Cytogenetics, Cytogenomics and Molecular Biology Unit

Justification

Genetic studies have become essential for the diagnosis, prognosis, monitoring or treatment selection of patients. There are different types of genetic variants (from point variants to large structural alterations) that require different methodological approaches for their identification. Likewise, the number of altered cells (up to the point of minimal detectable disease) means that the technological approach for detecting genetic variants may be very different. On this basis, the Cytogenetics, Cytogenomics and Molecular Biology Unit aims to provide scientific and technological support in these areas of genetics to the research groups of the Instituto de investigación sanitaria Gregorio Marañón (IiSGM), as well as to any external group.

Description of the facilities

The Cytogenetics, Cytogenomics and Molecular Biology Unit of IiSGM is located on Floor -1 of the Edificio Oncológico y de Terapias Avanzadas, within the Laboratorio de Genética Hematológica of the Haematology Department of Hospital General Universitario Gregorio Marañón.

The Unit has an excellent range of equipment, described below, both for sample preparation and for carrying out a significant battery of tests.

Sample processing:

• Maxwell CSC48 and Maxwell RSC (Promega), automatic extraction of DNA and RNA, cell-free plasma DNA and tissue DNA
• Auto-MACS (Miltenyi Biotec) for the purification of leucocyte lineages.
• Two Class 2 biological safety cabinets (Thermofisher)
• CO2 incubator for cell cultures (Thermofisher)
• Spectrophotometer (Nanodrop)
• Qubit fluorometer (Thermofisher)
• Refrigerated plate centrifuges, refrigerated Eppendorf centrifuge, heating block, vortex and mini-spins.
• Hulamixer (Thermofisher)

Cytogenetics and Cytogenomics studies:

• Conventional fluorescence microscope for the analysis of fluorescence in situ hybridisation (FISH)
• Automated metaphase capture system (Metafer) under the microscope
• For the specific analysis of karyotypes, we use the Ikaros software (2 licences)
• System for optical genome mapping, together with a server and specific software for data analysis (Bionano)

Molecular Biology (particularly techniques for detecting measurable residual disease, MRD).

• Conventional PCR (4 thermocyclers: 1 Verity from Applied Biosystems, 3 SimpliAmp)
• Real-time quantitative PCR (qPCR, LightCycler 480, LightCycler96 Roche)
• Digital PCR (dPCR, QIAcuity, Qiagen)
• Everything required for NGS, including automated library preparation (Hamilton Company, USA)

Service portfolio

• Nucleic acid extraction and quantification
• Automated purification of leukocyte lineages
• Cell cultures (mainly of haematopoietic cells)
• Fluorescence in situ hybridisation in fresh cells or paraffin-embedded samples. Processing, performance and interpretation of results
• Karyotyping of blood, bone marrow or tissue samples with G-banding (Conventional Cytogenetics). Processing, performance and interpretation of results
• Optical genome mapping. Processing (specialised in haematopoietic cells), analysis and interpretation of results (specialised in haematological diseases)
• Conventional PCR, quantitative PCR or digital PCR. Design and optimisation
• Massively parallel NGS sequencing panels for onco-haematology. Processing, performance (in collaboration with the Genomics Unit for sequencing) and interpretation of results
• Liquid biopsy (study of cell-free tumour DNA in plasma). Processing, performance and interpretation of results

Service Request

The IiSGM Service Request Form will be used.

The Service Request Form consists of 5 sections:

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

The procedure to be followed is as follows:

• Request for the study to be carried out.
• Preparation and delivery of the samples if necessary (it is also possible to request use of the machine only).
• Carrying out the analysis.
• Delivery of results.
• Sequencing results are archived in the Unit for 2 years so that the results can be reanalysed if necessary.

SAI Rates Cytogenetics, Cytogenomics and Molecular Biology 

Contact persons