MOLECULAR PATHOLOGY

STAFF:

Clinical Consultant
Dr. Gary Grubb
BMedSc, MBChB, PhD,
FRCPA, MBA

CONTACTS:

Email: pcr@gippspath.com.au

Telephone: 03 5174 0800

Fax: 03 5176 0281

MICROBIOLOGY TESTS OFFERED

Herpes simplex/zoster
A multiplexed PCR assay that detects herpes simplex (including typing) and herpes zoster.

Assayed daily (Monday-Friday)

SPECIMEN: dry swab or viral transport media - transport room temperature.

CMV
A qualitative PCR assay. A secondary confirmatory assay is employed when CMV-DNA is detected in low amounts.

Assayed daily (Monday-Friday)

SPECIMEN: dry swab, viral transport media or EDTA blood, transport room temperature.

Bordetella pertussis
A PCR assay.

Assayed daily (Monday-Friday)

SPECIMEN: dry swab or NPA transported at room temperature.

Trichomonas vaginalis
A PCR assay

Assayed daily (Monday-Friday)

SPECIMEN:
urine, tampon or dry swab transported at room temperature.

Chlamydia trachomatis
Roche Cobas Amplicor

Assayed daily (Monday-Friday)

SPECIMEN: - First void urine or swab transported at room temperature.

Neisseria gonorrhoeae screen
Roche Cobas Amplicor

Assayed daily (Monday-Friday)

SPECIMEN: - First void urine or swab transported at room temperature.

Neisseria gonorrhoeae confirmatory assay
A PCR targeting the porA pseudogene.

Assayed daily (Monday-Friday)

SPECIMEN: urine, tampon or dry swab transported at room temperature.

NO MBS item number. Charge: $25

MecA gene
A PCR multiplex assay targeting the mecA gene and S aureus specific gene Sa442.

Assayed daily (Monday-Friday)

SPECIMEN: - Sample of pure colony suspended in 1 ml of sterile saline. Transported at room temperature.

NO MBS item number. Charge: $50

HEPATITIS C VIRUS PCR
GPS offers HCV PCR screening (qualitative), viral load (quantitative) and genotyping

Assayed weekly

SPECIMEN: Serum separated from cells within 6 hours and frozen at -70C within 72 hrs

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GENETIC TESTS

HLAB27
A PCR assay targeting the HLA-B27 gene.

Assayed three times per week.

SPECIMEN: 4 - 5 ml EDTA whole blood transported at room temperature.

Factor V Leiden / Prothrombin 20210
A multiplexed PCR assay.

Assayed three times per week.

SPECIMEN: 4 - 5 ml EDTA whole blood transported at room temperature.

METHYLENETETRAHYDROFOLATE REDUCTASE (MTHFR)
A PCR assay for the C677T mutation

Assayed three times per week.

SPECIMEN: 4 - 5 ml EDTA whole blood transported at room temperature

HAEMOCHROMATOSIS (HFE)
A Multiplexed PCR assay that detects the C282Y,H63D and S65C mutations. A number of uncommon/
rare mutations are also detected by this assay which are confirmed by DNA sequencing.

Assayed daily (Monday - Friday)

SPECIMEN: 4 - 5 ml EDTA whole blood transported at room temperature.

FRAGILE X
This assay quantitates the number of CGG trinucleotide repeats in the FMR1 gene.

The PCR product is subsequently analysed by capillary electrophoresis using a DNA sequencer. Southern
blotting is employed in cases where PCR has not adequately defined the genotype or number of CGG
repeats.

Tested weekly.

SPECIMEN: 5-10ml EDTA blood transported at room temperature.

GILBERT'S SYNDROME
People with Gilbert's syndrome have mild, chronic unconjugated hyperbilirubemia in the absence of liver disease or overt hemolysis.

Although the syndrome is inherited, many people do not have a clear family history. The low grade hyperbilirubinemia is linked to mutations in the TATA box upstream of the uridine 5* -diphosphoglucose glucuronosyl-transferase (UGT1A1) gene leading to an impaired bilirubin glucuronidation.

From a clinical point of view it is highly desirable to distinguish between the different molecular causes of hyperbilirubinemia and to exclude potential genetic traits, such as Crigler-Najjar, Dubin-Johnson and/or GS. Carriers of the TATA-insertion-polymorphism may be at risk to suffer liver damage during drug treatment, particularly when glucuronidation is needed to ensure safe pharmacokinetics. This polymorphism is detected by real-time PCR.

Tested weekly.

SPECIMEN: 4 - 5 ml EDTA whole blood transported at room temperature

No MBS item number: Charge $50.

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HAEMATOLOGY TESTS

Immunoglobulin heavy chain rearrangement studies
This assay targets the FR3a and FR2 regions of the immunoglobulin heavy chain gene.

The PCR product is subsequently analysed by capillary electrophoresis using a DNA sequencer. The use of multiple primersets decreases the false negative rate seen with single primer set assays. Analysis by Genescan improves the sensitivity and specificity of this assay.

Tested weekly.

SPECIMEN: 4 - 5 ml EDTA whole blood or 1 ml of bone marrow or 5 - 6 paraffin sections ( 7- 10 microns)
transported at room temperature.

NO MBS item number. Charge: $100

T-cell receptor studies
This assay incorporates a multiplex PCR reaction that targets the T-cell gamma gene.

The PCR products are subsequently analysed by capillary electrophoresis using a DNA sequencer. The use of multiple primer sets decreases the false negative rate seen with single primer set assays. Analysis by Genescan improves the sensitivity and specificity of this assay.

Tested weekly.

SPECIMEN: 4 - 5 ml EDTA whole blood or 1 ml of bone marrow or 5 - 6 parrafin sections ( 7- 10 microns)
transported at room temperature.

NO MBS item number. Charge: $100

BCL1/ IgH translocation by PCR.
The translocation is found in the majority of cases of Mantle cell lymphoma.

Tested weekly.

SPECIMEN: 4 - 5 ml EDTA whole blood or 1 ml of bone marrow or 5 - 6 parrafin sections ( 7- 10 microns)
transported at room temperature.

NO MBS item number. Charge: $150

BCL2/ IgH translocation by PCR.
The translocation is found in the majority of cases of follicular lymphoma. This assay targets both the MBR and MCR breakpoints.

Tested weekly.

SPECIMEN: 4 - 5 ml EDTA whole blood or 1 ml of bone marrow or 5 - 6 paraffin sections ( 7- 10 microns)
transported at room temperature.

NO MBS item number. Charge: $200

BCR-ABL Translocation by PCR
The BCR-ABL translocation occurs in the vast majority of cases of chronic myeloid leukaemia (CML) and 10% - 20% of cases of adult acute lymphoblastic leukaemia (ALL).

The test performed by real-time PCR detects the transcripts found in both CML (b2a2 & b3a2). BCR-ABL is quantitated in CML patients.

Tested weekly.

SPECIMEN: 4-5ml EDTA whole blood or 1-2ml of bone marrow transported at room temperature. Specimens must reach the laboratory within 48hrs.

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TESTS TO BE RELEASED IN THE NEAR FUTURE

Cystic fibrosis
Cystic fibrosis is the most common autosomal recessive disease in the Caucasian population with a prevalance estimate of 1 in 2500 to 3300 live births.

The American College of Medical Genetics (ACMG) recommends screening of 25 different mutations as a minimum for population based carrier screening. Gippsland Pathology Service will shortly offer a screen based on oligonucleotide ligation molecular technology analysed using a DNA sequencer that exceeds the ACMG recommendation.