Download Coeliac tissue typing

Coeliac tissue typing
Test information sheet
About this test
Coeliac disease is caused by an immune response to gluten in genetically predisposed individuals.
Susceptibility to coeliac disease is linked to certain human leukocyte antigen (HLA) class II alleles,
especially in the HLA-DQ region. HLA molecules present gluten antigens to T-cells which in turn induce
tissue damage. Approximately 95% of patients with coeliac disease have the HLA-DQ2 heterodimer
encoded by the DQA1*05 and DQB1*02 alleles, while close to 5% have the HLA-DQ8 heterodimer
encoded by the DQA1*03 and DQB1*0302 alleles.
The presence of either heterodimer is not diagnostic of coeliac disease. Thus, the primary use of HLADQ typing is to rule out coeliac disease and genetic susceptibility for coeliac disease. Such typing is
particularly relevant when pathology of the small intestine is equivocal, serological testing is consistent
with coeliac disease but villous atrophy is absent, a gluten-free diet is being considered in the absence
of biopsy-proven coeliac disease, and when a first degree relative has been diagnosed with coeliac
disease.
Method
PCR amplification of the HLA DQ and DR
chains, followed by allele-specific identification
on a bead-based multiplex platform
Turnaround time
2 weeks
Billing information
This test is attracts a Medicare rebate
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
Constitutional Microarray
Test information sheet
About this test
Genetic tests are typically ordered for patients with conditions like developmental delay, intellectual
disability, and autism. Traditionally, this testing has included “karyotype analysis”, where each
chromosome of the patient’s genome is analysed under a microscope. This technique has been largely
replaced by “constitutional microarray analysis”, a new molecular method with higher resolution.
Constitutional microarray analysis detects copy number variations (CNVs); gains or losses of genetic
material, referred to as duplications or deletions, respectively. CNVs have been found to be the cause of
approximately 10-15% of cases of developmental delay.
Constitutional microarray analysis is useful in patients with developmental delay, intellectual disability,
autism, or with multiple (2 or more) congenital abnormalities. It is the recommended first tier test in
patients with these features. In addition, if a CNV is detected in a patient, family members may also be
tested, in order to help determine if the CNV is the cause of the patient’s features, and/or to determine if
the CNV was inherited from a parent or a new change in the patient.
Method
CGH microarray analysis of genomic DNA
extracted from a peripheral blood sample
Turnaround time
Two months
Billing information
There is a Medicare rebatable fee (if Medicare
criteria are met), plus a private gap payment
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
Familial Mediterranean Fever
Test information sheet
About this test
Familial Mediterranean fever is an inherited condition characterized by recurrent episodes of painful
inflammation in the abdomen, chest, or joints. These episodes are often accompanied by fever and
sometimes a rash or headache. Occasionally inflammation may occur in other parts of the body, such
as the heart, the membrane surrounding the brain and spinal cord, and in males, the testicles.
Familial Mediterranean fever primarily affects populations originating in the Mediterranean region,
particularly people of Armenian, Arab, Turkish, or Jewish ancestry. The disorder affects 1 in 200 to 1,000
people in these populations. It is less common in other populations.
Mutations in the MEFV gene cause familial Mediterranean fever. Familial Mediterranean fever is almost
always inherited in an autosomal recessive pattern, which means both copies of the MEFV gene in each
cell have mutations.
Method
Known and suspected disease causing
mutations within exon 2 and 10 of the pyrin/
marenostrin (MEFV) gene tested by bidirectional
DNA sequencing. Further screening of all exons
can be performed on request
Turnaround time
2 weeks
Billing information
This test is not covered by Medicare and
attracts a private fee. Clarification of the fee can
be requested by contacting 1800 010 447
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
Fragile X
Test information sheet
About this test
Inactivation of the FMR1 (Fragile X Mental Retardation 1) gene leads to Fragile X syndrome, the most
common single gene cause of intellectual disability/developmental delay. Fragile X syndrome can include
intellectual disability, autistic spectrum disorder and characteristic physical features.
Inactivation of the FMR1 gene is usually caused by expansion or lengthening of the gene in a section
called the CGG repeat tract (normally less than 45 repeats in size). Expansion of the repeat tract to full
mutation (FM) size (200 – over 1000 bp) results in abnormal protein and therefore interferes with normal
brain development. Presence of a full mutation results in Fragile X syndrome the in the vast majority of
FM males, and in approximately 50% of female ‘carriers’.
CGG repeat sizes of between 55-200 repeats in length are known as ‘premutation’ (PM) alleles,
because they can expand in length to a full mutation in a single generation, on transmission from
mother to offspring. In addtion, premutation alleles can themselves result in abnormal effects including
premature ovarian insufficiency (FXPOI) in females and older patients with premutation alleles may
develop Fragile X-associated tremor/ataxia syndrome (FXTAS), a neurological disorder (seen in 20–40%
of male and 8% of female premutation carriers over the age of 50).
