Microarray Analysis Service

The Microarray Analysis Service (SAM), with the AffymetrixGeneChip® research and diagnostics platform, offers an integrated service for cytogenetic, genomic and transcriptomic studies. The experimental services offered are the sample quality, quantification and microarray processing. Experimental design consultancy, statistical data analysis and orientation to its biological interpretation with specific tools are also included.

Arrays of human, mouse and other species are available.

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) and low quantity samples (from 500pg of total RNA)

Equipment

• Affymetrix Research Platform: GCS3000 with autoloader

• Affymetrix Diagnosis Platform: Molecular Diagnostic System Model GCS3000DX2

• Agilent Bioanalyzer 2100

• NanoDrop 2000 Spectrophotometer

• GeneAmp PCR System 9700 (gold block) Thermocycler

• Qubit Fluorometer

• Proflex Thermocycler

• 2720 GeneAmp PCR System

Activity

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The services carried out 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

• Giménez-Arnau A, Curto-Barredo L, Nonell L, Puigdecanet E, Yélamos J, Gimeno R, Rüberg S, Santamaria-Babí L, Pujol RM. Transcriptome analysis of severely active chronic spontaneous urticaria shows an overall immunological skin involvement. Allergy 2017; 72(11): 1778-1790. IF 7.361. Q1.

• Colomo L, Vázquez I, Papaleo N, Espinet B, Ferrer A, Franco C, Comerma L, Hernández S, Calvo X, Salar A, Climent F, Mate JL, Forcada P, Mozos A, Nonell L, Martínez A, Carrió A, Costa D, Dlouhy I, Salaverria I, Martín-Subero JI, López-Guillermo A, Valera A, Campo E; Grup per l’Estudi dels Limfomes de Catalunya i Balears (GELCAB). LMO2-negative Expression Predicts the Presence of MYC Translocations in Aggressive B-Cell Lymphomas. American Journal of Surgical Pathology 2017; 41(7): 877-886. IF 5.363. Q1.

• Garcia-Elias A, Alloza L, Puigdecanet E, Nonell L, Tajes M, Curado J, Enjuanes C, Díaz O, Bruguera J, Martí-Almor J, Comín-Colet J, Benito B. Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs. Scientific Reports 2017; 7: 7725. IF 4.259. Q1.

• Bustamante M, Hernández-Ferrer C, Sarria Y, Harrison GI, Nonell L, Kang W, Friedländer MR, Estivill X, González JR, Nieuwenhuijsen M, Young AR. The acute effects of ultraviolet radiation on the blood transcriptome are independent of plasma 25OHD3. Environmental Research 2017; 159: 239-248. IF 3.835. Q1.

• Lloreta J, Font-Tello A, Juanpere N, Frances A, Lorenzo M, Nonell L, de Muga S, Vázquez I, Cecchini L, Hernández-Llodrà S. FOXO1 downregulation is associated with worse outcome in bladder cancer and adds significant prognostic information to p53 overexpression. Human Pathology 2017; 62: 222-231. IF 3.014. Q1.

• Companioni O, Sanz-Anquela JM, Pardo ML, Puigdecanet E, Nonell L, García N, Parra Blanco V, López C, Andreu V, Cuatrecasas M, Garmendia M, Gisbert JP, González CA, Sala N. Gene expression study and pathway analysis of histological subtypes of intestinal metaplasia that progress to gastric cancer. PLoS ONE 2017; 12(4): e0176043. IF 2.806. Q1.

• Nomdedéu JF, Puigdecanet E, Bussaglia E, Hernández JJ, Carricondo M, Estivill C, Martí-Tutusaus JM, Tormo M, Zamora L, Serrano E, Perea G, de Llano MP, García A, Sánchez-Ortega I, Ribera JM, Nonell L, Aventín A, Solé F, Brunet MS, Sierra J. Feasibility of the AML profiler (Skyline™ Array) for patient risk stratification in a multicentre trial: a preliminary comparison with the conventional approach. Hematological Oncology 2017; 35(4): 778-788. IF 3.118. Q2.

• Alonso S, Mayol X, Nonell L, Salvans S, Pascual M, Pera M; Colorectal Cancer Research Group (Hospital del Mar Medical Research Institute). Peripheral blood leukocytes show differential expression of tumour progression-related genes in colorectal cancer patients who have a postoperative intra-abdominal infection: a prospective matched cohort study. Colorectal Disease 2017. 19(5); O115-O125. IF 2.689. Q2.

Participation in projects

• Grup de Recerca Translacional en neoplàsies hematològiques (GRETNHE). 2017-2019. Agència de Gestió d'Ajuts Universitaris i de Recerca (SGR 437). Lourdes Forensa, Lara Nonell, Eulàlia Puigdecanet

• 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. FIS (PI16PI15/00452). (2016-2018). Josep Lloreta, Lara Nonell

• Desarrollo y validación de un panel de secuenciación para translocaciones y mutaciones con relevancia clínica en neoplasias de células B maduras. FIS (PI15/00437). (2016-2018). Blanca Espinet, Lara Nonell, Eulàlia Puigdecanet

• Micro-RNA as a novel biomarker of cardiovascular fibrosis in patients with degenerative aortic stenosis. Marató 201519 10. (09/03/2016-08/03/2019). Miquel Gómez Pérez, Lara Nonell

• Regulación epigenética de la función inflamatoria del componente epitelial en la progresión metastática del carcinoma escamoso cutáneo (CEC) (PI15/00236) (2017-2018) Agustí Toll, Inmaculada Fernández, Marta Bódalo

• Alteraciones epigenéticas generadas por exposición prenatal al alcohol en pacientes con SAF (síndrome alcohol fetal). Antioxidante epigalocatequina (EGCG) como herramienta terapéutica (PI16/00566) (2017-2019) Òscar Garcia, Marta Bódalo.

