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Test ID: TPNUV Thiopurine Methyltransferase (TPMT) and Nudix Hydrolase (NUDT15) Genotyping


Advisory Information


For thiopurine methyltransferase (TPMT) enzyme activity testing, order TPMT3 / Thiopurine Methyltransferase (TPMT) Activity Profile, Erythrocytes.



Specimen Required


Multiple genotype tests can be performed on a single specimen after a single extraction. See Multiple Genotype Test List in Special Instructions for a list of tests that can be ordered together.

 

Submit only 1 of the following specimens:

 

Specimen Type: Whole blood

Container/Tube: Lavender top (EDTA)

Specimen Volume: 3 mL

Collection Instructions:

1. Invert several times to mix blood.

2. Send specimen in original tube.

Specimen Stability Information: Ambient (preferred) 9 days/Refrigerated 30 days

 

Specimen Type: Saliva

Patient Preparation: Patient should not eat, drink smoke, or chew gum 30 minutes prior to collection.

Supplies: Saliva Swab Collection Kit (T786)

Specimen Volume: One swab

Collection Instructions: Collect and send specimen per kit instructions.

Specimen Stability Information: Ambient 30 days

 

Specimen Type: DNA

Container/Tube: 2 mL screw top tube

Specimen Volume: 100 mcL

Collection Instructions:

1. The preferred volume is 100 mcL at a concentration of 50 ng/mcL.

2. Include concentration and volume on tube.

Specimen Stability Information: Frozen (preferred)/Ambient/Refrigerated


Forms

1. New York Clients-Informed consent is required. Please document on the request form or electronic order that a copy is on file. An Informed Consent for Genetic Testing (T576) is available in Special Instructions.

2. If not ordering electronically, complete, print, and send a Pharmacogenomics Test Request Form (T797) with the specimen (https://www.mayomedicallaboratories.com/it-mmfiles/pharmacogenomics-test-request-form-mc0767-15.pdf)

Useful For

Predicting potential for toxicity to thiopurine drugs (6-mercaptopurine, 6-thioguanine, and azathioprine)

Method Name

Real-Time Polymerase Chain Reaction (PCR) With Allelic Discrimination Analysis

Reporting Name

TPMT and NUDT15 Genotype

Specimen Type

Varies

Specimen Minimum Volume

Blood: 0.4 mL
Saliva: 1 swab

Specimen Stability Information

Specimen Type Temperature Time
Varies Varies

Clinical Information

The thiopurine drugs are purine antimetabolites that are useful in the treatment of acute lymphoblastic leukemia, autoimmune disorders (eg, Crohn disease, rheumatoid arthritis), and organ transplant recipients. The thiopurine drugs, 6-mercaptopurine (6-MP), 6-thioguanine (6-TG), and azathioprine (AZA) are prodrugs that require intracellular activation to 6-thioguanine nucleotides (6-TGN). This activation is catalyzed by multiple enzymes. The cytotoxic effects of thiopurine drugs are achieved mainly through incorporation of 6-TGN into DNA and RNA. The pathway that leads to synthesis of active cytotoxic 6-TGN is in competition with inactivation pathways catalyzed by thiopurine methyltransferase (TPMT). Evaluation of this pathway is important because the level of 6-TGN measured in red blood cells have been correlated with both thiopurine therapeutic efficacy and toxicity such as myelosuppression.

 

TPMT activity is inherited as a monogenic codominant trait, and variable TPMT activity is associated with TPMT genetic variants. The distribution of TPMT activity in red blood cells is trimodal in Caucasians, with approximately 0.3% of people having deficient (undetectable) TPMT activity, 11% low (intermediate) activity, and 89% normal TPMT activity. The allele for normal TPMT activity (wild-type) has been designated TPMT*1. Four TPMT alleles, comprised of a combination of 3 different single-nucleotide substitutions (SNP), account for the majority of inactivating alleles in some ethnicities, including Caucasians: TPMT*2, TPMT*3A, TPMT*3B, and TPMT*3C. Less frequently occurring TPMT alleles TPMT*4, TPMT*5, TPMT*8, and TPMT*12 also have been implicated as deficiency alleles. If no TPMT variant alleles are detected by this assay, the most likely genotype is that of TPMT*1/*1 although the presence of other rarer alleles cannot be excluded.

 

Nudix hydrolase (NUDT15) is thought to dephosphorylate the active metabolites of thiopurines, TGTP and TdGTP, which prevents their incorporation into DNA and decreases their cytotoxic effects. Genetic variants in NUDT15 that decrease this activity are strongly associated with thiopurine-related myelosuppression. NUDT deficiency is most common among East Asians (22.6%), followed by South Asians (13.6%), and Native American populations (12.5%-21.2%). Studies in other populations are ongoing. This test evaluates variants associated with NUDT15*2, NUDT15*3, NUDT15*4, and NUDT15 *5. If no NUDT15 variant alleles are detected by this assay, the most likely genotype is that of NUDT15*1/*1 although the presence of other rarer alleles cannot be excluded. Individuals with variants in both TPMT and NUDT15 have been identified and were significantly more sensitive to mercaptopurine than individuals with variants in only 1 gene. Integration of both TPMT and NUDT15 testing may allow for more accurate prediction of thiopurine-related toxicity risk to guide dosing, particularly among patients from diverse populations.

