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MP 2.04.19 Pharmacogenomic and Metabolite Markers for Patients Treated with Thiopurines

Medical Policy    
Original Policy Date
Last Review Status/Date

Reviewed with literature search/5:2014

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Our medical policies are designed for informational purposes only and are not an authorization, or an explanation of benefits, or a contract.  Receipt of benefits is subject to satisfaction of all terms and conditions of the coverage.  Medical technology is constantly changing, and we reserve the right to review and update our policies periodically. 


The use of thiopurines, medications for treating inflammatory bowel disease (IBD) and other conditions, is limited by a high rate of drug toxicity. Susceptibility to drug toxicity has been linked to the level of activity of the enzyme thiopurine methyltransferase (TPMT) which converts thiopurines into metabolites. There are 3 distinct TPMT mutations, and these are associated with the level of TPMT activity. Pharmacogenomic analysis of TPMT status is proposed to identify patients at risk of thiopurine drug toxicity and adjust medication doses accordingly. Measurement of metabolite markers has also been proposed.

Thiopurines or purine analogs are immunomodulators. They include azathioprine (AZA, Imuran), mercaptopurine (6-MP; Purinethol), and thioguanine (6-TG; Tabloid). Thiopurines are used to treat malignancies, rheumatic diseases, dermatologic conditions, IBD and are used in solid organ transplantation. In particular, they are considered an effective immunosuppressive treatment of IBD, particularly in patients with corticosteroid-resistant disease. However, the use of thiopurines is limited by both its long onset of action (3-4 months) and drug toxicities, which include hepatotoxicity, bone marrow suppression, pancreatitis, and allergic reactions.


Thiopurines are converted to 6-MP in vivo, where it is subsequently metabolized to 2 active metabolites; either 6-thioguanine nucleotides (6-TGN) by the enzyme IMPDH, or to 6-methyl-mercaptopurine ribonucleotides (6-MMRP) by the enzyme TPMT. TPMT also converts 6-MP to an inactive metabolite, 6- methyl-mercaptopurine (6-MMP). 6-TGNs are considered cytotoxic and thus are associated with bone marrow suppression, while 6-MMRP is associated with hepatotoxicity. In population studies, the activity of the enzyme TPMT has been shown to be trimodal, with 90% of subjects having high activity, 10% intermediate activity, and 0.3% with low or no activity. In patients with intermediate to low activity, the metabolism of 6-MP is shunted toward the IMPDH pathway with greater accumulation of 6-TGN; these patients are considered to be at risk for myelotoxicity (ie, bone marrow suppression).

This variation in TPMT activity has been related to 3 distinct TPMT mutations and has permitted the development of TPMT genotyping based on a polymerase chain reaction (PCR). For example, patients with high TPMT activity are found to have 2 normal (wild-type) alleles for TPMT; those with intermediate activity are heterozygous (ie, have a mutation on 1 chromosome), while those with low TPMT activity are homozygous for TPMT mutations (ie, a mutation is found on both chromosomes). Genetic analysis has been explored as a technique to identify patients at risk for myelotoxicity; those with intermediate TPMT activity may be initially treated with lower doses of thiopurines, while those with low TPMT activity may not be good candidates for thiopurine therapy.

TPMT activity can also be measured by phenotypic testing. Phenotypic testing determines the level of thiopurine nucleotides or TPMT activity in erythrocytes and can also be informative. Caution must be taken with phenotyping, because some coadministered drugs can influence measurement of TPMT activity in blood, and recent blood transfusions will misrepresent a patient’s actual TPMT activity.

Prospective TPMT genotyping or phenotyping may help identify patients who may be at increased risk of developing severe, life-threatening myelotoxicity.

Metabolite Markers

Monitoring of thiopurine therapy has been based on clinical assessment of response in addition to monitoring blood cell counts, liver function, and pancreatic function tests. However, there has been interest recently in monitoring intracellular levels of thiopurine metabolites (ie, 6-TGN and 6-MMRP) to predict response and complications, with the ultimate aim of tailoring drug therapy to each individual patient.

While genotyping and phenotyping of TPMT would only be performed once, metabolite markers might be tested at multiple times during the course of the disease ie, to aid in determining initial dose and to evaluate ongoing dosing.

