Table 3.

Comparison of pharmacogenetic genotyping methods

Method	Description	Cost per sample	Optimal Study Design	Drawbacks
TaqMan	Accurately assays the genotype of a single nucleotide variant	Low	Ideal for projects testing a small number of SNPs in a large population.	Cost approaches that of GWAs platform for more than ~330 ‡ of SNPs.
Genome-Wide Fixed Content Platforms	Current platforms range from 1-5 million common (MAF >1%) variants across the genome	Mid	Holistic approach that targets most of the genome. Best candidate for pharmacodynamic studies, especially if the HLA* complex is a candidate†	Overall highly accurate but drops in quality in repetitive genomic regions found around many CYP variants.
ADME Core andother PGX* Panels	Accurately targets 184-1,936§ variants in PGX genes	Mid-High	Selective coverage of functional variants in VIPs*. Results of PGX studies have so far converged around pharmacokinetic genes covered here (with the exception of HLA).	Large proportions of variants are too rare and lack statistical power in small to mid-range sized study designs.
Targeted, Exome, and Whole Genome Sequencing	Selective sequencing of targeted genes/regions, all coding regions, or the whole genome	High	Holistic approach to genome limited to coding regions. Most suitable for identifying the effect of burden of rare variants on drug response.	Massive data storage requirements and unfamiliar analysis tools available may be prohibitive for some investigators. Little information in the literature on performance in VIP variants.

^†Daly AK: Drug-induced liver injury: past, present and future. Pharmacogenomics. 11(5), 607-611 (2010)

^‡Estimated prices for one sample as follows: $0.72 per SNP assayed with TaqMan assay and $240.00 per genome-wide genotyping platform.

^§1,936 variants captured with the Affymetrix DMET (drug metabolism enzymes and transporters)

Abbreviations: Pharmacogenetics/Pharmacogenomics (PGX), Very Important Pharmacogene (VIP), and Human Leukocyte Antigen (HLA)