User:Dudley14/sandbox

APPLICATIONS
Several gene chips and systems for genotyping genes associated with drug metabolism have been developed. One of the chips, the first approved by the FDA, is the AmpliChip, which types alleles of the CYP2C19 and CYP2D6 genes, whose mutations are associated with decreased or increased drug metabolism. The AmpliChip, a product from Roche, was the first approved diagnostic genotyping product by the FDA. The product was approved in 2005 and can identifys up to 33 CYP2D6 alleles and 3 CYP2C19 alleles. It is a microarray and uses Polymerase chain reaction amplification of DNA isolated from the patient. The PCR products are applied to the AmpliChip. The chip contains oligonucleotide probes that hybridize with the PCR products. The probes represent the different polymorphism of the gene. In a clinical setting the information from the gene can be used as a component in determining prescribed drug dosage. Dudley14 (talk) 22:49, 28 April 2014 (UTC)

The ability of the gene chips to identify the degree of metabolism can be determined with the use of a probed drug. The probe drug is administered to the patient and then the drug and its resulting metabolites are measured from the patient’s urine. From this test a, a patient can be determined to be an, extensive (EM), poor (PM), ultra rapid (UM) or intermediate (IM) metabolizers. To determines these values the, ratio of dextromethorphan, the probe drug, to dextrorphan, the metabolite, can be determined from the urine. When the genotypes of samples obtained from PCR methods is compared with the genotype indicated by the AmpliChip the correspondence is nearly 100%. In determining whether a patient has an EM, UM, IM or Em phenotype, the amplichip was able to identify correctly 80% of samples. To separate the patients into phenotypes determined from the genotypes, the alleles reported by the AmpliChip were used. If a patient had one non-functional allele, one reduced activity allele or two reduced activity alleles, they were characterized as IM and EM, if they had at least one function allele, and UM if they had at least three copies of a functional allele.

Comparing the predicted phenotype from the chip with probe drug data, 15 out of 15 were correctly predicted. For IM, 8 out of 19 were correctly predicted, for EM 106 out of 111 were correctly identified and for UM only 1 out of 17 were correctly identified. The possible reasons for the poor result for UMmay be that factors independent of theCYP2D6 may be at play, such as other genes.

Other systems and gene chips on the market include the INFINITI 2C9 & VKORC1 Multiplex Assay for Warfarin, Tag-it mutation Detection System, and Invader UGT1A1 Molecular Assay. In tests to determine the accuracy of these systems, 112 subjects were genotyped. The Infinite system was found to be a 100% accurate for CYP2C9 *2 and *3 and VKORC1-1639 SNPs. the invader was also 100% accurate. The tag it mutation system was also 100% for CYP2C9*2 and *3 and 99% accurate for VKORCI genotyping.

AN important factor besides accuracy is turnaround time for a test, especially in a hospital setting. The three systems mentioned above were tested for turnaround time, the amount of time from the beginning of the test to results. The invader system had the lowest turnaround time at about 3 hours. The Infiniti and tag it systems both had system had a turnaround of 8 hours. Another important parameter is labor time. The invader system used 1.42 hours of labor time. To determine dose, dosing algoritms can be used, which incorporate clinical information and genotype information. A number of patients on a stable dose of warfarin were used as the subjects in a test to determine if dosing algorithms which incorporate genotypes were accurate. These algorithms incorporated the CYP2C9 and VKORC1 variants.

The average age of a patient was 67 years and 62% were male, 57% were Caucasian, 19% African American, Hispanic 14 % and 10% Asian. The 12 algorithms that incorporated genotypes explained between 33% and 55% of the variation in warfarin dosage

http://www.fda.gov/medicaldevices/productsandmedicalprocedures/invitrodiagnostics/ucm330711.htm#human Genetic Tests approved by FDA for determining genotype of drug metabolizing enzymes

Future Directions
In the future, high throughput tests genotypes of Metabolism enzymes and drug transporters that effect Absorption, distribution, metabolism and elimination (ADME) will be available. One such system, approved for clinical research, is the DMET system (Drug Metabolizing Enzyme and Transporters), which provides wide coverage of 1913 genetic variants, related to pharmacogenetics including drug transporters in cells and covers 225 genes. The system uses a molecular inversion probe, with the advantages that less and lower quality DNA can used. The results from DMET system was compared to lower through put genotyping systems. A total of 19,942 SNP patient pairs were tested, with DMET compared against at least one orthogonal method. The DMET system was able to identify genotypes with 99.9% accuracy.