Regulatory Status
Prometheus® is a commercial laboratory that offers thiopurine genotype, phenotype and metabolite testing for those undergoing thiopurine therapy. The tests are referred to as Prometheus TPMT Genetics, Prometheus TMPT enzyme, and Prometheus thiopurine metabolites, respectively. Other laboratories that offer TPMT genotyping include Quest (TPMT Genotype) and Specialty Laboratories (TPMT GenoTypR™).


One-time genotypic or phenotypic analysis of the enzyme TPMT may be considered medically necessary in patients beginning therapy with azathioprine (AZA), mercaptopurine (6-MP) or thioguanine (6-TG) OR in patients on thiopurine therapy with abnormal complete blood count (CBC) results that do not respond to dose reduction.

Genotypic and/or phenotypic analysis of the enzyme TPMT is considered investigational in all other situations.

Analysis of the metabolite markers of azathioprine (AZA) and mercaptopurine (6-MP), including 6-methyl-mercaptopurine ribonucleotides (6-MMRP) and 6-thioguanine nucleotides (6-TGN), is considered investigational. 

Policy Guidelines 

TPMT testing cannot substitute for complete blood count (CBC) monitoring in patients receiving thiopurines. Early drug discontinuation may be considered in patients with abnormal CBC results. Dosage reduction is recommended in patients with reduced TPMT activity. Alternate therapies may need to be considered for patients who have low or absent TPMT activity (homozygous for nonfunctional alleles). Accurate phenotyping results are not possible in patients who received recent blood transfusions. Genotyping and phenotyping of TPMT would only need to be performed once.

Effective in 2012, the analysis of common variants of the TPMT gene would be reported with CPT code 81401 - Molecular pathology procedure, Level 2 (e.g., 2-10 single nucleotide polymorphisms [SNPs], 1 methylated variant, or 1 somatic variant [typically using nonsequencing target variant analysis], or detection of a dynamic mutation disorder/triplet repeat).

There are no specific CPT codes for metabolite markers of azathioprine, mercaptopurine (6-MP) or thioguanine.

Before 2012, the laboratories offering this testing noted that they use a combination of the CPT codes listed below to code for this test (for example, Prometheus uses 83891, 83898 x3; 83896 x6; 83912):

83890: molecular diagnostics; molecular isolation or extraction, each nucleic acid type (i.e., DNA or RNA)

83891: isolation or extraction of highly purified nucleic acid, each nucleic acid type (i.e., DNA or RNA)

83892: enzymatic digestion, each enzyme treatment

83896: nucleic acid probe, each

83898: amplification, target, each nucleic acid sequence

83900: amplification, target, multiplex, first 2 nucleic acid sequences

83909: separation and identification by high resolution technique (e.g., capillary electrophoresis); each nucleic acid preparation

83912: interpretation and report

83914: mutation identification by enzymatic ligation or primer extension, single segment, each segment (e.g., oligonucleotide ligation assay [OLA], single base chain extension [SBCE] or allele-specific primer extension [ASPE])

Prior to 2013, there was also a CPT genetic testing modifier that is specific to TPMT:

-9A: TPMT, commonly called thiopurine methyltransferase (patients on antimetabolite therapy)

Benefit Application

BlueCard/National Account Issues

Genotypic, phenotypic, and metabolite markers are specialized laboratory tests typically performed in reference laboratories. 


This policy was originally created in 2000 and was updated regularly with searches of the MEDLINE database. The most recent literature search was performed through April 4, 2014. Following is a summary of the key literature to date:

As with any diagnostic technology, there are 3 steps in the technology assessment process: evaluation of technical feasibility, evaluation of ability to accurately diagnose a clinical condition in comparison with the gold standard, and determination of whether use of the test results in an improved patient outcome. These factors are discussed below, both for pharmacogenomics and metabolite markers.

Technical Performance


The genotypic analysis of the thiopurine methyltransferase (TPMT) gene is based on well-established polymerase chain reaction technology (PCR) to detect 3 distinct mutations. Currently, 3 alleles, TPMT*2, TPMT*3A and TPMT*3C, account for about 95% of individuals with reduced TPMT activity. Individuals homozygous for these alleles are TPMT-deficient and those heterozygous for these alleles have variable TPMT (low or intermediate) activity. A 2011 study from Sweden addressed the concordance between TPMT genotyping and phenotyping. (1) The investigators evaluated data from 7,195 unselected and consecutive TPMT genotype and phenotype tests. The genotype tests examined the 3 most common TPMT variants, noted above. TPMT genotyping identified 89% as TPMT wild type, 704 (10%) as TPMT heterozygous, and 37 (0.5%) as TPMT homozygous. The overall agreement between genotyping and phenotyping was 95%. Genotyping alone would have misclassified 3 of 37 (8%) homozygous patients as heterozygous; these 3 individuals were found to have uncommon mutations. All 3 had low TPMT activity. The phenotype test would have misclassified 4 of 37 (11%) of homozygous patients as they had test results above the cut-off level for low TPMT activity (<2.5 U/mL red blood cells).

