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Genomic genetics

Presentation

Last years’ research has shown that deciphering the genome was not the last step in the way. There is an estimation of about 20,000-24,000 human protein-coding genes, but several other points are raising importance: interactions in the genome (ncRNA, miRNA…), dynamic changes in DNA, methylation, interactions with the environment (intra- and extracellular, intra- and extra-organism). All these elements are studied by Genomics, which cannot be separated from Genetics anymore.

The Genetics-Genomics Facility at Biocruces Bizkaia Institute was thus created not only to study previous well-known genetic techniques (search for new genes or markers, mutation testing in patients, verification of new findings), but also, and in an important way as it is part of a Research Institute, to support innovating research in Genomics and its derivative Sciences: Epigenetics, Pharmacogenetics and all their applicability.

Facility management

The science of genetics has contributed decisively to the advancement of health sciences, especially since the decipherment of the Genome in 2000.

Applications to diagnosis and prevention are increasing significantly in medicine and public health, and the number of available genetic tests is growing exponentially. It is estimated that more than 100,000 people in the Basque Country may suffer or suffer from a genetic-based disease or are carriers of it.

With the existing screening and prevention programs, more and more Basque citizens have to make decisions that significantly affect themselves, their reproductive future and their family.

Mission

Provision of knowledge and technology in Genetics and Genomics for research and clinical assistance.

This provision of services is carried out to attend to the demand of patients and citizens, being connected through the work of basic and clinical researchers at Cruces University Hospital.

Vision

We aspire to be the benchmark Genetics-Genomics Facility in Euskadi, with areas of excellence both in Spain and internationally..

Values

  • Professionalism.
  • Commitment to quality.
  • Good organization and perfect relationship between basic research and clinical assistance (agreements, contracts…).
  • Customer-oriented services (provision of services to researchers, hospitals, technology-based companies, universities as UPV/EHU, private clinics, others).
  • Continuous innovating and investigating activity.

Services

Portfolio of services

  • Nucleic acid extraction and purification. Quantifying and preparation for subsequent studies.
  • PCR amplification of any requested amplicon.
  • Point mutation testing:
    • Sanger sequencing of DNA fragments (ABI3130 and ABI3130xl [Life Technologies] genetic Analyzers). EMQN certificate. Cert. 2017 - Cert. 2016 - Cert. 2015
    • Next Generation Sequencing. Gene panel design, preparation of libraries, capturing and sequencing. (Ion Torrent PGM-Life Tecnologies). Cert. 2017 - Cert. 2016
  • Search and determination of variations in the number of copies of a genome.
  • Gene expression studies:
    • Gene Expression Microarrays (SureScan Microarrays Scanner).
    • qRT-PCR. (7300 and 7900HT PCR Real Time Systems -Applied Biosystems-).
  • Nucleic acid and protein simultaneous detection: (FICTION technique: FISH and immunofluorescence staining).

Hereditary Cancer

  • Multiple Endocrine Neoplasia Type 1 (MEN1).
  • Multiple Endocrine Neoplasia Type 2 (MEN1).
  • Medullary thyroid cancer (MTC). Cert. 2017 - Cert. 2016 - Cert. 2015
  • Pheochromocytoma/Paraganglioma (RET).
  • Thyroid adenoma.
  • Wilms’ Tumor.

Imprinting Diseases

  • Uniparental Disomy chr6.
  • 6q Methylation.
  • 6q Duplication.
  • Uniparental Disomy chr20.
  • 20q13 Methylation.

Endocrinology

  • Monogenic Diabetes and Insulin Resistance. Cert. 2017 - Cert. 2016 - Cert. 2015
  • Neurogenic diabetes insipidus and nephrogenic diabetes insipidus.
  • Mitochondrial Diabetes.
  • Gonadal dysgenesis and hypogonadism.
  • Pseudohermaphroditism.
  • Other Disorders of Sex Development.
  • Congenital Adrenal Hypoplasia.
  • Panhypopituitarism.
  • Benign Hereditary Chorea.
  • Thyroid Hormone Resistance.
  • Allan-Herndon-Dudley Syndrome.
  • Hypothyroidism.
  • Pseudohypoparathyroidism.
  • Septo-optic dysplasia.
  • Hypercalciuric Hypocalcemia.
  • Type I Polyglandular Autoimmune Syndrome.
  • Glucocorticoid Resistance.

Other studies

  • Hyperferritinemia-cataract syndrome.
  • Type III Bartter Syndrome.
  • Branchio-Oto-renal Syndrome.

Infrastructures

Nowadays, the Genetics-Genomics Facility provides the following equipment:

ABI3130 and ABI3130xl Genetic Analyzers (Life Technologies)

Using capillary electrophoresis, they allow simultaneous runs of 4 and 16 samples, respectively. Daily performance of up to 82000 and 328000 bases in 24h; 5760 or 23040 genotypes in 24h (5 fluorophores), with optimal length of read (LOR) of up to 950bp.

