Central Support Units for Biomedical Research

Genomics

The aim of the IMIBIC Genomics Unit is to provide researchers with cutting-edge technologies and scientific/technical advice for the development of analytical techniques dedicated to the integral study of DNA and RNA. This allows researchers to obtain high-quality results for the development of biomedical research of excellence.

The Unit offers its services to researchers both at IMIBIC and other public and private institutions. The Genomics Unit collaborates closely with other Research Support Services, such as Bioinformatics, Cytometry, Microscopy and Mass Spectrometry (IMSMI).

The IMIBIC Genomics Unit is accredited as a ‘Clinical Genetics Unit’ (N.I.C.A.: 57798) and has a Quality Management System in accordance with the ISO 9001:2015 Quality Standard.

Personnel

Álvaro Jiménez Arranz

Head of Genomics Unit

• genomica@imibic.org
• alvaro.jimenez@imibic.org
• +34 957 21 37 59 (Corporative 3759)

Beatriz Domingo Escudero

Technical Specialist

• beatriz.domingo@imibic.org
• +34 957 21 37 59 (Corporative 3759)

Pilar Rubín González de Canales

Lab Technician

• pilar.rubin@imibic.org
• +34 957 21 37 58 (Corporative 3758)

María García Cruz

Lab Technician

• maria.garciacruz@imibic.org
• +34 957 21 37 58 (Corporative 3758)

Equipment and Facilities

NGS (Next Generation Sequencing)

The Unit currently has 2 NGS sequencers based on Illumina's Sequencing by Synthesis (SBS) technology:.

• MiSeq
• NextSeq 2000

The different capacities of both sequencers provide a high versatility to the NGS services of the Unit, allowing to offer applications ranging from the study of the bacterial 16S rRNA gene to the analysis of human genomes.

nCounter FLEX / NanoString technology

The NanoString´s nCounter system uses molecular barcodes linked to specific probes that enable the detection and counting of hundreds of targets in a single reaction without amplification or retrotranscription, thereby decreasing the associated bias and increasing reproducibility. Multiple applications include gene expression analysis, gene fusion, copy number variation (CNV) and simultaneous analysis of mRNAs and miRNAs. These applications, together with its Dx/CE-IVD certificate for the performance of analyses with healthcare-quality, as in the case of the Prosigna-PAM50 test, make NCounter a tool of great interest for clinical use.

Single-cell technologies

The Unit currently has 2 single-cell analysis platforms:

• Nadia
• C1

These technologies allow, among other possibilities, to analyse and compare gene expression profiles at the single-cell level thanks to the combination with the NextSeq 2000 NGS sequencer or the Biomark HD-Juno high-throughput qPCR platform.

Digital PCR (dPCR): QX200 Droplet Digital PCR System

The digital PCR offers a more precise and sensitive alternative to conventional qPCR for absolute quantification and detection of rare alleles without the need of standards or endogenous controls due to droplet partitioning.

Quantitative PCR (qPCR)

The Unit currently has 4 qPCR instruments aimed, among other applications, at genotyping and gene expression studies:

• Light Cycler 96 (96-well system)
• QuantStudio 5 (96-well system)
• QuantStudio 7 Flex (96-well, 384-well and Taqman Array Cards system)
• Biomark HD-Juno (High-throughput nanofluidics system)

With regard to IMIBIC research staff, the Unit offers the possibility of using the qPCR instruments under a "self-service" system (without a technical operator).

