and could suppose a clinically relevant tool to improve the mRCC patient management., Supported by Pfizer.

Next-generation sequencing (NGS) has overcome important limitations to the molecular diagnosis of Inherited Retinal Dystrophies (IRD) such as the high clinical and genetic heterogeneity and the overlapping phenotypes. The purpose of this study was the identification of the genetic defect in 32 Spanish families with different forms of IRD. With that aim, we implemented a custom NGS panel comprising 64 IRD-associated genes in our population, and three disease-associated intronic regions. A total of 37 pathogenic mutations (14 novels) were found in 73% of IRD patients ranging from 50% for autosomal dominant cases, 75% for syndromic cases, 83% for autosomal recessive cases, and 100% for X-linked cases. Additionally, unexpected phenotype-genotype correlations were found in 6 probands, which led to the refinement of their clinical diagnoses. Furthermore, intra- and interfamilial phenotypic variability was observed in two cases. Moreover, two cases unsuccessfully analysed by exome sequencing were resolved by applying this panel. Our results demonstrate that this hypothesis-free approach based on frequently mutated, population-specific loci is highly cost-efficient for the routine diagnosis of this heterogeneous condition and allows the unbiased analysis of a miscellaneous cohort. The molecular information found here has aid clinical diagnosis and has improved genetic counselling and patient management., This work was supported by the Instituto de Salud Carlos III (ISCIII), Spanish Ministry of Economy and Competitiveness, Spain (PI11-02923), CIBERER ACCI, CDTI FEDER-Innterconecta (EXP00052887/ITC-20111037), Regional Ministry of Economy, Innovation, Science and Employment of the Autonomous Government of Andalusia (CTS-1664) and the Foundation Ramon Areces (CIVP16A1856). The CIBERER is an initiative of the ISCIII, Spanish Ministry of Economy and Competitiveness. NB-G is supported by fellowship FI12/00545 from ISCIII.

Se describen los distintivos de los diseños de investigación epidemiológica que son utilizados con mayor frecuencia en los estudios de asociación genética. Los estudios de casos y controles proporcionan un método eficiente para evaluar asociaciones entre genes candidatos y enfermedad. Los estudios de cohorte, por su parte, si bien aportan un mayor grado de causalidad, no son eficientes para la exploración inicial en la identificación de las asociaciones gen-enfermedad. Los estudios transversales son menos costosos, requieren períodos de tiempo más cortos y son de utilidad para estimar la prevalencia de enfermedades, de factores de riesgo o de variantes genéticas. Los estudios basados en familias han sido exitosos para encontrar alelos que confieren mayor riesgo para el desarrollo de enfermedades de transmisión mendeliana.This article describes the features of the epidemiologic research designs most commonly used in genetic association studies. Case-control studies are efficient in evaluating associations between candidate genes and disease. Cohort studies, in contrast, yield a greater degree of causality but are not efficient for the initial exploration to identify gene-disease associations. Cross-sectional studies are less expensive, require less time, and are useful for estimating the prevalence of diseases, risk factors, and genetic variants. Family-based studies have been successful in finding alleles that confer greater risk for developing Mendelian inheritance disorders.

López-Mejías, Raquel et al., [Introduction] A study was conducted to determine whether the human leukocyte antigen (HLA) B alleles are implicated in the susceptibility to Henoch-Schönlein purpura (HSP) in the largest series of Caucasian HSP patients ever assessed for genetic studies., [Methods] The study population was composed of 349 Spanish patients diagnosed with HSP fulfilling the American College of Rheumatology and the Michel et al. classification criteria, and 335 sex and ethnically matched controls. HLA-B phenotypes were determined by sequencing-based typing (SBT) and analyzed by chi-square or Fisher exact test., [Results] A statistically significant increase of HLA-B*41:02 allele in HSP patients when compared with controls was found (8.3% versus 1.5% respectively; P = 0.0001; OR (odds ratio) =5.76 [2.15-19.3]). These results remained statistically significant after adjusting for Bonferroni correction (P = 0.0028). An internal validation also confirmed the susceptibility effect on HSP associated with HLA-B*41:02 (OR = 5.70 [1.98-16.44]). Since a former study described an association between HLA-DRB1*01:03 and HSP susceptibility, we also evaluated the implication of HLA-B*41:02 independently of HLA-DRB1*01:03. Interestingly, the association remained statistically significant (P = 0.0004, OR = 4.97 [1.8-16.9]). No HLA-B association with specific HSP clinical features was found., [Conclusions] Our study indicates that HLA-B*41:02 is associated with the susceptibility to HSP in Spanish patients irrespective of HLA-DRB1 status., This study was supported by a grant from ‘Fondo de Investigaciones Sanitarias’ PI12/00193 (Spain). RLM is a recipient of a Sara Borrell postdoctoral fellowship from the Instituto de Salud Carlos III at the Spanish Ministry of Health (Spain) (CD12/00425). FG and BU are supported by funds from the RETICS Program (RIER) (RD12/0009/0013).

