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Collection and Transportation of Genetics Specimens

Collection and Transportation of Genetics Specimens

All specimens submitted to the laboratory must be clearly identified by two unique patient identifiers. Please provide patient’s name and another patient identifier on all sample containers.

Please also ensure that the following details are provided on the request form:


  • The patient’s signed consent for the genetic test requested.*
  • The name and signature of the doctor performing the procedure to obtain tissue samples. The name of the doctor requesting the procedure should also be provided where applicable.
  • The clinic address to indicate where reports need to be sent
  • The name of the nurse or phlebotomist taking the blood sample for testing, as well as the date of the blood-taking. The relevant OT/Ward and Hospital name where applicable should also be provided.
  • The REFERRAL REASON(S) for the test (compulsory requirement). A history and/or intended purpose of the investigation allows us to select the exact culture regime or mode of analysis most appropriate for the clinical scenario.

*Note: Samples sent for karyotyping or molecular genetics testing require the patient’s signed consent on the appropriate form(s). If the patient is <21 year old, his/her parent or legal guardian may give consent for the child.

Samples should arrive in the laboratory within the same day of sample collection whenever possible. They must not be frozen nor fixed. Blood for most molecular DNA testing (except NIPS and ctDNA) should be taken into one or two 3ml EDTA containers. Collection containers must be closed tightly to prevent leakage of sample during transportation to the laboratory. Transport media or sterile bottles may be requested in advance from the laboratory (Genetics Laboratory Tel No: 62485873/4). Do not use expired collection containers or transport media for specimen collection.

KARYOTYPING OF ONCOLOGY SAMPLES

A number of specific chromosomal abnormalities have been found to be associated with particular haematological diseases or disease subgroups. For CLL, peripheral blood is recommended in preference to bone marrow. Indicate if lymphoproliferative disorders are likely to be derived from T- or B-cells as this information will help determine culture regimens employed, including the choice of mitogen.

Sample Requirement:

Bone marrow (Eve of PH and weekend charge applies)

1-5 mL in sterile universal container with transport media

Leukaemic Peripheral blood

5 mL in sodium/ lithium heparin vacutainer tube

KARYOTYPING OF PRENATAL SAMPLES

Cytogenetic prenatal diagnosis studies are performed usually on either chorionic villus or amniotic fluid samples. The discovery of a chromosomal abnormality allows the option of termination, preparation or appropriate obstetric management. Note: Cryptic subtelomeric deletions/duplications and microdeletions syndromes may not be detected with current chromosome resolution, and microarray or FISH is the preferred option when investigating for microdeletions.

  1. AMNIOTIC FLUID (AF)

    The AF sent should be clear and pale yellow in colour. A period in culture is required to obtain a sufficient number of metaphase cells for karyotyping. The chance of culture success is reduced in bloodstained or discoloured sample. The risk of maternal cell contamination may be minimised by discarding the first 1-2 mL of fluid obtained.

    Sample Requirement: 20 mL in sterile universal container

     

  2. CHORIONIC VILLUS SAMPLE (CVS)

    Please provide about 30 mg in sterile CVS transport medium. A period in culture is required to obtain a sufficient number of metaphase cells for karyotyping. Occasional interpretative problems of chromosomal mosaicism may occur. In most cases this is confined to the placental tissue and does not reflect the foetal karyotype. The rare interpretative problems which cannot be resolved after mesenchyme cell culture may require that a further evaluation on amniotic fluid and/or foetal blood sample. There is a small risk of maternal cell contamination.

    Sample Requirement: 30 mg villi in sterile universal container with transport media (Mon to Fri only)

  3. FOETAL CORD BLOOD

    Foetal cord blood for karyotyping is normally sampled only to resolve special interpretative problems.


Sample Requirement:
1-2 mL sodium/ lithium heparin vacutainer tube


KARYOTYPING OF BLOOD SAMPLES

Some Indications for Chromosome Analysis

  • Suspected Down or other chromosome abnormality syndrome
  • Family history of chromosome abnormality
  • Recurrent miscarriages
  • Ambiguous genitalia Abnormalities of secondary sexual development
  • Infertility or Subfertility
  • Azoospermia · Primary or Secondary Amenorrhoea

Sample Requirement:

Neonate Blood:          1-2 mL blood in sodium/ lithium heparin vacutainer tube
Peripheral Blood:       3-5 mL in sodium/ lithium heparin vacutainer tube


Note: Cryptic subtelomeric deletions/duplications and microdeletion syndromes may not be detected with current chromosome resolution, and microarray or FISH is the preferred option when investigating for microdeletions.


Note: Microarray methodologies are accepted as an appropriate first-tier test for the evaluation of imbalances associated with intellectual disability, autism, and/or multiple congenital anomalies (ACMG
standards; South et al., 20131). The International Standard Cytogenomic Array (ISCA) Consortium (Miller et al., 20102) recommended chromosome microarray testing as a first tier test for the investigation of developmental delay/intellectual disability (DD/ID), multiple congenital anomalies, and/or autism spectrum disorders (ASD) based on evaluation involving 21,698 patients in whom the diagnostic yield was found to be 12.2%, which is 10% higher than that of G-banded karyotyping.

