Genomics

The Genomics ECAI provides medium-high scale sequencing and genotyping services. In addition, our extensive experience in these techniques allows us to offer technical and methodological advice that is required at all times. There are two modes:

  1. Temporary access for researchers needing such facilities to carry out research projects funded by different programs.
  2. External services for public and private institutions at both the national and international level in activities related to genetic testing.
  • Objectives
  • Services
  • Members
  • Processing and genomic testing/sequencing of basic and clinical research samples.
  • Advise users in all genomic/sequencing techniques.
  • Training in genomics/sequencing through courses and outreach and specialization seminars.
  • Continuous improvement of services offered.
  • Incorporation of new techniques and updating of established techniques.

Sequencing

DNA sequencing using the Sanger method.

The 3130XL genetic analyzer provides automated DNA sequencing using capillary electrophoresis and the BigDyeTM fluorescent terminators system from Applied Biosystems, obtaining readings up to 1000 bases per reaction from plasmids, PCR products, cosmids, phages or BACs. This equipment can perform analysis of DNA fragments labeled with fluorochromes. It allows combinations of fluorochromes (6-FAM, HEX, NED, ROX, VIC, PET, LIZ) for multiple genotyping.

DNA sequencing using the Pyrosequencing method

Ultrasequencing on the 454 GS Junior. High-throughput sequencing technologies reduce analysis costs, simplifying the methodology and increasing the capacity and speed of sequencing to a large number of samples or samples that require studying a large number of genes. It uses the same long-read GS FLX Titanium sequencing chemistry to produce high quality long-read sequences that are easily analyzable with many bioinformatics tools. The small size of the various files and data allows direct analysis on the server that accompanies the GS Junior System, without complex IT infrastructures. With the simple sample preparation protocols, rapid sequencing and data processing with specialized software modules a large number of applications can be covered:

  • De novo sequencing of viruses, bacteria and fungi genomes .
  • Sequencing of full-length transcripts in microbial transcriptomes.
  • Sequencing of tens to hundreds of amplicons and loci.
  • Sequencing of regions captured with arrays of low density capture.
  • Discovery of pathogens
  • Metagenomics.

PyroMark Q96 ID. The PyroMark Q96 ID pyrosequencer is a fully integrated system that provides real-time sequencing and one of the reference systems for epigenetic research and genetic analysis. It also allows the preparation of single stranded DNA using the PyroMark Q96 ID vacuum workstation. The applications are:

  • Detection Tool for epigenetic research.
  • Quantification of individual CpG sites for differential gene expression in tumors.
  • Platform well suited to analysis of differences in genomic DNA, including mutation detection and SNP typing.
  • KRAS testing: mutations in genes involved in numerous human cancers.
  • In other disciplines: development studies on drug resistance in pathogenic polymorphisms in forensic samples of mitochondrial DNA.

Genotyping

Genotyping can be performed using applications on sequencing equipment. In addition to use specifically for genotyping, this ECAI has the high performance TaqMan OpenArray (Applied Biosystems) system.  Taqman probe chemistry can validate up to 256 assays in 12 samples simultaneously, in addition to other possible formats. The minimum order size is 960 samples and goes up in increments of 10 sets (the number of samples per set of ten arrays depends on the format).

The Sequencing and Genotyping Platform manages other equipment used autonomously, such as real-time PCR:

  • Roche LightCycler 480II, one system
  • 7500Fast from Applied Biosystems,
  • and Rotor Gene 6000

In addition to quantitative PCR experiments, the 7500 Fast system from Applied Biosystems and Rotor Gene 6000, can perform genotyping analysis based on high resolution melting curves (HRM analysis). This common structure supporting Genetics research (ECAI) is accredited in accordance with ISO/IEC 17025:2005). And participates in accredited external quality assessment of genetic testing for monogenic diabetes (ISO 17043) (EQA).

  • Juan Miguel Gomez Zumaquero
  • Pablo Rodriguez Bada
Genomics