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Genomic genetics

Presentation

Recent years have shown us that decoding the genome was not the only task. It is estimated at only 20-24,000 genes, but it exhibits impressive interactions with other parts of the genome (non-coding RNAs, miRNAs), with itself (methylation, dynamic changes), and with the environment (intra- and extracellular, intra- and extra-organism). This is the new science of Genomics, which can no longer be separated from Genetics.

The Genetics-Genomics Platform of the Biobizkaia Institute was created to serve not only all existing applications of genetics (gene screening, mutation screening in patients, verification of new findings, etc.), but also—and importantly because it belongs to a Research Institute—aims to support innovative research in Genomics and its derived sciences: Epigenetics, Pharmacogenetics, and all their corresponding applications.

Overview

Genetics has contributed decisively to the advancement of health sciences, especially since the decoding of the genome in 2000.

Applications for 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 disease or are carriers of one.

With existing screening and prevention programs, Basque citizens are increasingly having to make decisions that significantly affect themselves, their reproductive future, and their families.

Mission

Provision of knowledge and technology services in Genetics-Genomics for research and healthcare.

This service will be provided to meet the demands of citizens and patients, and will be channeled through the researchers and clinical researchers at Cruces University Hospital.

Vision

We aspire to be the benchmark Genetics-Genomics unit in the Basque Country, with exemplary areas of excellence throughout Spain and internationally.

Values

  • Professionalism.
  • Commitment to Quality.
  • Strong organization and impeccable research-assistance relationships (agreements, contracts, etc.).
  • Customer-focused: providing service to researchers, hospitals, technology companies, the University of the Basque Country (UPV/EHU), private clinics, and others.
  • Constantly researching and innovative.

Services

Portfolio of services

  • Manual and automated nucleic acid extraction.
  • Spectrophotometric and fluorimetric nucleic acid quantification.
  • Analysis of nucleic acids (DNA, RNA, libraries, etc.) using automated electrophoresis.
  • Design and setup of PCR amplification of any requested amplicon.
  • Conventional Sanger sequencing and results analysis, including the detection and interpretation of identified variants, both in sequence and fragment analysis.
  • Real-time PCR and digital PCR (ddPCR) assays, applied to detection, expression, or quantification.
  • Manual and automated library preparation from multiple sample types for massive sequencing:
    • Gene panels.
    • Whole exome.
    • Whole transcriptome or polyA capture.
    • Whole human genomes.
    • Methylome.
    • Metagenomics.
  • Mass-scale sequencing on the Ion S5 Plus and NovaSeq6000 systems.
  • Copy number variation (CNV) studies, array CGH, and microarray expression (CE-IVD marked system).
  • Population-wide genotyping studies on an array platform.
  • Preimplantation genetic diagnosis (PGT-A, PGT-M, PGT-SR), carrier screening studies.
  • Analysis of gene panel or whole exome results in genetic diseases.
  • Single-cell whole transcriptome studies Spatial transcriptomics studies from fresh or paraffin-embedded tissue (spatial transcriptomics).

Infrastructures

Currently, the Genetics-Genomics Platform has the following infrastructure:

Nucleic Acid Collection

Maxwell® CSC Instrument

The Maxwell® CSC is a compact platform with an intuitive graphical interface for automated nucleic acid purification, capable of processing up to 16 samples simultaneously. Using prefilled cartridges and preprogrammed methods, the Maxwell® CSC offers consistent and reliable DNA or RNA extraction in 25-60 minutes from multiple sample types. Furthermore, the system allows for use in IVD mode, ensuring quality and traceability in diagnostic processes. Learn more.

Applications

  • Obtaining consistently pure nucleic acids from multiple sample types.

Nucleic Acid Quantification

Spectrophotometer NanoDrop™ 2000

The NanoDrop™ 2000 measures microvolumes as small as 0.5 µL, allowing sample pipetting directly onto the optical measurement surface. It provides sample absorbance measurement. Learn more.

Qubit 2.0

Fluorimetric quantification of double-stranded deoxyribonucleic acid (dsDNA), ribonucleic acid, and protein samples in aqueous solution. More information.

Applications

  • Quantification of nucleic acids and proteins.

Molecule Quality Control

2100 Bioanalyzer Instrument

The Bioanalyzer is an automated electrophoresis system that enables the analytical evaluation of various types of biomolecules, using dedicated chips and the 2100 Expert Software. It enables objective assessment of the size, quantity, integrity, and purity of DNA, RNA, or protein samples, starting from minimal quantities. Learn more.

Applications

  • Next Generation Sequencing (NGS).
  • Gene expression.
  • Biopharmaceuticals.
  • Gene editing.

Automated Pipetting Systems

Integra ASSIST PLUS Pipetting Robot

El robot The ASSIST PLUS robot automates pipetting tasks in the laboratory using a variety of electronic pipettes. This minimizes potential pipetting errors, thereby increasing process reproducibility. Learn more.