Metabolite Markers

Metabolite markers have been assessed using high performance liquid chromatography (HPLC) technology. It would be optimal to assess metabolite markers in peripheral leukocytes, since they reflect the status of bone marrow precursors. However, it is technically easier to measure metabolites in red blood cells (RBCs) instead of leukocytes.

Diagnostic Performance


Several systematic reviews of studies on the diagnostic performance of TPMT genotyping have been published. Among the most recent studies was a 2011 review by Booth and colleagues that was sponsored by the Agency for Healthcare Research and Quality (AHRQ). (2) A total of 19 studies on test performance were identified; most were cross-sectional or prospective observational studies and approximately 70% included patients with inflammatory bowel disease. Among the 1,735 total patients, 184 were heterozygous and 16 were homozygous for variant alleles, a small total sample of individuals with variant alleles. A pooled analysis of data from 19 studies found a sensitivity of 79.9% (95% confidence interval [CI]: 74.8% to 84.6%) for correctly identifying individuals with subnormal (intermediate or low) enzymatic activity. The specificity of the wild-type genotype for correctly identifying individuals with normal or high enzymatic activity approached 100%. Seventeen studies addressed the association between TPMT status and thiopurine toxicity. The studies included a total of 2,211 patients, of which 357 had intermediate and 74 had low enzymatic activity. In a pooled analysis of 3 studies (92 patients, 10 events), there were greater odds of myelotoxicity with low TPMT enzymatic activity than intermediate activity (pooled odds ratio [OR]: 14.5, 95% CI: 2.78-76.0). Similarly, in a pooled analysis of 3 studies (403 patients, 29 events), there were greater odds of myelotoxicity with low TPMT enzymatic activity than normal levels (pooled OR: 19.1, 95% CI: 4.6-80.2). It is worth noting that confidence intervals were wide due to few events and small sample sizes.

Another systematic review published in 2011, by Donnan and colleagues, identified 17 studies that reported the performance characteristics of TPMT genotyping tests (12 studies) and phenotyping (6 studies) compared to a reference standard. (3) No true gold standard was available. The enzymatic test was used as the reference standard in 9 studies, and the remainder used a genotyping test; 3 studies compared 2 methods of genotyping. All of the studies used a method of genotyping as either the investigational test or the reference standard; the tests varied somewhat in the number and type of polymorphisms they were designed to detect. Sixteen of 17 studies either reported sensitivity and specificity, or reported sufficient data for these measures to be calculated. Only 3 studies considered confounding factors such as concurrent medications and blood transfusions in their exclusion criteria. The authors of the systematic review did not pool study findings. In the included studies, sensitivity of enzymatic tests ranged from 92% to 100% and specificity ranged from 86% to 98%. The sensitivity of the genotype tests ranged from 55% to 100% and the specificity ranged from 94% to 100%. In general, the enzymatic tests had a high sensitivity and low-positive predictive value when genotype tests were used as the reference standard. Genotype tests showed a lower sensitivity and high positive-predictive value when enzymatic tests were used as the gold standard. The inconsistent use of a reference standard complicated the interpretation of the findings.

