Genetic testing

 

The information and links provided on this page are for general guidance and information provision. Specific advice is available from either a Clinical Geneticist or Genetic Counsellor. Please phone Hunter Genetics (02) 4985 3100, or email HNELHD-Genetics@hnehealth.nsw.gov.au.
 

 

Diagnostic genetic testing is done when an individual is suspected of having a particular condition that is known to have a genetic basis.

 

Things to consider when ordering a genetic test
  • Testing may benefit individuals and families in a number of ways but it may also create dilemmas which need sensitive management.
  • Each test has distinct advantages, disadvantages and limitations and should only be used after the individual being tested (or their parent / legal guardian) has given full consideration to these issues.
  • As genetic disorders may be inherited, there may be implications for other family members.
  • Counselling is an essential element of genetic testing.
  • Medical practitioners requesting genetic testing are required to

- Have expertise in the disorder being tested
- Be able to interpret the results and the implications of both positive and negative results
- Arrange follow-up as appropriate

  • All testing should be carried out with informed consent

- Consent must be obtained from the person being tested (or their parent / legal guardian)
- The person giving consent must (1) consent freely without coercion by professional staff, family members, employers, insurers or others and (2) must be adequately informed about all relevant issues
- Consent may be withdrawn at any time
- Completion of an appropriate consent form is mandatory. Please refer to the 'Consent forms and patient information booklets' drop down menu below.

 

Research Testing
  • Must be done in accordance with NHMRC guidelines
  • Requires local ethics approval
  • The 'Genetic/Genomic consent form' must be used. Please refer to the 'Consent forms and patient information booklets' drop down menu below.
  • An additional sample must be analysed at an accredited diagnostic laboratory, before the results can be considered true or used for clinical purposes

 

Results and their implications


A positive test result in clinically affected patients

  • Will usually confirm that the individual is affected by the disease
  • Does not usually accurately predict severity or progression of the condition
  • May have implications for other family members
  • May affect future reproductive decisions
  • May have possible consequences for employment and insurance
  • The person (or their parent / legal guardian) should be offered a follow-up appointment with the clinician who ordered the test, at the earliest possible opportunity


An indeterminate result in clinically affected patients

  • Requires very specialised interpretation
  • Usually needs referral to a clinical geneticist at Hunter Genetics or elsewhere in NSW
  • An example may be where the laboratory reports a variation in a gene as “possibly causative” or ‘of unknown significance”
  • As testing moves from looking at individual genes to DNA sequencing of multiple genes,  more variations of unknown significance will be identified


A negative test result in clinically affected patients

  • May mean different things, depending on the clinical context
  • May require very specialised interpretation
  • In the situation where the genetic test is highly accurate and specific for a condition (eg methylation testing for Prader-Willi syndrome), will usually indicate that the person does not have the condition
    or
  • In the situation where the genetic test is not highly accurate (eg genetic testing for Noonan syndrome), a negative result does not exclude the condition. Possibilities include:

- The person does not have the condition
- A mutation may be present in the gene tested but not identified, either due to limitations in technology or insufficient testing methods. Consideration should be given to more detailed testing or repeat testing at a later date (as technology and pick up rates improve)
- A mutation may be present in another gene that is also known to cause the condition. Consideration should be given to testing of other possible genes that also cause the condition.

 

  • In this situation, the clinical diagnosis must be based on other factors (e.g. clinical diagnosis / radiological diagnosis / other investigations)
  • In the situation where another family member has a known mutation/s by previous genetic testing (eg cystic fibrosis), will indicate that the person does not have the condition.

 

Family Testing
  • In most situations, testing of other family members is most appropriately done by a Genetic Counsellor or Geneticist at Hunter Genetics or elsewhere in NSW
  • May include carrier testing for recessive conditions (e.g. cystic fibrosis or spinal muscular atrophy)
  • May include carrier testing for X-linked conditions (e.g. fragile X syndrome)
  • This may include the situation where family members are concerned that the sibling of an affected patient may develop the condition at a later date. This type of testing is called predictive testing and should only be done (if at all) after extensive genetic counselling.

    Predictive testing refers to testing in an individual who currently does not have symptoms or signs of disease, but who may be at risk due to their family history, and who requests more information about their risk. Predictive testing raises a number of complex issues and it is essential that prior to undertaking testing, the patient is fully informed about the implications of testing and is prepared for the results.

