Pharmacogenetics is the study of inherited genetic differences in drug metabolic pathways which can affect individual responses to drugs, both in terms of therapeutic effect as well as adverse effects. The term pharmacogenetics is often used interchangeably with the term pharmacogenomics which also investigates the role of acquired and inherited genetic differences in relation to drug response and drug behavior through a systematic examination of genes, gene products, and inter- and intra-individual variation in gene expression and function.
In oncology, pharmacogenetics historically is the study of germline mutations (e.g., single-nucleotide polymorphisms affecting genes coding for liver enzymes responsible for drug deposition and pharmacokinetics), whereas pharmacogenomics refers to somatic mutations in tumoral DNA leading to alteration in drug response (e.g., KRAS mutations in patients treated with anti-Her1 biologics).
Predicting drug-drug interactions
Much of current clinical interest is at the level of pharmacogenetics, involving variation in genes involved in drug metabolism with a particular emphasis on improving drug safety. The wider use of pharmacogenetic testing is viewed by many as an outstanding opportunity to improve prescribing safety and efficacy. Driving this trend are the 106,000 deaths and 2.2 Million serious events caused by adverse drug reactions in the US each year. As such ADRs are responsible for 5-7% of hospital admissions in the US and Europe, lead to the withdrawal of 4% of new medicines and cost society an amount equal to the costs of drug treatment.
Comparisons of the list of drugs most commonly implicated in adverse drug reactions with the list of metabolizing enzymes with known polymorphisms found that drugs commonly involved in adverse drug reactions were also those that were metabolized by enzymes with known polymorphisms (see Phillips, 2001).
Scientists and doctors are using this new technology for a variety of things, one being improving the efficacy of drugs. In psychology, we can predict quite accurately which anti-depressant a patient will best respond to by simply looking into their genetic code. This is a huge step from our previous way of adjusting and experimenting with different medications to get the best response. Antidepressants also have a large percentage of unresponsive patients and poor prediction rate of ADRs (adverse drug reactions). In depressed patients, 30% are not helped by antidepressants. In psychopharmacological therapy, a patient must be on a drug for 2 weeks before the effects can be fully examined and evaluated. For a patient in that 30%, this could mean months of trying medications to find an antidote to their pain. Any assistance in predicting a patient’s drug reaction to psychopharmacological therapy should be taken advantage of. Pharmacogenetics is a very useful and important tool in predicting which drugs will be effective in various patients. The drug Plavix blocks platelet reception and is the second best selling prescription drug in the world, however, it is known to warrant different responses among patients. GWAS studies have linked the gene CYP2C19 to those who cannot normally metabolize Plavix. Plavix is given to patients after receiving a stent in the coronary artery to prevent clotting.
Stent clots almost always result in heart attack or sudden death, fortunately it only occurs in 1 or 2% of the population. That 1 or 2% are those with the CYP2C19 SNP. This finding has been applied in at least two hospitals, Scripps and Vanderbilt University, where patients who are candidates for heart stents are screened for the CYP2C19 variants.
Another newfound use of Pharmacogenetics involves the use of Vitamin E. The Technion Israel Institute of Technology observed that vitamin E can be used to in certain genotypes to lower the risk of cardiovascular disease in patients with diabetes, but in the same patients with another genotype, vitamin E can raise the risk of cardiovascular disease. A study was carried out, showing vitamin E is able to increase the function of HDL in those with the genotype haptoglobin 2-2 who suffer from diabetes. HDL is a lipoprotein that removes cholesterol from the blood and is associated with a reduced risk of atherosclerosis and heart disease. However, if you have the misfortune to possess the genotype haptoglobin 2-1, the study shows that this same treatment can drastically decrease your HDL function and cause cardiovascular disease.
Pharmacogenetics is a rising concern in clinical oncology, because the therapeutic window of most anticancer drugs is narrow and patients with impaired ability to detoxify drugs will undergo life-threatening toxicities. In particular, genetic deregulations affecting genes coding for DPD, UGT1A1, TPMT, CDA and Cyp2D6 are now considered as critical issues for patients treated with 5-FU/capecitabine, irinotecan, mercaptopurine/azathioprine, gemcitabine/capecitabine/AraC and tamoxifen, respectively. The decision to use pharmacogenetic techniques is influenced by the relative costs of genotyping technologies and the cost of providing a treatment to a patient with an incompatible genotype. When available, phenotype-based approaches proved their usefulness while being cost-effective.
In the search for informative correlates of psychotropic drug response, pharmacogenetics has several advantages:
- The genotype of an individual is essentially invariable and remains unaffected by the treatment itself.
- Molecular biology techniques provide an accurate assessment of the genotype of an individual.
- There has been a dramatic increase in the amount of genomic information that is available. This information provides the necessary data for comprehensive studies of individual genes and broad investigation of genome-wide variation.
- The ease of accessibility to genotype information through peripheral blood or saliva sampling and advances in molecular techniques has increased the feasibility of DNA collection and genotyping in large-scale clinical trials.