A 2010 meta-analysis by Dong and colleagues evaluated the relationship between TPMT polymorphisms and adverse-drug reactions in patients with inflammatory bowel disease (IBD) taking thiopurine drugs. (4) The review included cross-sectional studies, prospective cohort studies, and case-control studies conducted in patients 18 years and older with IBD. In addition, studies needed to compare TPMT polymorphism frequencies in thiopurine-tolerant and thiopurine-intolerant patients and report at least one of several outcome measures related to adverse drug reactions. The investigators identified a total of 181 publications, 17 of which were considered potentially appropriate after applying initial eligibility criteria e.g. publication type and study population. Another 8 studies were excluded because relevant outcome variables were not reported or could not be calculated. The final sample consisted of 9 studies with 1,309 participants. In a pooled analysis of data from 6 studies, 39 of 273 (14%) patients with an adverse drug reaction were TPMT heterozygous or homozygous compared to 39 of 708 (55%) patients without an adverse drug reaction. This difference was statistically significant (OR: 2.93, 95% CI: 1.68-5.09). In analyses of specific adverse reactions, there was a statistically significant association between the presence of TPMT alleles and bone marrow toxicity, but not hepatotoxicity or pancreatitis. In the non-statistically significant analyses, the number of events was small and the analyses have been underpowered. For example, 3 of 37 (8%) IBD patients with hepatotoxicity were TPMT heterozygous/ homozygous compared to 82 of 1,017 (81%) patients without hepatotoxicity (OR: 1.51, 95% CI: 0.54 to 4.19).

No systematic reviews of studies on TPMT genotyping or phenotyping tests in patients undergoing solid organ transplantation were identified. One study was identified that addressed this population and provided support for genotype analysis. In 2013, Liang et al published data on 93 heart transplant patients treated with azathiopurine (AZA).(5) A total of 83 patients had the wild-type genotype, and 10 were heterozygous for mutations. The TMPT activity level was significantly lower in the heterozygous subjects (13.1, SD=2.8 U/mL) than in subjects with the wild-type genotype (21, SD=4.5 U/mL red blood cells; p<0.001). Moreover, there was a significantly higher rate of severe rejection in heterozygous
subjects (7/10, 70%) than in subjects with a wild-type genotype (12/83, 15%; p<0.001). In addition, heterozygous subjects developed severe rejection earlier than wild-type subjects, a median of 29 versus 36 days (p=0.046). There were not statistically significant associations between TMPT genotype and the development of hepatotoxicity or leukopenia.

Metabolite Testing

Studies on the diagnostic accuracy of metabolite testing have focused on assessing the association between metabolite levels and disease remission or adverse drug effects. One systematic review was identified and this focused on studies conducted in the pediatric population. In a literature search through January 4, 2013, Konidari et al identified 15 studies including a total of 1026 children with IBD.(6) There were 9 retrospective and 6 prospective case series and no RCTs. The authors did not pool study findings. Among studies that evaluated the association between metabolite markers and clinical remission, 5 found significantly higher rates of remission with higher levels of 6-thioguanine nucleotides (6-TGN), and 6 studies did not find significant differences in 6-TGN levels between responders and nonresponders. Moreover, 5 studies found significant associations between 6-methyl-mercaptopurine ribonucleotides (6-MMRP) levels and hepatotoxicity, and 3 studies did not find significant associations.

Several studies have considered the optimal therapeutic cutoff level of metabolites In 2000, Dubinsky et al measured 6-TGN, and 6-MMRP levels in 92 pediatric patients.(7) Higher median levels of 6-TGN were observed at points of clinical response versus nonresponse. Quartile analysis on all samples revealed that the best probability of treatment occurred when 6-TGN levels were greater than 235 (measured in pmol/8x108). The 6-methyl-mercaptopurine ribonucleotides (6-MMRP) levels did not correlate with disease activity, but elevated levels did correlate with hepatotoxicity, observed in 16 patients. Elevated 6-TGN levels were also associated with hematologic toxicity. Results of a study published in 2012 by Glissen et al in the Netherlands also found an optimal therapeutic 6-TGN cutoff level of 235 pmol/8x108. (8) This was a cross-sectional study with 100 IBD patients. Forty-one patients had an IBD exacerbation, and IBD was in clinical remission in 59 patients. Twenty-six of the 41 (63%) patients with an exacerbation had 6-TGN below the therapeutic threshold of 235 pmol/8x108 and 24 of 59 (41%) patients in remission had 6-TGN levels below this threshold. The association between 6-TGN level and remission was statistically significant (p=0.04).

