NOD1 rs2075820 (p.E266K) polymorphism is associated with gastric cancer among individuals infected with cagPAI-positive H. pylori

BACKGROUND: Helicobacter pylori is detected by pathogen recognition receptors including toll-like receptors (TLR) and nucleotide-binding oligomerization domain (NOD)-like receptors, eliciting an innate immune response against this bacteria. The aim of this study was to assess if polymorphisms of TLR2, TLR4, TLR5, NOD1 and NOD2 genes are associated with gastric cancer, in particular in individuals infected with H. pylori. RESULTS: A case-control study of 297 gastric cancer patients and 300 controls was performed to assess the association of 17 polymorphisms. Analyses performed under the allele model did not find association with gastric cancer. However, NOD1 rs2075820 (p.E266K) showed association with intestinal-type gastric cancer among H. pylori infected subjects (OR = 2.69, 95% CI 1.41-5.13, p = 0.0026). The association was not statistically significant in diffuse-type gastric cancer cases (OR = 1.26, 95% CI 0.63-2.52, p = 0.51). When the analyses were performed in patients carrying H. pylori strains harboring the cag pathogenicity island (cagPAI), we noticed significant association with NOD1 rs2075820 (OR = 4.90, 95% CI 1.80-3.36, p = 0.0019), in particular for intestinal-type gastric cancer cases (OR = 7.16, 95% CI 2.40-21.33, p = 4.1 × 10- 4) but not among diffuse-type gastric cancer cases (OR = 3.39, 95% CI 1.13-0.10, p = 0.03). CONCLUSIONS: NOD1 rs2075820 increases the risk of intestinal-type gastric cancer among individuals infected with H. pylori, particularly in those harboring the cagPAI.

Development of a small panel of SNPs to infer ancestry in Chileans that distinguishes Aymara and Mapuche components

BACKGROUND: Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. RESULTS: A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country's average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. CONCLUSIONS: We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.

Estudio de asociación de base familiar entre polimorfismos de MTHFR y mielomeningocele en Chile / Methylenetetrahydrofolate reductase polymorphisms as risk factors for myelomeningocele

Background: Mandatory fortification with folic acid (FA) was implemented in Chile in 2000. Thereafter, the rate of spina bifida decreased by 52 to 55%. Genetic abnormalities in folate metabolism may be involved in the etiology of spina bifida. Aim: To evaluate the association between myelomeningocele (MM) and c.A1298C and c.C677T polymorphisms within the coding gene for 5,10-methylenetetrahydrofolate reductase (MTHFR) in the Chilean population. Material and Methods: These polymorphisms were genotyped in 105 patients showing isolated MM, born after the onset of FA fortification, and in their parents. The transmission disequilibrium test (TDT) was performed to evaluate alterations in the transmission of both alleles and haplotypes MTHFR polymorphism. We also evaluated the presence of parent-origin-effect (POE) of alleles using the Clayton’s extension of the TDT. Results: TDT analysis showed no significant distortions in the transmission of alleles or haplotypes. Moreover, although the POE showed increased risk for maternally derived allele, this risk was not statistically significant. Conclusions: The studied variants in the MTHFR gene (c.C677T and c.A1298C) do not constitute risk factors for MM in this sample of Chilean patients and their parents.

Polimorfismos genéticos de interleuquina 6 (IL6), IL6R e IL18: asociación con componentes del síndrome metabólico en niños chilenos con obesidad / Association between genetic polymorphisms of interleukin 6 (IL6), IL6R and IL18 with metabolic syndrome in obese Chilean children

Background: Metabolic Syndrome (MS) is highly prevalent among obese children and adolescents and is considered a predictor for the development of type 2 diabetes mellitus and cardiovascular disease. Obesity is associated with an increase in circulating levels of interleukins 6 (IL6) and 18 (IL18), which in turn would depend on polymorphisms of IL6, IL6R and IL18 genes. Aim: To evaluate the association between genetic polymorphisms of IL6 (rs1800795, rs1800796 and rs1800797), IL6R (rs2228145) and IL18 (rs360719, rs187238 and rs204355) and MS and/or its components in a sample of Chilean obese children. Patients and Methods: These polymorphisms were genotyped in 259 obese children aged 10 ± 2 years with a body mass index of 26.1 ± 4.1 kg/m². Sixty eight had metabolic syndrome (26.3%). The association of their alleles, genotypes and haplotypes with the MS and its components was assessed. Results: IL6, IL6R and IL18 variants showed no association with SM nor with any of the phenotypes that compose it. However, IL18 haplotypes (rs360719-rs187238-rs204355) TCT and CGT were associated with triglycerides ≤ 110 mg/dL and HDL < 40 mg/dL, respectively. Conclusions: IL6 and IL6R variants are not associated with MS or with any of its phenotypes. Although an association between IL18 haplotypes and certain MS component has been detected herein, it is necessary to replicate our findings in independent studies due to the low frequency of these allele combinations detected in our sample.