The FOXP3 gene encodes for a protein (Foxp3) involved in the development and functional activity of regulatory T cells (CD4+/CD25+/Foxp3+), which exert regulatory and suppressive roles over the immune system. After allogeneic stem cell transplantation, regulatory T cells are known to mitigate graft versus host disease while probably maintaining a graft versus leukemia effect. Short alleles (, This work was partially supported by the Ministry of Economy and Competitiveness ISCIII-FIS grants PI08/1463, PI11/00708, PI14-01731 and RD12/0036/0061, co-financed by ERDF (FEDER) Funds from the European Commission, as well as grants from the Fundacion LAIR and Asociacion Madrilena de Hematologia y Hemoterapia (AMHH). Sequencer 3130xl Genetic Analyzer was partially supported by ISCIII-FIS grants PI01-3624, PI08-36173. VN and CML were partially supported by a Post-Residency Research Fellowship from the Instituto de Investigacion Sanitaria Gregorio Maranon (IiSGM).

Neurofibromatosis type 1 (NF1) is one of the most frequent genetic disorders, affecting 1:3,000 worldwide. Identification of genotype-phenotype correlations is challenging because of the wide range clinical variability, the progressive nature of the disorder, and extreme diversity of the mutational spectrum. We report 136 individuals with a distinct phenotype carrying one of five different NF1 missense mutations affecting p.Arg1809. Patients presented with multiple cafe-au-lait macules (CALM) with or without freckling and Lisch nodules, but no externally visible plexiform neurofibromas or clear cutaneous neurofibromas were found. About 25% of the individuals had Noonan-like features. Pulmonic stenosis and short stature were significantly more prevalent compared with classic cohorts (P, We thank the patients, their family and their referral physicians for the information. We thank the genetics counselor students who helped to re-contact all referral physicians for confirming information. This work was supported though the Children's Tumor Foundation by the Isaac and Sadie Fuchs Genotype-Phenotype Study (to L.M.) and by internal funds from the Medical Genomics Laboratory at UAB.

Background Some association studies, as the implemented in VEGAS, ALIGATOR, i-GSEA4GWAS, GSA-SNP and other software tools, use genes as the unit of analysis. These genes include the coding sequence plus flanking sequences. Polymorphisms in the flanking sequences are of interest because they involve cis-regulatory elements or they inform on untyped genetic variants trough linkage disequilibrium. Gene extensions have customarily been defined as ± 50 Kb. This approach is not fully satisfactory because genetic relationships between neighbouring sequences are a function of genetic distances, which are only poorly replaced by physical distances. Results Standardized recombination rates (SRR) from the deCODE recombination map were used as units of genetic distances. We searched for a SRR producing flanking sequences near the ± 50 Kb offset that has been common in previous studies. A SRR ≥ 2 was selected because it led to gene extensions with median length = 45.3 Kb and the simplicity of an integer value. As expected, boundaries of the genes defined with the ± 50 Kb and with the SRR ≥2 rules were rarely concordant. The impact of these differences was illustrated with the interpretation of top association signals from two large studies including many hits and their detailed analysis based in different criteria. The definition based in genetic distance was more concordant with the results of these studies than the based in physical distance. In the analysis of 18 top disease associated loci form the first study, the SRR ≥2 genes led to a fully concordant interpretation in 17 loci; the ± 50 Kb genes only in 6. Interpretation of the 43 putative functional genes of the second study based in the SRR ≥2 definition only missed 4 of the genes, whereas the based in the ± 50 Kb definition missed 10 genes. Conclusions A gene definition based on genetic distance led to results more concordant with expert detailed analyses than the commonly used based in physical distance. The genome coordinates for each gene are provided to maintain a simple use of the new definitions. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-408) contains supplementary material, which is available to authorized users.