Charging Policy
  • Most specialised DNA tests do not have an associated Medicare Benefits Schedule (MBS) Item number.
  • Genetic tests typically cost between $400 and $2000.
  • The cost of testing for public or privately referred inpatients and outpatients is billed to the department of the Doctor who signs the request form.
  • As per NSW Health Policy PD2005_335, costs will be covered by the Local Health District of the patient.

Laboratory requirements
  • Pathology North is a NATA accredited laboratory. In accordance with New South Wales and Australasian guidelines, the HAPS laboratory will only commence processing/testing of samples on receipt of all required information:

- All requests are to be completed on the standard Pathology North request form. 

- All sample requests require written consent on a NSW Health genetic testing consent form. Please refer to the 'Consent forms and patient information booklets' drop down menu below. The original must be placed in the patient notes and a copy provided to the patient.

- Requests with incomplete / illegible information will not be processed. In this situation, DNA will be stored until the referring doctor can be contacted.

  • Susan Dooley and Andrew Ziolkowski, Molecular Genetics, are available to help with DNA genetic testing requests. They can be contacted on
    • Susan (02) 4921 4312 or by email.
    • Andrew (02) 4921 4078 or by email.
  • Nicole Bain, Cytogeneticist, is available to help with chromosome microarray testing requests. She can be contacted on (02) 49214077 or by email.

Patterns of Inheritance


Autosomal Dominant Inheritance

 

 

For more details read the fact sheet on autosomal dominant inheritance

 

Autosomal Recessive Inheritance
 

 

For more details read the fact sheet on autosomal recessive inheritance

 

X-Linked Inheritance
 


For more details read the fact sheets on X-Linked recessive or dominant inheritance.

For other information regarding medical genetics and patterns of inheritance, refer to the NSW Health Centre for Genetics Education website.

 

Guide to ordering a genetic test

Diagnostic genetic testing is done when an individual is suspected of having a particular condition that is known to have a genetic basis.

Should you have any questions relating to this document, please do not hesitate to speak with:

  • Susan Dooley and Andrew Ziolkowski, Molecular Genetics, regarding DNA genetic tests. They can be contacted on
    • Susan (02) 4921 4312 or by email.
    • Andrew (02) 4921 4078 or by email.
  • Nicole Bain, Cytogeneticist, regarding chromosome microarray tests. She can be contacted on (02) 49214077 or by email.

 

 Step 1: Finding your gene

  • Determine the genetic disorder / gene and laboratory for which testing is required.
  • Common disorders/genes listed in Table 1 (below).
  • If the disorder / gene of interest is not found in the table, then:
  1. Look at the RCPA website for genetic tests that are performed in Australia
  2. If the disorder / gene is not available within Australia, then look at overseas websites; this may include but not limited to

 

Step 2: Forms

  • Fill out the Pathology North request form.
  • Fill out the appropriate consent form (see consent forms section). File original in the patient's medical record and give a copy to the patient / parent / legal guardian.
  • Give the original Pathology North request form to the patient for blood / sample collection.

 

Table 1: Common genetic tests

 

Test Name

Gene / Chromosome

Lab

Cost

Turn Around Time

Consent form Needed

Beckwith Wiedemann Syndrome

11p15 critical region, Imprinting Centres, UPD

Clinical Haematology + Oncology, RCH, Melbourne

$480

4 weeks

Yes


Cryopyrin associated periodic fever syndromes (CAPS)
 
NLRP3 (CIAS1) Molecular Genetics, Children's Hospital at Westmead (CHW) $300 for sequencing of Exon 3 4 weeks Yes

Cystic fibrosis F508del

CFTR

PaLMs

$50

2 weeks

Yes

Cystic fibrosis panel

 

CFTR panel of ~50 mutations

PaLMs

$250

2 weeks

Yes

Deafness -  Congenital

Connexin 26 /30

PaLMs

$250 =Cx26 full sequencing; or $400 (+ Cx30 MLPA)

2-4 weeks

Yes

DNA Storage

n/a

HAPS

$105

1 week

Yes

Duchenne Muscular Dystrophy / Becker Muscular Dystrophy

Dystrophin (DMD)

