MARGenomics

MARGenomics is an integrated translational platform that includes microarrays, qPCR and Next-Generation Sequencing technologies.

This new platform was launched on 1 January 2019 and includes the Microarray Analysis Service (SAM) as well as offering wider services for biomedical research.

The AffymetrixGeneChip® research and diagnostics platform offers an integrated service for cytogenetic, genomic, and transcriptomic studies. Arrays for human, mouse and other species are available.

Services

MARGenomics offers a wide range of services covering all phases of the genomic analysis process, from the initial phase of project advice, to final analysis of the data, validation of the results and expert support with their interpretation.

The request for these services is coordinated by a Central Management Unit that supports application management procedures, the preparation of ethical/legal documents, sample or data transfer agreements (MTAs), and prepares budgets and billing.

The request may include all phases of genomic analysis or just some of them. This means that it is also possible to initiate a request in the intermediate points of the service offered.

• Advice on experiment design

• Extraction of DNA and/or RNA from different types of samples (whole blood, frozen or FFPE tissue, etc.)

• DNA/RNA quality analysis (quantification and integrity):

- Quantification of DNA or RNA by fluorimetry and/or spectrophotometry

- Analysis of DNA integrity by agarose gels and/or Bioanalyzer

- Analysis of RNA integrity by Bioanalyzer

• Real-time quantitative 4-PCR (qPCR)

• Microarrays:

- Expression (human, mouse, and other species)

- Genomics

• Next Generation Sequencing (library preparation):

- Whole Genome Sequencing

- Exome Sequencing

- RNA Sequencing

- Small RNA sequencing

- Panel Sequencing

- ChIP Sequencing

- Bisulphite Sequencing

• Data analysis:

- Sequence alignment

- Variant calling and copy number analysis from genomic data

- Identification of differentially expressed genes, alternative splicing and fusion genes in transcriptomic data

- Study of small RNAs through microtranscriptome analysis

- Identification of regions with peak protein-DNA interaction in chromatin immunoprecipitation sequencing experiments (ChIP-seq)

- Identification of methylated DNA positions or regions in methylome data

- Integration of data obtained from different “omic” platforms using specific methodology

- Microarray analysis

- qPCR analysis

Applications

• Discovery of biomarkers involved in biological processes

• Gene expression profile studies

• Detection of genes and pathways involved in diseases and pharmacological treatments

• Pharmacogenomics and toxicogenomics studies

• Alternative splicing detection

• Dose-effect studies

• Classification of samples based on gene signatures

• Predictive models associated with genes

• miRNA analysis

• Microarray analysis of degraded samples (ex: FFPE) or/and low quantity samples (from 500pg of total RNA)

• Genomic analysis

• Integrative analysis

Equipment

• Affymetrix Research Platform: GCS3000 with autoloader

• Agilent Bioanalyzer 2100

• NanoDrop 2000 Spectrophotometer

• GeneAmp PCR System 9700 (gold block) Thermocycler

• Qubit Fluorometer

• Proflex Thermocycler

• 2720 GeneAmp PCR System

• Qubit Fluorometer 2.0 and 4.0

• SimpliAmp Thermocycler

Activity

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The 54 projects attended correspond to the following centers:

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The Microarray Analysis Service is subscribed to the European Microarray Quality Control Programme, organized by the CEQA (Cytogenic European Quality Assessment).

Publications

• García-Díez I, Hernández-Muñoz I, Hernández-Ruiz E, Nonell L, Puigdecanet E, Bódalo-Torruella M, Andrades E, Pujol RM, Toll A. Transcriptome and cytogenetic profiling analysis of matched in situ/invasive cutaneous squamous cell carcinomas from immunocompetent patients  Genes Chromosome Canc 2019; 58(3): 164-174. FI: 2.94. Q2

• Hardy-Werbin M, Simoes da Rocha P, Arpí O, Taus A, Nonell L, Durán X, Villanueva X, Joseph-Pietras D, Nolan L, Danson S, Griffiths R, López-Botet M, Rovira A, Albanell J, Ottensmeier C, Arriola E. Serum cytokine levels as predictive biomarkers of benefit from ipilimumab in small cell lung cancer OncoImmunology 2019; 8(6): e1593810. FI: 5.333. Q1.