Applications

  • Transfers from tubes to plates (96/384) and vice versa.
  • Serial dilutions.
  • Multiple dispensings.
  • Customizable protocols with high reproducibility, repeatability, and traceability.

Microlab STARlet ivd Robotic Workstation

With over 15 years on the market and a benchmark in the industry, Hamilton's Microlab STAR line is a robotic pipetting platform available in different working capacities for the automation of all types of assays and sample preparation. It allows customization of various workflows through compatible operating modules and intuitive programming via VENUS software. Learn more.

Applications

  • Library preparation (RNAseq, whole genome).
  • Genomics, proteomics, etc.
  • Diagnostics.
  • Sample transfer.
  • Replicates.

Microarray analysis and mass genotyping

SureScan Microarray Scanner

Microarray scanner, combined with software tools such as CytoGenomics (Agilent Technologies), Genoglyphix® (Perkin Elmer), etc. It allows the use of a wide range of commercial and custom arrays, with flexible formats ranging from one 1Mb array per crystal to eight 60Kb arrays per crystal, and can detect changes up to 100-150Kb. Learn more.

GeneChip™ System 3000Dx

The GeneChip 3000Dx platform consists of a hybridization oven, a fluidics system, and an array scanner and can analyze both DNA and RNA samples in genotyping and expression studies. It is worth noting that, when used with Affymetrix Molecular Diagnostics Software, it enables the analysis of various arrays for clinical diagnostics in compliance with the IVDR regulation. Learn more.

GeneTitan™ MC Scan Instrument

The GeneTitan is a high-performance instrument comprising an integrated hybridization oven, microfluidics system, and imaging system, capable of processing 16, 24, or 36 arrays at once. 96 arrays. Minimal user intervention allows for highly reproducible results. Learn more.

Applications

  • Expression analysis and microRNAs
  • Genotyping studies and CNV detection (SNArrays)
  • Pharmacogenomics
  • Polygenic diseases (Risk score)
  • Customized assays

SANGER Sequencing

ABI3500 Genetic Analyzer

The ABI3500 Genetic Analyzer uses capillary electrophoresis technology in simultaneous runs of 8 capillaries, capable of detecting 6 fluorophores, to perform Sanger sequencing and analyze fluorescently labeled fragments. With a 24-hour throughput of up to 368 samples (220,000 bp) in Sanger mode, and genotyping of 280 fragments of up to 600 bp, its optimal ranges reach up to 850 bp. Learn more.

SeqStudio Genetic Analyzer

The SeqStudio Genetic Analyzer uses capillary electrophoresis technology in simultaneous runs of 4 capillaries, with the capacity to detect 6 fluorophores, to perform Sanger sequencing and analyze fluorescently labeled fragments. With a 24-hour throughput of up to 192 samples (67,000 bp) in Sanger, and genotyping of 128 fragments of up to 460 bp, its optimal ranges reach up to 800 bp. Learn more.

Applications

  • Sanger sequencing: resequencing, NGS confirmation, indels, heterozygote detection, minor variant detection, microbial identification, gene editing validation, etc.
  • Fragment analysis: microsatellite analysis, MLPA, SNaPshot applications, line checking cell phones, etc.

Genotyping and Gene Expression Analysis Systems

QuantStudio™ 12K Flex Real-Time PCR System Multi-Well Plates and Array Card Experiments

The Applied Biosystems QuantStudio 12K Flex is a real-time PCR platform that can simultaneously analyze up to four 3072-reaction QuantStudio 12K Flex OpenArray plates in approximately four hours. When combined with the AccuFill QuantStudio 12K Flex OpenArray system, the QuantStudio 12K Flex system can produce up to 110,000 data points or more in one day (8 hours) with as little as 20 minutes of handling per run. It has a touchscreen interface with numerous functions and software analysis tools. Learn more.

The QuantStudio 12K Flex system has five interchangeable block formats, of which the platform has the following:

  • QuantStudio 12K Flex System, OpenArray plate.
  • QuantStudio 12K Flex System, TaqMan array card.
  • QuantStudio 12K Flex System, 384 wells.
  • QuantStudio 12K Flex System, 96 wells (0.1 ml).

Applications

  • Gene expression: Comparative CT (ΔΔCT) or Relative Standard Curve Method
  • Genotyping
  • Melt Curve Analysis
  • Presence/Absence Experiments
  • Standard Curve Experiments

QX200 Droplet Digital PCR system

The QX200 Droplet Digital PCR (ddPCR) system provides absolute quantification of DNA or RNA molecules using EvaGreen as the intercalating fluorophore or specific probes. The QX200 system consists of two instruments, the QX200 droplet generator and QX200 droplet reader, and QuantaSoft software. Learn more.

Applications

  • Measuring copy number variations (CNVs).
  • Detecting rare sequences.
  • Gene expression analysis.
  • Quantification of NGS libraries.
  • Viral load determination.
  • Single-cell gene expression analysis.
  • Absolute quantification.
  • Detecting rare mutants.
  • Analysis of miRNAs.
  • Detection of GMO (genetically modified organisms).
  • Detection of genome editing.