 

TPMT Allele

cDNA Nucleotide Change

Effect on Enzyme Metabolism

*1

None (wild type)

Normal function

*2

c.238G->C

No activity

*3A

c.460G->A and c.719A->G

No activity

*3B

c.460G->A

No activity

*3C

c.719A->G

No activity

*4

c.626-1G->A

No activity

*5

c.146T->C

No activity

*8

c.644G->A

Reduced activity

*12

c.374C->T

Reduced activity

 

The US Food and Drug Administration, the Clinical Pharmacogenetics Implementation Consortium, and some professional societies recommend consideration of TPMT genotype or TPMT erythrocyte testing prior to the initiation of therapy with thiopurine drugs. There is substantial evidence linking TPMT genotype to phenotypic variability. Dose adjustments based upon TPMT genotype have reduced thiopurine-induced adverse effects without compromising desired antitumor and immunosuppressive therapeutic effects in several clinical settings.

 

Genotyping is not impacted by other medications known to inhibit TPMT activity. Complementary clinical testing is available to measure TPMT enzymatic activity in erythrocytes (TPMT3 / Thiopurine Methyltransferase (TPMT) Activity Profile, Erythrocytes) if the clinician wants to check for lower TPMT enzyme activity, regardless of cause. Although there currently aren't guidelines or professional society recommendations related to NUDT15 genotyping to guide thiopurine use, this practice is substantially supported by the literature. Testing for TPMT enzyme activity is not impacted by variants in NUDT15.

NUDT15 Allele

cDNA Nucleotide Change

Effect on Enzyme Metabolism

*1

None (wild type)

Normal activity

*2 or *3

c.415C>T

No activity

*4

c.416G>A

No activity

*5

c.52G>A

No activity

Reference Values

An interpretive report is provided.

Interpretation

An interpretive report will be provided.

 

The TPMT genotype, with associated star alleles, is assigned using standard allelic nomenclature as published by the TPMT Nomenclature Committee.(1) NUDT15 genotype and associated star alleles are as described by Moriyama et al.(2)

 

For additional information regarding pharmacogenomic genes and their associated drugs, see the Pharmacogenomics Associations Tables in Special Instructions. This resource also includes information regarding enzyme inhibitors and inducers, as well as potential alternate drug choices.

Clinical Reference

1. TPMT nomenclature committee. Available at www.imh.liu.se/tpmtalleles

2. Moriyama,T., Nishii, R., Perez-Andreu, V., et al: NUDT15 polymorphisms alter thiopurine metabolism and hematopoietic toxicity. Nature Genetics 2016;48:367-373

3. Appell ML, Berg J, Duley J, et al: Nomenclature for alleles of the thiopurine methyltransferase gene. Pharmacogenet Genomics 2013;23(4):242-248

4. Nguyen CM, Mendes MA, Ma JD: Thiopurine methyltransferase (TPMT) genotyping to predict myelosuppression risk. PLoS Curr 2011;3:RRN1236

5. Relling MV, Gardner EE, Sandborn WJ, et al: Clinical Pharmacogenetics Implementation Consortium guidelines for thiopurine methyltransferase genotype and thiopurine dosing. Clin Pharmacol Ther 2011;89(3):387-391

6. Weinshilboum R: Thiopurine pharmacogenetics clinical and molecular studies of thiopurine methyltransferase. Drug Metab Dispos 2001 Apr;29(4 Pt 2):601-605

7. Zaza G, Cheok M, Krynetskaia N, et al: Thiopurine pathway. Pharmacogenet Genomics 2010 Sep;20(9):573-574

Day(s) and Time(s) Performed

Monday through Friday; 8 a.m.

Analytic Time

1 day (not reported on Saturday or Sunday)

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

0034U

LOINC Code Information

Test ID Test Order Name Order LOINC Value
TPNUV TPMT and NUDT15 Genotype In Process

 

Result ID Test Result Name Result LOINC Value
BA0211 TPMT Genotype In Process
BA0212 TPMT Phenotype 79713-4
BA0213 NUDT15 Genotype In Process
BA0214 NUDT15 Phenotype In Process
BA0215 Interpretation 69047-9
BA0216 Additional Information 48767-8
BA0217 Method 49549-9
BA0218 Disclaimer 62364-5
BA0219 Reviewed by 18771-6
Mayo Medical Laboratories | Genetics and Pharmacogenomics Catalog Additional Information:

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