[Background] The Fas apoptotic pathway has been implicated in type 2 diabetes and cardiovascular disease. Although a polymorphism (rs7138803; G > A) near the Fas apoptotic inhibitory molecule 2 (FAIM2) locus has been related to obesity, its association with other cardiovascular risk factors and disease remains uncertain., [Methods] We analyzed the association between the FAIM2-rs7138803 polymorphism and obesity, blood pressure and heart rate in 7,161 participants (48.3% with type 2 diabetes) in the PREDIMED study at baseline. We also explored gene-diet interactions with adherence to the Mediterranean diet (MedDiet) and examined the effects of the polymorphism on cardiovascular disease incidence per diabetes status after a median 4.8-year dietary intervention (MedDiet versus control group) follow-up., [Results] We replicated the association between the FAIM2-rs7138803 polymorphism and greater obesity risk (OR: 1.08; 95% CI: 1.01-1.16; P = 0.011; per-A allele). Moreover, we detected novel associations of this polymorphism with higher diastolic blood pressure (DBP) and heart rate at baseline (B = 1.07; 95% CI: 0.97-1.28 bmp in AA vs G-carriers for the whole population), that remained statistically significant even after adjustment for body mass index (P = 0.012) and correction for multiple comparisons. This association was greater and statistically significant in type-2 diabetic subjects (B = 1.44: 95% CI: 0.23-2.56 bmp; P = 0.010 for AA versus G-carriers). Likewise, these findings were also observed longitudinally over 5-year follow-up. Nevertheless, we found no statistically significant gene-diet interactions with MedDiet for this trait. On analyzing myocardial infarction risk, we detected a nominally significant (P = 0.041) association in type-2 diabetic subjects (HR: 1.86; 95% CI:1.03-3.37 for AA versus G-carriers), although this association did not remain statistically significant following correction for multiple comparisons., [Conclusions] We confirmed the FAIM2-rs7138803 relationship with obesity and identified novel and consistent associations with heart rate in particular in type 2 diabetic subjects. Furthermore, our results suggest a possible association of this polymorphism with higher myocardial infarction risk in type-2 diabetic subjects, although this result needs to be replicated as it could represent a false positive. © 2014 Corella et al.; licensee BioMed Central Ltd., This study has been supported by The Spanish Ministry of Health (Instituto de Salud Carlos III) and the Ministry of Economy and Innovation, Spain and Fondo Europeo de Desarrollo Regional (projects PI051839, PI070240, PI1001407, G03/140, CIBER 06/03, RD06/0045 PI07-0954, CNIC-06, PI11/02505, SAF2009-12304 and AGL2010-22319-C03-03), by contracts 53-K06-5-10 and 58-1950-9-001 from the US Department of Agriculture Research, USA and by the Generalitat Valenciana, Spain (AP111/10, AP-042/11, BEST11-263, BEST/ 2011/261, GVACOMP2011-151, ACOMP/2011/145 and ACOMP/2012/190).

Context: Recently irisin (encoded by Fndc5 gene) has been reported to stimulate browning and uncoupling protein 1 expression in sc adipose tissue of mice. Objective: The objective of the study was to investigate FNDC5 gene expression in human muscle and adipose tissue and circulating irisin according to obesity, insulin sensitivity, and type 2 diabetes. Design, Patients, and Main Outcome Measure: Adipose tissue FNDC5 gene expression and circulating irisin (ELISA) were analyzed in 2 different cohorts (n = 125 and n = 76); muscle FNDC5 expression was also evaluated in a subcohort of 34 subjects. In vitro studies in human preadipocytes and adipocytes and in induced browning of 3T3-L1 cells (by means of retinoblastoma 1 silencing) were also performed. Results: In both sc and visceral adipose tissue, FNDC5 gene expression decreased significantly in association with obesity and was positively associated with brown adipose tissue markers, lipogenic, insulin pathway-related, mitochondrial, and alternative macrophage gene markers and negatively associated with LEP, TNFα, and FSP27 (a known repressor of brown genes). Circulating irisin and irisin levels in adipose tissue were significantly associated with FNDC5 gene expression in adipose tissue. In muscle, the FNDC5 gene was 200-fold more expressed than in adipose tissue, and its expression was associated with body mass index, PGC1α, and other mitochondrial genes. In obese participants, FNDC5 gene expression in muscle was significantly decreased in association with type 2 diabetes. Interestingly, muscle FNDC5 gene expression was significantly associated with FNDC5 and UCP1 gene expression in visceral adipose tissue. In men, circulating irisin levels were negatively associated with obesity and insulin resistance. Irisin was secreted from human adipocytes into the media, and the induction of browning in 3T3-L1 cells led to increased secreted irisin levels. Conclusions: Decreased circulating irisin concentration and FNDC5 gene expression in adipose tissue and muscle from obese and type 2 diabetic subjects suggests a loss of brown-like characteristics and a potential target for therapy.