The first observations of genetic variation in drug response date from the 1950s, involving the muscle relaxant suxamethonium chloride, and drugs metabolized by N-acetyltransferase. One in 3500 Caucasians has less efficient variant of the enzyme (butyrylcholinesterase) that metabolizes suxamethonium chloride. As a consequence, the drug’s effect is prolonged, with slower recovery from surgical paralysis. Variation in the N-acetyltransferase gene divides people into "slow acetylators" and "fast acetylators", with very different half-lives and blood concentrations of such important drugs as isoniazid (antituberculosis) and procainamide (antiarrhythmic). As part of the inborn system for clearing the body of xenobiotics, the cytochrome P450 oxidases (CYPs) are heavily involved in drug metabolism, and genetic variations in CYPs affect large populations. One member of the CYP superfamily, CYP2D6, now has over 75 known allelic variations, some of which lead to no activity, and some to enhanced activity. An estimated 29% of people in parts of East Africa may have multiple copies of the gene, and will therefore not be adequately treated with standard doses of drugs such as the painkiller codeine (which is activated by the enzyme). The first study using Genome-wide association studies (GWAS) linked age-related macular degeneration (AMD) with a SNP located on chromosome 1 that increased one’s risk of AMD. AMD is the most common cause of blindness, affecting more than seven million Americans. Until this study in 2005, we only knew about the inflammation of the retinal tissue causing AMD, not the genes responsible.
Thiopurines and TPMT (thiopurine methyl transferase)
One of the earliest tests for a genetic variation resulting in a clinically important consequence was on the enzyme thiopurine methyltransferase (TPMT). TPMT metabolizes 6-mercaptopurine and azathioprine, two thiopurine drugs used in a range of indications, from childhood leukemia to autoimmune diseases. In people with a deficiency in TPMT activity, thiopurine metabolism must proceed by other pathways, one of which leads to the active thiopurine metabolite that is toxic to the bone marrow at high concentrations. Deficiency of TPMT affects a small proportion of people, though seriously. One in 300 people have two variant alleles and lack TPMT activity; these people need only 6-10% of the standard dose of the drug, and, if treated with the full dose, are at risk of severe bone marrow suppression. For them, genotype predicts clinical outcome, a prerequisite for an effective pharmacogenetic test. In 85-90% of affected people, this deficiency results from one of three common variant alleles. Around 10% of people are heterozygous - they carry one variant allele - and produce a reduced quantity of functional enzyme. Overall, they are at greater risk of adverse effects, although as individuals their genotype is not necessarily predictive of their clinical outcome, which makes the interpretation of a clinical test difficult. Recent research suggests that patients who are heterozygous may have a better response to treatment, which raises whether people who have two wild-type alleles could tolerate a higher therapeutic dose. The US Food and Drug Administration (FDA) have recently deliberated the inclusion of a recommendation for testing for TPMT deficiency to the prescribing information for 6-mercaptopurine and azathioprine. Hitherto the information has carried the warning that inherited deficiency of the enzyme could increase the risk of severe bone marrow suppression. Now it will carry the recommendation that people who develop bone marrow suppression while receiving 6-mercaptopurine or azathioprine be tested for TPMT deficiency.
A polymorphism near a human interferon gene is predictive of the effectiveness of an artificial interferon treatment for Hepatitis C. For genotype 1 hepatitis C treated with Pegylated interferon-alpha-2a or Pegylated interferon-alpha-2b (brand names Pegasys or PEG-Intron) combined with ribavirin, it has been shown that genetic polymorphisms near the human IL28B gene, encoding interferon lambda 3, are associated with significant differences in response to the treatment. Genotype 1 hepatitis C patients carrying certain genetic variant alleles near the IL28B gene are more probable to achieve sustained virological response after the treatment than others, and demonstrated that the same genetic variants are also associated with the natural clearance of the genotype 1 hepatitis C virus.
Integrating pharmacogenetics into the health care system
Despite the many successes, most drugs are not tested using GWAS. However, it is estimated that over 25% of common medication have some type of genetic information that could be used in the medical field. If the use of personalized medicine is widely adopted and used, it will make medical trials more efficient. This will lower the costs that come about due to adverse drug side effects and prescription of drugs that have been proven ineffective in certain genotypes. It is very costly when a clinical trial is put to a stop by licensing authorities because of the small population who experiences adverse drug reactions. With the new push for pharmacogenetics, it is possible to develop and license a drug specifically intended for those who are the small population genetically at risk for adverse side effects. 
As the cost per genetic test decreases, the development of personalized drug therapies will increase. However, as of now, we only have access to single-gene test and which is currently quite expensive. In the future, more advanced sequencing will be able to test for multiple genes in a short amount of time. A disposable DNA sequencing device, which will retail for under $900 has recently been announced. The device was made to be the size of a USB memory drive to make it portable and easy to use  Likewise, companies like deCODE genetics, Navigenics and 23andMe offer genome scans. The companies use the same genotyping chips that are used in GWAS studies and provide customers with a write-up of individual risk for various traits and diseases and testing for 500,000 known SNPs. Costs range from $995 to $2500 and include updates with new data from studies as they become available. The more expensive packages even included a telephone session with a genetics counselor to discuss the results.
