Translational Genomics

Genetics Analysis Service

The genomics platform allows the study of genetics of organisms through the use of several techniques:

a) Approximations based on new generation deep sequencing (NGS)

This is carried out using a latest generation MiSeq® Personal Sequencer.  NGS allows for simultaneous qualitative (determination of the sequences of bases) and quantitative (recounting the number of sequences) analysis in several samples.  This can be applied to genomic DNA (whole genome and exome), enriched fragments of DNA, simple whole genomes (small genomes), metagenomics profiles (16s or others), RNA, transcriptomics, RNA profiling), small RNAs/miRNAs, immunoprecipitated chromatin (Chip-Seq), etc.

Samples will need appropriate preparation in function of the technique requested.

b)     Approximations based on capillary electrophoresis

Gold standard techniques are used to analyse specific areas of the genome.  The facility carries out these analyses using 2 genetic analysers ABI3130Xl which allow for sequencing based on the Sanger method and gene fragments (genescan).  The most usual applications are: de novo DNA sequencing; detection of mutations; allele discrimination studies (SNPS); analysis of gene methylation profiles in DNA CpG islands (MSP); analysis of the variable number of gene copies (CNVs); analysis of microsatellites (STRs, VNTR); ligation PCR and multiplex ligation dependent probe amplification (MPLA).

Additionally we have a bioanalyzer 2200 Tapestation.  This is an automatized system for qualitative and quantitative analysis of DNA, DNA and RNA fragments in standard and highly sensitive formats.

c)    Approximations based on nucleic amplification

  • Real time PCR

Using monitoring of fluorescence emitted during the amplification reaction simultaneously in all the samples in every cycle in a Thermocylcer LC480 (Roche) the quantity of RNA or DNA in a sample can be determined (qPCR) or we can identify specific areas of DNA qualitatively.  This is carried out using: DNA intercalators, hydrolysis probes, hybridization probes, LNA probes and other modifications.  The principle applications are: absolute/relative quantification of differential gene expression profiles; allelic discrimination studies (SNPs); analysis of gene methylation profiles; in CPG islands, determination of the number of gene copies in genomic or viral DNA (CNVs); quanitification of gene dosage (QFPCR for aneuploidy detection) and high resolution melting (HRM) for gene scanning

  • Amplification of single cell nucleic acids

Carried out in a Amplispeed Thermocycler (Beckman Coulter) in slide format (Ampligrid) , where cell or tissue fragments (from FACS cell sorting or microdissection) are deposited.  The principle applications of the system include: single cell genetic analysis in heterogeneous populations, study of heteroplasmy in mitochondrial DNA, analysis of chromosomic disorders in polar bodies.

Additional Services

Consultations on design, analysis and interpretation of data