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.

 

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. 

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.

 

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.

 

Sample Stability

Molecular Genetic Samples

Whole blood collected in EDTA should be sent to the laboratory between 4˚C-28˚C within 48 hours.

Long term storage should be at 2-8°C.

Extracted DNA samples should be sent to the laboratory between 4˚C-28˚C. 

 

Cytogenetic Samples

Cytogenetic studies require living cells, please ensure that samples reach the laboratory as soon as possible. 

If a delay before dispatch is unavoidable, samples may be stored in a refrigerator (4°C) but they must not be frozen.

Samples sent more than 48 hours after sampling, or kept at temperatures below 4˚C and greater than 38˚C may have inhibited growth.

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

 

Requesting additional tests

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

  • 1 week for tests requiring prenatal culture or cultured cells
  • 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, See sample stability section for cytogenetic samples. 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.

 

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. See sample stability section for cytogenetic samples.

b)  chorionic villus – 5mg+ in sterile transport medium. Suitable containers containing medium can be provided by the laboratory. The specimen must not be frozen. See sample stability section for cytogenetic samples.

c)  fetal blood – 1-2ml LITHIUM HEPARIN whole blood, gently mixed to prevent clotting. The specimen must not be frozen. See sample stability section for cytogenetic samples.

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. For all other prenatal tests, please contact the laboratory prior to taking samples.

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 abnormalities 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. See sample stability section for
cytogenetic samples.

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 note: a laboratory processing charge of £100+VAT is applicable to those cases wherein
a successful analysis cannot be obtained. Please contact the laboratory for further details.



Statement Regarding Measurement Uncertainty (MU)

Measurement Uncertainty is determined for each measurement procedure in the examination phase used to report
measured quantity values on patients’ samples. This is determined during verification of this assay for service
introduction; creation of laboratory standard operating procedures (SOP) and interpretation of the results.

Where examinations include a measurement step but do not report a measured quantity value, the laboratory calculates
the uncertainty of the measurement step where it has utility in assessing the reliability of the examination procedure
or has influence on the reported result.

Estimates of measurement uncertainty are regularly reviewed and are available upon request to laboratory users.