02478nas a2200325   4500008004100000022001400041245015000055210006900205260000900274300000700283490000600290520144200296653001401738653000901752653001901761100002301780700001701803700001901820700002401839700002601863700002001889700002801909700002601937700002601963700002001989700002502009700002002034700001902054856007902073       2015                        eng d  a1755-879400aIdentification of epistatic interactions through genome-wide association studies in sporadic medullary and juvenile papillary thyroid carcinomas.0 aIdentification of epistatic interactions through genomewide asso  c2015  a830 v83 aBACKGROUND: The molecular mechanisms leading to sporadic medullary thyroid carcinoma (sMTC) and juvenile papillary thyroid carcinoma (PTC), two rare tumours of the thyroid gland, remain poorly understood. Genetic studies on thyroid carcinomas have been conducted, although just a few loci have been systematically associated. Given the difficulties to obtain single-loci associations, this work expands its scope to the study of epistatic interactions that could help to understand the genetic architecture of complex diseases and explain new heritable components of genetic risk. METHODS: We carried out the first screening for epistasis by Multifactor-Dimensionality Reduction (MDR) in genome-wide association study (GWAS) on sMTC and juvenile PTC, to identify the potential simultaneous involvement of pairs of variants in the disease. RESULTS: We have identified two significant epistatic gene interactions in sMTC (CHFR-AC016582.2 and C8orf37-RNU1-55P) and three in juvenile PTC (RP11-648k4.2-DIO1, RP11-648k4.2-DMGDH and RP11-648k4.2-LOXL1). Interestingly, each interacting gene pair included a non-coding RNA, providing thus support to the relevance that these elements are increasingly gaining to explain carcinoma development and progression. CONCLUSIONS: Overall, this study contributes to the understanding of the genetic basis of thyroid carcinoma susceptibility in two different case scenarios such as sMTC and juvenile PTC.10aepistasis10aGWAS10aThyroid cancer1 aLuzón-Toro, Berta1 aBleda, Marta1 aNavarro, Elena1 aGarcía-Alonso, Luz1 aRuiz-Ferrer, Macarena1 aMedina, Ignacio1 aMartín-Sánchez, Marta1 aGonzalez, Cristina, Y1 aFernández, Raquel, M1 aTorroglosa, Ana1 aAntiňolo, Guillermo1 aDopazo, Joaquin1 aBorrego, Salud  uhttp://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-015-0160-702712nas a2200325   4500008004100000022001400041245015600055210006900211260001300280300001000293490000700303520157800310653002801888653002201916653004201938653001301980653003401993653001302027653003602040653001302076653002802089100002002117700002402137700001702161700002402178700002002202700002602222700002002248856011802268       2012                        eng d  a1362-496200aVARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.0 aVARIANT Command Line Web service and Web interface for fast and   c2012 Jul  aW54-80 v403 a<p>The massive use of Next-Generation Sequencing (NGS) technologies is uncovering an unexpected amount of variability. The functional characterization of such variability, particularly in the most common form of variation found, the Single Nucleotide Variants (SNVs), has become a priority that needs to be addressed in a systematic way. VARIANT (VARIant ANalyis Tool) reports information on the variants found that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes, and disease-related variants from the Genome-Wide Association Study (GWAS) catalog, Online Mendelian Inheritance in Man (OMIM), Catalog of Somatic Mutations in Cancer (COSMIC) mutations, etc). VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNA-binding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied. Contrarily to other tools, VARIANT uses a remote database and operates through efficient RESTful Web Services that optimize search and transaction operations. In this way, local problems of installation, update or disk size limitations are overcome without the need of sacrifice speed (thousands of variants are processed per minute). VARIANT is available at: http://variant.bioinfo.cipf.es.</p>10aDatabases, Nucleic Acid10aGenetic Variation10aHigh-Throughput Nucleotide Sequencing10aInternet10aMolecular Sequence Annotation10amutation10aPolymorphism, Single Nucleotide10aSoftware10aUser-Computer Interface1 aMedina, Ignacio1 aDe Maria, Alejandro1 aBleda, Marta1 aSalavert, Francisco1 aAlonso, Roberto1 aGonzalez, Cristina, Y1 aDopazo, Joaquin  uhttp://clinbioinfosspa.es/content/variant-command-line-web-service-and-web-interface-fast-and-accurate-functional