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Pharmacogenetics in Oncology

Pharmacogenetic Markers in Oncology

Pharmacogenomics can play an important role in identifying responders and non-responders to medications, avoiding adverse events and optimising drug dose. Drug labelling may contain information on genomic biomarkers and can describe:

Drug exposure and clinical response variability Mechanisms of drug action
Risk for adverse events Polymorphic drug target and disposition genes
Genotype-specific dosing Trial design features

In addition to RAS, BRAF, EGFR, ERBB2 (HER2), PK3CA, KIT mutation and PD-1, ROS, ALK, and BCR-ABL fusion genes, other genetic pharmacogenetic biomarkers play a role in patients’ responses to oncology therapy.

Pharmacogenomics, an important part of precision medicine, is the study of how a person’s genetic makeup can affect their response to a drug. Healthcare providers can use pharmacogenomic information to help decide the most appropriate treatment for each individual.

The cytochrome P450 (CYP450), a family of enzymes, catalyses the metabolism of many drugs and xenobiotics. The genes that code for these enzymes are polymorphic, which can significantly affect drug metabolism in certain individuals. CYP2D6, CYP2C19 and CYP2C9 are responsible for the metabolism of a large number of commonly prescribed drugs, including warfarin, analgesics, clopidogrel, codeine, tamoxifen, some antidepressants, statins, proton pump inhibitors (PPI) and anti-emetics.

More than 70 allelic variants have been described for the gene that codes CYP2D6. These variants result in four distinct phenotypes: poor metabolisers, intermediate metabolisers, extensive metabolisers and ultrarapid metabolisers. Both the CYP2C9 and the CYP2C19 genes have two major variant alleles that result in enzyme deficiency.

Differences in drug metabolism due to CYP450 gene variants influence plasma levels of both the active drug and its metabolites. Poor metabolisers treated with drugs that are metabolised by these enzymes are at increased risk for prolonged therapeutic effect or toxicity, while ultrarapid metabolisers may not achieve therapeutic plasma levels.

Thiopurine methyltransferase (TPMT) is the primary enzyme responsible for thiopurine drugs (azathioprine, 6-mercaptopurine and 6-thioguanine) metabolism. These drugs are converted in the body to thioguanine nucleotides (TGNs).

Thiopurine therapy targets the replicating cells without overly harming normal cells. TPMT activity is significantly affected by polymorphisms found in the TPMT gene and can lead to different responses to thiopurine therapy.

DPYD gene
DPD stands for dihydropyrimidine dehydrogenase, an enzyme made by the liver that breaks down uracil and thymine. The molecules created when pyrimidines are broken down (5,6-dihydrouracil and 5,6-dihydrothymine) are excreted by the body or used in other cellular processes.

More than 50 mutations in the DPYD gene have been identified in people with dihydropyrimidine dehydrogenase deficiency. DPYD gene mutations interfere with the breakdown of uracil and thymine and result in excess quantities of these molecules in the blood, urine, and the fluid that surrounds the brain and spinal cord (cerebrospinal fluid).

Mutations in the DPYD gene also interfere with the breakdown of drugs with structures similar to the pyrimidines, such as the cancer drugs 5-fluorouracil and capecitabine (two common chemotherapy drugs used as a treatment for a number of different cancers). As a result, these drugs accumulate in the body and cause the severe reactions and neurological manifestations as a result of DPD deficiency.


 

Pharmacogenetic Testing at Australian Clinical Labs

Our comprehensive Pharmacogenetic tests can detect polymorphisms in genes coding for drug-metabolising enzymes that predispose individuals to metabolising drugs inadequately.

