NEW YORK – The Association for Molecular Pathology Pharmacogenetics Working Group this week published new consensus recommendations to assist lab professionals in designing and validating clinical TPMT and NUDT15 genotyping assays, frequently used to determine an individual's likely response to certain chemotherapeutics in acute lymphoblastic leukemia and to immunosuppressive agents in disorders such as inflammatory bowel disease and rheumatoid arthritis.
The recommendations, published in the Journal of Molecular Diagnostics, are meant to promote testing standardization across different laboratories and improve patient care.
The group noted that the number of variant alleles currently being tested for vary widely across available commercial assays and sometimes fail to include those variants most relevant to clinical care.
This, the group wrote, can result in labs reporting a patient's genotype as a *1 normal allele or no variants detected, when such variants are actually present, leading to discrepancies in interpretation, complicating the implementation of pharmacogenomic testing, and adversely impacting patient care due to increased risk of thiopurine toxicity.
Thiopurine medications include Prometheus' Imuran (azathioprine), Rare Disease Therapeutics' Purixan (6-mercaptopurine), and GlaxoSmithKline's Tabloid (6-thioguanine).
Similar to prior recommendations from the same AMP working group, such as for CYP2C19, the group established two tiers of allele selection, based upon an allele meeting certain criteria.
"Our pan-ethnic testing approach is based on criteria such as allele frequencies in people of different genetic ancestries, the availability of reference materials, and other technical considerations," Victoria Pratt, co-chair of the AMP PGx Working Group, said via email.
Technical considerations include the feasibility for clinical laboratories to accurately investigate these variants.
Tier 1 comprises five alleles that the group recommends for inclusion in all clinical TPMT and NUDT15 genotyping tests. These alleles are TPMT*2, *3A, *3B, and *3C, and NUDT15*3, all of which are considered "no-function," meaning that their corresponding proteins are poor metabolizers of thiopurine compounds.
"AMP intends to update these recommendations as new data and/or reference materials become available," Pratt said.
Tier 2 consists of optional alleles that do not currently meet one or more of the Tier 1 inclusion criteria. These alleles are TPMT*11, *29, and *42, and NUDT15 *2, *4, *6, *9, and *14. Some of these are no-function alleles while others are likely no-function or are of uncertain function but are likely to affect the same amino acid or are useful in accurately detecting and differentiating a Tier 1 allele.
Despite Tier 2 alleles not meeting all the Tier 1 criteria, there is good evidence for and confidence in their function.
The group noted that there are over 100 NUDT15 alleles and over 150 TPMT alleles and that more continue to be discovered. The functions of those not assigned to Tier 1 and Tier 2, however, and their clinical significance are less clear.
Although the adoption of AMP recommendations is voluntary, Pratt said that the group has received "positive feedback" from labs that have implemented them.
"AMP typically formally assesses implementation approximately two to three years after recommendations are published because the time to adoption by laboratories can be heterogeneous," she said.
Although she didn't specify which genes the group is focusing on next, she noted that AMP collaborates with the broader laboratory community, prioritizing genes largely by the frequency with which they are used in pharmacogenomic assays.
"We are focused on developing guidelines for the most frequently used PGx genotyping assays," she said, "to help ensure that they investigate the most clinically relevant variant alleles and enable healthcare professionals to provide high-quality patient care."