Method
Sizing PCR and triplet repeat primed PCR
Turnaround time
2 weeks
Billing information
This test is covered by Medicare if specific
criteria for testing is met. Clarification of the fee
or criteria can be requested by contacting
1800 010 447
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
Hereditary
Angioedema type III
Test information sheet
About this test
Type III Hereditary Angioedema (HAE III) is the rarest type, compared to Type I and II. It is caused in
most cases by mutations in the F12 gene. This gene provides instructions for making a protein called
coagulation factor XII. In addition to playing a critical role in blood clotting (coagulation), factor XII is also
an important stimulator of inflammation and is involved in the production of bradykinin.
Method
Real Time PCR for screening of the Thr328Lys
(c.1032C<A) mutation present in the
Coagulation Factor XII gene.
Turnaround time
2 weeks
Billing information
This test is not covered by Medicare and
attracts a private fee. Clarification of the fee can
be requested by contacting 1800 010 447
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
HLA B27
Test information sheet
About this test
HLA-B27 occurs in up to 8% of Caucasians, 2-9% of Chinese and 0.1-0.5% of persons of Japanese
decent. HLA-B27 adds weight to the diagnosis of seronegative arthritis, ankylosing spondylitis, anterior
uveitis, iritis, psoriatic arthritis, Reiter’s syndrome and Cröhn’s disease. HLA-B27 appears to be the
greatest genetic cause of spondyloarthropathies and plays an important role in the pathogenesis of
arthritis.
Method
PCR amplification of the HLA DQ and DR
chains, followed by allele-specific identification
on a bead-based multiplex platform
Turnaround time
2 working days
Billing information
This test is covered by Medicare
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
JAK2
Test information sheet
About this test
The JAK2 (Janus kinase 2) gene provides instructions for making a protein that promotes the growth
and division (proliferation) of cells. Somatic mutations in the JAK2 gene are associated with essential
thrombocythemia, polycythemia vera, primary myelofibrosis and is occasionally found in people with
cancer of blood-forming cells (leukemia) or other bone marrow disorders. The most common mutation
(written as Val617Phe or V617F) replaces the protein building block (amino acid) valine with the amino
acid phenylalanine at position 617 in the protein.
Method
Real Time PCR for the screening of the
Val617Phe mutation present in Janus Kinase 2
(JAK2) Tyrosine Kinase
Turnaround time
2 weeks
Billing information
This test is not covered by Medicare and
attracts a private fee. Clarification of the fee can
be requested by contacting 1800 010 447
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
Non-invasive Prenatal DNA testing
(for trisomies 21, 18, 13 and sex chromosomes)
Test information sheet
About this test
The verifiTM prenatal test is a non-invasive test that detects multiple fetal chromosomal aneuploidies. The
test detects three primary chromosomal aneuploidies for trisomies 21, 18 and 13 from a single blood
draw as early as 10 weeks estimated gestational age. Trisomies occur when three, instead of the usual
two, copies of a chromosome are present. The sex chromosomes test option is available at the request
of the referring Obstetrician, which includes the detection of Turner syndrome (Monosomy X), Triple X
(XXX), Klinefelter syndrome (XXY), and Jacobs syndrome (XYY).
This test is available for singleton and twin pregnancies.
Method
Massively parallel DNA sequencing
Turnaround time
3-6 working days from sample receipt in lab
Billing information
This test is not covered by Medicare and
attracts a private fee. Clarification of the fee can
be requested by contacting 1800 010 447
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
Pharmacogenomics
Test information sheet
About this test
Pharmacogenetics tests analyse the genes that affect a person’s response to medications. Whether a
medication works well for you, or causes serious side effects, can depend on your genes. There are
many genes that are involved in drug metabolism. The cytochrome P450 (CYP) family is a group of
enzymes which are important for the metabolism of more than 50% of commonly prescribed drugs.
These include drugs for depression, anxiety, pain relief, blood thinners and breast cancer. Sonic
Genetics tests can establish a person’s “Pharmacogenetic Profile”, which includes genetic analysis of
the CYP2D6, CYP2C19, CYP2C9 and VKORC1 genes. Additional genetic testing is available for other
genes involved in the metabolism of specific drugs including the TPMT, CYP3A4, CYP3A5, DPYD
and UGT1A1 genes. At Sonic Genetics, our pharmacogenetic test menu continues to expand, as
information on the role of different genes in drug metabolism becomes clinically useful.
