Ferran Casals

Web Site

Research Outline

One of the missions of the Genomics Core Facility is the development of new technologies and methodologies for genomic analyses. The Genomics Core Facility at the UPF performs collaborative research projects with labs at the Experimental and Health Sciences Department of the UPF, to develop and implement novel methodological approaches.

Services

The Genomics Core Facility at the UPF provides a wide variety of methods for DNA and RNA analyses. Available equipments include liquid handling robots to automate pipeting tasks, capillary sequencers for Sanger sequencing and fragment analysis, DNA quantification and quality control with Picogreen and Bioanalyzer, real-time PCR and OpenArray system for absolute and relative quantification of nucleic acids (genotyping and gene expression), and four next-generation sequencing platforms: MiSeq (Illumina), ideal for targeted and small genome sequencing; MiSeqFGx (Illumina), for population and forensic genetics analyses; NextSeq (Illumina), a highly flexible platform performing a broad range of applications, from targeted resequencing to RNA profiling and whole-exome or genome sequencing.; and MinION (Oxford Nanopore), a new single-molecule technology ideal for de novo sequencing and the study of structural variation .

The laboratory also offers the service of library preparation for most of the next-generation sequencing applications. The Genomics Core Facility organizes courses and workshops on the new sequencing methodologies and pioneers some of their applications to medical and population genomics research.

Team during 2017-18

• PhD students: Laura Batlle-Masó, Manuel Solís-Moruno.
• Technicians: Roger Anglada, Núria Bonet, Raquel Rasal, Marc Tormo.
   

Selected publications 2017-18

• De Valles-Ibañez G, Esteve-Solé A, Piquer M, González-Navarro A, Hernández-Rodríguez J, Laayouni H, González-Roca E, Plaza-Martin AM, Deyà-Martínez A, Martín-Nalda A, Martínez-Gallo M, García-Prat M, del Pino L, Cuscó I, Codina-Solà M, Marquès-Bonet T, Bosch E, López-Granados E, Aróstegui JI, Soler-Palacín P, Colobrán R, Yagüe J, Alsina L, Juan M,  and Casals F. 2018. Evaluating the genetics of common variable immunodeficiency: monogenetic model and beyond. Frontiers in Immunology 14;9:636.

• Hernandez-Rodriguez J, Arandjelovic M, Lester J, de Filippo C, Weihmann A, Meyer M, Angedakin S, Casals F, Navarro A, Vigilant L, Kühl HS, Langergraber K, Boesch C, Hughes D, Marques-Bonet T. 2017. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Mol Ecol Resour 18 (2):319-333.

• Casals F, Anglada R, Bonet N, Rasal R, van der Gaag KJ, Hoogenboom J, Solé-Morata N, Comas D, Calafell F. 2017. Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations. Forensic Sci Int Genet. 30:66-70.

• Mondal M, Bergström A, Xue Y, Calafell F, Laayouni H, Casals F, Majumder PP, Tyler-Smith C, Bertranpetit J. 2017. Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Hum Genet. 136(5):499-510.

• Spataro N, Roca-Umbert A, Cervera-Carles L, Vallès M, Anglada R, Pagonabarraga J, Pascual-Sedano B, Campolongo A, Kulisevsky J, Casals F, Clarimón J, Bosch E. 2017. Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients. Mov Disord. 32(1):165-169.

Other relevant information 2017-18

Illumina & Verogen Forensic Genomics Workshop, at the Genomics Core Facility (Universitat Pompeu Fabra, Barcelona). 20-21 March 2018.Organized by the Genomics Core Facility & Illumina&Verogen.