Methods:

The CYP2D6 allele frequency tables (CYP2D6 frequency table; link to PharmGKB) are updates of those previously published in CPIC guidelines (PMID: 25974703, 24458010). Updates to the CYP2D6 allele frequency tables were made by searching the PubMed® database (1995 to 2018). The following criteria were used for CYP2D6: (CYP2D6 or 2D6 or cytochrome P4502D6) AND (genotype OR allele OR frequency OR minor allele OR variant OR ethnic OR race OR racial OR ethnicity) with filter limits set to retrieve "full-text" and "English" literature. In addition, reports were also identified from citations by others or review articles. Studies were considered for inclusion in the CYP2D6 frequency table if: (1) the ethnicity of the population was clearly indicated, (2) either allele frequencies or genotype frequencies were reported, (3) the method by which the genes were genotyped was indicated, (4) the sample population consisted of at least 50 individuals with a few exceptions (e.g., smaller cohorts that were part of larger studies) and (5) the study represented an original publication (no reviews or meta-analyses).
Diplotype and phenotype frequencies were estimated using the equation describing Hardy Weinberg equilibrium based on reported allele frequencies. Because the frequencies for each allele are averages from all studies for that population, allele frequencies may not add up to100%. To account for this in diplotype and phenotype frequencies calculations, *1 frequency was calculated as 1 - sum (non *1 allele frequency).


Caveats to estimated allele, diplotype and phenotype frequencies:

Sampling. Allele frequencies collected by CPIC for the supplemental tables are based on published literature reports which typically study small groups of people based on a geographic location (e.g. Malaysia, Berlin, Cairo). Almost no studies use genetic markers to estimate ancestry. Manuscripts are often focused on a specific phenotype (e.g. disease) or study only individuals taking a particular drug. Such samples would not be considered a random sample of the general population. Another consideration is that sample size is important, and PGx studies are typically not large. The frequencies collected from these studies are then used to estimate general estimates of entire ethnic population allele frequencies. Therefore, frequencies from larger groups of subjects and frequencies averaged from many sample populations probably result in better estimates.

Estimation of *1 frequency. In general, there are no population studies that test for all known variant alleles. Because CYP2D6*1 is not genotyped directly, all alleles that are negative for a sequence variation are defaulted to a CYP2D6*1 assignment. Likewise, sequence variations of alleles that are not tested may default to a CYP2D6*1 assignment and hence contribute to the frequencies reported for this allele. Therefore, the inferred frequency for CYP2D6*1 was calculated as an average from studies describing allele frequencies for the most common alleles found in a particular ethnic group.

Diplotype/Phenotype frequency estimates. When calculating diplotype frequencies from these allele frequencies, the margin of error is compounded based on the margin of error on each allele in the diplotype. So, the margin of error will necessarily increase for diplotype frequency estimates compared to allele frequency estimates. For allele frequencies with already large margins of error due to small and non-random sampling, the diplotype margin of error could potentially be quite large. On the other hand, for well-studied alleles, the margin of error is likely low.

Biogeographical groups. Biogeographical groups are derived from PMID 30506572. Further details, including the definitions of each group, can be found at https://www.pharmgkb.org/page/biogeographicalGroups. We strongly recommend that users use either the publication or the PharmGKB link provided to familiarize themselves with the grouping system before using these allele frequencies. These tables group individuals from particular geographic locations into larger biogeographical groups. It is difficult to group populations with certainty, because some populations are often admixed, or at the least, a combination of different ethnicities. Therefore, the margin of error is increased when different subpopulations are grouped together.

Overestimation of allele frequencies. CYP2D6*2 is a 'default' assignment and, unless tested and discriminated for CYP2D6*8, *11, *17, *35,*41 and other variants, will default to a CYP2D6*2 assignment. The frequencies shown here may therefore be over-estimated. CYP2D6*10 is a 'default' assignment and, unless tested and discriminated for, CYP2D6*14 and *36 and other variants, will default to a CYP2D6*10 assignment. The frequencies shown here may therefore be over-estimated. CYP2D6*17 is a 'default' assignment and, unless tested and discriminated for, CYP2D6*40 and *58 will default to a CYP2D6*17 assignment. The frequencies shown here may therefore be over-estimated. CYP2D6*41 has not consistently been determined by its defining SNP (2988G>A) across studies; some platforms still use the -1584C>G SNP to discriminate between CYP2D6*2 and *41. This may lead to an overestimation of the CYP2D6*41 frequency, especially in those of African ancestry.

CNV alleles. Many studies do not specify the exact copy number of duplicated alleles found in their study population and instead report the total frequency of observed CNVs as "xN". Where possible, these frequencies have been included in the CNV column for that allele (e.g. *1xN frequencies are included in the *1x2 column, *4xN frequencies are included in the *4x2 column). Users should be aware that this will lead to an overestimation of the frequency of that exact copy number in the population.