Core Facilities

Genomics Unit

Justification

Nucleic acid sequencing has become a fundamental tool in the diagnosis of numerous diseases, patient stratification according to risk, disease monitoring and the identification of therapeutic targets.

Nucleic acid sequencing has enabled significant development of genetic diagnosis in the laboratory, as well as the knowledge generated by research into the genetic bases of a wide range of diseases.

On this basis, the Genomics Unit’s mission is to provide scientific and technical support to research groups both within and outside the Gregorio Marañón Health Research Institute (IiSGM) in the field of genomics.

Description of the facilities

The Genomics Unit is located on Floor -1 of the Maternal and Child Building of Hospital General Universitario Gregorio Marañón. For carrying out massively parallel sequencing studies, it has high-end equipment dedicated to clinical and research studies. This includes two Miseq massively parallel sequencers, one MiSeqi100, one NextSeq 550, one NextSeq 2000 and one NovaSeq 6000 (Illumina). We have two Microlab STARLET robots (Hamilton) and one Magnis robot (Agilent) for automating library preparation for NGS sequencing. The Unit also has three genetic analysers: ABI 3130xl (16 capillaries), ABI3730xl (96 capillaries) and one SeqStudio Flex (48 capillaries; Applied Biosystem), one Qubit fluorometer and one Nanodrop for nucleic acid quantification, one Tape Station 4150 fragment analyser (Agilent), two nucleic acid extraction systems (Maxwell, Promega) and one single-cell separation system (iChromium).

In addition, the Genomics Unit is equipped with four conventional thermocyclers with a 96-well block (GeneAmp 9700 PCR System, 2 SimpliAmp and Touch ThermoCycler C1000), one Qubit fluorometer (Thermo), one Nanodrop spectrophotometer (Thermo), one Labchip fragment analyser (PerkimElmer), Speed-Vac (Thermo), refrigerated plate centrifuges, a refrigerated Eppendorf centrifuge, a heating block, vortex and mini-spins.

The Genomics Unit occupies an area of 85m² and has computing resources with high data storage and processing capacity.

Service Portfolio

Sample quantification

Fluorescence-based nucleic acid sample quantification method (Qubit).

Fragment size

DNA fragment size analysis (Labchip).

Primer design

Advice on primer and probe design for PCR studies.

Sequencing

Automated sequencing of purified PCR products and cloned DNA in vectors by capillary electrophoresis using BigDye Terminator v3.1 chemistry (Applied Biosystem 3130xl and 3730xl). All samples are purified to prevent background noise and remove the remaining terminators. The primers used for the sequencing reaction are specific to the region under study.

Interpretation of conventional sequencing results

  

Fragment analysis

Analysis of fluorescently labelled fragments by capillary electrophoresis (Applied Biosystem 3130xl and 3730xl). In-house or commercially designed fluorescently labelled fragments up to 1200 bp.

Interpretation of fragment analysis results

  

MLPA

Multiplex ligation probe amplification. Probe binding-ligation reaction with the homologous region of interest, followed by PCR amplification.

Interpretation of MLPA results

  

Library preparation

DNA library preparation (enrichment, indexing and library quality control)

Massive sequencing

Sequencing-by-synthesis technology (MiSeq and NextSeq NovaSeq ). Preparation of the application-specific library; an already prepared library can also be provided, provided that it is compatible with the Illumina sequencing system.

Gene panel design

Design of gene panels intended to study one or more phenotypes.

Procedure for requesting a specific service

The form Hoja de Encargo IM-SPE-06 or IM-SPE-07 of the IiSGM will be used. The Hoja de Encargo consists of 5 parts:

  1. SAI identification
  2. Applicant identification*
  3. Details of the service required and budget**
  4. Comments: Indicate whether it is a self-invoice or not***
  5. Signatures

* Applicant identification: where the researcher to whom the cost of the service is to be charged is a new user, they must complete and attach the signed billing details form with the first Hoja de Encargo.

**Details of the services provided:

  • Sample quantification
  • Fragment size
  • Primer design
  • Sequencing
  • Interpretation of conventional sequencing results
  • Fragment analysis
  • Interpretation of fragment analysis results
  • MLPA
  • Interpretation of MLPA results
  • Library preparation
  • Massive sequencing
  • Interpretation of massive sequencing results
  • Gene panel design

***Where it is necessary to justify expenditure in public projects, the PNT Autofacturación procedure PR-SPE-06 of the IiSGM will be applied.

IMPORTANT: the expenditure must have been approved by the funding agency, either because it was included in the budget of the initial application (ideal situation), or because the expenditure was subsequently approved after a formal written request.

The procedure to be followed is as follows:

  • Request for the study to be carried out.
  • Preparation and delivery of the samples.
  • Performance of the analysis.
  • Delivery of results.
  • Sequencing results are archived in the Genomics Unit for 2 years so that the results can be reanalysed if necessary.

SAI Genomics Unit Rates

Contact people

Julia Suárez González
Technical Manager of the Genomics Unit
Email: julia.suarez(ELIMINAR)@iisgm.com
Tel: 91 529 01 51
Gregorio Marañón General University Hospital (HGUGM)
Calle Doctor Esquerdo 46, 28007 Madrid

Belén Beteré Cubillo
Medical Specialist of the Genomics Unit

Laura Martínez Figueras
Medical Specialist of the Genomics Unit

Elena Lamparero Hernández
Laboratory Technician of the Genomics Unit

María Isabel Pérez Martínez
Laboratory Technician of the Genomics Unit

Marta Sánchez Carrillo
Laboratory Technician of the Genomics Unit

Marta Sánchez Gómez
Laboratory Technician of the Genomics Unit

Ahinoa Simón Zarate
Laboratory Technician of the Genomics Unit