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MP 2.04.50

Genetic Testing for Helicobacter pylori Treatment

Medical Policy

Original Policy Date

Last Review Status/Date
Reviewed with literature search/7:2011
Return to Medical Policy Index


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.


Helicobacter pylori (H. pylori) is a bacterium associated with a range of gastrointestinal (GI) disorders such as peptic ulcer disease, chronic gastritis, and gastric malignancy. Eradication of H. pylori has been proven beneficial for a number of indications.

Currently, multiple regimens are available for treating H. pylori infection. These include proton pump inhibitors (PPIs), as well as similar medication(s), to suppress acid production, in combination with antibiotic treatment, consisting of one or more agents such as amoxicillin, clarithromycin, or metronidazole. These first-line regimens generally achieve eradication rates in the 70–90% range. Differences in eradication rates are dependent on the regimen used and the population being treated. Treatment failures are most often attributed to antibiotic resistance or poor patient compliance. Resistance to clarithromycin is an important factor associated with treatment failure, with high rates of treatment failure for standard first-line regimens in patients infected with clarithromycin-resistant strains of H. pylori. A 2002 survey from the U.S. estimated that 13% of H. pylori strains are resistant to clarithromycin and that the rate of resistance was rising in comparison to earlier studies.

Genetic factors may influence the success of H. pylori treatment through effects on PPI metabolism. Individuals with polymorphisms in the CYP2C19 gene, a component of the cytochrome P450 (CYP450) system, metabolize PPIs more slowly than normal. Genetic variation in the CYP450 enzyme system is one of the most extensively studied in the field of pharmacogenomics. This family of enzymes is found in the liver and is important for metabolizing and eliminating a large number of pharmacologic agents. Differences in PPI metabolism lead to variability in gastric acid suppression, with associated variability in gastric pH, and potential impact on the efficacy of H. pylori treatment. Observational research suggests that patients who are extensive metabolizers of PPIs have lower eradication rates following standard treatment for H. pylori, compared with poor metabolizers.

Three major CYP2C19 alleles determine enzymatic activity, as shown in Table 1. The *1 allele is the wild-type found in most individuals, while the *2 and *3 alleles are the most common polymorphisms that are known to impact enzymatic activity. Both the *2 and *3 alleles are examples of “null” alleles, which ave no enzymatic activity. Each null allele is caused by a single nucleotide change that results in a plice defect or a stop codon (1) 
Table 1. CYP2C19 polymorphisms**          Table 2. CYP2C19 phenotypes**




Predicted Enzyme Activity























** Adapted from AmpliChip package insert
EM           extensive metabolizers
IM             intermediate metabolizers
PM           poor metabolizers

Polymorphisms of the CYP2C19 gene are relatively common and vary by ethnicity. Patients with no polymorphisms of CYP2C19 have two wild-type alleles and no reduction in their ability to metabolize PPIs. These patients are typically called extensive metabolizers (EM) (Table 2). Heterozygous polymorphisms are found in 27–37% of the Caucasian population and 46–50% of the Asian population. These patients have a minor reduction in their ability to eliminate PPIs, and are called intermediate metabolizers (IM). Homozygous polymorphisms of the CYP2C19 gene are found in 3–6% of Caucasians and in 12–20% of Asians. These patients eliminate PPIs from the circulation substantially much more slowly than unaffected patients, and are termed poor metabolizers (PM).

In patients treated with PPIs, intragastric pH has been shown to correlate with CYP2C19 status. Patients homozygous for a CYP2C19 mutation (PM) exhibit a less acidic pH when compared to patients without a CYP2C19 mutation, with heterozygous patients exhibiting intermediate values. Intragastric pH has important implications for treating H. pylori. H. pylori is more sensitive to antibiotics at less acidic pH levels. Less acidic pH levels also lead to greater stability and bioavailability of antibiotics. Therefore, it is expected that treatment of H. pylori will be more successful if there is maximal suppression of gastric acid production and higher intragastric pH levels.
Therefore, it has been proposed that a pharmacogenomics-based treatment regimen individualized by CYP2C19 status may improve the success rate of treatment for H. pylori. If CYP2C19 status is known prior to treatment, adjustments can be made in the selection of PPI and/or the dosing schedule in order to achieve optimal acid suppression in all patients. Improved eradication rates for H. pylori could lead to improved health outcomes by reducing the need for re-treatment following treatment failure, reducing recurrences of H. pylori -associated disorders, and reducing the morbidity and mortality associated with disease recurrence.

At least one commercially available genetic test, the Roche AmpliChip Cytochrome P450® Genotyping test, has been approved by the U.S. Food and Drug Administration (FDA) as a class II medical device. This test examines polymorphisms in CYP2D6 and CYP2C19 isoenzymes of the cytochrome P450 enzyme system. Approval for this device was originally granted in December 2004 as an aid in determining treatment choice and individualizing treatment dose for therapeutics that are metabolized primarily by the CYP2D6 enzyme. The use of information on CYP2C19 polymorphisms was not addressed as part of the FDA approval process.