Funded projects

• Regulación epigenética de la función inflamatoria del componente epitelial en la progresión metastática del carcinoma escamoso cutáneo (CEC)

- Financing Institution: Fondo de Investigación Sanitaria (PI15/00236)

- Period: from 2016 to 2019

- Principal investigators: Toll, Agustí; Hernández, Inmaculada

- Research collaborator: Bódalo Torruella, Marta

• Validación clínica y mecanismos de acción de las alteraciones moleculares con valor predictivo de progresión en el cáncer de próstata: algoritmo molecular de la carcinogénesis prostática

- Financing Institution: Fondo de Investigación Sanitaria (PI15/00452)

- Period: from 2016 to 2019

- Principal investigator: Lloreta, Josep

- Research collaborator: Nonell Mazelón, Lara

• Desarrollo y validación de un panel de secuenciación para translocaciones y mutaciones con relevancia clínica en neoplasias de células B maduras

- Financing Institution: Fondo de Investigación Sanitaria (PI15/00437)

- Period: from 2016 to 2020

- Principal investigator: Espinet, Blanca

- Research collaborator: Nonell Mazelón, Lara; Puigdecanet Riubujent, Eulàlia

• Micro-RNA as a novel biomarker of cardiovascular fibrosis in patients with degenerative aortic stenosis

- Financing Institution: Marató (201519 10)

- Period: from 2016 to 2019

- Principal investigator: Gómez Pérez, Miguel

- Research collaborator: Nonell Mazelón, Lara

• Ajuts per donar suport a les activitats dels grups de recerca (SGR) (12202)

- Financing Institution: Grup de Recerca Traslacional en Neoplàsies Hematològiques (GRETNHE) SGR

- Period: from 2017 to 2020

- Principal investigator: Espinet, Blanca

- Research collaborator: Nonell Mazelón, Lara; Puigdecanet Riubujent, Eulàlia

• Influencia de las concentraciones de compuestos tóxicos persistentes sobre la mortalidad, la incidencia de trastornos crónicos y la expresión de miARN en población general

- Financing Institution: Fondo de Investigación Sanitaria (PI17/00088)

- Period: from 2018 to 2020

- Principal investigator: Porta, Miquel

- Research collaborator: Bódalo Torruella, Marta

• Alteraciones epigenéticas generadas por exposición prenatal al alcohol en pacientes con SAF (síndrome alcohol fetal). Antioxidante epigalocatequina (EGCG) como herramienta terapéutica

- Financing Institution: Fondo de Investigación Sanitaria (PI16/00566)

- Period from 2017 to 2019

- Principal investigator: García, Óscar

- Research collaborator: Bódalo Torruella, Marta

• Red de salud maternoinfantil y del desarrollo

- Financing Institution: RETIC (RD16/0022/0002)

- Period: from 2017 to 2021

- Principal investigator: García, Óscar

- Research collaborator: Bódalo Torruella, Marta

Fundings

• Grants for Thechnical Support Personnel Contracts. MINECO (PTA2014-09119-I). 2015-2019.

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BIOBANK MARBiobanc

The biobank of the Parc de Salut Mar (MARBiobanc) is a public, non-for-profit facility which stores various collections of biological samples available to the whole scientific community. It is organized as a technical unit with regards to quality, order and destination.

It has restricted access facilities which are equipped with the security control mechanisms necessary to ensure the correct storage of the biological samples, their confidentiality and their traceability in accordance with all the Spanish ethical and legal regulations.

The Biobank Service is certified by AENOR to ISO 9001:2015.