South East Area Laboratory Services (SEALS)

$400 (MLPA)

4 weeks

Yes

Family testing in clinically affected individuals *3

Previously identified gene mutation

Various (via HAPS)

$250-$400

~4 weeks

Yes

Fragile X

FRAXA

SEALS

Medicare*1

2 weeks

No

Haemochromatosis

C282Y

HAPS

Medicare*2

2 weeks

No

Haemophilia A

Factor VIII sequencing

SA Pathology

$1500

6 weeks

Yes


Hyper-IgD syndrome
/ Periodic Fever /
Mevalonic aciduria

MVK Molecular Genetics, Children's Hospital at Westmead (CHW) $300. Sequence all coding exons (2 to 11) 3 weeks Yes

Mediterranean Fever
 
MEFC (Pyrin) Molecular Genetics, Children's Hospital at Westmead (CHW) $200 (Exons 2, 3, 5 & 10); $800 (sequencing) 4 weeks Yes

Microarray (molecular karyotype)

Chromosomes

HAPS

Medicare *4

2 months

No

Myotonic dystrophy

DMPK

VCGS

$460

6-8 weeks

Yes

Spinal muscular atrophy (SMA)

SMN1

South East Area Laboratory Services (SEALS)

$300

2 weeks

Yes

Thalassaemia – alpha

Alpha globin producing genes (HBA1 &  HBA2; Gap PCR +/- DNA sequencing +/- MLPA)   

RPAH (Royal Prince Alfred Hospital), Sydney

$400

6-8 weeks

Yes

Thalassaemia – beta

Beta globin producing genes (HBB; DNA sequencing +/- MLPA)

RPAH

$400

6-8 weeks

Yes


TRAPS (Tumor Necrosis Factor Receptor-Associated Periodic Syndrome)
 
TNFRSF1A (Tumor necrosis factor receptor superfamily, member 1A) Molecular Genetics, CHW $250 (sequencing of exons 2-5 and intron boundaries) 6 weeks Yes

DVT Risk (Factor V Leiden)

Factor V

HAPS

Medicare *5

2 weeks

No

DVT Risk

Prothrombin gene 20210G>A mutation

HAPS

Medicare *5

2 weeks

No

*1. #73300: Detection of mutation of the FMR1 gene where: (a) the patient exhibits intellectual disability, ataxia, neurodegeneration, or premature ovarian failure consistent with an FMRI mutation; or (b) the patient has a relative with a FMR1 mutation

*2. #73317: Detection of the C282Y genetic mutation of the HFE gene and, if performed, detection of other mutations for haemochromatosis where: (a) the patient has an elevated transferrin saturation or elevated serum ferritin on testing of repeated specimens; or (b) the patient has a first degree relative with haemochromatosis; or (c) the patient has a first degree relative with homozygosity for the C282Y genetic mutation, or with compound heterozygosity for recognised genetic mutations for haemochromatosis

*3.  Hunter Genetics staff available to help with testing / counselling if required

*4. #73292: Analysis of chromosomes by genome wide microarray including targeted assessment of specific regions for constitutional genetic abnormalities in diagnostic studies of a person with developmental delay, intellectual disability, autism, or at least two congenital abnormalities

*5.#73308: Characterisation of the genotype of a patient for Factor V Leiden gene mutation, or detection of the other relevant mutations in the investigation of proven venous thrombosis or pulmonary embolism. If the request is for more than 1 gene/mutation, the patient will only receive a Medicare rebate for one gene.

 

Information on chromosomes and genes
  • Chromosomes are thread-like structures within each cell nucleus and contain the body's genetic blueprint.
  • Each chromosome contains thousands of genes in specific locations.
  • Genes are responsible for a person’s inherited physical characteristics and they have a profound impact on growth, development and function.
  • Humans have 46 chromosomes, present as 23 pairs. Twenty-two pairs are found in both genders (autosomes), and one pair (sex chromosomes) is present as either XY (in males) or XX (in females).

 

Traditional testing methods

Chromosome analysis (karyotyping) is a test that evaluates the number and structure of a person's chromosomes in order to detect abnormalities.

