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AMP, CAP Develop Guidelines for CYP2C9 PGX Assay Design


NEW YORK (360Dx) – The Association for Molecular Pathology (AMP) and the College of American Pathologists have issued guidelines for developing CYP2C9 genotyping assays.

Presented in a paper published last month in the Journal of Molecular Diagnostics, the guidelines provide recommendations for what CYP2C9 variant alleles should be included in clinical pharmacogenomic tests assessing that gene.

The guidelines are the second such issued by AMP's PGx Working Group, which last year published recommendations on variant alleles that should be included in clinical PGx tests for CYP2C19.

The AMP PGx working group started with those two genes "due to the widespread adoption of [PGx panels analyzing those genes] and our desire to help physicians, pharmacists, researchers, and other stakeholders better understand what these panels include and what the test results mean," said Victoria Pratt, associate professor, director of pharmacogenetics and molecular genetics laboratories at the Indiana University School of Medicine and chair of the AMP PGx Working Group.

CYP2C9 codes for the cytochrome P4502C9 protein, which Pratt noted is one of the "most abundant and important drug metabolizing enzymes" and is involved in "Phase I metabolism of many commonly prescribed medications, including the anticoagulant warfarin and the anticonvulsant phenytoin."

CYP2C9 is listed by the US Food and Drug Administration as a PGx biomarker for 10 FDA-approved drugs, and there are seven commercially available CYP2C9 tests ranging from research-use only offerings from companies including Affymetrix and Agena Biosciences to FDA-cleared tests from GenMark Diagnostics and TrimGen. Additionally, many clinical laboratories have developed their own PGx panels testing CYP2C9.

These tests are not consistent, however, in terms of what alleles they analyze, which may impact their performance. Because different alleles have been linked to different levels of drug response, with these links supported by varying levels of evidence, the composition of PGx test panels is a potentially important consideration. The AMP effort aimed to identify minimal sets of CYP2C9 alleles that all tests would ideally include.

The researchers followed the template they developed through their previous work on CYP2C19, identifying a set of Tier 1 alleles that they recommend testing for in all populations and a Tier 2 set of alleles for which testing may be appropriate in particular circumstances or subpopulations.

According to the guidelines established in the original CYP2C19 work, Tier 1 alleles are those that "have been well characterized and shown to significantly affect the function of the protein and/or gene leading to an alteration in a drug response phenotype … have an appreciable minor allele frequency in a population/ethnicity group, and … have publicly available reference materials."

Tier 2 alleles are those that meet "at least one but not all three" of the Tier 1 requirements, the authors wrote, noting that Tier 2 alleles may be moved into the Tier 1 category if reference materials or additional evidence supporting their linkage to drug response becomes available.

The AMP-CAP guidelines identified six CYP2C9 variant alleles (*2, *3, *5, *6, *8, and *11 ) as Tier 1 and three variants (*12, *13, *15) as Tier 2. All three of the Tier 2 alleles have been shown to "have either decreased function or no function," the authors wrote, but they have low frequency (< 0.5 percent) in the general population and reference materials are not available for *13 and *15.

Pratt said that she and her colleagues were "not aware of any significant changes in the field with regards to CYP2C19 testing," since they published their variant allele guidelines for that gene last year. However, she noted that the feedback they have received "has been positive" and added that most commercially available CYP2C19 testing platforms already correlated well with the group's recommendations.

Adoption of the CYP2C9 guidelines could present more of a challenge, Pratt said, as only two of the seven commercial platforms available at the time the JMD paper was published included all of the recommended Tier 1 alleles.

Of particular concern are the Tier 1 alleles *5, *6, *8, and *11 that are particularly prevalent among people with African ancestry.

Pratt said that she and her colleagues on the working group were aware that their recommendations to include these alleles would be difficult to implement using existing genotyping platforms.

"However, we concluded that failure to include these alleles could lead to inaccurate CYP2C9phenotype prediction among individuals with known or unknown African ancestry and could potentially contribute to existing healthcare disparities in these populations," she said.

The CYP2C19and CYP2C9recommendations are the first stages of the AMP working group's project to develop guidelines for as many pharmacogenomic-relevant genes as possible.

Pratt said that the group's recommendations are "not to be interpreted as restrictive but to provide a reference guide" for test developers, though she added that the group "urge[s] the FDA and other regulatory agencies to consider the Tier 1 alleles when reviewing new commercially available testing platforms."