Genotyping to determine cytochrome p450 (CYP2C19) genetic polymorphisms is considered investigational for the purpose of managing the treatment of H. pylori infection.

Policy Guidelines

There are specific CPT codes for array-based evaluation of multiple molecular markers:

88384: Array-based evaluation of multiple molecular probes: 11 through 50 probes
88385: 51 through 250 probes
88386: 251 through 500 probes

When less than 11 probes are prepared and evaluated, the services are coded using CPT codes 83890-83914 as appropriate.

There is also a CPT genetic testing modifier that is specific to CYP2 genes:
-9B: CYP2 genes, commonly called cytochrome p 450 (drug metabolism)

Benefit Application

State or federal mandates (e.g., FEP) may dictate that all FDA-approved devices may not be considered investigational and thus these devices may be assessed only on the basis of their medical necessity.


This policy was originally based on a February 2008 TEC Assessment. (2)
Validation of genotyping to improve pharmacologic treatment outcomes is a multistep process. In general, important steps in the validation process address the following:

  • Analytic validity: measures technical performance, i.e., whether the test accurately and reproducibly detects the gene markers of interest.
  • Clinical validity: measures the strength of the associations between the selected genetic markers and dose, therapeutic efficacy, and/or adverse events.
  • Clinical utility: determines whether the use of genotyping for specific genetic markers to guide prescribing and/or dosing improves patient outcomes such as therapeutic effect, time to effective dose, and/or adverse event rate compared to standard treatment without genotyping.

The AmpliChip Cytochrome P450® Genotyping test, tests for known polymorphisms of two isoenzymes of the cytochrome P450 system, CYP2D6 and CYP2C19. This system uses DNA extracted from whole blood and a PCR-based GeneChip Microarray Instrumentation system to determine the presence or absence of genetic polymorphisms. (1)

For the CYP2C19 gene, the test examines for the two common polymorphisms associated with enzymatic activity (Table 1). Information from the manufacturer claims greater than 99% accuracy in detecting these common polymorphisms. (2) However, there are a number of rare polymorphisms that have been identified that are not tested for by the AmpliChip system. The results of the test are included in a report to the ordering physician that includes potential clinical implications of the result.

Numerous case series and re-analyses of clinical trials completed for other reasons have suggested that there is a correlation between CYP2C19 status and success rates for eradication of H. pylori. For the most part, these are studies in which a single treatment regimen was used and in which patients were tested for CYP2C19 status. These studies then report eradication rates for H. pylori according to CYP2C19 status. (3-5, 9,10)

The majority of studies that did not use rabeprazole reported lower eradication rates in extensive metabolizer (EM) patients compared with poor metabolizer (PM) patients. Rabeprazole is the only PPI that is not metabolized by the CYP2C19 enzyme, and therefore eradication rates with regimens including rabeprazole may not vary according to CYP2C19 status. For studies not using rabeprazole, eradication rates in PM patients are consistently in the 95–100% range. The eradication rates for EM patients are substantially lower, ranging from 29–80%, with eradication rates for intermediate metabolizer (IM) patients generally intermediate between the two. For trials that used rabeprazole, eradication rates according to CYP2C19 group were generally similar, although at least 1 study did report lower eradication rates for EM patients. (6)

A meta-analysis from 2006 (7) confirmed these findings. This analysis included clinical trials of H. pylori eradication that used dual or triple therapy antibiotic regimens, reported eradication rates by CYP2C19 status, and had a Jadad quality score of 2 or greater. The authors identified 19 trials that met their inclusion criteria and reported pooled eradication rates by genetic status and specific PPI agent. For all PPIs, the pooled eradication rate was highest in the PM group (89%), intermediate in the IM group (83%), and lowest in the EM group (71%), with the difference between these groups significant at the p <0.0001 level. The difference in eradication rates by CYP2C19 status also appeared to vary by the specific PPI used. The greatest difference in eradication rates between EM groups and PM groups was seen for omeprazole (93% vs. 63%, respectively). The difference in eradication rates was less pronounced for lansoprazole (88% vs. 74%, respectively), and least evident for rabeprazole (81% vs. 77%, respectively).

A second meta-analysis reported similar findings. This study (16) reviewed 20 studies that evaluated the relationship between CYP2C19 genetic status and H. pylori eradication rates. Poor metabolizers had the highest rates of eradication when compared to either heterozygous extensive metabolizers (odds ratio [OR] 1.73, p =0.002) or homozygous extensive metabolizers (OR 2.79, p <0.001). Among the individual PPIs included in these studies, CYP2C19 status was associated with eradication rates for treatment regimens using omeprazole and lansoprazole but not for regimens using rabeprazole.