Applications:

  • Sanger sequencing (‘de novo’ sequencing and resequencing).
  • Analysis of microsatellites.
  • Amplified fragment length polymorphisms (AFLP).
  • Loss of heterozygosity (LOH).
  • Detection and validation of SNP, MLPA, MS-MLPA, QMPSF…

Quantitative Real Time PCR systems: 7300 and 7900HT Fast (LifeTechnologies)

They allow real-time PCR experiments in a 96- or 384-wells format or TaqMan Low Density Arrays (TLDA) for absolute and relative nucleic acid quantification, high resolution melting and low-yield SNPs genotyping.

Applications:

  • PCR and real time PCR.
  • Gene expression analysis (absolute or relative).
  • Allelic discrimination (SNPs genotyping).
  • Detection and quantification of pathogens.
  • Gene copy number quantification.

SureScan Microarray Scanner (Agilent Technologies)

Scanner for microarrays, either for CGH arrays (Comparative Genomic Hybridization Arrays) or for expression microarrays. Analysis is provided by different software: CytoGenomics (Agilent Technologies) and Genoglyphix® (Perkin Elmer). A big range of commercial or customized arrays are available. Formats are quite flexible, from one array of 1Mb per slide, to 8 arrays of 60Kb per slide. Detected changes can be as small as 5.4Kb.

Applications:

  • Copy number and/or SNP detection.
  • Use of aCGH for the study of microdeletion syndromes.
  • Gene expression analysis in somatic or germline samples.

IonTorrent PGM (Life Technologies)

Next Generation Sequencer. This platform is an accurate tool to detect genomic variants, allowing simultaneous sequencing of several genes in a unique assay, which saves time and money. It is a scalable technology; this is, hundreds of genes can be analyzed using up to 6144 primer pairs in an ultrahigh-multiplex PCR. It allows sequencing up to 2Gb in nearly 5 million-read, in a single assay. . Another important advantage is the very small amount of sample that is required . This technique can be used with several sample types: blood cells, frozen tissues, FFPE, amniotic fluid or even a single blastomere for preimplantation diagnosis.

Applications:

  • Massive parallel sequencing of commercial gene panels.
  • Design and massive parallel sequencing of customized gene panels.
  • Detection of copy number variations (CNVs) and aneuploidies. A single assay allows simultaneous analysis of aneuploidies and point mutations in several genes.
  • RNA sequencing (RNAseq).
  • Metagenomic studies (microorganism typing).

QX200 Droplet Digital PCR System (BioRad)

This system allows absolute quantification of DNA and RNA molecules with a great precision and sensibility.

Aplicaciones:

  • Absolute quantification of DNA copies. Also applicable to viral load and microbial quantification.
  • Analysis of CNVs. Analysis of copy-sensitive genes responsible for diseases.
  • Rare sequence detection. For example, tumor cells detection in a healthy tissue.
  • Gene expression and analysis of microRNA (miRNA). It detects target genes even in low quantity samples, as miRNA.
  • Applications in NGS: Quantification of DNA libraries; validation of SNPs or CNV through absolute quantification.
  • Single cell analysis, due to its high precision for low copy number quantification.

2100 Bioanalyzer (Agilent)

It is a nanofluidic system that discriminates by size small DNA, RNA and proteins. It also performs flow cytometry of a small number of cells in the same equipment, through electrophoresis in small chips, providing high-quality digital data.

It is capable of quantifying and analyzing RNA quality in a more reliable and rigorous way than traditional systems. RIN algorithm (RNA Integrity Number) is supplied, determining eukaryotic RNA sample quality in a numeric range from 1 to 10.

Applications:

  • RNA quality determination: total RNA data. Sizing and quantification.
  • DNA analysis: Separation and high-resolution quantification of DNA. Quantification and analysis of quality of DNA libraries for NGS experiments.
  • An alternative to SDS-PAGE for protein analysis: rapid and reliable method to determine quantity and purity of proteins in a high range of sensibility.

Qubit 2.0 Fluorimeter (Thermofisher)

It allows high precision and sensibility in DNA, RNA and protein quantification. Fluorescence is released by a fluorochrome in a target-specific way, avoiding the negative effect of contaminants (including degraded DNA or RNA) in quantification.

Applications:

  • Nucleic acid quantification for subsequent techniques (qPCR, NGS…).
  • Protein quantification.
  • Analysis of the quality of NGS libraries, before and after the enrichment of the positive Ion Sphere Particles.

Platform members

Rates

Download Rates (PDF) (Updated 2015/10)

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