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Laboratory Services

Genetic testing

  • Genetic Review process

    Laboratory Services has an established process for review and referral of high-cost genetic test requests for RCH patients. The process ensures patients have access to high quality genetic tests which are likely to yield a diagnosis and answer the clinical question posed by the treating team.

    A multidisciplinary meeting is held each month, attended by the laboratory-based Genetic Counsellor, geneticists, Laboratory Director and Specimen Reception Manager and subspecialists. Clinicians seeking genetic testing for patients are welcome to attend. Communication to clinicians relating to test requests which are changed or declined is communicated via email or Staff in-box message in EPIC.

    Subject to available budget to cover test costs, the review process supports testing in the following circumstances;

    • When confirmation of a clinical diagnosis will lead to a change in management for an RCH patient ( <18years). Examples of change in management may include access to a treatment or drug, surveillance for disease complications, a change in direction of care  
    • To confirm a clinical or genetic diagnosis in a patient where it is relevant to screening for potential disease complications (including predictive testing for at risk siblings)  
    • Where genetic testing would prevent the need for expensive or invasive alternate investigations (such as brain MRI under GA, nerve or muscle biopsy, lumbar puncture)  
    • Where molecular confirmation of a clinical diagnosis will facilitate predictive testing for at-risk siblings, thereby avoiding unnecessary surveillance.

    The Medical Benefits Schedule (MBS) provides reimbursement for a small number of genetic tests for eligible out-patients (private patients, or those attending MBS clinics), but not for hospital in-patients. Examples include whole exome sequencing for childhood syndromes for eligible children aged 10 years or younger (MBS Items 73358, 73359, 73360), genetic testing in suspected Alport syndrome (MBS Item 73298) and in familial hypercholesterolaemia (MBS Item 73352 and 73353). See below for more details on how to order an MBS funded exome.

    Ordering a genetic test

    Genetic tests are requested as pathology orders in EPIC.

    Given the large numbers of genes in the human genome, and the subsequent high number of genetic testing options, it is not possible to have a specific order name for every genetic test. A number of commonly ordered specific gene or syndrome tests are available as well as generic tests.

    The table shows frequently ordered examples;

    EPIC test name (synonym) 
    Test utilisation 
    Microarray (molecular karyotype)   
    Chromosomes (karyotype)   
    Fragile X nucleic acid detection   
    Genetic test (miscellaneous genetic test) 

    Used for single genes or gene panels.
    The disorder, gene list or gene panel can be specified in the order 

    Immunology genetic test 

    Used for ordering genetic tests for specific genes or panels associated with immunology genetic disorders
    such as those associated with autoinflammatory or periodic fever, TRAPS, Familial Mediterranean
    Fever, Primary immunodeficiencies, Haemophagocytic Lymphohistiocytosis, etc. 

    AGHA Immunology Flagship  Used for ordering whole exome sequencing for immunodeficiency disorders.
    This test requires prior discussion and approval from the Immunopathologists (Dr Sharon Choo, 

    Dr Stephanie Richards) 

    Whole Exome Sequencing (Exome, Clinical Exome)  Used for singleton or Trio WES including when MBS funded or other funding source 
    Whole Exome Sequencing parent sample  Used to order parent samples in trio testing 
    Neuromuscular panel  Used for neuromuscular related disorders 
    Cardiomyopathy, Aortopathy, Arrhythmia gene panels  For cardiac genetic disorders (exome backbone) 

     

    RCH paediatricians are able to order Medicare-funded whole exome sequencing for eligible patients with certain phenotypes.  For other patients who may benefit from whole exome sequencing, referral for a clinical genetics consultation should occur, as some funding options for testing remain restricted to tests ordered by the clinical genetics team.

    For exome sequencing tests, RCH paediatricians and specialists are expected to have undertaken online learning by completing the Learning Hero Genomics Module

    Support and advice

    Yana Smagarinsky

    Yana Smagarinsky BScBA MGenCouns

    Email: Labservices.genetics@rch.org.au

    Yana is the laboratory-based genetic counsellor and is available for advice and support.

    The lab-GC reviews and triages genetic and genomic test requests and liaises with clinicians to obtain further details to ensure that the requested test is the most appropriate test and is likely yield the required information. The lab-GC is supported by a clinical geneticist and a range of subspecialists with genomic knowledge.

    The lab-GC assists in the selection of the most appropriate testing laboratory based on the following principles;

    • The laboratory is accredited to perform the requested test and produces high quality results and accessible reports
    • Clinically appropriate test turn-around time
    • Value for money

    Laboratory Services gratefully acknowledges the RCH Foundation in supporting Yana’s role.

    Sue White

    A/Prof Sue White MBBS, FRACP

    A/Prof White is the clinical geneticist providing support to the lab-GC and guiding the selection of tests and referral laboratories.