Riesgo de diabetes mellitus tipo 2 asociado al uso de estatinas: evidencias y posibles mecanismos / Risk of type 2 diabetes mellitus associated with statin therapy: evidence and possible mechanisms

In the last decade, an increased number of new cases of type 2 diabetes mellitus (T2DM) among patients who use statins have been reported. The aim of the present review is to compile the most relevant information about the risk of T2DM associated with the use and dose of different statins, especially based on meta-analysis considering different studies worldwide. To explain this relationship, several studies have reported the effect of statins on insulin resistance in dyslipidemic non-diabetic patients, reporting different findings according to the types of statins. In addition, some reports -based on culture of β pancreatic cells- have evaluated the effect of these drugs in certain cellular events that are essential for insulin secretion. Clearly, further studies in humans are needed -applying more robust tests than those used up to date- in order to define more precisely the potential mechanisms explaining the higher incidence of T2DM among statin users.

Análisis molecular de Sonic hedgehog (Shh) en la etiología de la fisura labiopalatina no sindrómica en tríos caso-progenitores chilenos / Molecular analysis of Sonic hedgehog (Shh) in the etiology of nonsyndromic cleft lip and palate in Chilean case-parent trios

introducción: la fisura labio palatina no sindrómica, NSCLP (del inglés Nonsyndromic cleft lip and palate) es una de las malformaciones congénitas más frecuentes tanto en Chile como en el resto del mundo. Presenta un modo de herencia multifactorial, en la que interactúan varios genes y el medio ambiente. Evidencias experimentales han demostrado la participación de Sonic hedgedhog (Shh) en la migración de las células de la cresta neural, en la transformación epitelio-mesénquima y en la formación de las estructurasmedias craneofaciales durante el desarrollo embrionario, es probable una asociación entre variantes de Shh y la NSCLP. Métodos: el objetivo de este trabajo fue evaluar las regiones exónicas e intrónicas adyacentes de Shh, en una muestra de 150 tríos caso-progenitores para hallar la asociación con NSCLP. Se utilizó el método PCR-RFLP para determinar la presencia de heterodúplex. Luego, se utilizó la técnica de Conformation Sensitive Gel Electrophoresis (CSGE) para ver la distorsión del ADN en los heterodúplex. Como método alternativo, se hizo un análisis de polimorfismos de un solo nucleótido (del inglés single-nucleotide polymorphism SNP) para determinar asociación entre NSCLP y Shh, para lo cual se utilizaron los SNP: rs1233555 y rs1233556, ubicados en el primer intrón de Shh. Resultados:no se observaron heterodúplex en ninguno de los segmentos de Shh analizados en 150 tríos, el análisis de SNP tampoco mostró asociación con Shh y FLPNS. conclusión: la no asociación puede deberse a que la frecuencia de distribución de los SNP en la población chilena es diferente a la de las poblaciones referidas, o a que el número de SNP analizados fue insuficiente, o la no inclusión para el análisis de otras regiones de Shh.

introduction: nonsyndromic cleft lip and palate (NSCLP) is one of the most common congenital malformations not only in Chile but also worldwide. It has a multifactorial inheritance pattern with interaction of several genes and the environment. Several experimental studies have proven the participation of Sonic hedgedhog (Shh) in the migration process of cells from the neural crest,in the epithelium-mesenchyme transformation, and in the formation of middle craniofacial structures during embryo development; an association between Shh variants and NSCLP is probable. Methods: the goal of this study was to evaluate both exonic and intronic regions adjacent to Shh, in a sample of 150 case-parent trios in order to find possible associations with NSCLP. The PCR-RFLP method was used to determine the presence of heteroduplex. Afterwards, the Conformation Sensitive Gel Electrophoresis (CSGE) technique wasused to visualize DNA distortion at the heteroduplexes. As an alternative method, a single-nucleotide polymorphism (SNP) analysis wasperformed in order to determine NSCLP-Shh associations, by means of these SNPs: rs1233555 and rs1233556, located at the first Shhintron. Results: no heteroduplexes were found in any of the analyzed Shh segments in 150 trios; SNP analysis did not show associations between Shh and NSCLP either. conclusions: this lack of association may be due to the fact that SNP distribution frequency among Chilean population is different to that of reference populations, or because the number of SNPs analyzed was not sufficient, or even because this study did not include other Shh regions.

Assessment of the association between SMAD1 and HHIP gene variation and non-syndromic cleft-lip palate in Chilean case-parent trios

Nonsyndromic cleft lip/palate (NSCLP) is a congenital malformation with features of a complex genetic trait. Several studies have reported positive association and linkage between NSCLP and microsatellite markers in the 4q28-4q33 region particularly with the D4S192 (4q31) marker. We hypothesized that the candidate genes SMAD1 and HHIP (4q31) could be involved in the etiology of NSCLP based on previous positive linkage results and their important role in maxillofacial development. We evaluated the possible association between microsatellite markers located at less than 1 cM from these genes and NSCLP using a sample of 58 Chilean case-parent trios. Microsatellite markers were analyzed using the polymerase chain reaction (PCR) with fluorescent labeled primers. Electrophoresis of the PCR products was performed on a laser-fluorescent automatic DNA sequencer. The extended transmission disequilibrium test (ETDT) was used to analyze allelic transmissions from the parents to their affected progeny. No significant association due to linkage disequilibrium was detected between both markers and NSCLP.