Bioinformatics Analysis Unit

CNAG-CRG

HEAD OF THE UNIT: Sergi Beltran

PRODUCTION BIOINFORMATICS TEAM: Matthew Ingham (Manager), Raul Alcántara, Eloi Casals

FUNCTIONAL GENOMICS TEAM: Simon Heath (Manager), Anna Esteve-Codina, Marc Dabad, Marcos Fernández, Angelika Merkel

DATA ANALYSIS TEAM: Sergi Beltran (Manager), Felipe Camacho (from June), Jordi Camps, Steven Laurie, Damian Loska (until June), Inés Martínez, Leslie Matalonga, Anastasios Papakonstantinou, Genís Parra (from July), Daniel Picó (from April), Davide Piscia, Joan Protasio, Raul Tonda, Jean-Rémi Trotta.

Summary

The Unit collaborates with external and internal groups on the analysis of large-scale genomics data and develops state-of-the-art pipelines, methods and tools. The activity is carried out by highly skilled data analysts, software engineers and bioinformaticians divided into three teams. The Production Bioinformatics team develops and operates the Laboratory Information Management System (LIMS) and pipelines to process, control the quality and transfer the data generated by the laboratory. The Data Analysis team develops and operates bioinformatics pipelines to analyse sequencing data, mainly related to germinal variant and somatic mutation identification and annotation. Finally, the Functional Genomics team has a production aspect in the handling of the processing, analysis and interpretation of RNA expression experiments produced at the CNAG-CRG. The team also has a research aspect in the development and deployment of a diverse array of expression analysis pipelines, as well as participating in European research projects. The team interacts closely with the Bioinformatics and Statistical Development team (in particular with the development of the analysis pipelines, choice of statistical analyses, and in the larger collaborative projects) and with the genome assembly and annotation team (for expression analysis in species lacking a comprehensive genome annotation). Notably in 2017 the team has been involved in the analysis of the European funded project IBD-Character.

The Unit partners in or provides support to several European and National projects and initiatives, such as RD-Connect, ELIXIR-Excelerate, B-CAST, GA4GH MatchMaker Exchange, URD-Cat, MEDPERCAN and Navarra 1000 Genomes.

Services

  • Collaborative analyses
  • Experimental design
  • Data processing and quality control
  • Genetic variant identification and annotation
  • Genotyping by Sequencing (GBS)
  • Identification of methylation profil·les
  • RNA-Seq QC, alignment and quantifications
  • Differential expression analysis
  • Differential alternate splicing analysis
  • Detection of gene fusion events
  • Small and micro-RNA analysis
  • SNP calling from RNA-Seq data
  • Analysis of co-expression modules
  • Transcriptome assembly
  • Genome annotation improvement

Research lines

  • Bioinformatics for Clinical Research (Rare Diseases and Cancer)
  • Development of support systems for Personalised Medicine
  • Development of pipelines and tools
  • Benchmarking of data analysis methods
  • Variant annotation Systems
  • Omics data Integration
  • Agrogenomics (GBS)

Selected Publications

González-Vela MD, Curiel-Olmo S, Derdak S, Beltran S, Santibañez M, Martínez N, Castillo-Trujillo A, Gut M, Sánchez-Pacheco R, Almaraz C, Cereceda L, Llombart B, Agraz-Doblas A, Revert-Arce J, López Guerrero JA, Mollejo M, Marrón PI, Ortiz-Romero P, Fernandez-Cuesta L, Varela I, Gut I, Cerroni L, Piris MÁ, Vaqué JP.
“Shared Oncogenic Pathways Implicated in Both Virus-Positive and UV-Induced Merkel Cell Carcinomas.“
J Invest Dermatol, 37(1):197-206 (2017).

Feliubadaló L, Tonda R, Gausachs M, Trotta JR, Castellanos E, López-Doriga A, Teulé À, Tornero E, Del Valle J, Gel B, Gut M, Pineda M, González S, Menéndez M, Navarro M, Capellá G, Gut I, Serra E, Brunet J, Beltran S, Lázaro C.
“Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer.”
Sci Rep, 4;7:37984 (2017).

Curiel-Olmo S, Mondéjar R, Almaraz C, Mollejo M, Cereceda L, Marès R, Derdak S, Campos-Martín Y, Batlle A, González de Villambrosía S, Gut M, Blanc J, Traverse-Glehen A, Verney A, Baseggio L, Camacho FI, Wotherspoon A, Stamatopoulos K, Xochelli A, Papadaki T, Kanellis G, Ponzoni M, García-Cosío M, Vaqué JP, Beltrán S, Gut I, Piris MA, Martínez N.
“Splenic diffuse red pulp small B-cell lymphoma displays increased expression of cyclin D3 and recurrent CCND3 mutations.”
Blood, 129(8):1042-1045 (2017).

Esteve-Codina A, Arpi O, Martinez-García M, Pineda E, Mallo M, Gut M, Carrato C, Rovira A, Lopez R, Tortosa A, Dabad M, Del Barco S, Heath S, Bagué S, Ribalta T, Alameda F, de la Iglesia N, Balaña C; GLIOCAT Group.
“A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.”
PLoS One, 2(1):e0170632 (2017).

Campos-Sanchez E, Deleyto-Seldas N, Dominguez V, Carrillo-de-Santa-Pau E, Ura K, Rocha PP, Kim J, Aljoufi A, Esteve-Codina A, Dabad M, Gut M, Heyn H, Kaneda Y, Nimura K, Skok JA, Martinez-Frias ML, Cobaleda C.
“Wolf-Hirschhorn Syndrome Candidate 1 Is Necessary for Correct Hematopoietic and B Cell Development.”
Cell Rep, 23;19(8):1586-1601 (2017).