Journal Article; OBJECTIVE Endogenous uveitis is a major cause of visual loss mediated by the immune system. The protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene encodes a lymphoid-specific phosphatase that plays a key role in T-cell receptor (TCR) signaling. Two independent functional missense single nucleotide polymorphisms (SNPs) located within the PTPN22 gene (R263Q and R620W) have been associated with different autoimmune disorders. We aimed to analyze for the first time the influence of these PTPN22 genetic variants on endogenous non-anterior uveitis susceptibility. METHODS We performed a case-control study of 217 patients with endogenous non-anterior uveitis and 718 healthy controls from a Spanish population. The PTPN22 polymorphisms (rs33996649 and rs2476601) were genotyped using TaqMan allelic discrimination assays. The allele, genotype, carriers, and allelic combination frequencies were compared between cases and controls with χ(2) analysis or Fisher's exact test. RESULTS Our results showed no influence of the studied SNPs in the global susceptibility analysis (rs33996649: allelic P- value=0.92, odds ratio=0.97, 95% confidence interval=0.54-1.75; rs2476601: allelic P- value=0.86, odds ratio=1.04, 95% confidence interval=0.68-1.59). Similarly, the allelic combination analysis did not provide additional information. CONCLUSIONS Our results suggest that the studied polymorphisms of the PTPN22 gene do not play an important role in the pathophysiology of endogenous non-anterior uveitis. Yes

Journal Article; Hypertension and congenital aortic valve malformations are frequent causes of ascending aortic aneurysms. The molecular mechanisms of aneurysm formation under these circumstances are not well understood. Reference genes for gene activity studies in aortic tissue that are not influenced by aortic valve morphology and its hemodynamic consequences, aortic dilatation, hypertension, or antihypertensive medication are not available so far. This study determines genes in ascending aortic tissue that are independent of these parameters. Tissue specimens from dilated and undilated ascending aortas were obtained from 60 patients (age ≤70 years) with different morphologies of the aortic valve (tricuspid undilated n = 24, dilated n = 11; bicuspid undilated n = 6, dilated n = 15; unicuspid dilated n = 4). Of the studied individuals, 36 had hypertension, and 31 received ACE inhibitors or AT1 receptor antagonists. The specimens were obtained intraoperatively from the wall of the ascending aorta. We analyzed the expression levels of 32 candidate reference genes by quantitative RT-PCR (RT-qPCR). Differential expression levels were assessed by parametric statistics. The expression analysis of these 32 genes by RT-qPCR showed that EIF2B1, ELF1, and PPIA remained constant in their expression levels in the different specimen groups, thus being insensitive to aortic valve morphology, aortic dilatation, hypertension, and medication with ACE inhibitors or AT1 receptor antagonists. Unlike many other commonly used reference genes, the genes EIF2B1, ELF1, and PPIA are neither confounded by aortic comorbidities nor by antihypertensive medication and therefore are most suitable for gene expression analysis of ascending aortic tissue. Yes

Introduction HLA-B27 has a modifier effect on the phenotype of multiple diseases, both associated and non-associated with it. Among these effects, an increased frequency of clinical enthesitis in patients with Rheumatoid Arthritis (RA) has been reported but never explored again. We aimed to replicate this study with a sensitive and quantitative assessment of enthesitis by using standardized ultrasonography (US). Methods The Madrid Sonography Enthesitis Index (MASEI) was applied to the US assessment of 41 HLA-B27 positive and 41 matched HLA-B27 negative patients with longstanding RA. Clinical characteristics including explorations aimed to evaluate spondyloarthrtitis and laboratory tests were also done. Results A significant degree of abnormalities in the entheses of the patients with RA were found, but the MASEI values, and each of its components including the Doppler signal, were similar in HLA-B27 positive and negative patients. An increase of the MASEI scores with age was identified. Differences in two clinical features were found: a lower prevalence of rheumatoid factor and a more common story of low back pain in the HLA-B27 positive patients than in the negative. The latter was accompanied by radiographic sacroiliitis in two HLA-B27 positive patients. No other differences were detected. Conclusion We have found that HLA-B27 positive patients with RA do not have more enthesitis as assessed with US than the patients lacking this HLA allele. However, HLA-B27 could be shaping the RA phenotype towards RF seronegativity and axial involvement. The study was supported by grants 10CSA918040PR from the Xunta de Galicia (http://www.sergas.e/MostrarContidos_N3_T01.aspx?IdPaxina=10142) and PI08/0744 of the Instituto de Salud Carlos III (http://www.isciii.es/) that are partially financed by the European Regional Development Fund of the European Union SI

