Test Catalog

Test Id : TPNUQ

Thiopurine Methyltransferase (TPMT) and Nudix Hydrolase (NUDT15) Genotyping, Varies

Useful For
Suggests clinical disorders or settings where the test may be helpful

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

Highlights

This test includes genotyping of TPMT and NUDT15, both of which affect metabolism of thiopurine drugs.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

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

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

TPMT and NUDT15 Genotype, V

Aliases
Lists additional common names for a test, as an aid in searching

6-Mercaptopurine

6-Thioguanine

Acute Lymphoblastic Leukemia (ALL)

Azathioprine

Crohn's Disease

Inflammatory Bowel Disease (IBD)

NUDT15

Rheumatoid Arthritis

Thiopurine

TPMT

Ulcerative Colitis

mercaptopurine

thioguanine

tmpt

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

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

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

Multiple genotype tests can be performed on a single specimen after a single extraction. See Multiple Genotype Test List 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 whole blood specimen in original tube. Do not aliquot.

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: 1 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. Provide concentration of DNA and volume on tube.

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

Special Instructions
Library of PDFs including pertinent information and forms related to the test

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:

-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)

Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the Testing Laboratory

Blood: 0.4 mL

Saliva, extracted DNA: see Specimen Required

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

Specimen Type Temperature Time Special Container
Varies Varies (preferred)

Useful For
Suggests clinical disorders or settings where the test may be helpful

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

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

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 3 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.

 

Table 1. TPMT Enzyme Activity of Individual Star Alleles

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

 

Table 2. NUDT15 Enzyme Activity of Individual Star Alleles

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
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation
Provides information to assist in interpretation of the test results

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. This resource also includes information regarding enzyme inhibitors and inducers, as well as potential alternate drug choices.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Rare variants may be present that could lead to false-negative or false-positive results. 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. In addition, 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.

 

If genotype results obtained do not match the clinical findings, additional testing should be considered for thiopurine methyltransferase enzyme activity (TPMT3 / Thiopurine Methyltransferase Activity Profile, Erythrocytes). A corresponding activity assay for NUDT15 is not currently available.

 

Samples may contain donor DNA if obtained from patients who received non-leukoreduced blood transfusions or allogeneic hematopoietic stem cell transplantation. Results from samples obtained under these circumstances may not accurately reflect the recipient's genotype. For individuals who have received blood transfusions, the genotype usually reverts to that of the recipient within 6 weeks. For individuals who have received allogeneic hematopoietic stem cell transplantation, a pretransplant DNA specimen is recommended for testing.

 

The results do not rule out the possibility that a patient harbors another variant in TPMT, NUDT15, or another gene that can impact drug response or drug side effects. These genotyping procedures will not distinguish between heterozygous TPMT*3A from the rare TPMT*3B/*3C, which has an estimated frequency of 1:120,890. This rare genotype is associated with low enzyme activity. Enzyme activity evaluation is necessary to definitively identify this rare genotype (TPMT3 / Thiopurine Methyltransferase Activity Profile, Erythrocytes).

 

This test will not detect all TPMT or NUDT15 genetic variants. A negative result does not rule out the possibility of toxicity if thiopurines are used, since multiple factors (eg, other genetic factors, drug-drug interactions) are known to play a role. Co-prescription of allopurinol might inhibit TPMT activity. Other drugs that have been shown to inhibit TPMT activity include naproxen, ibuprofen, ketoprofen, furosemide, sulfasalazine, mesalamine, olsalazine, mefenamic acid, thiazide diuretics, and benzoic acid inhibitors.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

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

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Description
Describes how the test is performed and provides a method-specific reference

Genomic DNA is extracted from whole blood or saliva. Genotyping for the TPMT and NUDT15 alleles is performed using a polymerase chain reaction (PCR)-based 5'-nuclease assay. Fluorescently labeled detection probes anneal to the target DNA. PCR is used to amplify the segment of DNA that contains the polymorphism. If the detection probe is an exact match to the target DNA, the 5'-nuclease polymerase degrades the probe, the reporter dye is released from the effects of the quencher dye, and a fluorescent signal is detected. Genotypes are assigned based on the allele-specific fluorescent signals that are detected.(Instruction manual: TaqMan SNP Genotyping Assay User Guide. Applied Biosystems; Revision A.0, 01/2014)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Monday through Friday

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

1 to 4 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Whole blood/Saliva: 2 weeks; Extracted DNA: 2 months

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their Regional Manager. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

0034U

LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
TPNUQ TPMT and NUDT15 Genotype, V 93193-1
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
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

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