Other studies have identified somewhat different optimal 6-TGN cutoffs. Gupta et al reported discordant results in 54 patients with IBD being treated with AZA.(9) A total of 36% of patients in relapse had 6-TGN levels greater than 230, compared with 30% of those in remission. Conversely, 57% of patients with 6- TGN levels less than 230 were in remission, versus 50% of patients with 6-TGN levels greater than 230. In 2012, Dhaliwal et al in the UK published findings of a study that included 70 patients with autoimmune hepatitis who were at the maintenance of remission stage of treatment and were being treated with AZA.(10) Blood samples were taken at baseline and at each clinic visit over the following 2 years. During the study period, 53 of 70 patients (76%) maintained remission. Levels of 6-TGN were significantly higher in patients who maintained remission compared with those who did not (mean of 237 vs 177 pmol/8x108, p=0.025). According to receiver operating curve analysis, a cutoff of 220 pmol/8x108 best discriminated between patients who did and did not stay in remission. Sixty-two percent of patients in remission and 18% of those not in remission had a 6-TGN concentration higher than 220 pmol/8x108.

A 2010 cross-sectional study by Waljee et al compared the ability of metabolite tests and a clinical algorithm using routine laboratory values (complete blood count [CBC], chemistry panel) and patient age to predict the clinical response of patients with IBD to thiopurines.(11) The study included 346 patients taking thiopurines who underwent thiopurine metabolite analysis, a CBC, and a comprehensive chemistry analysis in one 24-hour period. Clinical response was determined through medical record review. Data on clinical response were available for 240 patients; 119 (49.6%) were classified as responders. Using area under the curve (AUC) analysis, an  algorithm using patient age and laboratory values differentiated clinical responders from nonresponders with an AUC of 0.86. In comparison, the metabolite marker 6- TGN had an AUC of 0.59 for differentiating between clinical response and nonresponse. The difference between these 2 areas was statistically significant (p<0.001). The variables with the strongest independent associations with clinical response were neutrophil count, alkaline phosphatase, red cell distribution width, age, and white blood cell count. When 6-TGN levels were added as an independent variable to a model containing the above variables, it did not significantly improve the AUC (which increased from 0.856 to 0.862). The authors noted that a limitation of the study was that data were obtained from a tertiary care center, and it is possible that patients in whom metabolites performed poorly were likely to be referred to that center. The authors concluded that the algorithm they developed and tested using routine laboratory tests for differentiating thiopurine clinical responders and nonresponders performed significantly better than metabolite monitoring in predicting clinical response.

Improvement in Health Outcomes
The use of pharmacogenomics and thioprine metabolite testing creates the possibility of tailoring a drug regimen for each individual patient, with the ultimate goal of attaining disease remission and elimination of steroid therapy. The preferred study design would compare patient management (eg, drug choice) and health outcomes in patients managed with and without testing.


A randomized controlled trial (RCT), known as the TARGET study, randomized 333 patients to receive TPMT genotyping or usual care (no genotyping) before AZA therapy.(12) Study eligibility included age 16 years or older with a diagnosis of IBD. In the testing arm, test results were generated within 1 week, and the study clinician was informed of the results. Clinicians were advised to recommend the following: maintenance dose of AZA (ie, 1.5 to 3 mg/kg/d) for patients with wild-type TPMT, low-dose AZA (ie, 25 to 50 mg/d) titrated to a maintenance dose for patients with heterozygous TPMT variant alleles, and an alternative therapy (no AZA) for patients homozygous for TPMT variant alleles. All final treatment decisions were at the discretion of the individual provider (ie, this was a pragmatic RCT). Genotyping was also done on samples from patients in the control group, but results were not made available until the end of the study.

Data were available for 322/333 (97%) patients at 4 months. The primary study end point was stopping AZA at any adverse drug reaction in the first 4 months of treatment. At 4 months, a total of 91 of 322 (28%) patients had stopped taking AZA because of an adverse drug reaction, 47 of 163 (29%) in the genotyping group and 44 of 159 (28%) in the nongenotyping group. The difference between groups was
not statistically significant (p=0.74). In the genotyping arm, the average starting dose of AZA was significantly lower in TPMT heterozygotes than wild-type patients (p=0.008), suggesting that clinicians were following dosing recommendations. However, at 4 months, the mean dose was similar across both arms (1.68 mg/kg/d, p=0.25), and there was no difference in dose between patients heterozygous or wild type for TPMT variant alleles (p=0.99). Moreover, at 4 months, there was not a significant difference between groups in the level of clinical symptoms between groups. The mean Harvey-Bradshaw symptom index score was 4.5 in each group (p=0.80) (54 patients in the genotyping group and 56 patients in the nongenotyping group were included in this analysis). It is important to note that, in this study, few patients had non-wild type gene variants. In the genotyping group, there were 7 heterozygous patients and in the non-genotyping group, there were 2 heterozygous patients and 1 homozygous patient. Thus, the study was underpowered to evaluate the impact of TPMT genotyping on patients with variant alleles.

