| Services & Data |
|GCAT | Panel|
The GCAT project aims to fill the existent gap in the development of haplotype panels by generating a dense haplotype map focused on the identification, characterization, and phasing of structural variants (SVs), the GCAT|Panel. In addition, we developed a comprehensive and detailed guide for the systematic inclusion of SVs in this type of study. |
In this way, this resource will help improve the Genome-Wide Association Studies (GWAS) resolution, giving a step towards the inclusion of SVs into GWAS to start understanding the role of these variants in complex diseases. ( Jordi Valls-Margarit, Iván Galván-Femenía 2 , Daniel Matías-Sánchez, et. al. Nucleic Acids Res. 2022 ).
|The TIGER resource (Translational human pancreatic Islet Genotype tissue-Expression Resource), developed within the T2DSystems consortium, enables an integrative exploration of the genetic and epigenetic basis of the development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in the biology and the role of pancreatic beta cells. To that aim, the TIGER Data Portal offers browsing and interrogation possibilities through different pancreatic beta cell spaces, helping identifying the molecular mechanisms behind cell dysfunction and T2D. As a result, this resource provides academia and industry with a powerful new tool for investigating the molecular basis of pancreatic beta cell failure and T2D, identifying potential new therapeutic targets, and providing information on possible responses to therapeutic agents. ( Lorena Alonso, Anthony Piron, Ignasi Morán, et. al. Cell Reports 2021 ).|
|GUIDANCE is an integrated framework that is able to perform haplotype phasing, genotype imputation, association testing assuming different models of inheritance and phenome-wide association analysis (PheWAS) analysis of large GWAS datasets. Moreover, this application allows performing all these steps in a single execution, as well as in a modular way with optional user intervention. (M. Guindo-Martínez, R. Amela et al, Nat Commun. 2021).|
|SMuFin (Somatic MUtation FINder) is a reference-free method designed to identify somatic variation on tumor genomes from the direct comparison with the corresponding normal genome of the same patient. Through a single execution SMuFin is able to identifying somatic single nucleotide variants (SNVs) and structural variants (SVs) of any size. (Moncunill V. & Gonzalez S., et al, Nature Biotechnology 2014).|
|ReLA (REgulatory region Local Alignment tool) is a method optimized with the Smith-Waterman algorithm that identifies gene regulatory regions in genomic DNA sequences through local searches of clusters of coincident transcription factor binding sites between two or more DNA sequences. ReLA can identify these regulatory regions through the comparison of homologous (orthologs and paralogs) or co-expressed sequences. Our server also allows the identification of more than one regulatory region (alternative promoters) within the reference sequence (Gonzalez S., et al, Bioinformatics 2012).|