  • For individuals with intellectual disability, the diagnostic yield is 3-4%.
  • High resolution banding detects loss (deletion) or gain (duplication) of chromosome segments > 5Mb in size.
  • Can detect balanced translocations / complex rearrangements.
     

Normal male karyotype

       Normal male karyotype

 

FISH (fluorescent in situ hybridization)
  • Uses fluorescently labeled DNA probes bound to a specific chromosomal region; e.g. velocardiofacial syndrome = 22q11.2 deletion, William syndrome = 7q11.23 deletion.
  • Detects much smaller losses / gains of chromosome material (50-100 Kb).
  • Subtelomere FISH deletion testing uses FISH probes at the tips of the chromosomes.
  • For individuals with intellectual disability; diagnostic yield is 2 - 6%.
  • Superseded by chromosome microarray testing.

FISH

 

What is chromosome microarray (CMA) testing?
  • Involves examining many thousands of very small segments of DNA along each chromosome to see if there is more or less DNA than would normally be expected. Typically, we see 2 copies of each DNA segment.
  • Used at Pathology North since 2008.
  • Has, in most instances, replaced karyotyping and FISH testing.
  • Pathology North use a reporting resolution of 200kb for deletions and 200kb for duplications.
  • In 2016, HAPS upgraded the microarray testing platform from Bluegnome oligonucleotide array to the Illumina CytoSNP-12 Beadchip SNP array. 
  • The Illumina CytoSNP-12 BeadChip array includes a complete panel of ~300,000 markers targeting all regions of known cytogenetic importance.  This includes dense coverage of around 250 genomic regions commonly screened in cytogenetics laboratories, including subtelomeric regions, pericentromeric regions, sex chromosomes, and targeted coverage in around 400 additional disease-related genes.  
  • The cartoon below is representative of the design used at HAPS.
  • Results will typically take around 3-4 weeks for a normal result, abnormal results may take longer.

Targeted with Backbone

 

What does CMA test for?
  • Detects all gains and losses that can be seen by conventional karyotyping plus detects much smaller (>200kb) chromosomal losses and gains.
  • Referred to as a copy number variant (CNV).
  • Mosaicism may be detected.
  • The SNP array is also able to detect copy-neutral loss of heterozygosity (LOH). Note LOH is only reported when above 5Mb (to minimise the number of clinically insignificant variants reported). 
  • For individuals with intellectual disability; the diagnostic yield is 15% -20%.
  • For individuals with autism, the diagnostic yield is ~10%.
     

ArrayCGHtesting



What does CMA not test for?
  • Does not detect fragile X syndrome - molecular genetic testing is required.
  • Does not detect single base pair variations / mutations - molecular genetic testing is required.
  • Does not detect triplet repeat disorders - molecular genetic testing is required.
  • Does not detect very low level mosaicism.
  • Does not detect balanced chromosome rearrangements - karyotype is required.

When should I order a CMA test?

It is usually ordered for individuals where it is possible that missing or extra pieces of genetic material is the cause of their health problem, such as:

  • Individuals with intellectual disability +/- facial dysmorphism.
  • Individuals with multiple congenital abnormalities.
  • Individuals with Autism.

The laboratory staff will usually request for testing to be performed in parents of an individual with an abnormality found on microarray testing.


Samples required
  • A blood sample is required; 3-5 mls sodium or lithium heparin and 3-5 mls EDTA.
  • In difficult samples an absolute minimum of 1 ml sodium or lithium heparin tube.
  • In cases where a blood sample cannot be taken, cheek cells (buccal swab) may be used.  These have a lower success rate for obtaining a result.  Please discuss with the laboratory prior to collecting a buccal swab.

How do I fill out the test request?
  • Use a Pathology North request form.
  • Medicare details must be filled in and signed by patient / parent (costs are covered by Medicare*).
  • It is important to include a brief summary of clinical details on the request form in order to ensure the patient meets the Medicare criteria as outlined above.
  • A consent form is not required.

How much does CMA cost?

Medicare details must be filled in and signed by patient / parent (Costs are covered by Medicare*).

* #73292: Analysis of chromosomes by genome wide microarray including targeted assessment of specific regions for constitutional genetic abnormalities in diagnostic studies of a person with developmental delay, intellectual disability, autism, or at least two congenital abnormalities.