Las enfermedades cardiovasculares (ECV) constituyen la principal causa de mortalidad en todo el mundo. Su etiología es multifactorial y compleja e incluye la interacción de factores de estilo de vida, ambientales y genéticos. Mediante estudios de asociación acerca de la influencia de polimorfismos de un sólo nucleótido (SNP) sobre fenotipos intermedios y finales de ECV, es posible identificar rutas metabólicas implicadas en ECV. De todos los factores de riesgo modificables de ECV, la dieta es de particular relevancia, tanto porque la gente come y bebe a diario como por su potencial para interactuar con factores de riesgo no modificables, tales como factores genéticos. En esta tesis se presentan cinco estudios: cuatro de ellos de asociación genética en dos cohortes diferentes y una revisión sistemática sobre herramientas informáticas disponibles para la medida de la dieta en grandes estudios epidemiológicos, que facilitan su estudio como factor de riesgo de diversas enfermedades, incluidas las ECV. El primer estudio se llevó a cabo en una muestra de población mediterránea española de alto riesgo cardiovascular (estudio PREDIMED-Valencia, n = 940). Mediante un diseño transversal, se investigó la relación con obesidad de la variante genética rs4988235 (C/T), localizada a 13910 pares de bases del gen que codifica la β-galactosidasa Lactasa (LCT). Así mismo de determinó su possible modulación por consumo de productos lácteos. Este polimorfismo, ha sido consistentemente relacionado con la persistencia del enzima lactasa y es además un candidato emergente de obesidad. A pesar de que el consumo de productos lácteos no varió sustancialmente de acuerdo a genotipo, los participantes homocigotos para el alelo C, presentaron menor índice de masa corporal (29.7±4.2 vs 30.6±4.2 kg/m2; P = 0.003) y perimétro de de cintura (101.1±11.8 vs 103.5±11.5 cm, P = 0.005) que los portadores del alelo T. La prevalencia de obesidad fue también significativamente mayor en los portadores del alelo T, sin embargo, sólo entre aquellos participantes cuyo consumo de lactosa fue moderado o alto (>8g/día). En el segundo estudio, desarrollado en la cohorte de Potsdam del Estudio Europeo Prospectivo sobre Cáncer y Nutrición (EPIC), se investigó la asociación de la variante genética rs2943634 (C/A) con incidencia de infarto de miocardio y accidente cerebrovascular isquémico. El polimorfismo rs2943634 se localiza en una región no codificante del cromosoma 2q36.3, sin embargo, había sido asociado con enfermedad arterial coronaria en dos GWAS previos. Se utilizó un diseño caso-cohorte, que incluyó una submuestra aleatoria de 2500 participantes y todos los casos de infarto de miocardio (n = 211) y accidente cerebrovascular isquémico (n = 144) ocurridos en EPIC-Potsdam durante un periodo de seguimiento medio de 8.2 años. Dado que el mecanismo por el que rs2943634 podría modular el riesgo de ECV es desconocido, también se investigó de forma transversal su posible asociación con 12 fenotipos intermedios disponibles de ECV. El alelo C fue asociado de manera aditiva con menor riesgo de accidente cerebrovascular isquémico (ratio de riesgo (HR) por alelo 0.66, intervalo de confianza IC al 95%: 0.50-0.87), pero no con infarto de miocardio [1.02 (82-1.28)]. Además los portadores de este alelo, también presentaron mayores niveles plasmáticos de adiponectina (CC 6.94, CA 7.27, AA 7.86 μg/ml, P = 0.0002) y de cholesterol-HDL (CC 52.08, CA 53.05, AA 55.27mg/dl, P = 0.002). Sin embargo, el ajuste por adiponectina y cholesterol-HDL de los análisis de asociacion del SNP con accidente cerebrovascular hisquémico, no atenuó la asociación. El enzima Estearoil-CoA Desaturasa-1 (SCD1) cataliza la conversión de los ácidos grasos saturados palmítico y esteárico a los monoinsaturados palmitoléico y oléico, respectivamente. Su actividad se ha asociado con rasgos del síndrome metabólico en ratones y seres humanos, pero también con la prevención de la acumulación de ácidos grasos saturados y posterior inflamación, mientras que para contenido de grasa del hígado los resultados hasta ahora publicados son inconsistentes. En el tercer estudio de esta tesis, en una muestra aleatoria (n = 2500) de la cohorte del studio EPIC-Potsdam, a través de 7 tagging-SNPs y 5 haplotipos inferidos, se investigó el efecto de la heterogeneidad genética común del gen que codifica la enzima SCD1 (SCD1), en la modulación de 8 factores de riesgo metabólico vinculados a la actividad de: SCD1: triglicéridos, índice de masa corporal, circunferencia de cintura, hemoglobina glicosilada, proteína-C-reactiva, gamma-glutamil transferasa, alanina aminotransferasa y fetuina-A. No se encontraron asociaciones estadísticamene significativas entre los genotipos y fenotipos estudiados. La proteína microsomal transferidora de triglicéridos (MTTP), participa en el ensamblaje y secreción de lipoproteínas con apolipoproteína-B. Esta proteína está codificada por el gen MTTP, que se regula mediante colesterol. Polimorfimos en la zona promotora de este gen, tales como el -164 T>C, han sido inconsistentemente asociados con ECV en distintos estudios. En el cuarto estudio de esta tesis, utilizando un diseño caso-cohorte, se investigó la asociación del polimorfismo -164T> C con riesgo de padecer un evento cardiovascular, en función de los niveles de colesterol (subcohorte, n = 1978; casos de infarto de miocardio, n = 193; casos de ictus isquémico, n = 131). Los resultados obtenidos fueron replicados en la cohorte del estudio Heinz Nixdorf Recall (30 casos, 1188 controles). Los participantes de EPIC-Potsdam con niveles de colesterol inferiores a 200 mg/dL, mostraron un incremento significativo del riesgo cardiovascular [HRaditivo 1.38 (1.07-1.78)], mientras que para participantes con niveles de colesterol ≥200 mg/dL se observó una disminución del riesgo [HRadditvo = 0.77 (0.58-1.03)]. En el estudio Heinz Nixdorf Recall, los respectivos HR para niveles de colesterol 8 g/day). The second study investigated whether the gene variant rs2943634 (C/A), located in a non-coding region of chromosome 2q36.3, and recently associated with coronary artery disease in two GWA studies, was associated with myocardial infarction and ischemic stroke in the Potsdam arm of the European Prospective Investigation into Cancer and Nutrition (EPIC). A case-cohort design was used, with a subsample of 2500 persons randomly drawn from the total population of 27,548 middle-aged men and women, along with all incident cases of myocardial infarction (n = 211) and ischemic stroke (n = 144), occurring during a mean follow-up of 8.2 years. Because the mode of mechanism by which this SNP may increase CVD risk is unknown, associations of this SNP with 12 available intermediate risk phenotypes of CVD were also investigated. The minor allele of rs2943634 was associated in an additive fashion with lower risk of ischemic stroke after adjustment for age and sex (per-allele hazard ratio 0.66, 95% CI 0.50-0.87) but not with myocardial infarction (per-allele hazard ratio 1.02, 95% CI 0.82-1.28). Furthermore, the minor allele was related to slightly higher levels of plasma adiponectin (CC 6.94, CA 7.27, AA 7.86μg/ml, P=0.0002) and HDL-cholesterol (CC 52.08, CA 53.05 and AA 55.27mg/dl, P=0.002) in an additive fashion. Adjustment for adiponectin and HDL-cholesterol did, however, not attenuate the association between the SNP and ischemic stroke risk. In contrast, adjustment for adiponectin abolished the association between the SNP and HDL-cholesterol and adjustment for HDL-cholesterol attenuated the association between the SNP and adiponectin. In the third study, the impact of common genetic variation in the Stearoyl-CoA desaturase-1 (SCD1) gene, captured by means of 7 tagging SNPs and 5 inferred haplotypes, on the modulation of 8 metabolic risk factors linked to the activity of SCD1 (triglycerides, body mass index, waist circumference, glycated haemoglobin, high-sensitivity C-reactive protein, gamma-glutamyltransferase, alanine aminotransferase and fetuin-A) was investigated. SCD1 is the rate limiting enzyme catalyzing the conversion of the endogenous and dietary saturated fatty acids palmitic and stearic into the monounsaturated palmitoleic and oleic, respectively. Its activity has been associated with traits of the metabolic syndrome in mice and humans, but also with the prevention of saturated fatty acids accumulation and subsequent inflammation, whereas for liver fat content inconsistent results have been reported. In the EPIC-Potsdam Study (n = 2157), however, no associations between common variants of SCD1 or its inferred haplotypes and the investigated metabolic risk factors were observed. The fourth study was conducted in EPIC-Potsdam following a case-cohort design (193 incident myocardial infarction, 131 incident ischemic stroke cases and 1978 non-cases). Further, the Heinz Nixdorf Recall Study (30 CVD cases and 1,188 controls) was used to replicate findings. The microsomal triglyceride transfer protein (MTTP), encoded by the MTTP gene, plays an important role in the assembly and secretion of apolipoprotein-B containing lipoproteins as chylomicrons in the intestine, and of very low density lipoproteins in the liver. MTTP is regulated by cholesterol. In this study the investigated hypothesis was that, the -164T>C polymorphism, located in the promoter region of MTTP, could modify the risk of CVD, depending on cholesterol levels. This SNP had inconsistently been associated with CVD in previous studies. In the EPIC-Potsdam study, individuals with cholesterol levels

