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Test ID: TPNUQ Thiopurine Methyltransferase (TPMT) and Nudix Hydrolase (NUDT15) Genotyping, Varies


Ordering Guidance


For thiopurine methyltransferase (TPMT) enzyme activity testing, order TPMT3 / Thiopurine Methyltransferase Activity Profile, Erythrocytes; however, this test (TPNUQ) should also be ordered because TPMT enzyme activity testing cannot detect variants in NUDT15, which also impact thiopurine metabolism.



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: Extracted 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. Document on the request form or electronic order that a copy is on file. The following documents are available in Special Instructions:

-Informed Consent for Genetic Testing (T576)

-Informed Consent for Genetic Testing-Spanish (T826)

2. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:

-Neurology Specialty Testing Client Test Request (T732)

-Gastroenterology and Hepatology Client Test Request (T728)

-Therapeutics Test Request (T831)

-Gastroenterology and Hepatology Patient Insurance Test Request (T908)

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, V

Specimen Type

Varies

Specimen Minimum Volume

Blood: 0.4 mL
Saliva: 1 swab

Specimen Stability Information

Specimen Type Temperature Time Special Container
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 the white population, 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 three different single-nucleotide variants (SNV), account for the majority of inactivating alleles in some ethnicities, including whites: TPMT*2, TPMT*3A, 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. NUDT15 deficiency is most common among East Asian (22.6%),  South Asian (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 heterozygous for a variant in only one 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

(NM_000367.4)

Amino acid change

Effect on enzyme metabolism

*1

None (wild type)

None (wild type)

Normal function

*2

c.238G>C

p.Ala80Pro (p.A80P)

No activity

*3A

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

p.Ala154Thr (p.A154T) and p.Tyr240Cys (p.Y240C)

No activity

*3B

c.460G>A

p.Ala154Thr (p.A154T)

No activity

*3C

c.719A>G

p.Tyr240Cys (p.Y240C)

No activity

*4

c.626-1G>A

Not applicable, splice site

No activity

*5

c.146T>C

p.Leu49Ser (p.L49S)

No activity

*8

c.644G>A

p.Arg215His (p.R215H)

Reduced activity

*12

c.374C>T

p.Ser125Leu (p.S125L)

Reduced activity

 

 

NUDT15 allele

cDNA nucleotide change

(NM_018283.3)

Amino acid change

Effect on enzyme metabolism

*1

None (wild type)

None (wild type)

Normal activity

*2 or *3

c.415C>T

p.Arg139Cys (p.R139C)

No activity

*4

c.416G>A

p.Arg139His (p.R139H)

No activity

*5

c.52G>A

p.Val18Ile (p.V18I)

No activity

 

The US Food and Drug Administration, the Clinical Pharmacogenetics Implementation Consortium, and some professional societies recommend consideration of TPMT and NUDT15 genotype testing or TPMT enzyme activity testing along with NUDT15 genotype testing prior to the initiation of therapy with thiopurine drugs. There is substantial evidence linking TPMT and NUDT15 genotype to phenotypic variability. Dose adjustments based upon TPMT and NUDT15 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 Activity Profile, Erythrocytes) if the clinician wants to check for lower TPMT enzyme activity, regardless of cause. Testing for TPMT enzyme activity is not impacted by variants in NUDT15.

Reference Values

An interpretive report will be 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) and catalogued in the Pharmacogene Variation Consortium (www.pharmvar.org).

 

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 (TPMT Alleles): Linkoping University; Updated May 2019. Accessed October 14, 2020. 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. Nat Genet. 2016;48(4):367-373. doi: 10.1038/ng.3508

3. Appell ML, Berg J, Duley J, et al: Nomenclature for alleles of the thiopurine methyltransferase gene. Pharmacogenet Genomics. 2013;23(4):242-248. doi:1 0.1097/FPC.0b013e32835f1cc0

4. Nguyen CM, Mendes MA, Ma JD: Thiopurine methyltransferase (TPMT) genotyping to predict myelosuppression risk. PLoS Curr. 2011;3:RRN1236. doi: 10.1371/currents.RRN1236

5. Relling MV, Schwab M, Whirl-Carrillo M, et al: Clinical Pharmacogenetics Implementation Consortium Guideline for Thiopurine Dosing Based on TPMT and NUDT15 Genotypes: 2018 Update. Clin Pharmacol Ther. 2019;105(5):1095-1105. doi: 10.1002/cpt.1304

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

7. Zaza G, Cheok M, Krynetskaia N, et al: Thiopurine pathway. Pharmacogenet Genomics. 2010;20(9):573-574. doi: 10.1097/FPC.0b013e328334338f

Day(s) Performed

Monday through Friday

Report Available

1 to 4 days

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 US Food and Drug Administration.

CPT Code Information

0034U

LOINC Code Information

Test ID Test Order Name Order LOINC Value
TPNUQ TPMT and NUDT15 Genotype, V 93193-1

 

Result ID Test Result Name Result LOINC Value
610159 TPMT Genotype 41048-0
610160 TPMT Phenotype 79713-4
610161 NUDT15 Genotype 93194-9
610162 NUDT15 Phenotype 93195-6
610163 Interpretation 69047-9
610164 Additional Information 48767-8
610165 Method 85069-3
610166 Disclaimer 62364-5
610167 Reviewed by 18771-6
Mayo Clinic Laboratories | Genetics and Pharmacogenomics Catalog Additional Information:

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