Genomics and Bioinformatics

genoma humano

Platform for Genomics and Bioinformatics

  • Responsible for the Platform: María de Toro
  • Postdoctoral Researcher: Rosario López
  • Laboratory technician: María Bea Escudero

CIBIR's Genomics and Bioinformatics Platform is a central support service in which complete genome analysis services are provided through massive sequencing.

The platform enables the strengthening of the scientific and technical capacities of the research groups, providing them with the infrastructures and the necessary equipment to boost their international leadership in the generation of frontier knowledge, the development of emerging technologies and the generation of priority knowledge oriented to the resolution of the present and future needs of our society.

General objective:

  1. Performing massive sequencing analysis for the characterization and reconstruction of different organisms genomes.
  2. Study of point mutations.
  3. Study of the activation of genes.
  4. Microbial diversity exploration.

Other lines:

  • Provision of basic and applied research services.
  • Provision of care services.

Contact data

María de ToroResponsible for the Platform
María Pilar Bea EscuderoLaboratory technician
  • Centro de Investigación Biomédica de La Rioja (CIBIR)
  • Calle Piqueras, 98
  • 26006, Logroño, La Rioja
  • Dra. María de Toro; This email address is being protected from spambots. You need JavaScript enabled to view it.
  • Telf: 941 278 876

Massive Sequencing

Custom solutions (Illumina Technology)

De novo sequencing

De novo sequencing is used to characterise new genomes, when no reference genome is available, or to analyze singular structural variants in previously characterised genomes.

Our bioinformatic analysis includes read assembly, CDS and ORFs prediction, annotation, resistome, virulome and mobilome analysis, when possible. We will provide raw reads, as well as all analysis results.

Resequencing

Genome resequencing by Next Generation Sequencing (NGS) is one of the most reliable methods to identify genomic variants (SNPs and indels) from known reference genomes.

This type of analysis is of great relevance to detect phenotypic correlations, phylogenetic analysis and mutations associated to disorders.

Our reports include raw reads, alignment files and variant reports, adapted to type of analysis, organism and the aim of work.

Exome capture (whole- or focused-exome) and sequencing

Exome analysis is used to selective capture and sequencing of genome coding regions. It is used to identify functional variants that are involved in common and Mendelian diseases.

In our service we perform complete and focused exome analysis, by using Agilent’s SureSelect protocols for library preparation and enrichment, followed by paired-end 100bp sequencing in a HiSeq platform (Illumina). This protocol is available for exome analysis for human, mouse, bovine and zebra fish.

Our reports include raw reads, alignment files and variant reports, containing allelic frequencies, protein function effect predictors, splicing prediction…

Custom design, gene capture and sequencing (custom panels)

Selective capture is also used to sequence specific genomic regions. This method is widely employed to analyse a great number of genes, associated to disease, or analyse a great number of samples in an economic way.

In the same way as complete exome analysis, our Platform use SureSelect Agilent protocols to generate genomic libraries and selective gene capture, in combination with paired-end 100bp sequencing in Illumina MiSeq.

We perform gene panel analysis from previously designed ones, or even custom design, to different organisms which available reference genomes. Our reports include raw reads, alignment files and variant reports, containing allelic frequencies, protein function effect predictors, splicing prediction...

Transcriptomic analysis

RNAseq technique is a powerful tool for expression analysis and transcript quantification. It does not require primers or specific probes, so it could be useful in a great number of applications and organisms. It is widely used to analyze gene expression and transcript discovery, as well as splicing variants and SNP identification in genome coding regions.

We offer several types of transcriptomic analysis, including mRNA, totalRNA, small RNAs and directional studies. Our reports include raw read files, alignment files, normalize expression quantification, differential expression and functional enrichment analysis. For miRNA studies se also perform target prediction (for available species).

Metagenomics analysis

Metagenomics includes the analysis of species variation in complex microbial samples. By massive sequencing it is possible to study bacterial communities without previous culture techniques. This enables microbial diversity identification from natural habitats, functional gene recognition and new metabolic pathway discovery, among others.

Our Platform performs 16S and shotgun sequencing, comprising taxonomic and functional analysis. Delivered reports include biological diversity analysis and taxonomic identification: identification and assignment of Operational Taxonomic Units (OTUs), rarefaction curves, alpha- and beta-diversity analysis, and relative OTU abundance, including biological diversity graphs.

Amplicon sequencing

Amplicon sequencing consists of massive sequencing from PCR products. It is employed not only in metagenomics studies, but also to discover, validate and analyze genetic variation in an efficient and fast manner. Our reports are adapted to the type of project.

Technical equipment

  • MiSeq (Illumina) sequencing system
  • BioRad Experion Station
  • Nanodrop ND-1000
  • Qubit Fluorometer
  • ABIGene Amp PCR System 9700
  • 7300 Real Time PCR System ABI
  • Covaris S2
  • Other common laboratory equipment
© 2020 Rioja Salud - C/ Piqueras, 98 – 3ª Planta · 26006 · Logroño · La Rioja · Telf.: 941 278 855 · Fax: 941 278 887