    Laboratory Services gratefully acknowledges the support of the following subspecialists with genomic expertise who assist in the review process;

    Professor Monique Ryan (Neurological disorders), Professor John Christodoulou (Biochemical genetics and metabolic disorders), Dr Heidi Peters (Metabolic disorders), Dr Sharon Choo (Immunological disorders), Dr Michele O’Connell (Endocrine disorders), and Dr Katherine Howell (genetic epilepsies).

    Once a test request has been approved and a referral laboratory selected, the Lab Services specimen reception team managed by Mr Paul Marcus (paul.marcus@rch.org.au) are responsible for transport of specimens to a range of local, interstate and international laboratories as well as receipt of results.

    Samples for genetic testing

    Testing is most commonly performed on DNA extracted from peripheral blood, although saliva, skin fibroblasts and tumour tissues are sometimes used

    • EDTA blood sample (minimum 2.5 mL)
    • Saliva (suitable for some tests)
    • DNA (extracted in a NATA accredited laboratory)

    Helpful hints:

    If the patient has previously had a microarray test performed at VCGS, it is likely that stored DNA can be used for testing and no additional pathology collection is required.  

    • In the test order select ‘extracted DNA’ as the specimen type
    • If sample collection is not required, sign the order, perform the ‘collection’, print the order and forward this to RCH Laboratory Services. Please note, the test can only proceed if a physical hard-copy of the pathology order is received in the laboratory.
    • You will be informed if there is insufficient or unsuitable stored DNA and a recollection is required
    • You can confirm whether there is sufficient DNA stored for a patient at VCGS by emailing dna.extractions@vcgs.org.au.
    • For predictive testing, a second, independently collected specimen may be required for confirmatory testing. It is best practice to ensure the patient’s parent confirms the patient’s identity and name on the specimen tube and signs the label to verify this check. Check with the lab-GC or testing laboratory if you are unsure.

    Consent for genetic testing

    Obtaining informed consent for complex genetic tests (such as multi gene panel testing, exome and genome sequencing) is especially important because of potential implications for other family members, reproductive risks and future well-being (for example for subsequent children, or the ability to obtain insurance).  There are limitations to genetic testing that need to be understood. In many cases, not all genes that predispose to a certain condition are known, so a negative result does not necessarily mean that an individual does not have a genetic cause for their condition. Genomic testing may result in identification of variants of uncertain significance that can be difficult to interpret, the implications of which should be clearly understood by families prior to agreeing to the testing. Genomic testing may identify variants associated with diseases that are not related to the indication for testing.

    https://www.vcgs.org.au/sites/default/files/forms/MGF164-consent-form-genomics.pdf

    Finding Genetic results in EPIC

    • Tests performed by RCH Laboratory Services or by VCGS are available in EPIC in the Chart Review (Labs) or Results Review sections. In most cases the report will be in pdf format and must be opened to view the result.
    • Amended reports- Many laboratories issue amended reports as new information becomes available. New information may alter the classification of variants and arise from research or family member testing. Always check you are viewing the latest report. Where an amended report has been received a statement “Amended Report” with date of new report and reason for amendment will be added to the original report.
    • If the test is performed by an external laboratory, or was performed many years ago, a scanned image of the report will be available in EPIC either in the Media Tab- under “External Pathology Results” or “External Investigations scanned”, or in the Chart Review or results review sections linked to the original order.

    FAQ

    When should I order a genetic test?

    A genetic test is best used to answer a specific clinical question

    Genetic tests are generally poor at “ruling things out” (so it is best not to use as a test of exclusion) for a variety of reasons:

    • Mutation mechanisms can be diverse
    • Variants outside coding regions may affect splicing or promoter regions
    • Many conditions may be caused/influenced by as yet uncharacterised genes  

    Consider how sure are you that the child’s presentation is due to a gene change that this test can identify.

    If you are seeing a patient who is (or may be) undergoing genetic testing, hold off on other investigations where possible (for example in a stable outpatient) until genetic testing is completed.

    Consider the most likely fit for child’s phenotype and order the most appropriate test. Concurrent or sequential testing is not good clinical practice, the lab-GC is available to assist in test selection.

    Common definitions

    Predictive testing – testing of unaffected, at-risk relatives for a pathogenic variant known to cause disease

    Segregation testing – testing of biological relatives for a variant of unknown significance with the aim of clarifying the pathogenicity (usually at the request of the testing laboratory or clinical geneticist)

    Cascade testing – genetic testing of healthy biological relatives for a known pathogenic variant in order to avoid/inform of risk of disease

    Panel testing – where there is a clinical suspicion of a condition which can be caused by a number of genes. Eg. Cardiomyopathy panel, RASopathy panel, arrhythmia panel

    Proband  the first person in a family to receive genetic counselling and/or testing for suspected hereditary risk. This person is usually (but not always) affected with the disease in question.

    Trio testing – genomic testing of a proband in conjunction with their biological parents. This can be particularly useful where there is consanguinity or where the family is from an ethnic minority. 


    Click here for detailed information on how to order MBS funded Whole Exome Sequencing (attachment)

    Click here to see an expanded version of the EPIC smart phrase ".exome" (attachment)