Systemic lupus erythematosus (SLE) is a chronic and systemic autoimmune disease that primarily affects women during the childbearing years. SLE is characterized by the production of autoantibodies against nucleic acids and their interacting proteins. The exact molecular mechanisms leading to the breakdown of self-tolerance remain to a large extent unknown, but it is well established that they are influenced by both non-genetic (i.e. environmental and hormonal) and genetic factors. SLE is a complex, polygenic disease. Several susceptibility variants have been identified in SLE. However, the functional role in disease pathogenesis for the majority of them remains largely unknown. This thesis includes case-control association studies where the role of the genes TNFSF4 (Paper I), STAT4 (Paper II), CD226 (Paper III), and BLK (Papers IV and V) in the susceptibility of developing SLE was investigated. The primary focus was on the identification of the functional variants underlying the association. For each of these genes, fine mapping was performed using single nucleotide polymorphisms (SNPs), the linkage disequilibrium (LD) was characterized, and the association was narrowed down to specific haplotypes by means of several different statistical genetic strategies. Candidate variants were prioritized for further functional analysis on the basis of their potential effect on the gene function, their association, and/or biological plausibility. In Paper I, the association of TNFSF4 with SLE was validated and attributed to a risk haplotype tagged by SNPs rs1234317-T and rs12039904-T. Paper II provides evidence supporting the presence of at least two independent genetic effects within the STAT4 gene represented by rs3821236-A and rs7574865-A, which correlated with increased levels of gene expression. In Paper III, a functional allele in CD226 (rs727088-C) was identified, which was responsible for decreased levels in both mRNA and protein expression. In Paper IV, two independent genetic effects in the BLK gene were demonstrated. The first one comprised multiple regulatory variants in high LD that were enriched for NFκB and IRF4 binding sites and correlated with low BLK mRNA levels. The second was a low-frequency missense substitution (Ala71Thr) that decreased the BLK protein half-life. In Paper V, a genetic epistatic interaction between BANK1 rs10516487 (GG) and BLK rs2736340 (TT+TC) was demonstrated. Additional molecular analyses established that these molecules interact physically. These studies have contributed to the dissection of the genetic architecture of SLE. They highlight the allelic heterogeneity of the disease and provide functional links to the associated variants, which has significantly aided in the understanding of SLE disease pathogenesis.