Several prospective studies examining variation in the efficacy of medication according to patient’s TPTM status have also been published. For example, in a study that involved 131 patients with IBD, investigators from Europe did not find that the choice of AZA/mercaptopurine (6-MP) dose based on RBC TPMT activity prevented myelotoxicity; no patients in this study exhibited low activity.(13) In a 2008 study from New Zealand, Gardiner et al noted that initial target doses to attain therapeutic levels in patients with IBD might be 1 mg/kg/d and 3 mg/kg/d in intermediate (heterozygous) and normal (wild-type) metabolizers.(14) This conclusion was based on a study of 52 patients with IBD who were started on AZA or 6-MP and who were followed up for 9 months, while 6-TGN levels and clinical status were assessed. This study suggested that knowledge of TPMT activity can assist with initial dosing. In a study from Europe including 394 patients with IBD, Gisbert et al noted that the probability of myelotoxicity was 14.3% in the TPMT intermediate group compared with 3.5% in those with high (wild-type) activity.(15) These authors concluded that determining TPMT activity before initiating treatment with AZA could help to minimize the risk of myelotoxicity.

Metabolite Testing
No prospective comparative trials were identified in which use of metabolite markers was compared with current approaches to care. In 2012, Kennedy et al published a study retrospectively reviewing medical records of patients who had undergone metabolite testing after it was introduced in South Australia.(16) The analysis reported on 151 patients with IBD who had been taking a thiopurine for at least 4 weeks, underwent at least 1 metabolite test, and were managed at 1 of the study sites. The 151 patients had a total of 157 tests. Eighty of 157 tests (51%) were done because of flare or lack of medication efficacy, 18 (12%) were for adverse effects, and 54 tests (34%) were routine tests. Forty-four of the 80 patients (55%) who had a metabolite test due to flare or lack of efficacy had improved outcomes after the test was
performed. Outcomes were also improved after testing for 5 of 18 patients (28%) with a suspected adverse reaction to a thiopurine. For patients who had routine metabolite tests, 7 of 54 (13%) had improved outcomes following testing. The rate of benefit was significantly higher in patients tested because of flare or lack of efficacy compared with those who underwent routine metabolite testing (p<0.001). Changes in patient management included medication dose adjustments, change in medication, and surgical treatment. The study lacked a control group and thus, outcomes cannot be compared with patients managed without metabolite testing. It is possible that, even in the absence of metabolite testing, patients who were not experiencing efficacy or who were experiencing adverse events would have had their treatments adjusted, which could lead to improved outcomes.

Other relevant studies have examined the association between drug dose and the level of metabolite markers. In general, studies have reported that there is only weak correlation between metabolite levels and dose of drug.(17) One 2013 retrospective study, however, found a positive correlation between levels of 6-TGN and 6-MMP and weight-based AZA dose in children with IBD.(18) In addition, studies have reported that levels obtained with testing are often outside of the therapeutic range. For example, the Gearry et al study reported that 41% of values were within the therapeutic range.(19) and Armstrong et al found that 32% of values were within therapeutic levels.(20)

There are a large number of studies on the diagnostic performance of thiopurine methyltransferase (TMPT) genotyping and phenotyping tests. A recent meta-analysis found a pooled sensitivity of about 80% and specificity near 100% for identifying patients with subnormal enzymatic activity. In addition, studies have found a greater likelihood of adverse drug reactions with low TPMT activity. One randomized controlled trial reporting evidence on health outcomes was identified; this study did not find a significant difference in outcomes in patients managed with and without TPMT genotyping testing, but the study may have been underpowered. One-time genotype or phenotype testing is considered medically necessary in select patients.

There is insufficient evidence from prospective studies on whether metabolite markers will lead to improved outcomes (primarily improved disease control and/or less adverse drug effects). Moreover, there is a lack of consensus among studies on the optimal cutoff to use when measuring 6-thioguanine nucleotides (6-TGN) levels. Thus, analysis of metabolite markers is considered investigational.