Quality Control equipment

The Unit has different technologies for quantification, quality analysis and size determination of nucleic acid fragments:

• DeNovix DS-11 (Spectrophotometer)
• Quantus (Fluorometer)
• 2200 TapeStation (Microelectrophoresis)

Services

• Technical support and scientific and methodological advice on the choice and optimization of genomic techniques
• Design support for NGS or NCounter targeted panels
• Technical and scientific support in the use of qPCR platforms and probe design
• Nucleic acid quality controls (spectrophotometry, fluorometry and microelectrophoresis)
• Analysis of targeted gene expression panels (up to 800 genes) using NCounter System
• PAM50-signature Analysis (ProsignaTM) for breast cancer prognosis
• Analysis of custom panels for detection of targeted fusion genes by NCounter System
• Screening of up to 800 miRNAs in tissue, peripheral blood cells and serum/plasma by NCounter System
• Gene expression and genotyping studies using real-time PCR
• Absolute quantification by Droplet Digital PCR System (viral load analysis…)
• Liquid biopsy (cfDNA): Rare mutation detection by ddPCR and analysis of SNVs, Indels, CNVs and fusions by NGS
• Analysis of SNVs, Indels and CNVs in peripheral blood cells and tissue by NGS or Ncounter System
• Characterization of bacterial populations by 16S rRNA and shotgun sequencing
• Targeted sequencing for the characterization of Mycobacteria and SARS-CoV-2 (epidemiological monitoring protocol)
• RNA-Seq
• Single-cell RNA-Seq and single-nuclei RNA-Seq
• ATAC-Seq
• ChIP-Seq
• DNA methylation analysis by NGS
• NGS library preparation
• NGS by Illumina Miseq and NextSeq 2000
• Training and support in the use of data analysis software related to the Unit’s technology

Projects

Some of the projects in which the IMIBIC Genomics Unit is participating or has recently participated are:

• High-performance diagnostic platform for personalised medicine in patients with Acute Myeloblastic Leukaemia. Pethema Foundation Group. Carlos III Health Institute.
• Molecular characterisation of Gestational Breast Cancer. IMIBIC. Carlos III Health Institute.
• EMBARCAM. Ambispective observational study of pregnancy and Breast Cancer registry. Spanish Breast Cancer Research Group (GEICAM).
• EpiGEICAM. Molecular subtypes of Breast Cancer: risk factors and their prognostic influence in EpiGEICAM. Spanish Breast Cancer Research Group (GEICAM).
• RETUD. Descriptive multicentre observational epidemiological study on digestive tumours. NGS programme in Cholangiocarcinomas. Spanish Group for the Treatment of Digestive Tumours (TTD).
• VISNÚ. CTCs, molecular alterations and their correlation with treatment in mCRC. Spanish Group for the Treatment of Digestive Tumours (TTD).
• ONCO-NGS. Evaluation of the usefulness of NGS in the molecular analysis of tumours through a multidisciplinary board. Reina Sofia University Hospital (HURS).
• PERSEIDA. Determination of RAS mutational status in liquid biopsies from subjects with first-line non-mutated RAS Metastatic Colorectal Cancer: an observational, prospective, multicentre study in Spain. Amgen.

Highlights

• Since the creation of the Unit in 2015, the number of projects and researchers using our services has increased progressively, currently analysing more than 23.000 samples/year with the Unit's technologies.
• The Genomics Unit of IMIBIC is accredited since 2021 as "Clinical Genetics Unit" (N.I.C.A.: 57798) and participates in a multidisciplinary team, together with several departments of the Reina Sofia University Hospital (HURS), aimed at the implementation of genomic diagnostic protocols in the Andalusian Public Health Service. The Unit carries out services developed together with the Departments of Anatomic Pathology, Oncology and Haematology of the HURS and is part of the Research Committee in Molecular Clinical Oncology, focused on the evaluation of NGS as a diagnostic, prognostic and therapeutic tool for oncology patients.
• The Genomics Unit participates as a collaborator laboratory in projects of the Pethema Foundation and the TTD (Spanish Group for the Treatment of Digestive Tumours) and GEICAM (Spanish Breast Cancer Research Group) groups. In addition, the Unit collaborates in different clinical trials with the pharmaceutical industry and in inter-laboratory validations of genetic/genomic diagnostic kits from different companies.
• The Unit is part of several laboratory networks, such as the EATRIS network (European Infrastructure for Translational Medicine), Innolabs and the Novartis laboratory network.