Introduction CD226 genetic variants have been associated with a number of autoimmune diseases and recently with systemic sclerosis (SSc). The aim of this study was to test the influence of CD226 loci in SSc susceptibility, clinical phenotypes and autoantibody status in a large multicenter European population. Methods A total of seven European populations of Caucasian ancestry were included, comprising 2,131 patients with SSc and 3,966 healthy controls. Three CD226 single nucleotide polymorphisms (SNPs), rs763361, rs3479968 and rs727088, were genotyped using Taqman 5'allelic discrimination assays. Results Pooled analyses showed no evidence of association of the three SNPs, neither with the global disease nor with the analyzed subphenotypes. However, haplotype block analysis revealed a significant association for the TCG haplotype (SNP order: rs763361, rs34794968, rs727088) with lung fibrosis positive patients (P Bonf = 3.18E-02 OR 1.27 (1.05 to 1.54)). Conclusion Our data suggest that the tested genetic variants do not individually influence SSc susceptibility but a CD226 three-variant haplotype is related with genetic predisposition to SSc-related pulmonary fibrosis., This work was supported by the following grants: JM was funded by GEN-FER from the Spanish Society of Rheumatology, SAF2009-11110 from the Spanish Ministry of Science, CTS-4977 from Junta de Andalucía, Spain, in part by Redes Temáticas de Investigación Cooperativa Sanitaria Program, RD08/0075 (RIER) from Instituto de Salud Carlos III (ISCIII), Spain and by Fondo Europeo de Desarrollo Regional (FEDER).

