Pharmacogenomics

Pharmacogenomics is the study of how genes affect a person’s response to drugs. This relatively new field combines pharmacology (the science of drugs) and genomics (the study of genes and their functions) to identify effective, safe medications and doses that will be tailored to a person’s genetic makeup. Pharmacogenomic testing helps evaluate which drugs will be more suited to an individual, and therefore be more effective, as well as identify drugs which will have less adverse effects on the individual.

DYPD (DPD) Genotyping (5FU Assay)

This test is used to determine the DPYD genotype of patients being considered for treatment
with medications metabolized by DPYD. This is a pharmacogenomics test associated with 5-
fluorouracil and capecitabine drug sensitivity. These drugs are all part of chemotherapy
treatments of colorectal cancer and other solid tumors.

 

Genetic variants tested for DPYD are as follow.

 

  • *2A (c.1905+1G>A)
  • *13 (c.1679T>G)
  • rs67376798 (c.2846A>T)
CYP2D6 Genotyping

This test is used to determine the CYP2D6 genotype of patients being considered for treatment with medications metabolized by CYP2D6. CYP2D6 acts on 25% of all prescription drugs. Drugs that CYP2D6 metabolizes include selective serotonin reuptake inhibitors (SSRI), tricyclic antidepressants (TCA), beta-blockers, opiates, neuroleptics, antiarrhythmics, and a variety of toxic plant substances.

 

Genetic variants tested for CYP2D6 are as follow.

 

  • CYP2D6*2 g.4180G>C
  • CYP2D6*29 g 3183G>A
  • CYP2D6*41 g.2988G>A
  • CYP2D6*7 g.2935A>C
  • CYP2D6*2 g.2850C>T
  • CYP2D6*9 g.2615_2617delAAG
  • CYP2D6*3 g.2549delA
  • CYP2D6*20 g.1973_1974insG
  • CYP2D6*4 g.1846G>A
  • CYP2D6*14 g.1758G>A
  • CYP2D6*8 g.1758G>T
  • CYP2D6*6 g.1707delT
  • CYP2D6 g.1661G>C
  • CYP2D6*29/*70 g. 3183G>A
  • CYP2D6*17 g.1023C>T
  • CYP2D6*11g.883G>C
  • CYP2D6*15 g.137-138insT
  • CYP2D6*10 g.100C>T
  • CYP2D6*35 g.31G>A
  • CYP2D6*2A g.-1584C>G
CYP2C19 Genotyping

This test is used to determine the CYP2C19 genotype of patients being considered for treatment with medications metabolized by CYP2C19. CYP2C19 is an important drug metabolizing enzyme that catalyzes the biotransformation of many other clinically useful drugs including antidepressants, barbiturates, proton pump inhibitors, antimalarial, and antitumor drugs.

 

Genetic variants tested for CYP2C19 are as follow.

 

  • CYP2C19 *2 (681 G>A)
  • CYP2C19*3 (636 G>A)
  • CYP2C19*4 (1 A>G)
  • CYP2C19*10 (680C>T)
TPMT Genotyping

This test is used to determine the TPMT genotype of patients being considered for treatment with medications metabolized by Thiopurine methyltransferase (TPMT). TPMT plays a role in the elimination of thiopurine drugs, including mercaptopurine, azathioprine and thioguanine. These drugs are typically used to treat acute lymphoblastic leukemia, autoimmune disorders, inflammatory bowel disease and organ transplant rejection.

