Bioinformatics Unit

The main mission of the Unit is to develop and operate state-of-the-art pipelines, tools and databases to manage and analyse the sequencing data generated at the CNAG-CRG in collaboration with the Sequencing Unit and National and International collaborators. Over 3254 samples from 178 collaborative projects have been analysed by the Unit in 2018. In addition, the Unit participates in several infrastructural and research projects. RD-Connect (www.rd-connect.eu), a hallmark FP7 project on rare diseases, was successfully concluded in 2018. However, Solve-RD (http://solve-rd.eu) has started to use the RD-Connect Genome-Phenome Analysis Platform developed by the Unit as a key infrastructure to collate and re-analyse 19.000 undiagnosed rare disease exomes. Furthermore, the Unit has effectively contributed to reach at least a 10% diagnosis by re-analysing previously unresolved rare disease patient exomes and panels collated in the platform deployed by the Unit for the URD-Cat (www.urdcat.cat) project on Personalised Medicine. In a similar context, collaboration with the Navarra 1000 Genomes (https://www.nagen1000navarra.es) project on Personalised Medicine has progressed significantly, with hundreds of genomes already analysed. In ELIXIR, the Unit has contributed in the co-coordination of the ELIXIR Rare Disease Community and the EXCELERATE project and new Implementation Studies have been granted. In summer 2018, the PerMedOmics REDES project coordinated by Sergi Beltran to promote the usage of omics technologies for Personalised Medicine kicked off. The project brings together the CNAG-CRG with the Center of Omics Sciences in Reus, which constitute the Infrastructure for Omics Technologies (IOT) ICTS. Regarding cancer genome analysis, an automated pipeline to process the thousands of breast cancer samples from the B-Cast project has been developed, and the first steps to adapt the RD-Connect platform for cancer have been made within the MedPerCan project (www.medpercan.cat). The Unit has contributed to 12 peer-reviewed publications in 2018.

• Collaborative analyses
• Experimental design
• Data processing and quality control
• Genetic variant identification and annotation
• Genotyping by Sequencing (GBS)
• Identification of methylation profiles
• RNA-Seq QC, alignment and quantifications
• Differential expression analysis
• Differential alternate splicing analysis
• Detection of gene fusion events
• SNP calling from RNA-Seq data

• 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
• Omics data Integration
• Agrogenomics (GBS)

• Solve-RD (EU H2020, PI: Sergi Beltran)
• URD-Cat (Generalitat PERIS,  PI: Sergi Beltran)
• PerMedOmics (MCIU REDES ICTS, PI: Sergi Beltran)
• ELIXIR Implementation Studies (PI: Sergi Beltran)
• EXCELERATE (EU H2020; task leads, PI: Ivo Gut)
• RD-Connect (EU FP7; team members, PI: Ivo Gut)
• B-Cast (EU H2020; team members, PI: Ivo Gut)
• MedPerCan (Generalitat PERIS; team members, PI: Ivo Gut)
• Members of GA4GH and MatchMaker Exchange working groups

D. Genis et al.
“Heterozygous STUB1 mutation causes familial ataxia with cognitive affective syndrome (SCA48).”
Neurology, 91(21):e1988–e1998, 2018.

S. Köhler et al.
“Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.”
Nucleic Acids Res., Nov. 2018.

S. Franch-Expósito et al.
“Rare germline copy number variants in colorectal cancer predisposition characterized by exome sequencing analysis.”
Journal of Genetics and Genomics, 45(1):41–45, 2018.

T. Gstrein et al.
“Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans.”
Nat. Neurosci., 2018.