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Genetic Testing

The importance of Clinical Details

Clinical details are very important when providing genetic analysis. The more clinical information that is available (e.g. details of ultrasound information, phenotypic features or family history) the better the service we can provide. Failure to provide this information for cytogenetic studies may result in an inaccurate analysis.

CYTOGENETICS

Cytogenetic analysis is performed according to the Professional Guidelines for the Association of Clinical Genetic Science and the recommendations provided are dependent on the clinical indications given for each case.

 

Clinical details inform the investigation at all stages:

  • Prior to analysis, clinical details may indicate, for example, that procedures such as chromosome breakage or leukaemic studies are required, which must be referred to a specialist centre.
  • During analysis they may indicate that extra cells should be screened to investigate the possibility of mosaicism, for example in a diagnosis of suspected Turner syndrome, or that particular chromosomes must be targeted for high-resolution study, for example chromosome 4 in suspected Wolf-Hirschhorn syndrome.
  • When the analysis has been completed they may help to provide an accurate interpretation of the findings and in some instances prompt further investigations, for example FISH or molecular genetic studies.

When clinical details are not available a routine analysis will be performed and a conditional report issued.

MOLECULAR GENETICS

Clinical details can be extremely important for clinical interpretation of a molecular genetic test.

For example, the clinical comments accompanying a cystic fibrosis screening report will vary depending on whether the patient is a potential gamete donor or a person exhibiting a cystic fibrosis phenotype. Similarly, the interpretative comment accompanying Factor II and V studies may vary depending on whether the investigation is prompted by a history of recurrent miscarriage or the need to determine a thrombotic risk.

It may also be crucial, where a mutation has already been shown to be segregating in a family, to be provided with information concerning the mutation and a family pedigree to ensure the correct analysis is performed and reliable risk figures calculated.


Notes for Cytogenetics

As cytogenetic studies require living cells, please ensure that samples reach the laboratory quickly. If a delay before despatch is unavoidable, samples may be stored in a refrigerator (4°C) but they must not be frozen.

Information concerning packaging, transportation, and labelling of samples is provided on the inside cover of our TDL Genetics Request Form Pad.

On completion of analyses, fixed cell suspensions are stored for a minimum of three months and are available for additional follow-up studies (for example, FISH), if necessary.


Requesting additional tests
Any further tests not requested at the time of sample receipt must be requested within:

  • 2 weeks for DNA testing
  • 2 weeks for cell culture testing
  • 3 months for FISH testing

Samples can be stored for longer periods if specifically requested at the time of sample receipt.

POSTNATAL DIAGNOSIS (BLOOD CULTURE)

Reasons for analysis: Chromosome studies are requested where problems that may have a cytogenetic basis are suspected, e.g. babies with birth defects; children with developmental delay and physical handicaps, or adults with fertility problems. Additionally, prospective gamete donors are screened to detect carriers of balanced chromosome rearrangements.

 

Sample requirements: Lithium heparin whole blood specimens are required – gently mixed to prevent clotting and must not be frozen, or exposed to temperatures greater than 38°C. Sample volumes may be reduced for children (2-4ml) and neonates (1-2ml).

 

Turnaround time: The usual turnaround time is 2-3 weeks however the laboratory will endeavour to respond to
urgent requests. Where a major trisomy is suspected, a rapid PCR screen may be performed to provide an urgent provisional result.

 

Notes
a) Rarely, blood samples fail to culture (<1%);
b) The culture may yield chromosomes of insufficient quality. This will be indicated on the report and a repeat study suggested;
c) The laboratory should be informed if the patient has recently received a blood transfusion.
d) The laboratory should be informed if the patient has EVER had a bone marrow transplant.

LEUKAEMIC STUDIES (BONE MARROW)

Sample requirements: 5-10ml bone marrow in preservative free heparin and RPMI medium. This can be supplied by the laboratory.

 

Clinical information: Please complete the Leukaemic Studies Request form at the back of the laboratory guide, including WBC, reason for referral, stages of disease/treatment and analysis required e.g. karyotype and/or FISH or PCR.

