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Sequencing and Genotyping Unit

Research Area: 
Life & Medical Sciences
Location: 

University of the basque country UPV/EHU
Science and technology faculty
Basement Building CD4
Bº Sarriena, s/n 48940 Leioa (Vizcaya)

Contact: 

Dr. Irati Miguel / Dr. Fernando Rendo
Phone: 94 601 3561 / 3471
E-mail: irati.miguel@ehu.es / fernando.rendo@ehu.es

Available for external users?: 
Yes
Access protocol: 

An essential requirement is to register as a user research group of the Sequencing and Gernotyping Unit by completing the User Register form. This form will contain information about the scientist in charge of the group and its line of research, the department, institution, a list of users authorised by the scientist in charge for the request for services with contact details, and invoicing details. The form only needs to be handed over the first time a service is requested from the Unit, and in the event that there should be any change to the group's details (authorised user, invoicing details). The User Register form must be signed by the scientist in charge of the group.
The authorised user requests the service by completing the request form for the relevant service, which will be handed over together with the samples to be analysed. The samples must be delivered duly labelled with the name of the sample in accordance with that indicated on the request form. For further information about sending specific samples for each analysis, please visit the Services offered section.
Once the experiment has been completed, the Sequencing and Genotyping Unit will then inform the user of completion of the later, and the results will be sent to them by email.
The samples and primers sent by the user will be kept for a maximum period of 3 months following completion of the service and delivery of the results.
General rules
Access to the unit of Sequencing and Genotyping involves meeting the requirements set forth in the Protocol for access to SGIker and the services it provides.

Description: 

Numerous research groups are currently involved in projects that incorporate genetic studies. However, the high cost of the equipment and the specialist nature of the techniques makes it difficult for each research group to be able to ensure that the equipment necessary for expression analyses and massive genotyping is at their disposal.

The Sequencing and Genotyping Unit of the University of the Basque Country, UPV/EHU, has been set up in order to provide both the knowledge and equipment necessary to researchers from the Basque Network of Science, Technology and Innovation, biocompanies from the milieu and to public and private institutions throughout Spain and overseas, in activities related to genetic analysis. To this end, it has qualified personnel at its disposal together with state-of-the-art techniques and equipment in automatic DNA sequencing and genotyping, and a recently-created laboratory designed in accordance with the recommendations of laboratory good practices.

The wide experience and importance of this university service is evidenced by the high number of users that are currently using it, and by the large volume of work that is being administered in this section.
This unit carries out a series of services such as:

extraction, quantification and normalization of genomic and mitochondrial DNA from different tissues.
amplification, purification and quantification reactions of PCR and plasmic DNA products.
DNA sequencing,
genotyping of different DNA markers: RFLPs, STRs or microsatellites, SNPs, CNVs, etc.
The quality of Sequencing and Genotyping is backed up by international genetic analysis societies via the participation of the UPV/EHU Service in numerous quality controls and authorisations for domestic animal genotyping (Comparation test of the Internatinal Society of Animal Genetic; ISAG) and genotyping in humans (officially approved by the Spanish and Portuguese Group of the International Society of Forensic Genetics; GEP-ISFG)

Services: 

The Genomics Facility provides technical support and advice for those non-expert users who wish to introduce these molecular techniques in their field. In addition , training courses will be organized for users, mainly aimed at optimization of protocols and analysis of data generated.

Extraction of genomic DNA from various tissues
Quantification ( spectrophotometry and fluorimetry ) ,quality check , standardization of DNA
Standard amplification reactions ( PCR ) and Whole Genome amplification ( WGA )
Purification and quantitation of PCR products and plasmid DNA (see the document)
DNA sequencing
Genotyping of fragments, STRs and indels by capillary electrophoresis (see the document):
Amplified size determinationof fluorescently labeled DNA
Microsatellite multiplex genotyping (STRs ) : simultaneous detection of up to 5 colors
Genotyping of SNPs and Indels , techniques :
TaqMan - simple tests ( 1 SNP per reaction, analysis by real-time PCR ) (see the document)
Kaspar probes - simple tests ( 1 SNP per reaction, analysis by real-time PCR ) (see the document)
TaqMan OpenArray ( multiplex 16, 32 , 64, 128 , 192, 256 SNPs, high number of samples) (see the document)
BioMark HD System - Fluidigm ( 48-96 multiplex SNPs, number low / medium sample ) (see the document)
SNaPshot (1-20 multiple SNPs by PCR and detection by capillary migration ) (see the document)
Digital PCR ( Fluidigm BioMark HD System ) : quantification of target sequences in a given DNA sample, study of copy number variation ( CNV ), loss of heterozygosity , rare mutations , ...
Individual identification and parentage or kinship controls in humans
Genotyping of human mitochondrial haplotype (Human mtDNA HVR -I hypervariable regions , HVR - II )
Identification of human cell lines ( AuthentiFiler ™ PCR Amplification Kit)
Individual identification , traceability and control of parentage or kinship controls in different animal species (ovine , bovine, equine , canine , avian , ... )
Detection of alleles responsible for chestnut coat color in horses (using snapshot)
MLPA: DNA methylation analysis , CNVs , detection of large deletions / duplications detection ( predesigned kit for disease detection , analysis pre and post -natal , tumor characterization , hereditary cancer disorders , pharmacogenetics , ... ) (see the document)
Personalized services : specific analysis of research projects in population genetics , forensic genetics , evolutionary genetics , Intercalibration between laboratories, ...
Others