* Array can be performed on samples that do not meet these guidelines, however the referring clinic or the patient will be billed $600. 


What results can be expected from a CMA?

1. No copy number variant (CNV) is found

  • This is the most common result.
  • The cause of the individual’s developmental or physical concern remains unexplained.

OR

2. A CNV is found


What does it mean when a CNV is found?

A. The CNV will explain the individual’s health or developmental concern (pathogenic CNV)

  • This type of result is called a pathogenic CNV.
  • Testing of the parents may be requested to see if the variant is only present in the child (de novo) or was inherited from a parent.
  • The individual should be referred to Hunter Genetics.
     

B. A CNV is found but its impact on health or development is unclear

  • This type of result is called a Variant of Unknown Significance (VOUS).
  • The individual should be referred to Hunter Genetics after parental testing is arranged.
  • Parental testing should be requested to determine if the CNV is only present in the child or was inherited from a parent.
  • If one of the parents also has the CNV:
    • If the parent has the same condition as the child, the variant is likely to be the cause of the health or developmental concern.
    • If the parent does not have the same condition as the child, the variant is unlikely to be the cause of the health or developmental concern.
    • Further testing of other family members may be indicated.
  • If neither of the parents has the CNV:
    • The CNV must have occurred during or soon after the child’s conception (a de novo variant).
    • The CNV may then be considered to be the cause of the developmental or health concern OR the relevance of the CNV may remain uncertain.


C. Rarely, a CNV is found that contains a gene or genes unrelated to the developmental or health concerns, but which could potentially cause other health problems in the future

  • This is called an incidental finding.
  • The individual should be referred to Hunter Genetics.


D.  A region (or regions) of homozygosity is found

  • Small regions of homozygosity are normal and present in all individuals.
  • Large regions of homozygosity (>5Mb) are less common and may increase the risk of a genetic disease.
  • A single large region of homozygosity may indicate uniparental disomy (UPD) – where a person inherits two copies of a chromosome from one parent rather than one from each parent.
  • Lots of large regions of homozygosity (excessive homozygosity) may indicate that the person’s parents are related. This does not mean that they have a genetic disease but have an increased risk of genetic conditions, such as autosomal recessive diseases.
  • In this situation, the laboratory will indicate where follow up parental studies are recommended.

How does the lab determine whether a CNV is Significant?
  • Sometimes, it is difficult to determine what is normal variation (we all have ~1000 CNVs that contribute to our individuality) verses which CNVs cause disease / pathology.
  • Generally, the larger the gain or loss of chromosome material, the more genes are involved, and the more likely the CNV is to be significant.
  • Losses (deletions) are frequently more significant than gains (duplications).
  • Prior knowledge and experience helps with interpretation.
  • Analysis of parental samples (where available) to help determine if the CNV is inherited from a parent or has occurred as a new event (de novo) in the individual.
  • Reference to online public databases of CNVs, such as Decipher or the Toronto Database of Genomic Variation.
  • International Standards for Cytogenomic Arrays (ISCA).
  • Input from a Clinical Geneticist may be required.

Information sheets for patients / families

Chromosomes and genes
Microarray Testing


Need help completing the request?

Nicole Bain, Cytogeneticist, is available to help. She can be contacted on (02) 49214077 or by email.

Advice is available from either the Clinical Geneticist or Genetic Counsellor on call. Please phone Hunter Genetics (02)49 853100, or email HNELHD-Genetics@hnehealth.nsw.gov.au.


 
 

 

Patients must be provided with the relevant Information Booklet to allow for informed consent to be undertaken (see below)

Consent (Diagnostic, predictive and genetic carrier DNA testing)
Patient Information
For 16 years and below (SMR020.111)
 
Diagnostic, predictive and
genetic carrier DNA testing
For 14 years and above (SMR020.110)
 
For 16 years and above, under the Guardianship Act (SMR020.112)
 

 

Consent (Genetic/Genomic testing)
Patient Information
For 16 years and below (SMR020.106)
 
Genetic/genomic testing
For 14 years and above (SMR020.105)
 
For 16 years and above, under the Guardianship Act (SMR020.107)

Consent for collection, testing and storage for research requires completion of the Genetic/Genomic paperwork (see above)