Transl Clin Pharmacol.  2016 Mar;24(1):13-21. 10.12793/tcp.2016.24.1.13.

Brief introduction to current pharmacogenomics research tools

Affiliations
  • 1Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 47392, Korea. hosuegi@gmail.com
  • 2Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Busan 47392, Korea.

Abstract

There is increasing interest in the application of personalized therapy to healthcare to increase the effectiveness of and reduce the adverse reactions to treatment. Pharmacogenomics is a core element in personalized therapy and pharmacogenomic research is a growing field. Understanding pharmacogenomic research tools enables better design, conduct, and analysis of pharmacogenomic studies, as well as interpretation of pharmacogenomic results. This review provides a general and brief introduction to pharmacogenomics research tools, including genotyping technology, web-based genome browsers, and software for haplotype analysis.

Keyword

Genotyping technology; Pharmacogenomics research tools; Software for haplotype analysis; Web-based genome browsers

MeSH Terms

Delivery of Health Care
Genome
Haplotypes
Humans
Pharmacogenetics*

Figure

  • Figure 1. Schematic representation of SNP detection method. (A) TaqMan probe method. The template DNA is combined with primers and fluorophore-labeled allele specific probes, such as FAM labeled-allele 1 probe and VIC labeled-allele 2 probe. When a FAM-labeled allele 1 probe perfectly complements the target SNP site at allele 1, the FAM is released by the 5' nuclease activity of Taq polymerase. Release of the FAM separates the 3' quencher, allowing FAM to be emitted and subsequently detected as homozygotes of SNP at allele 1. In contrast, the VIC signal indicates homozygotes of SNP at allele 2. Fluorescences from both signals indicate heterozygotes. (B) Single base extension method. Extension primers are designed a single base upstream from the target SNP. During polymerase reactions, extension primers are bound a single base upstream of SNP site and ddATP are bound and extended to the target SNP site at allele 1, and the reaction is terminated. In contrast, ddTTP are bound and terminated to the target SNP site at allele 2. The incorporated base is detected using fluorescence. (C) Goldengate assay. Genomic DNA is activated by binding streptavidin/biotin beads. Both primers (ASOs and LSO) are hybridized to the genomic DNA-bound streptavidin/biotin beads. Extension of the appropriate ASO and ligation of the LSO generates ligation products. This product is amplified using dye-labeled universal PCR primers, and then fluorescence is used for signal detection. (D) GeneChip Microarray. ① Two genomic-specific flank regions are hybridized at genomic DNA ② The gap is filled with complementary base of target SNP and ③ ligated ④ cleavage site is digested by exonuclease, then the inversion probe is amplified by PCR reaction.

  • Figure 2. An example of what a Linkage Disequilibrium (LD) Map looks like (triangle format). This is a Linkage disequilibrium (LD) blocks structure of the inflammatory bowel disease 5 (IBD5) gene in chromosome 5q31-q33. The white line on top represents a strand of a chromosome. The black bars on the white line of the chromosome are SNPs (Single nucleotide polymorphism) that have been identified and sequenced. These SNP locations or loci are labeled in this picture as 1, 2, 3 and so on (#1∼20 in this case). The kilobase (kb) in each LD blocks means the distance between first of SNP and end of SNP. The values in diamond represent the D' values (×100) between the two SNPs. For example, the diamond in which the columns leading from SNP#1 and SNP#7 intersect has a number, 95 with red color. Thus SNP#1 and SNP#7 have a D' value of 0.95 and are in high linkage disequilibrium with each other. The color is categorized according to D' value (D' ≥ 0.80, red; 0.5 ≤ D' < 0.8, pink; 0.2 ≤ D' < 0.5, blue; and D' < 0.2, white).


Reference

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