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. © 2012 Alcina et al.

Tesis leida dentro del Master de "Ingeniería Computacional y Sistemas Inteligentes"

En general, en los estudios de asociación sólo se obtiene un número reducido de SNPs con p significativas (p

Traditionally, QTL mapping has been used as methodology to understand the genetic control of polygenic traits and has been useful for identifying QTL in different species, however QTL mapping presents limitations, such as the difficulty to build segregating populations in some species, the presence of only one meiotic generation and the reduced genetically diversity derived of just two parental. Recently, association genetics studies are becoming an important methodology to identify quantitative trait loci and to find diagnostic molecular markers associated with complex traits. This methodology overcomes some barriers of QTL mapping and it is an alternative to apply in plant breeding in direct way. However, it is necessary to considerer important aspects in this methodology to avoid false associations between trait-markers. Association genetics employs as parameter linkage disequilibrium to find these associations. Here we present methods to analyze and establish population structure, factors that affect linkage disequilibrium and how to measure it and methods to perform association mapping

BACKGROUND: Colorectal cancer (CRC) is the second cause of cancer-related death in the Western world. Much of the CRC genetic risk remains unidentified and may be attributable to a large number of common, low-penetrance genetic variants. Genetic linkage studies in CRC families have reported additional association with regions 9q22-31, 3q21-24, 7q31, 11q, 14q and 22q. There are several plausible candidate genes for CRC susceptibility within the aforementioned linkage regions including PTCH1, XPA and TGFBR1 in 9q22-31, and EPHB1 and MRAS in 3q21-q24. METHODS: CRC cases and matched controls were from EPICOLON, a prospective, multicentre, nationwide Spanish initiative, composed of two independent phases. Phase 1 corresponded to 515 CRC cases and 515 controls, whereas phase 2 consisted of 901 CRC cases and 909 controls. Genotyping was performed for 172 single-nucleotide polymorphisms (SNPs) in 84 genes located within regions 9q22-31 and 3q21-q24. RESULTS: None of the 172 SNPs analysed in our study could be formally associated with CRC risk. However, rs1444601 (TOPBP1) and rs13088006 (CDV3) in region 3q22 showed interesting results and may have an effect on CRC risk. CONCLUSIONS: TOPBP1 and CDV3 genetic variants on region 3q22 may modulate CRC risk. Further validation and meta-analysis should be undertaken in larger CRC cohorts. British Journal of Cancer (2011) 105, 870-875. doi: 10.1038/bjc.2011.296 www.bjcancer.com Published online 2 August 2011, We are sincerely grateful to all patients participating in this study who were recruited in 25 (EPICOLON 1) and 14 (EPICOLON 2) Spanish hospitals as part of the EPICOLON project. We are also grateful to the Spanish National Genotyping Center (CEGEN-ISCIII)-USC and UPF nodes, and the Genome Analysis Platform of the CIC-BioGUNE. The work was carried out (in part) at the Esther Koplowitz Centre, Barcelona. SC-B, CF-R and MDG are supported by contracts from the Fondo de Investigacion Sanitaria (CP 03-0070 to SC-B, CM10/00084 to MDG, and PS09/02368 to CF-R). JM is supported by a contract from the CIBERehd. Both CIBERehd and CIBERER are funded by the Instituto de Salud Carlos III. This work was supported by grants from the Fondo de Investigacion Sanitaria/FEDER (06/1384, 08/0024, 08/1276, PS09/02368, 10/00918), Instituto de Salud Carlos III (Accion Transversal de Cancer), Xunta de Galicia (07PXIB9101209PR), Ministerio de Ciencia e Innovacion (SAF2010-19273), Asociacion Espanola contra el Cancer (Fundacion Cientifica y Junta de Barcelona), Fundacio Olga Torres (SCB and CRP) and FP7 CHIBCHA Consortium (LC-C, ACar and SC-B).