References:

1. Genet Med. 2013 Nov;15(11):901-9

2. Am J Hum Genet. 2010 May 14; 86(5): 749–764


KARYOTYPING OF SAMPLES FROM TERMINATION OF PREGNANCY

Chromosomal abnormality is a significant finding in spontaneous abortions, accounting for approximately 60% of first trimester miscarriages. After a termination of pregnancy, the products of conception (in appropriate transport medium) can be sent to the laboratory for chromosomal analysis. It may take two to four weeks for a result. In occasional samples, a result may take longer or fail due to lack of viable tissues. Success in culture largely attributed to “viability and sterility” of the tissues sent. Avoid endometrial tissue/ deciduas basalis, which is mainly maternal in origin. Avoid sending skin samples as chance of culture failure is high.

Sample Requirement: 30-50 mg villi in sterile universal container with transport media

If there is an evacuation planned in the OT or Labour Ward, check to see that you have our sterile transport media ready. These media bottles are to be kept frozen at -20°C and thawed before use. You may obtain them from your respective hospital site outpatient laboratories or by calling the Genetics Lab (62485873/4). (The latter option needs a minimum of a working day notice to deliver the transport media to you).

Sample must be immersed in POC transport medium in a sterile, universal container with transport medium obtainable from the laboratory.

Karyotyping can only be carried out on live healthy tissues. Never preserve the specimen in formalin nor freeze the sample while in storage.

Please obtain the POC sample as aseptically as possible. Use sterile forceps and scalpel to obtain tissue to avoid infection of the cultures.

For spontaneous abortuses, please send villi tissues so we that can be certain they are foetal in origin and not maternal tissue.

Where possible, rinse the POC sample in sterile saline (this may also help the spotting of placental tissue more easily) before storing in our transport media. However, please avoid sending the sample in saline as this may encourage cell membrane breakdown. Place a small portion of the chorion containing villi (about 50mg) in the tube of transport medium. A 10 -15 mm2 piece of tissue will be sufficient if villi is present. Submerge the tissue completely in the transport media provided.

Send samples without delay to the laboratory whenever possible. If unable to, please keep sample in 4°C refrigerator to minimise infection/ bacterial proliferation and send to us by the next working day.

Other Genetics Tests ordered on POC samples apart from Karyotyping may be QF-PCR and Microarray. Please tick “POC” on our request form, the test(s) ordered, and provide us with the gestational age (if available) and any other relevant information. Ensure patient has signed the consent section (before the OT procedure).

For hospital sites, please bill at inpatient (refer to the relevant CDM codes) before patient is discharged. Please call our Genetics Lab (62485873/4) before the procedure if there is uncertainty about tests ordered.


QUALITATIVE FLUORESCENT POLYMERASE CHAIN REACTION (QF- PCR) ANEUPLOIDY

This is a DNA based PCR test designed to detect specific chromosome numerical abnormality in the panel selected and has a rapid turnaround time. It can also be used to pick up the presence or absence of the Y chromosome and *SRY gene. (*Note: A negative result may not indicate absence of the SRY gene if a rare variant is present in the patient.) This technique involves the amplification of DNA which is quantified by means of a fluorescent capillary DNA sequencer. However, it should be noted that structural and chromosome structural abnormalities as well as mosaicism cannot be recognised using this test, and only a full chromosome analysis by culture approach will be able to provide those information. If karyotyping has also been requested concurrently with QF-PCR to exclude other conditions, please provide additional sample material for chromosome testing.

Sample Requirement for QF-PCR:

Amniotic Fluid:                            5 mL in sterile universal container

Blood:                                           3-5 mL in EDTA vacutainer tube

Chorionic Villus / POC:               5 mg villi, or foetal tissue in sterile universal container with transport media 

CONSENT TAKING AND GENETIC COUNSELLING

For all karyotyping, QF-PCR chromosome microarray, non-invasive prenatal screening (NIPS) and personalised genomics tests, there should be adequate pre- and post- counseling done by the clinician/ other healthcare professionals trained in genetics/ a genetic counselor so that the report is properly interpreted. For example, a “normal” result or absence of a mutation just implies that there was no specific alteration detected in the designed sites of the gene(s) interrogated. The patient may still have a mutation in a gene other than the gene(s) that was tested. Thus, the patient needs to be helped through to understand the implications of his/her report.

Genetic counselors are available at NUHS, KKCWCH, NCC or Compass Genetics. Please contact our genetics laboratory for the contact numbers at the respective organisations, if required.

SAMPLE STORAGE AND TRANSPORT

Samples for karyotyping/cytogenetic investigations should not be frozen or exposed to excessive heat as they require living cells. It is important to send samples without delay to Parkway Laboratory Services (Genetics Department).

Collect amniotic fluid in sterile universal containers provided. Place chorionic villi, products of conception (POC) and bone marrow samples in their respective sterile transport media bottles obtainable from the laboratory. Please immerse POC tissues in the transport media provided. Do not use collection containers or transport media that have passed its expiry date. Transport media may be stored frozen and thawed before use.

Samples should arrive at our laboratory within the same day if possible, if not, then within 24-48 hours of sample collection. If unable to send within the same day, please store prenatal, blood and bone marrow samples in a cool place overnight (20°- 30°C) and send to us by the next working day. Store POC tissues collected in transport media at 4°C to minimise bacterial contamination/proliferation. These samples may be transported to Parkway Laboratory Services (Genetics Department) at 20°- 30°C.