Microarray; FISH; QF-PCR; Infertility; dd_PCR


Tel: 0131 537 2998

Referral Indications

Microarray testing will only be performed for patients meeting the following criteria:

  • Moderate or severe intellectual disability or global developmental delay
  • OR
  • Two or more major malformations

  • OR
    at least TWO of the following:
  • Growth disorder (> or < 2.57 SD for birth weight OR length/height OR head circumference)
  • Severe physiological instability (including epilepsy)
  • Severe behavioural phenotype
  • Major craniofacial dysmorphism
  • Single major malformation

For referral with limited clinical details, blood samples in both lithium heparin and EDTA will be processed and stored and a Phenotype Information Form will be issued.   This can be completed and returned if microarray testing is still considered appropriate and testing will be actioned upon receipt.  Repeat samples will not be necessary.


  • Characterisation of prenatal abnormalities (e.g. abnormal ultrasound or increased risk from Serum Screen)
  • Solid Tissue samples where there is a fetal anomaly/parental chromosomal rearrangement/history of recurrent miscarriage
                 NB This test is not available for ?mosaicism screen on live skin samples

  • Characterisation of 1p 19q co-deletion in anaplastic oligodendroglioma

Specimen Requirements

Two specimen tubes are required; one a lithium Heparin specment tubes, the other an EDTA (KE) tube.

Arrange for immediate transport to the Cytogenetics Laboratory.  if this is not available, blood specimens should be refrigerated. (DO NOT FREEZE)

Reporting Times and success rates


National Target

Proband (no follow up studies required)

Within 28 days from receipt of sample or DNA

Proband and parental blood samples referred together (follow up material held by laboratory)

Within 28 days of receipt of sample or DNA

Parental blood samples requested after detection of imbalance in proband

Within 28 days from receipt of parental blood samples

Referring clinicians are requested to comply with NHS Lothian policy on Mandatory Data Sets:  Failure to do so will result in delays in processing or rejection of the sample.

FISH (Fluorescent In Situ Hybridisation)

Tel: 0131 537 1944

Microdeletion syndromes.

Fluorescent IN SITU Hybridization (FISH) can be used to detect missing pieces of DNA, known as microdeletions that are beyond the resolution of routine cytogenetic techniques

Structural abnormalities

Complex chromosome rearrangements and sub-microscopic rearrangements can be studied by molecular cytogenetic techniques using chromosome paints.

Cancer Cytogenetics

The same techniques used to study structural abnormalities and aneuploidy in constitutional samples can also be used to study cancer cells. There are specific probes available to detect gene fusions that have arisen as a result of the rearrangement of specific genetic material.
Gene fusions currently detectable by FISH include:

  • BCR/ABL in chronic myeloid leukaemia
  • PML/RARA in acute promyelocytic leukaemia
  • ETV6/RUNX1 in acute lymphoblastic leukaemia
  • t(14;18) in follicular lymphoma

Click here to see the Repertoire of tests

QF-PCR (Quantitative Fluorescence Polymerase Chain Reaction)

Small sections of DNA from the sample are amplified, labelled with fluorescent tags and the amounts measured by electrophoresis.

QFPCR is used to measure gene dosage.  It can be used to test for aneuploidy of whole chromosomes.

For Prenatal samples aneuploidy for chromosomes 13,18,21,X and Y are tested

For Tissue samples aneuploidy for chromosomes 13,15,16,18,21,22,X and Y are tested.

For neonatal blood: The laboratory offers a rapid aneuploidy test for Chromosome 21. Referrals must be discussed with a Consultant Clinical Geneticist prior to sending the sample.

Male Factor Infertility Kit

Y chromosomal microdeletions are the second most common cause of male infertility after Klinefelter’s syndrome with deletion frequencies varying between 2 and 10% in azoospermic men, dependent on patient selection (Krausz et al., 2013).
Clinically relevant deletions have been identified in three regions of the Y chromosome, AZFa, AZFb and AZFc.

Testing of Y microdeletion by QF-PCR is available for patients with azoospermia (sperm concentrations < 2x10^6/ml).

Please note:  This test requires 2-5mL of peripheral blood in an EDTA tube.


dd_PCR (Droplet Digital Polymerase Chain Reaction)

This technique is used to confirm copy number abnormalities detected by microarray analysis of the whole genome.

Use of probe based assays gives an absolute count of the number of target sequences compared to a reference sequence from the same sample to give a highly accurate value of the copy number status.

Assays are designed 'in house' to target particular copy number variants or target genes within a deletion or duplication.

Referral are internal only.  External requests must be discussed with a Consultant Clinical Geneticist prior to sending the sample.

Last Reviewed: 23/05/2017