7300 Plus Real-Time PCR

The 7300Plus Real-Time PCR System is a 96-well, four-color instrument that uses fluorescence-based polymerase chain reaction (PCR) reagents. Learn more.

Applications

  • Quantitative real-time detection of target nucleic acid sequences.
  • Qualitative target detection by post-PCR (endpoint) analysis.
  • Qualitative PCR product analysis (Melt Curve Analysis).

Next-generation sequencing (NGS

Ion GeneStudio S5 Plus System. Ion Chef. Ion Reporter (Ion Torrent)

Next-generation semiconductor-based sequencing system optimized for a simple workflow in targeted sequencing using gene panels. With great flexibility and scalability, it can be adapted to the sequencing needs of both research and clinical applications. Reagents are cartridge-based, using chips of varying capacities (Ion 510-540), achieving between 2 and 80 million reads per cycle.

High efficiency with difficult samples: formalin-fixed, paraffin-embedded (FFPE) tissue, retrospective fine needle aspirate samples, and cell-free DNA extracted from blood (cfDNA). You can start with as little as 1 ng of DNA or RNA.

This platform provides the software tools for primary and secondary analysis of the obtained sequences (Torrent Suite software) and connects to the Ion Reporter software for annotation and interpretation of variants.

The platform also has a local server with the Ion Reporter software. Ion Chef, in addition to annealing the libraries and loading them onto the chip, also offers automated library preparation.

Links of interest

Ion GeneStudio™ S5 System - Ion Chef™ Instrument - Torrent Suite Software - Ion Reporter Software - Ion AmpliSeq Designer

NovaSeq 6000 (Illumina)

Offers increased capacity and speed for data acquisition, at a more cost-effective price. With high throughput, it meets virtually any analytical need, thanks to a variety of loading flow cell types, a dual loading flow system, and a wide variety of read length combinations. It is a scalable and flexible system that can generate from 80 GB of data and 800 million reads, making it possible to sequence from a trio of exomes in one day to 48 genomes in approximately two days with complete coverage.

To load samples quickly, this device offers a standardized workflow, where libraries are automatically loaded into a tube that attaches to pre-configured reagent cartridges, which are then loaded directly into the system.

Another advantage is its compatibility with different library preparation kits, supporting a wide variety of capture methods.

It integrates simple data storage and analysis tools that assist with sequence analysis work. Data analysis and preparation can be optimized directly within BaseSpace Sequence Hub, an easy-to-use genomics informatics platform optimized for processing large volumes of data. BaseSpace offers simplified data management, analysis, and storage solutions. From it, you can access the DRAGEN™ (Dynamic Read Analysis for Genomics) bioinformatics technology platform for ultra-fast secondary analysis of NGS data or various BaseSpace applications, including sequence alignment, variant detection, annotation, and visualization. To facilitate data interpretation, Illumina offers comprehensive and intuitive tools for visualizing, classifying, and interpreting variants associated with genetic diseases.

Applications

  • Targeted sequencing using gene panels.
  • Clinical exome or complete exome (individual or in trios).
  • Complete genome.
  • Transcriptome.
  • Methylome.

Links of interest

NovaSeq 6000 System - Illumina Control Panel - Sequencing Coverage Calculator - Basespace - DRAGEN secondary analysis

Single-Cell Analysis System

Chromium X

The Chromium X system enables the analysis of single cells, facilitating an understanding of cellular diversity, its intracellular mechanisms, and its applications in health and disease. The Chromium X can analyze hundreds to hundreds of thousands of cells in a single run, making studies of millions of cells routine.

Its patented NextGEM technology allows the generation of hundreds of thousands of partitions containing a single cell, with each partition containing an identification barcode for subsequent analysis. Combined with an innovative reagent management system and software analysis tools, this enables the discovery of previously inaccessible biological information.

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In addition, the Chromium X features fully integrated automated system support in the 10x Genomics Cloud, complete with temperature control and enhanced access to support. Learn more.

Applications

  • Single-cell gene expression.
  • Chromatin accessibility studies.
  • Single-cell immune profiling.
  • Biomarker studies.
  • Advances in the study of oncological processes, neurodegenerative diseases, etc.

Spatial transcriptomics system

Visium CytAssist

The Visium CytAssist system is integrated into the spatial transcriptome processing protocol of Visium (10X Genomics) assays, which allow the user to start from tissue sections, both frozen (fresh and fixed) and paraffin-embedded tissue, on standard slides. The CytAsssist system allows for easy transfer of probes already hybridized to the tissue onto the Visium slide, which will be used until elution and subsequent indexing of the libraries for sequencing. Learn more.

Applications

  • Differential gene expression analysis in both humans and mice.
  • Discovery applications using polyA capture assays regardless of the species being studied.

Platform members

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