Translational Genomics

Genetic Analysis Service

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

 a) Deep Sequencing (NGS)

This consists of the preparation of libraries and the subsequent high throughput of deep sequencing of the region of interest. The possibility to make multiple reads makes the detection of rare clonal types, cells or microbes that only represent 1% of the original sample. The preparation of libraries is carried out using different approaches all aimed at obtaining fragments of the right size to which bar codes have been attached (identifiers on each sample) and the adapters to read them.

Applications: this technology is applicable to:

  • Genomic DNA (who genome, exome)
  • Fragments of enriched DNA
  • Simple whole genomes
  • Metagenomic Profiles (16s or others)
  • RNA (transcriptomic, RNA profiling)
  • Small RNAs/miRNAs
  • Immunoprecipitated chromatin (Chip-Seq.) etc.

Sequencing is carried out in an MiSeq® Personal Sequencer (Illumina), a NextSeq-1000 (Illumina) and a MinION Sequencer (Oxford Nanopore).

b) Capillary electrophoresis for sequencing

These are the gold standard for genetic diagnostics when specific regions of the genome need to be analyzed. They permit both Sanger sequencing and the analysis of genic 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).

This is carried out using the genetic analyzes ABI 3130 and ABI 3130xl (Applied Biosystems).

c) Capillary electrophoresis for analysing nucleic acid quality

To study nucleic acid quality we have a bioanalitzador 2200 TapeStation (Agilent) and a QIAxcel Advanced System (Izasa). Both are automated systems for quantitative and qualitative analysis of nucleic acids based on capillary electrophoresis.

The applications offered are: analysis of quantity/quality of gDNA (including DNA integrity number (DIN), DNA fragments (150-5,000bp) and standard format or high sensitivity RNA analysis (including RNA integrity number (RIN)).

d) Amplification of nucleic acids

  • Real time PCR, based on monitoring fluorescence emitted during the amplification reaction in each cycle simultaneously in all samples. It permits the determination of quanities of DNA, RNA or MiRNAs present in the original sample (qPCR) or the qualitative identification of specific DNAs (genotyping).

The principle applications are: absolute/relative quantification of differential gene expression profiles; allele discrimination studies (SNPS); analysis of gene methylation profiles in DNA CpG islands (MSP); analysis of the variable number of gene copies in genomic or viral DNA(CNVs), quantification of gene dose (QF-PCR to detect aneuploidies); High Resolution Melting (HRM) for gene scanning.

  • Droplet digital PCR (ddPCR) is a technology that fragments each sample into more than 20,000 drops individually wrapped in a layer of oil, within which the polymerase reaction takes place. It can be carried out alternating with double chain or marked fluorescent probes and provides an absolute and ultra-sensitive quantification of nucleic acids. It is particularly useful to quantify low abundance genic fragments, allele variants (SNP), viruses and bacteria poorly represented in the heterogenous mixture. Etc.

Complementary Services

  • Fluorometric quantification using a Quantus™

Fluorometer (Promega). An optimized two channel fluorometer to measure nucleic acids (RNA and DNA) pre- and post- generation of sequencing libraries

  • Robotic liquid dispensing using an EpMotion 5070 station (Eppendorf). This can prepare serial dilutions, PCR trials, transfer samples from tubes to plaques (96w and 384w), reformatting of plaques etc.

Consulting on experimental design, sample preparation and analysis of results and global interpretation of data are also available services.