Genes Offered:

Cytochrome P450 including:
- CYP2D6, CYP2C9, CYP2C19, CYP3A4, CYP3A5, CYP1A2, SLCO1B and VKORC
TPMT
DPYD
UGT1A1

List of Oncology Related Genotypes:

GENE Oncology Drug Medicare Rebate
CYP2D6 Tamoxifen
Codeine
Tramadol
Oxycodone (lesser extent)
Gefitinib
Rucaparib
N/A
CYP2C9 Tacrolimus
Erdafitinib
N/A
CYP2C19 Clopidogrel N/A
CYP2C9/VKORC1 Warfarin N/A
CYP3A5 Tacrolimus N/A
DPYD Fluorouracil
capecitabine
tegafur
N/A
UGT1A1 Belinostat
Binimetinib
Irinotecan
Nilotinib
Pazopanib
N/A
Thiopurine Methyltransferase (TPMT) Mercaptopurine,
Azathioprine and
Thioguanine
Cisplatin
YES

Please note that the panel Cytochrome P450 Genes can be ordered separately or together
(CYP2D6, 2C9, 2C19, CYP3A4, CYP3A5, CYP1A2, SLCO1B1 and VKORC1)

When to Order: Before therapy, with adverse reaction or resistance.
How to Order: Fill out our routine Clinical Labs testing request form, list the gene required or group of genes.
Turnaround Time: Results will be available after 7-10 business days from the sample receipt date.
Specimen Required: 2x EDTA blood samples.
Test Cost:
CYP2D6: No Medicare rebate available. An out-of-pocket fee of $180 applies.
CYP2C19: No Medicare rebate available. An out-of-pocket fee of $140 applies.
Analgesic Dosing (CYP2D6): No Medicare rebate available. An out-of-pocket fee of $100 applies.
Clopidogrel Predictar (CYP2C19): No Medicare rebate available. An out-of-pocket fee of $90 applies.
Taxoxifen Predictar: No Medicare rebate available. An out-of-pocket fee of $100 applies.
Warfarin Predictarn (CYP2C9/VKORC1): No Medicare rebate available. An out-of-pocket fee of $90 applies.
Variconazole (CYP2C19): No Medicare rebate available. An out-of-pocket fee of $90 applies.
Proton Pump Inhibitors (CYP2C19): No Medicare rebate available. An out-of-pocket fee of $90 applies.
CYP3A5: No Medicare rebate available. An out-of-pocket fee of $90 applies.
DPYD: No Medicare rebate available. An out-of-pocket fee of $90 applies.
UGT1A1: No Medicare rebate available. An out-of-pocket fee of $60 for UG1 test and $35 for GIL test applies.
Thiopurine Methytltransferase (TPMT): Medicare rebate available.

Download Clinical Labs Request Form


 

The content on our Molecular Cancer Services page is written by National Clinical Director of Molecular Genetic Pathology at Australian Clinical Labs, Associate Professor Mirette Saad

 

Assoc. Prof. Mirette Saad

MBBS (Hons), MD, MAACB, FRCPA, PhD
Lab: Clayton
Speciality: Chemical Pathology and Molecular Genetics
Areas Of Interest: Cancer Genetics, Antenatal Screening, NIPT, Endocrine, Fertility Testing and Research, Medical Teaching
Phone: 1300 134 111
Email: mirette.saad@clinicallabs.com.au

Associate Professor Mirette Saad is a Consultant Chemical Pathologist and the National Clinical Director of Molecular Genetic Pathology at Australian Clinical Labs. Associate Professor Saad obtained her fellowship in Chemical and Molecular Pathology with a clinical Microbiology sub-specialty in Egypt.

After several posts, she worked as a Medical Laboratory Director in private labs and as an Associate Professor and Examiner of Clinical Chemistry for postgraduate and undergraduate medical and nursing students at various institutions. Upon receiving the National Health and Medical Research (NHMRC) Scholarship in 2006, Associate Professor Saad commenced her PhD studies at Melbourne University and Peter MacCallum Cancer Institute in Cancer Genetics. Associate Professor Saad undertook her specialty training at Healthscope Pathology (now Australian Clinical Labs) and Monash Health and obtained the Chemical Pathology Fellowship (FRCPA) and the Membership (MAACB) by examination from the Royal College of Pathologists of Australasia (RCPA) and the Australasian Association of Clinical Biochemists (AACB) respectively.

She is currently a member of the Chemical Pathology Advisory Committee at RCPA. At Clinical Labs, A/P Saad supervises the antenatal screening program including combined First Trimester Screening and Non-Invasive Prenatal Testing (NIPT) along with the Molecular Genetic testing for hereditary disorders, personalised drug therapy and cancer.

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