Sequencing Unit

The Sequencing Unit acts as a nexus for collaboration in national and international genomics research projects and has the proficiency and infrastructure to provide clinical grade next generation sequencing assays. The Unit is working in three intersecting lines: first, bringing the most pertinent selected sequencing technologies towards maturity; second, as genomic sequencing has already reached the diagnostic level, the Unit serves to deliver standardized, ISO accredited high quality data for research and for clinics; and third, the close collaboration with leading companies for keeping the processes up to date, with a strong commitment to quality and economy of the operation.

The efficiency of the processes, the reliability and reproducibility of the execution of each of individual project are measurable registered periodically to answer the most exigent audits of the ISO 9001:2015 certification and the ISO/IEC 17025:2017 accreditation.

The equipment infrastructure of the Unit is kept at state of the art level, the personal is regularly trained for high technical competence and new technologies are constantly implemented, such as Oxford Nanopore sequencing and single cell sequencing increased our collaboration potential among new and existing users.

• Integration of miniaturized Kapa Hyper Prep (Roche) low input protocol using Mantis (Formulatrix) and Sciclone (PerkinElmer) automation with Hybridization-Based Target Custom Enrichment using SeqCap EZ Prime Choice Probes (Roche) for the B-CAST (Breast CAncer Stratification) consortium project.
• Establishing of the high throughput Covaris instrument (Covaris) fragmentation using the oneTUBE-10 plates, as one of the first centres in Europe to acquire the LE220-Plus upgrade.
• Implementation of Sage HLS (Sage Science) for ultra HMW DNA extraction from yeast spheroplasts
• Benchmarking of three capillary based electrophoretic systems: 2100 Bioanalyzer (Agilent), Fragment Analyzer (AATI) and 4200 Tapestation (Agilent) platforms. As a result, Fragment Analyzer was implemented into the quality control processes decreasing the need of ethidium bromide.
• Increase of the platform sequencing capacity to over 4 Tb/day by introduction of a second Illumina HiSeq4000 and Illumina NovaSeq6000.
• Introduction of automatic report-generation summarizing run and basecalling quality parameters of the Oxford Nanopore MinION sequencing runs.
• Basic incorporation of the nanopore sequencing into CNAG-CRG Laboratory Information Management System (LIMS), to improve the process traceability.   
• Generation of a pipeline to improve MinION runs data management to allow a real-time data transfer to the CPD (Centro de Procesamiento de Datos).
• Large-scale benchmarking single-cell RNA-seq methods (Human Cell Atlas project).
• Installation of a Chromium Controller (10x Genomics).
• Leadership of RNASeq interlaboratory comparison among five ISO 17025 accredited centres.
• Quality control protocols standardization and interlaboratory comparison assessment projects were conducted in collaboration with IBBL (Integrated Biobank of Luxembourg) within the scope of the SPIDIA4P project.
• Preparation and passing the re-certification audit of ISO9001:2015.
• Preparation and re-certification audit ISO10725:2017 (including the transition to last revision of the standard).