A single randomized, controlled trial was identified for use of genetic testing in selecting the treatment regimen for H. pylori infection. (8) This study randomly assigned 300 Japanese patients to a pharmacogenomics-based treatment regimen versus a standard treatment regimen. The pharmacogenomics regimen included testing for CYP2C19 genetic status, esophagogastroduodenoscopy (EGD), and H. pylori culture with sensitivity testing to clarithromycin. In the pharmacogenomics group, the dose of PPI was adjusted according to CYP2C19 genetic status, and the antibiotic regimen was adjusted according to H. pylori sensitivity to clarithromycin.

Eradication rates following initial treatment were 96% (95% confidence interval [CI]: 91.5% –98.2%) in the pharmacogenomics-based treatment group versus 70.0% (95% CI: 62.2% –77.2%) in the standard therapy group (p <0.001). When analyzed according to genetic status, the improvement in eradication rates in the pharmacogenomics group was greater for EM patients (100% vs. 58%, respectively) and IM patients (95% vs. 72%, respectively), compared to PM patients (91% vs. 91%, respectively). Eradication rates also varied by clarithromycin-resistant status, with particularly low eradication rates occurring in the standard treatment group for EM patients with clarithromycin resistance (0%) and IM patients with clarithromycin resistance (48%).

Patients who failed eradication following first-line treatment were re-treated. By intent-to-treat analysis, eradication rates following re-treatment were 97.8% (95% CI: 94.3 –99.6%) for the pharmacogenomics group compared to 88.0% (95% CI: 81.7 –92.7%) for the standard regimen group (p <0.001). When analyzed by per-protocol, the eradication rates were 99.3% (95% CI: 96.3 –100%) for the pharmacogenomics group compared to 95.7% (95% CI: 90.8–98.4%) for the standard treatment group (p =NS).

Several more recent trials have directly compared the eradication rates of a treatment regimen containing rabeprazole to a treatment regimen containing an alternative PPI in Asian populations (Kuo 2010, Zhang 2010). Kuo et al. (12) enrolled 195 patients who had previously failed initial treatment, and reported an eradication rate of 78.7% (95% CI 72.5-84.9%) for the rabeprazole regimen compared to 72.9% (95% CI 64.9-80.9%, p =0.05) for the esomeprazole-based regimen group. These results remained significant after controlling for the effect of antibiotic resistance. Zhang et al. (13) studied 240 Chinese patients with peptic ulcer disease, and compared eradication rates for rabeprazole-based regimens compared with omeprazole-based regimens. The eradication rates were significantly higher for the rabeprazole-based regimens among EMs, but not among patients with wild-type CYP2C19 (p =0.01).

While the single available randomized, controlled trial reports an increased rate of H. pylori eradication in the pharmacogenomics strategy compared with a standard approach, this study does not provide definitive evidence that use of a pharmacogenomics-based treatment regimen improves health outcomes. There are numerous variations in the treatment regimen within the experimental group that make it difficult to determine which specific aspects of the treatment regimen may have led to benefit. In particular, it appears that clarithromycin resistance is an important factor in treatment success and that there may be an interaction between clarithromycin resistance and CYP2C19 status. From the data reported in the study, it is hard to separate the potential impact of clarithromycin resistance on eradication rates from the impact of pharmacogenomically tailored PPI dosage schedules.

Alternative treatment strategies exist for eradicating H. pylori that address some of the issues raised by CYP2C19 variability but do not rely on testing for CYP2C19 status. For example, empiric treatment with higher-dose PPI for all patients might be reasonable, particularly for non-Asian populations in which CYP2C19 mutation rates are lower. This approach may be as effective as regimens tailored by pharmacogenomics, with little additional risk. The use of a PPI that is less susceptible to CYP2C19 status, such as rabeprazole, has been associated with higher eradication rates compared to other PPI’s. This may be the preferred regimen, given that there is no reason to suspect other advantages to use of omeprazole or lansoprazole. Ideally, a clinical trial will evaluate whether a tailored pharmacogenomics approach is superior to other empiric approaches such as these.