Method
INFINITI Autogenomics assays
Turnaround time
2 weeks
Billing information
This test is not covered by Medicare and
attracts a private fee. Clarification of the fee can
be requested by contacting 1800 010 447
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
Thrombophilia Genetic Testing
Test information sheet
About this test
Thrombophilia is a general term to describe an increased tendency to develop blood clots. Patients with
thrombophilia are at a higher risk of developing venous thrombosis (such as deep vein thrombosis-DVT)
and pulmonary embolisms. Mutations in two genes are known to be associated with thrombophilia.
Factor V Leiden Thrombophilia is caused by a mutation, known as the Leiden mutation (c.1691G>A)
in the Factor V gene. Prothrombin-Related Thrombophilia is caused by a mutation in the Prothrombin
gene (c.20210G>A). Factor V and Prothrombin genes encode proteins that are involved in the clotting
cascade. For both conditions, the risk of developing blood clots increases with the number of mutated
copies of the gene. For example, one copy of the Factor V Leiden mutation is associated with an
approximately 3-8 times risk of developing venous thromboembolism, and having two copies results
in a 9-80 times risk. It is important to note that the mutations indicate an increased risk of blood clots,
but are not predictive of blood clots occurring. Testing for thrombophilia is useful in patients who
have had a venous thrombosis or pulmonary embolism or in first degree relatives of patients with a
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Method
The Factor V Leiden (c.1691G>A) and
Prothrombin (c.20210G>A) gene mutations are
detected using a real time PCR-based endpoint
genotyping method
Turnaround time
2 weeks
Billing information
Thrombophiia testing is rebatable by Medicare,
if specific criteria are met
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
TPMT Genotype
(Thiopurine S-methyltransferase)
Test information sheet
About this test
For many patients with chronic inflammatory disorders, transplanted organs, as well as severe eczema,
immunosuppression with thiopurine medications has significant clinical utility. However, despite good
management, a small but significant number of patients have trouble tolerating these medications.
Azathioprine, mercaptopurine and thioguanine are inactivated by
ThioPurine S-MethylTransferase (TPMT). This enzyme exhibits co-dominant genetic polymorphism.
Consequently, 90% of persons have high or normal levels, nearly 10% have intermediate levels and
1 in 300 are profoundly deficient in this enzyme. Treatment of profoundly deficient persons can be
life threatening, due to severe and possibly fatal myelosuppression. Nearly 10% of persons have an
intermediate risk of toxicity.
Successful therapeutic regimes with reduced doses of these medications have been described for
deficient patients.
Method
Detection of TPMT variants (LightSNiP). Alleles
identified are *1, *2, *3A, *3B and *3C
Turnaround time
2 weeks
Billing information
This test is covered by Medicare
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
TRAPS
Test information sheet
About this test
TRAPS or Tumor necrosis factor Receptor Alpha Polymorphism Syndrome is an inherited disorder which
results from mutations in the gene coding the TNF receptor (TNFRSF1A gene). TRAPS is a condition
characterized by recurrent episodes of fever. These fevers typically last about 3 weeks but can last
from a few days to a few months. Abdominal symptoms are common and include pain, diarrhoea,
constipation and, occasionally, peritonitis.
TRAPS is the second most common inherited recurrent fever syndrome, following Familial
Mediterranean fever (FMF). More than 1,000 people have been diagnosed with TRAPS worldwide.
TRAPS is inherited in an autosomal dominant pattern, which means one copy of the altered gene in
each cell is sufficient to cause the disorder.
Method
Complete TRNFRSF1a exon 2, 3 and
4 mutation screening is performed by
bi-directional DNA
Turnaround time
2 weeks
Billing information
This test is not covered by Medicare and
attracts a private fee. Clarification of the fee can
be requested by contacting 1800 010 447
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au
Chromosome Y Microdeletions
(YDAZ)
Test information sheet
About this test
Key regions of the Y-Chromosome are suspected to contain genes which have important roles
in spermatogenesis. The general regions relevant to infertility are found on the long arm of the
Y-chromosome. Genes termed azoospermia factor (AZF) are found in this region. Currently there are
three identified regions termed AZFa, AZFb and AZFc.
This procedure tests for the presence or absence of microsatellite loci within threse three regions of
the Y chromosome. Deletions in these regions can cause severe spermatogenic defects ranging from
non-obstructive azoospermia to oligospermia. About 7% of male infertility has been attributed to Y
chromosome submicroscopic deletions including the “Deleted in Azoospermia” or DAZ genes. The most
common microdeletion is in the AZF-c region encompassing the DAZ genes.
Method
PCR amplification of selected regions of the
Y chromosome to determine the presence of
deletions.
Turnaround time
2 weeks
Billing information
This test is not covered by Medicare and
attracts a private fee. Clarification of the fee can
be requested by contacting 1800 010 447
Further information
www.sonicgenetics.com.au
www.sonicgenetics.com.au