Available human biospecimen collections

• DNA bank for cardiovascular diseases

• Cerebral infarction (ictus) sample bank

• FORTIAM, acute myocardial infarction sample collection

• DNA bank for oncological diseases

• Bank of samples from influenza A (H1N1) patients

• Bank of lung disease samples (Lung Biobank Platform)

• Hematological malignancies bank

• Left over diagnose sample bank

• Cryopreserved tumour bank

• Collection Alzheimer and families (Alfa Study)

• ERyME: Sample collection from patients with rheumatic or muscle-skeletal disease

• GLOSEN: Glomerular diseases sample collection

• Colorectal cancer

Two new collections were incorporated:

• Plasma and serum samples (liquid biopsy) collection from patients with solid and haematological neoplasms

• Tumoroids collection from human colorectal cancer

Research line collections

• Nine new research line collections have been added to the Biobank facility to be managed under biobank standards.

Activity

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There were 47 other services including general assessment in legal and ethical aspects, new collections, National Register of Biobancs (ISCIII), informed consent (IC), revision of documents, etc.

It is important to highlight that in 2019 the biobank obtained 6,514 new donors from patients of the hospital. These donations allow the biobank to transfer their diagnostic/treatment left-over samples to research projects after the approval of biobank external scientific and ethics committees.

The biobank is subscribed to the Biobanks European Quality Control Program, organized by the IBBL (Integrated Biobank of Luxembourg).

Fundings

• Concession of the Biobanks Platform. Instituto de Salud Carlos III/FEDER (PT17/0015/0011). Period: 2018-2020.

Dissemination to society

• 14 MARBiobanc dissemination sessions, including Open Day and student visits.

• MARBiobanc Website. This website has been operational since June 2016. The website received a total of 1,732 visits from January to December 2019, with 734 new users. The pages most visited are in the Spanish language, followed by English.

• MARBiobanc has also available an Instagram channel, and Twitter and LinkedIn profiles.

New Informed Consent (IC) adapted to personal data protection regulation

The new IC models have been developed and distributed, which include Regulation (EU) 2016/679 of the European Parliament and of the Council, and Organic Law 3/2018, on the protection of personal data and the guarantee of digital rights in 2019.

Publications 2019 with MARBiobanc samples

A total of 15 scientific publications have been done with samples obtained from MARBiobanc.

Microdissector Laser (microscopy area)

The ArcturusXT™ microdissection system offers a combination of infrared (IR) laser capture using standard slides, or a combination of both infrared and ultraviolet (IR and UV) laser, using polyethylene naphthalate (PEN) membrane slides laser enabled.

The instrument has a proprietary combination of a gentle IR laser and a powerful UV laser that work in conjunction to efficiently isolate cells without changing morphology or integrity of the biological content. The IR laser helps to capture the cells of interest, and the UV laser microdissects the captured cells. This is done without affecting the morphology of the cells, and allows for visual inspection of the remaining specimen to help ensure the quality of the sample collected. A wide-slide stage format is available for neurobiology researchers working with very large sections of brain tissue. The petri dish stage insert has opened the door for live-cell microdissection applications such as stem cell research and other rare-cell isolations.

The LCM technique can be used on formalin-fixed, paraffin-embedded (FFPE) sections, allowing the use of archival pathological material. In addition, frozen sections of tissue and cytological specimens are also suitable for laser microdissection. The technique causes no apparent alteration to the morphology of the chosen cells, which can be directly visualized after microdissection.

Key features

• Dual laser system-enables a wide range of applications ranging from single-cell isolation to large biopsy extractions.

• IR laser capture microdissection preserves morphology of isolated samples and integrity of biological material for downstream applications.

• Software enables rapid isolation of specific cells in five simple steps, provides quality control feature that allows users to visualize collected sample.

• Flexible sample prep-wide range of slide types and sample preparation formats supported.

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