The scientific evidence does not permit conclusions on whether the use of a pharmacogenomics-based treatment regimen for H. pylori improves eradication rates. In general, eradication rates of H pylori vary by CYP2C19 status. In the single randomized controlled trial comparing a pharmacogenomics-based treatment regimen with a standard regimen, eradication rates after first-line treatment were higher for the pharmacogenomics group compared with the standard treatment group. However, because of numerous variations in treatment protocol within the pharmacogenomics group, it is not possible to determine whether the improvement resulted from the tailored PPI dosages according to CYP2C19 genetic status or due to other variations in the treatment protocol unrelated to CYP2C19 status. It is possible that other clinical factors, such as clarithromycin resistance, or other treatment factors, such as length of antibiotic treatment, may have influenced eradication rates. The use of a PPI that is less susceptible to CYP2C19 status, such as rabeprazole, has been associated with higher eradication rates compared to other PPIs. Therefore, additional trials are needed to address the issues noted above, including alternative treatment regimens, before conclusions can be made on whether a pharmacogenomics-based treatment regimen improves H. pylori eradication rates compared to a standard treatment regimen. Therefore, the use of genetic testing for Helicobacter pylori treatment is considered investigational.

Practice Guidelines and Position Statements

Medicare National Coverage



  1. AmpliChip CYP450 test package insert. Roche Diagnostics/Roche Molecular Systems. Indianapolis, IN; July 2006. Available online at Last accessed February 2008.
  2. Blue Cross and Blue Shield Association Technology Evaluation Center (TEC). Pharmacogenomics-based treatment of Helicobacter pylori infection. TEC Assessments 2008; vol. 23, tab 2.
  3. Sapone A, Vaira D, Trespidi S et al. The clinical role of cytochrome P450 genotypes in Helicobacter pylori management. Am J Gastroenterol 2003; 98(5):1010-5.
  4. Schwab M, Schaeffeler E, Klotz U et al. CYP2C19 polymorphism is a major predictor of treatment failure in white patients by use of lansoprazole-based quadruple therapy for eradication of Helicobacter pylori. Clin Pharmacol Ther 2004; 76(3):201-9.
  5. Sheu BS, Kao AW, Cheng HC et al. Esomeprazole 40mg twice daily in triple therapy and the efficacy of Helicobacter pylori eradication related to CYP2C19 metabolism. Aliment Pharmacol Ther 2005; 21(3):283-8.
  6. Kang JM, Kim N, Lee DH et al. Effect of the CYP2C19 polymorphism on the eradication rate of Helicobacter pylori infection by 7-day triple therapy with regular proton pump inhibitor dosage. J Gastroenterol Hepatol 2008; 23(8 Pt 1):1287-91.
  7. Miehlke S, Schneider-Brachert W, Kirsch C et al. One-week once-daily triple therapy with esomeprazole, moxifloxacin, and rifabutin for eradication of persistent Helicobacter pylori resistant to both metronidazole and clarithromycin. Helicobacter 2008; 13(1):69-74.
  8. Furuta T, Shirai N, Takashima M et al. Effects of genotypic differences in CYP2C19 status on cure rates for Helicobacter pylori infection by dual therapy with rabeprazole plus amoxicillin. Pharmacogenetics 2001; 11(4):341-8.
  9. Padol S, Yuan Y, Thabane M et al. The effect of CYP2C19 polymorphisms on H. pylori eradication rate in dual and triple first-line PPI therapies: a meta-analysis. Am J Gastroenterol 2006; 101(7):1467-75.
  10. Zhao F, Wang J, Yang Y et al. Effect of CYP2C19 genetic polymorphisms on the efficacy of proton pump inhibitor-based triple therapy for Helicobacter pylori eradication: a meta-analysis. Helicobacter 2008; 13(6):532-41.
  11. Furuta T, Shirai N, Kodaira M et al. Pharmacogenomics-based tailored versus standard therapeutic regimen for eradication of H. pylori. Clin Pharmacol Ther 2007; 81(4):521-8.
  12. Kuo CH, Wang SS, Hsu WH et al. Rabeprazole can overcome the impact of CYP2C19 polymorphisms on quadruple therapy. Helicobacter, 2010; 15(4):265-72.
  13. Zhang L, Mei Q, Li QS et al. The effect of cytochrome P2C19 and interleukin-1 polymorphism on H. pylori eradication rate of 1-week triple therapy with omeprazole or rabeprazole, amoxicillin and clarithromycin in Chinese people. J Clin Pharm Ther, 2010; 35(6):713-22.





CPT    See Policy Guidelines section
ICD-9 Diagnosis    investigational for all codes 
ICD-10-CM (effective 10/1/13)    investigational for all codes 
ICD-10-PCS (effective 10/1/13)    Not applicable. No ICD procedure codes for laboratory tests.


H.pylori Treatment, Genetic Testing

Policy History

Date Action Reason
03/13/08 Add policy to Medicine section, Pathology, Laboratory subsection New Policy
3/12/09 Replace policy  Policy updated with literature search; no change to policy statement. Reference numbers 9 through 12 added 
07/08/10 Replace policy Policy updated with literature search; no change to policy statement. Reference numbers 13 through 16 added
7/14/11 Replace policy Policy updated with literature search; rationale section rewritten and streamlined; no change to policy statement. Reference numbers 12 and 13 added

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