• Red de Salud Materno-Infantil y del Desarrollo (RD16/0022/0002) (2017-2021) Òscar Garcia, Marta Bódalo (no projecte té data de fi 03/01/2017)

Funding

• Grants for Thechnical Support Personnel Contracts.  MINECO (PTA2014-09119-I). (2015-2018)

• Grants for the promotion of “empleo joven e implantación de la Garantía Juvenil”: Implementation of new protocols for difficult samples and microarray data analysis. MINECO (PEJ-2014-A-15816)

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BIOBANC 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

Research line collections

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

Activity

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

MARBiobanc is the first biobank in Spain to implement an evaluation as a way of controlling samples transferred to clinical trials and their future uses.

In addition, MARBiobanc reviews all the agreements with the pharmaceutical industry to prevent surpluses being used for unspecified research. This special and urgent evaluation system guarantees the necessary speed and control of samples used in clinical trials.

The Reference Laboratory of Catalonia (Laboratori de Referència de Catalunya – LCR) has been included in the MARBiobanc since 24 May 2017 as a new node. This new node includes all residual samples obtained at the phlebotomy department.

Funding

• Biobanks Platform. Instituto de Salud Carlos III/FEDER (PT13/0010/0005). (2015-2017).

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

• Network of Tumour Banks (Xarxa de Bancs de Tumors-XBTC) sponsored by the Master Plan for Oncology of Catalonia.

• Grants for the promotion of “youth employment and implementation of the Youth Guarantee”: Implementation of new protocols in the Biobank: cryopreservation, immortalization, microdissection. PEJ-2014-A-40109. MINECO.

Dissemination

• MARBiobanc Website. This website has been operational since June 2016. The website received a total of 1,449 visitors from January to December 2017, with 892 new users. The pages most visited are in the Spanish language, followed by English.

• Creation of the new MarBiobanc Twitter channel in September 2017.

Publications 2017 with MARBiobanc samples

• Sabbaghi M, Gil-Gómez G, Servitja S, Arpí O, García-Alonso S, Menéndez S, Arumí M, Serrano L, Salido M, Muntasell A, Martínez-García M, Zazo S, Chamizo C, González-Alonso P, Madoz-Gúrpide J, Eroles P, Arribas J, Tusquets I, Lluch A, Pandiella A, Rojo F, Rovira A, Albanell J. Defective cyclin B1 induction in trastuzumab-emtansine (T-DM1) acquired resistance in HER2-positive breast cancer. Clin Cancer Res 2017; 23(22): 7006-7019. IF 9.619. Q1.

• Mateu-Jiménez M, Curull V, Pijuan L, Sánchez-Font A, Rivera-Ramos H, Rodríguez-Fuster A, Aguiló R, Gea J, Barreiro E. Systemic and Tumor Th1 and Th2 Inflammatory Profile and Macrophages in Lung Cancer: Influence of Underlying Chronic Respiratory Disease. J Thorac Oncol 2017; 12(2): 235-248. IF 6.595. Q1.

• Álvarez-Larrán A, Senín A, Fernández-Rodríguez MC, Pereira A, Arellano-Rodrigo E, Gómez M, Ferrer-Marín F, Martínez-López J, Camacho L, Colomer D, Angona A, Navarro B, Cervantes F, Besses C, Bellosillo B, Hernández-Boluda JC. Impact of genotype on leukaemic transformation in polycythaemia vera and essential thrombocythaemia. Br J Haematol 2017; 178(5): 764-771. IF 5.67. Q1.

• Puiggros A, Collado R, Calasanz MJ, Ortega M, Ruiz-Xivillé N, Rivas-Delgado A, Luño E, González T, Navarro B, García-Malo M, Valiente A, Hernández JÁ, Ardanaz MT, Piñán MÁ, Blanco ML, Hernández-Sánchez M, Batlle-López A, Salgado R, Salido M, Ferrer A, Abrisqueta P, Gimeno E, Abella E, Ferrá C, Terol MJ, Ortuño F, Costa D, Moreno C, Carbonell F, Bosch F, Delgado J, Espinet B. Patients with chronic lymphocytic leukemia and complex karyotype show an adverse outcome even in absence of TP53/ATM FISH deletions. Oncotarget 2017; 8(33): 54297-54303. IF 5.168. Q1.

• Gómez-Acebo I, Dierssen-Sotos T, Fernández-Navarro P, Palazuelos C, Moreno V, Aragonés N, Castaño-Vinyals G, Jiménez-Monleón JJ, Ruiz-Cerdá JL, Pérez-Gómez B, Ruiz-Domínguez JM, Molero JA, Pollán M, Kogevinas M, Llorca J. Risk Model for Prostate Cancer Using Environmental and Genetic Factors in the Spanish Multi-Case-Control (MCC) Study. Sci Rep 2017; 7: 8994. IF 4.259. Q1.

• Casadevall D, Clavé S, Taus A, Hardy-Werbin M, Rocha P, Lorenzo M, Menéndez S, Salido M, Albanell J, Pijuan L, Arriola E. Heterogeneity of Tumor and Immune Cell PD-L1 Expression and Lymphocyte Counts in Surgical NSCLC Samples. Clin Lung Cancer 2017; 18(6): 682-691.e5. IF 3.434. Q2.

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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