Areas of activity

The sequencing, genotyping and analysis of expression and regulation enable the identification of genes associated with physiological and pathological processes. These techniques provide information that makes possible the development of new early detection systems, the assessment of the genetic predisposition to have a disease, and the development of new and more efficient drugs to combat complicated diseases.

Sequencing

DNA sequencing is a technique used to study the genetic information of individuals. It is able to determine the order of nucleotides within DNA channels. Different methods have been developed to obtain the precise sequence of DNA nucleotides. The predominant methods used nowadays for DNA sequencing have been the enzymatic method and automated sequencing based on the Sanger method, which made possible the development of genomics within the last 3 decades.

A new generation of sequencing technologies, different from the Sanger method, has revolutionized the field of genomics, increasing enormously the velocity and the information provided.

Today, the new technologies have implemented the conventional techniques, such as sequencing by synthesis together with pyrosequencing, polymerase, or ligation based- sequencing.

In this field, the scientific board of GENYO had decided to provide the Genomics and Genotyping Unit with SOLID next-generation sequencing technology (Applied Biosystems by Life Technologies), based on the fragments generation and sequencing by ligation. This Unit also provides researchers with multicapillary electrophoresis systems.

Genotyping

Genotyping is the process of determining the genetic information of an organism- called genotype- and be able to differentiate it from the rest.

We understand genotyping as the analysis of one or several regions or positions. This technique was traditionally based on the study of the change of a specific position-nucleotide- which is called SNP, of a region or a repeat fragment (depending on their size: VNTR, STR, ...). There are several techniques that allow to examine one position alone or millions positions.

There are different types of genotyping:

  • Depending on the type of study to be performed, small-scale studies, studies of high-thoughput technologies for the study of massive SNPs (up to million positions) allowing Genome-Wide Association Studies (GWAS).
  • If SNPs are selected by the researcher (Custom SNPs) or if the researcher prefers to use matrices (arrays or biochips) or pre-designed panels of SNPs.
  • Depending on the technology selected to perform the study.

The Genotyping Unit covers all the possible demands of the researchers, providing different types of technologies and all the kits or microarrays pre-designed by the best trade houses. Some of these technologies are BeadArray™ (Illumina®) and Targeted Resequencing, SNPlex™, Taqman™,… (Applied Biosystems by Life Technologies™), among others.

Although genotyping can be addressed from different platforms, real Time-PCR, capillary or massive sequencing, DNA matrices, (arrays or biochips)... , the microarrays Illumina® make possible the use of BeadArray™ (Infinium and GoldenGate) technology for SNPs analysis, in the analysis of variability selected by the researcher. This system has several products available such as the Infinium iSelect HD Custom Genotyping BeadChip which allows the study of SNPs and structural variations. The array is offered on a 24-sample and 12-sample BeadChip (24-sample format with 3,000 to 68,000 analysis, or the 12-sample format with 68,000 to 200,000 positions).. Illumina offers a semi-custom product called the Human1M-Duo DNA Analysis BeadChip; it is a biochip that allows researchers to analyze two samples, with nearly 1.2 million markers per sample; of them, more than 60,800 SNPs are of the user’s choice. On the other hand, there are other biochips designed to Whole-Genome Genotyping studies or biochips specific for gene association studies, SNPs, regions of interest… of a particular disease, such as cáncer, using the GoldenGate technology.

Expression and Regulation

Although cells of the organism all have the same genetic content, each one has a different phenotype. Cellular differentiation depends on the genome expression and regulation. We define expression and regulation as the molecular processes by which information encoded in an organism’s DNA is expressed. Each gene must be expressed at the right time and in the right place for a correct cellular function. To know the function of genes, we must know when, where, and how they are expressed. Changes in gene expression patterns provide information about the regulatory mechanisms, cell functions and metabolic pathways. To know the regulation of gene expression and its interactions provides information about diseases of different complexity such as cancer, neurodegenerative,or autoimmune diseases.

Gene expression analysis and large-scale methylation studies can be carried out using next-generation sequencers or high-density oligonucleotide microarray technology. However, today one of the most used techniques providing other complementary information is the real-time or quantitative PCR, which is able to detect the increase in the number of copies of DNA fragments in a cycle of PCR.

Our Unit has chosen Applied Biosystems by life technologies, based on the detection of fluorescence combined with PCR reaction. For the detection of PCR product, two types of chemistry are used: SYBR Green fluorochrome, and TaqMan specific fluorescent probes.;