 

Genetic variants tested for TPMT are as follow

 

  • TPMT*1S (474T>C)
  • TPMT*2 (238G>C)
  • TPMT*3A (460G>A) (719A>G)
  • TPMT*3B (460G>A)
  • TPMT*3C (719A>G)
  • TPMT*3D (292G>T) (460G>A) (719A>G)
  • TPMT*7 (681T>G)
  • TPMT*8 (644G>A)
  • TPMT*9 (356A>C)
  • TPMT*10 (430G>C)
  • TPMT*16 (488 G>A)
  • TPMT*19 (365A>C)
  • TPMT*20 (712A>G)
  • TPMT*22 (488 G>C)
  • TPMT*25 (634T>C)
  • TPMT*27 (319T>G)
  • TPMT*28 (349G>C2)
  • TPMT*32 (340G>A)
  • TPMT*33 (487 C>T)
  • TPMT*34 (244 C>T)
HLA-A*3101/HLA-B* 1502 Genotyping

Carbamezapine is an anticonvulsant prescribed most often in the treatment of epilepsy, as well as trigeminal neuralgia and bipolar disorder. It is also known to show incidences of cutaneous adverse drug reactions (cADRs) including Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN) and drug-induced hypersensitivity syndrome (DIHS). Severe forms of these hypersensitivity reactions can also cause death. In genome wide association studies, a few SNPs were found to be associated with these cADRs. Among these, the HLA-A*3101 allele has been found to have maximum association with hypersensitivity reactions induced by carbamezapine. The HLA-B*1502 allele is also associated with SJS and TEN in Asian populations.

HLA-B* 5701 Genotyping

Abacavir is a core part of anti retroviral therapy used for the treatment of HIV. Patients with a HLA-B*5701 allele can have increased hypersensitivity to abacavir. In order to avoid the hypersensitivity in these patients, it is important to conduct HLA-B* 5701 genotyping prior to administration of Abacavir.

MTHFR Genotyping

The methylenetetrahydrofolate reductase (MTHFR) catalyzes the reaction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, which is involved in folate metabolism. The variant 677C>T in MTHFR gene causes production of a thermolabile enzyme with reduced enzymatic activity.

 

As a result, reduced conversion of homocysteine to methionine leads to an  accumulation of homocysteine in the plasma (hyperhomocysteinaemia). Enhanced homocysteine plasma concentration is a risk factor for coronary heart disease, thrombosis, and arterosclerosis. In addition, the variant MTHFR 1298A>C in the MTHFR gene has been associated with increased risk for cardiovascular diseases.

 

The presence of both variant (C677T and A1298C) in same patient is described as a risk factor for defects of the neural tube. MTHFR genotyping is an important pharmacogenomic test used to assess whether few therapies will be effective on patients who may have a MTHFR gene polymorphism as mentioned above.

Tacrolimus Mutation Study for CYP3A4

Tacrolimus is an immunosuppressive drug whose main use is after organ transplant to reduce the activity of the patient’s immune system and so the risk of organ rejection. It is also used in a topical preparation in the treatment of severe atopic dermatitis, severe refractory uveitis after bone marrow transplants, and the skin condition vitiligo. Tacrolimus dosing is often a challenge, as its complex pharmacokinetics can result in either drug toxicity or insufficient immunosuppressive activity.

 

Tacrolimus is metabolized by cytochrome CYP3A enzymes and hence genetic variants of the CYP3A4 gene can cause faulty metabolism of this drug. This pharmacogenomic test is hence important to assess whether or not Tacrolimus can be administered to a patient.

Warfarin Genotyping

Warfarin has a narrow therapeutic window; under medicating increases the risk for thrombosis and overmedicating increases the risk for cerebrovascular accidents. Warfarin therapy has one of the highest rates of severe adverse drug reactions. The cytochrome P450 2C9 gene (CYP2C9) encodes an enzyme that metabolizes the more active isomer of warfarin (S-Warfarin) to inactive products. Polymorphisms in this gene decrease the activity of the enzyme and may cause increases in serum warfarin and overmedicating, driving INR above the therapeutic target level. The second gene (VKORC1) encodes vitamin K epoxide reductase complex subunit-1 (VKORC1), the target of warfarin therapy.

 

A polymorphism within the promoter of VKORC1 decreases expression of the gene, decreasing the availability of vitamin K. This may cause increases in serum warfarin and overmedicating, driving INR above the therapeutic target level.Therefore, understanding genotype of these two genes helps in deciding the warfarin dosage for a patient.

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Accreditations

CLIA No. 34D2205781