PRENATAL DIAGNOSIS

Reasons for analysis: Chromosome studies are requested where pregnancies are identified as being at risk of a cytogenetic abnormality e.g. advanced maternal age; positive maternal serum screening; fetal abnormalities found on ultrasound; or where a parent is a known carrier of a chromosome anomaly, or where a high risk trisomy has been found by NIPT. As false positive NIPT results may arise from placental mosaicism, amniocentesis is the suggested sample type for confirmation of NIPT results.

 

Sample requirements:
a) amniotic fluid – 10ml+ in a plain sterile, leak-proof container. Suitable containers can be provided by the laboratory. The specimen must not be frozen.
b) chorionic villus – 5mg+ in sterile transport medium. Suitable containers containing medium can be provided by the laboratory. The specimen must not be frozen.
c) fetal blood – 1-2ml LITHIUM HEPARIN whole blood, gently mixed to prevent clotting. The specimen must not be frozen.


Turnaround time:
This is dependent on the rate of cell growth, however, the usual turnaround time is approximately 2 weeks. A number of circumstances now occur more frequently, as invasive prenatal diagnosis becomes less common, that may result in delayed reporting time. These include:

a) A delay in transportation in order to collect a batch of samples to reduce courier costs. Even when couriered promptly, sample growth may be slower than that seen in samples sent immediately.

b) Sampling at early or late gestations, for example to confirm non-invasive tests or follow up anomaly scans.

c) A tendency to take smaller quantities of sample or to take insufficient sample for multiple techniques.

d) The request for karyotyping as an add-on after an initial PCR test.

Fetal blood results will usually be reported by 10 calendar days.

 

Notes

a) Maternal contamination, and mosaicism may complicate the analysis and may lead to the suggestion
that a second invasive test is performed.

b) Rarely, cultures fail to grow (overall <1%)

c) Very small chromosome abnormalities may not be detected (this is why the phrase ‘No trisomies or major chromosome abnormalites detected…’ is used in our reports).

d) for TTTs or heavily blood stained amniocentesis samples, please provide a maternal EDTA blood sample
for comparison studies.

SOLID TISSUE

Reasons for analysis: Fibroblast cultures may be used in addition to blood cultures, for example where tissue specific mosaicism is suspected, or where blood samples cannot be obtained. POC samples may be requested for early spontaneous miscarriages, stillbirths, or to confirm a prenatal diagnosis.

 

Sample requirements: All specimens should be placed in a sterile container, preferably containing transport medium. This can be supplied by the laboratory. Sterile normal saline can be used if transport medium is not available. Samples must not be placed in formaldehyde or other preservative and must not be frozen.


Turnaround time:
This is dependent on the rate of cell growth, however, the usual turnaround time is approximately 4 weeks.


Notes
a) Material from miscarriages has a relatively high culture failure rate (around 20%). Where failure occurs, alternative molecular methods may be attempted, usually a KaryoLite Bacs-on-Beads assay that can detect whole monosomy or trisomy of any chromosome, if possible.

b) If no villus or fetal parts are identified in supposedly POC material and a normal female chromosome result is found, this may indicate that maternal tissue has been cultured (this will be noted on our report)

c) Material from miscarriages can be returned for sensitive disposal if requested at the time of receipt. If no special request is made, fetal material will be sent for incineration separate from general clinical waste. Placental and other POC material will be disposed of in general clinical waste for incineration.

FLUORESCENCE IN SITU HYBRIDISATION (FISH)

Where FISH studies for specific microdeletion syndromes are required this must be indicated on the request form.

Note: FISH studies for a rapid pre or postnatal aneuploidy screen have now been superseded in our laboratory by multiplex-PCR technology. Subtelomeric screens are now performed by Array CGH as part of developmental delay investigations. Common microdeletion syndrome testing is now performed by BOBs analysis.

CELL LINE KARYOLOGY

The cytogenetics laboratory can perform cell line karyology on live cultures or fixed cells suspensions (recommended) on a research basis. Please contact laboratory for further details.

 

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