Biotechnology Programme

Genomics Core Unit

Head of Unit:  Orlando Domínguez
Research highlights

The Genomics Unit contributes to the advancement of research projects conducted by multiple CNIO Research Groups. We provide services at 2 levels of complexity. The genomic wide level is addressed by both deep-sequencing (NGS) and microarray technologies. NGS permits a variety of applications, such as whole genome or whole exome tumour sequencing, transcriptome analyses by RNAseq, or location of interacting protein factors on chromosomal DNA by ChIPseq. On the other hand, DNA microarray technology is a powerful platform for transcriptome determinations or for the detection of chromosomal copy number aberrations. Its use, however, has diminished over the last few years in favour of NGS. This year, the demand for NGS services has been stable and the number of samples processed has been similar to those processed in 2016. At the single locus level other services are provided. A traditional DNA capillary sequencing service, based on a 3730xl DNA Analyzer from Applied Biosystems, is being used to find and confirm mutations in candidate genes, or for the verification of cloned genes or inserts. The Unit also provides a transgenic mouse genotyping service, based on allelespecific quantitative PCR for a quick and efficient turnaround time. The catalogue of available tests for genetic modifications has expanded, upon demand, from 30 to close to 90 in 2017. The genotyping service has seen an increase in demand in 2017 that nearly doubled that of former years.

An extended contribution, in the framework of a collaborator’s project, has led to a report being published with the co-authorship of some of the Unit’s members. A novel NGS analysis pipeline that facilitates forward genetic screenings on haploid mammalian cell lines has been described. The new RNA sequencing-based method, named TrapSeq, maps insertions that lead to productive trapping by recognising chimeric mRNAs containing gene-trap sequences spliced to an exon. The method provides a fast and cost-effective way that, not only identifies the insertion site but also, reveals its impact on the expression of the trapped gene (Mayor-Ruiz et al.).