Practice Guidelines and Position Statements
In 2013, the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition Committee on IBD published consensus recommendations on the role of TMPT and thiopurine metabolite testing in pediatric IBD. (21) Recommendations included:

  • TPMT testing is recommended before initiation of thiopurines, and individuals who are homozygous recessive or have extremely low TPMT activity should avoid use of thiopurines because of risk of leucopenia.
  • Individuals on thiopurines should have routine monitoring of blood counts to evaluate for leucopenia regardless of TPMT testing results.
     Metabolite testing can be used to determine adherence to thiopurine activity.
  • Metabolite testing can be used to guide dosing changes in patients with active disease.
  • Routine and repeat metabolite testing has little or no role in patients who are responding well to medication and taking an acceptable dose of thiopurines.

A 2011 guideline from the British Association of Dermatologists addressed the safe and effective prescribing of azathioprine.(22) The guideline included the following recommendations on analysis of TMPT activity:

  • There is strong evidence that baseline testing before starting azathioprine predicts severe neutropenia in patients with absent TMPT activity
  • There is good evidence that intermediate TMPT activity is associated with myelotoxicity in patients using conventional doses of azathioprine
  • There is a continued need for regular monitoring of blood counts in addition to TMPT testing.

A 2010 guideline from the National Academy of Clinical Biochemistry (NACB) stated, “thiopurine methyltransferase (TPMT) genotyping is recommended as a useful adjunct to a regimen for prescribing azathioprine.”(23) This is an “A-I” recommendation, indicating that the NACB strongly recommends adoption and the recommendation is based on evidence with consistent results from well-designed, well-conducted studies in representative populations.

A 2006 position statement from the American Gastroenterological Association included the following ecommendations(24):

  • “Current U.S. Food and Drug Administration (FDA) recommendations suggest that individuals should have thiopurine methyltransferase (TPMT) genotype or phenotype assessed before initiation of therapy with AZA or 6-MP in an effort to detect individuals who have low enzyme activity (or who are homozygous deficient in TPMT) in an effort to avert AZA or 6-MP therapy and thus avoid potential adverse events. Individuals who have intermediate or normal TPMT activity (wild type or heterozygotes) need measurement of frequent complete blood counts (as above) in addition to TPMT assessment because these individuals may still develop myelosuppression
    subsequent to use of AZA or 6-MP (Grade B)”.
  • “Thiopurine metabolite monitoring in the treatment of patients with 6-MP or AZA is useful when attempting to determine medical noncompliance and may be helpful for optimizing dose and monitoring for toxicity (Grade C).”

Evidence grades used in this guideline are:

  • “Grade A: Homogeneous evidence from multiple well-designed, randomized (therapeutic) or cohort (descriptive) controlled trials, each involving a number of participants to be of sufficient statistical power.
  • Grade B: Evidence from at least 1 large well-designed, clinical trial with or without randomization from cohort or case-control analytic studies or well-designed meta-analysis.
  • Grade C: Evidence based on clinical experience, descriptive studies, or reports of expert committees.”

Medicare National Coverage
There is no national coverage determination (NCD). In the absence of an NCD, coverage decisions are left to the discretion of local Medicare carriers. 


