EL ESTUDIO GENÓMICO DEL CACAO (Theobroma cacao L.); BREVE RECOPILACIÓN DE SUS BASES CONCEPTUALES

The cacao plant (Theobroma cacao L.) has been cultivated since more than 2,000 years ago by different Mesoamerican cultures. This species represents a significant biocultural resource for the world, due mostly to its importance in the production and commercialization of chocolate. Nowadays, the use and application of genomic tools make relatively possible the characterization of “genotypes” as well as the elucidation of genetic differences between hundreds of individuals at the population level. Current methods of molecular diagnosis, such as microarrangements, massive sequencing of new generation, assemblage and annotation of genomes and genetic expression, help generate data, as well as programming languages and mathematical algorithms that are used in biotechnological processes, whose objective is to improve the understanding and exploitation of the biology of this type of specimens.La planta de cacao (Theobroma cacao L.) ha sido cultivada desde hace más de 2,000 años por distintas culturas Mesoamericanas. Esta especie representa un recurso biocultural significativo para el mundo, debido principalmente a su importancia en la producción y comercialización del chocolate. Hoy en día, el uso y aplicación de herramientas genómicas facilitan relativamente la caracterización de “genotipos” al igual que la dilucidación de diferencias genéticas entre cientos de individuos a nivel poblacional. Métodos actuales de diagnóstico molecular, como microarreglos, secuenciaciones masivas de nueva generación, ensamblado y anotación de genomas y expresión génica, ayudan a la generación de datos, así como lenguajes de programación y algoritmos matemáticos que son utilizados en procesos biotecnológicos, cuya finalidad es mejorar el entendimiento y explotación de la biología de este tipo de especímenes

A Large-Scale Genetic Analysis Reveals a Strong Contribution of the HLA Class II Region to Giant Cell Arteritis Susceptibility

We conducted a large-scale genetic analysis on giant cell arteritis (GCA), a polygenic immune-mediated vasculitis. A case-control cohort, comprising 1,651 case subjects with GCA and 15,306 unrelated control subjects from six different countries of European ancestry, was genotyped by the Immunochip array. We also imputed HLA data with a previously validated imputation method to perform a more comprehensive analysis of this genomic region. The strongest association signals were observed in the HLA region, with rs477515 representing the highest peak (p = 4.05 × 10−40, OR = 1.73). A multivariate model including class II amino acids of HLA-DRβ1 and HLA-DQα1 and one class I amino acid of HLA-B explained most of the HLA association with GCA, consistent with previously reported associations of classical HLA alleles like HLA-DRB1∗04. An omnibus test on polymorphic amino acid positions highlighted DRβ1 13 (p = 4.08 × 10−43) and HLA-DQα1 47 (p = 4.02 × 10−46), 56, and 76 (both p = 1.84 × 10−45) as relevant positions for disease susceptibility. Outside the HLA region, the most significant loci included PTPN22 (rs2476601, p = 1.73 × 10−6, OR = 1.38), LRRC32 (rs10160518, p = 4.39 × 10−6, OR = 1.20), and REL (rs115674477, p = 1.10 × 10−5, OR = 1.63). Our study provides evidence of a strong contribution of HLA class I and II molecules to susceptibility to GCA. In the non-HLA region, we confirmed a key role for the functional PTPN22 rs2476601 variant and proposed other putative risk loci for GCA involved in Th1, Th17, and Treg cell function