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Oxford University Hospitals NHS Foundation Trust

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Cytogenetics Laboratory

The Cytogenetics Laboratory investigates the whole genome for loss or gain of chromosomal material and structural rearrangements of the chromosomes.

Our laboratory provides a comprehensive genetic testing service for a broad range of clinical conditions, both constitutional and cancer, and accepts referrals from a broad spectrum of medical disciplines.

Our constitutional service spans prenatal diagnosis, neonatal and paediatric investigations for recognised syndromes, investigation of developmental delay and learning difficulties, multiple congenital abnormalities or dysmorphism as well as investigating infertility and reproductive problems in adults. In conjunction with Clinical Geneticists, also based at the OUH, we also undertake specialist tests for rarer genetic syndromes.

Our oncology service includes chromosomal investigations for haematological malignancy and a range of other tumour types such as paediatric tumours, sarcomas and oligodendrogliomas. Cytogenetics helps to provide an accurate diagnosis and assist with clinical management and treatment selection. Cytogenetic markers can monitor the course of disease and provide an early indication of relapse.

The Cytogenetics Laboratory participates in the Genomics Quality Assessment Schemes for each aspect of our service (

Research and development

Genetics is a rapidly evolving field and our laboratory is involved in translating research into diagnostics. We are collaborating with the Oxford Biomedical Research Centre (OxBRC) - a partnership between the Oxford University Hospitals and the University of Oxford - in developing targeted array CGH for brain malformations, for cardiac abnormalities and for speech and language impairment.

Range of investigations

Karyotyping (chromosome analysis)

Karyotyping involves the microscopic examination of the chromosomes. This test can detect loss or gain of material in any region of any chromosome as well as both balanced and unbalanced structural rearrangements such as translocations and inversions. As this test examines the chromosomes microscopically, the level of detail is limited by the resolution of the microscope and imbalances of ~ 5 Mb or greater can be detected.

Living cells are required for cell culture to produce the chromosome preparations hence frozen or fixed material cannot be processed.

Please select below for:

Array Comparative Genome Hybridisation (Array CGH)

Array CGH involves labelling the patient's DNA with a fluorescent dye, hybridising against 'normal' control DNA labelled with a different dye, using a laser scanner to measure the ratio of the two dyes across sequential segments of the genome and hence detect loss or gain of chromosomal material in the patient. This technique allows examination of the whole genome in greater detail and can detect imbalances of 100 - 200Kb or greater. The software allows cross referencing to international databases to allow identification of the genes in the region of imbalance. This test detects imbalance and does not detect balanced rearrangements.

This test can detect chromosomal imbalance and can also be used to further define the breakpoints and gene content of known chromosome abnormalities.

Referrals are routinely made in conjunction with Clinical Genetics.

This test is primarily undertaken on blood and tissue samples (please discuss with the laboratory for other sample types).

Please select below for:

Postnatal blood sample information

Fluorescence in situ hybridisation (FISH)

FISH is the microscopic examination of either interphase cells or chromosomes for the presence or absence of a fluorescently tagged probe. The probe is specific for the region of a chromosome containing the genes for an explicit genetic syndrome or condition (e.g. examination of 22q11 for DiGeorge syndrome or outflow cardiac abnormalities).

Interphase analysis can also be undertaken as a rapid investigation for whole chromosome trisomy 13,18 or 21.

Each FISH probe is specific to a region of DNA (and associated syndrome) and therefore the syndrome or region for investigation must be specified on the referral card.

FISH investigations are available for most microdeletion syndromes and conditions.

FISH can be undertaken on preparations from cultured or uncultured cells (e.g. prenatal and postnatal investigations) or from paraffin embedded fixed material (e.g. tumour sections).

Please select below for:

Quantitative Fluorescence PCR (QF-PCR)

QF-PCR measures the number of alleles for specific regions of DNA and by examining a series of alleles along a specific chromosome, the copy number for that chromosome can be established. This test is used as a rapid test to screen for trisomy of chromosome 13, 18 or 21, primarily in prenatal diagnosis.

Please select below for:

Please contact the laboratory for test details and sample information:

  • Buccal interphase FISH
  • Breakage Syndromes - As of the 1st October, referrals for cytogenetic investigations of breakage syndromes from our region which would previously have been processed in Oxford, will now be processed and reported by the West Midlands Regional Genetics Laboratory (WMRGL) in Birmingham. Please click here for more information.


All reports are sent by post or e-mail (where agreed) to the referring clinician: hospital consultant, community paediatrician, GP.

For discussion of the result and report, please contact our Cytogenetic office:

Tel: 01865 226001

They will forward your call to the appropriate person.

Contact details for the laboratory can be found on our Home Page

Last updated: April 4, 2019 by Claire Scott