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  2. Booth RA, Ansari MT, Loit E et al. Assessment of thiopurine S-methyltransferase activity in patients prescribed thiopurines: a systematic review. Ann Intern Med 2011; 154(12):814-23, W-295-8.
  3. Donnan JR, Ungar WJ, Mathews M et al. Systematic review of thiopurine methyltransferase genotype and enzymatic testing strategies. Ther Drug Monit 2011; 33(2):192-9.
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  5. Liang JJ, Geske JR, Boilson BA et al. TPMT genetic variants are associated with increased rejection with azathioprine use in heart transplantation. Pharmacogenet Genomics 2013; 23(12):658-65.
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  14. Gardiner SJ, Gearry RB, Begg EJ et al. Thiopurine dose in intermediate and normal metabolizers of thiopurine methyltransferase may differ three-fold. Clin Gastroenterol Hepatol 2008; 6(6):654-60;quiz 04.
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  17. Morales A, Salguti S, Miao CL et al. Relationship between 6-mercaptopurine dose and 6-thioguanine nucleotide levels in patients with inflammatory bowel disease. Inflamm Bowel Dis 2007;13(4):380-5.
  18. Nguyen TV, Vu DH, Nguyen TM et al. Relationship between azathioprine dosage and thiopurine metabolites in pediatric IBD patients: identification of covariables using multilevel analysis. Ther Drug Monit 2013; 35(2):251-7.
  19. Gearry RB, Barclay ML, Roberts RL et al. Thiopurine methyltransferase and 6-thioguanine nucleotide measurement: early experience of use in clinical practice. Intern Med J 2005; 35(10):580-5.
  20. Armstrong L, Sharif JA, Galloway P et al. Evaluating the use of metabolite measurement in children receiving treatment with a thiopurine. Aliment Pharmacol Ther 2011; 34(9):1106-14.
  21. Benkov K, Lu Y, Patel A et al. Role of thiopurine metabolite testing and thiopurine methyltransferase determination in pediatric IBD. J Pediatr Gastroenterol Nutr 2013; 56(3):333-40.
  22. Meggitt SJ, Anstey AV, Mohd Mustapa MF et al. British Association of Dermatologists' guidelines for the safe and effective prescribing of azathioprine 2011. Br J Dermatol 2011; 165(4):711-34.
  23. National Academy of Clinical Biochemistry. Laboratory medicine practice guidelines: guidelines and recommendations for laboratory analysis and application of pharmacogenetics to clinical practice 2010. Available online at: Last accessed March, 2014.
  24. Lichtenstein GR, Abreu MT, Cohen R et al. American Gastroenterological Association Institute medical position statement on corticosteroids, immunomodulators, and infliximab in inflammatory bowel disease. Gastroenterology 2006; 130(3):935-9.




CPT    See policy guidelines section
ICD-9 Procedure     
ICD-9 Diagnosis  555.0–555.9  Regional enteritis code range 
  556.0 – 556.9  Ulcerative colitis code range 
ICD-10-CM (effective 10/1/15) K50.0-K50.019 Crohn's disease (regional enteritis) code range
  K51.00-K51.319 Ulcerative colitis, code range
ICD-10-PCS (effective 10/1/15)    Not applicable. ICD-10-PCS codes are only used for inpatient services. There are no ICD procedure codes for laboratory tests.
Type of Service  Pathology/Laboratory 
Place of Service  Physician’s Office 



Azathioprine, Management of
Genotypic Analysis of TPMT
Metabolite Markers, Azathioprine
6-mercaptopurine, Management of
6-MMP, Levels of, in Inflammatory Bowel Disease
6-TG, Levels of, in Inflammatory Bowel Disease

Policy History


Date Action Reason
12/15/00 Add to Medicine section New policy
07/12/02 Replace policy Policy reviewed; expanded discussion, additional references, no change in policy statement
12/17/03 Replace policy Policy reviewed; no change in policy statement
07/15/04 Replace policy Policy updated with literature review; no change in policy statement
08/17/05 Replace policy Policy updated with literature review; no change in policy statement. References 9, 10, 21, and 22 added
10/10/06 Local Policy Policy updated. Removed “with Inflammatory Bowel Disease” from the title. Information added to Description section about azathioprine prescribing and TMPT testing. Policy statement unchanged. Reference numbers 23 to 26 added. CPT modifier -9A added,
09/07/07 Updated Local Policy added med nec section to policy
08/14/08 Replace policy  Policy updated with literature search, reference numbers 27 to 31 added. Policy statement on TPMT gene testing changed to medically necessary; other policy statements unchanged. (Local Policy status removed)
09/10/09 Replace policy Policy updated with literature search July 2007 to July 2009; reference numbers 33 to 37 added; Policy statement on TPMT testing changed to “One-time genotypic OR phenotypic testing” as medically necessary; other policy statements unchanged. Policy title changed – azathioprine (6-MP) taken out, replaced with “Thiopurines”.
6/9/11 Replace policy Policy updated with literature search through March 2011. Rationale extensively rewritten. References 1,3,4,17 and 25 added; other references renumbered or removed. The word “enzyme” added to first policy statement for clarification; no changes to intent of policy statements.
06/14/12 Replace policy Policy updated with literature search through April 2012. References 1, 2, 9, 16 and 17 added; other references renumbered or removed. Policy statements unchanged.
6/13/13 Replace policy Policy updated with literature search through May 9, 2013. References 7, 8, 15 and 20 added; other references renumbered or removed. Policy statements unchanged.
5/22/14 Replace policy Policy updated with literature review through April 4, 2014. References 5-6 and 18 added Statement added that genotypic and/or phenotypic analysis of the enzyme TPMT is considered investigational in all other situations.

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