An alternative approach to SNP genotyping is haplo-typing. Gene-based haplotypes are composed of the nucleotides that occur at SNP positions on a single chromosome at the locus of a single gene. Haplotypes are the most precise markers possible for a given gene because they contain all the variations in a gene. Hap-lotyping is a way of characterizing combinations of SNPs that might influence response and is considered to be a more accurate measure of phenotypic variation. However, SNP-based tests have greater power when the number of causative SNPs (a subset of the total set of SNPs) is smaller than the total number of haplotypes. One limitation of haplotyping is that haplotypes need to be determined for each individual, as SNPs detected from a pool of DNA from a number of individuals cannot yield haplotypes. Clinical trials using haplotyped individuals are the first genetically personalized medical treatments.
Table 1 Pharmacogenetic vs. pharmacogenomic studies
Focus of studies Scope of studies
Methods of study Relation to drugs Examination of drug effects
Application relevant to personalized medicine
Study of sequence variations in genes suspected of affecting drug response
SNP, expression profiles, and biochemistry
One drug and many genomes (patients)
Study of one drug in vivo in different patients with inherited gene variants
Studies encompass the whole genome
Many drugs and one genome
Examination of differential effects of several compounds on gene expression in vivo or in vitro
Drug discovery and development or drug selection
Source: Modified and expanded from Ref. .
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