Pharmacogenetics has become a controversial issue in the area of bioethics. It's a new topic to the medical field, as well as the public. This new technique will have a huge impact on society, influencing the treatment of both common and rare diseases. As a new topic in the medical field the ethics behind it are still not clear. However, ethical issues and their possible solutions are already being addressed.
There are three main ethical issues that have risen from pharmacogenetics. First, would there be a type equity at both drug development and the accessibility to tests. The concern of accessibility to the test is whether it is going to be available directly to patients via the internet, or over the counter. The second concern regards the confidentiality of storage and usage of genetic information. Thirdly, would patients have the control over being tested.
One concern that has risen is the ethical decision health providers must take with respect to educating the patient of the risks and benefits of medicine developed by this new technology. Pharmacogenetics is a new process that may increase the benefits of medicine while decreasing the risk. However clinicians have been unsuccessful in educating patients regarding the concept of benefits over risk. The Nuffield Council reported that patients and health professionals have adequate information about pharmacogenetics tests and medicine. Health care providers will also encounter an ethical decision in deciding to tell their patients that only certain individuals will benefit from the new medicine due to their genetic make-up. Another ethical concern is that patients who have not taken the test be able to have access to this type of medicine. If access is given by the doctor the medicine could negatively impact the patient's health. The ethical issues behind pharmacogenetics tests, as well as medicine, are still a concern and policies will need to be implemented in the future.
- Personalized medicine
- Structural genomics
- Klotz, U. (2007). "The role of pharmacogenetics in the metabolism of antiepileptic drugs: pharmacokinetic and therapeutic implications.". Clin Pharmacokinet 46 (4): 271–9. doi:10.2165/00003088-200746040-00001. PMID 17375979.
- "Center for Pharmacogenomics and Individualized Therapy". Retrieved 2014-10-28.
- Roses AD (June 2000). "Pharmacogenetics and the practice of medicine". Nature 405 (6788): 857–65. doi:10.1038/35015728. PMID 10866212.
- Lazarou J, Pomeranz BH, Corey PN (April 1998). "Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospective studies". JAMA 279 (15): 1200–5. doi:10.1001/jama.279.15.1200. PMID 9555760.
- Ingelman-Sundberg M, Rodriguez-Antona C (August 2005). "Pharmacogenetics of drug-metabolizing enzymes: implications for a safer and more effective drug therapy". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 360 (1460): 1563–70. doi:10.1098/rstb.2005.1685. PMC 1569528. PMID 16096104.
- Kirchheiner J, Seeringer A, Viviani R (2010). "Pharmacogenetics in psychiatry--a useful clinical tool or wishful thinking for the future?". Curr. Pharm. Des. 16 (2): 136–44. doi:10.2174/138161210790112728. PMID 20205659.
- Alazraki M (2011). "The 10 Biggest-Selling Drugs That Are About to Lose Their Patent". DailyFinance. Retrieved 2012-05-06.
- Shuldiner AR, O'Connell JR, Bliden KP, Gandhi A, Ryan K, Horenstein RB, Damcott CM, Pakyz R, Tantry US, Gibson Q, Pollin TI, Post W, Parsa A, Mitchell BD, Faraday N, Herzog W, Gurbel PA (August 2009). "Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy". JAMA 302 (8): 849–57. doi:10.1001/jama.2009.1232. PMID 19706858.
- The Creative Destruction of Medicine: How the Digital Revolution Will Create Better Health Care. New York: Basic Books. 2012. ISBN 0-465-02550-1.
- Farbstein D, Blum S, Pollak M, Asaf R, Viener HL, Lache O, Asleh R, Miller-Lotan R, Barkay I, Star M, Schwartz A, Kalet-Littman S, Ozeri D, Vaya J, Tavori H, Vardi M, Laor A, Bucher SE, Anbinder Y, Moskovich D, Abbas N, Perry N, Levy Y, Levy AP (November 2011). "Vitamin E therapy results in a reduction in HDL function in individuals with diabetes and the haptoglobin 2-1 genotype". Atherosclerosis 219 (1): 240–4. doi:10.1016/j.atherosclerosis.2011.06.005. PMC 3200506. PMID 21722898.
- Yang CG, Ciccolini J, Blesius A, Dahan L, Bagarry-Liegey D, Brunet C, Varoquaux A, Frances N, Marouani H, Giovanni A, Ferri-Dessens RM, Chefrour M, Favre R, Duffaud F, Seitz JF, Zanaret M, Lacarelle B, Mercier C (January 2011). "DPD-based adaptive dosing of 5-FU in patients with head and neck cancer: impact on treatment efficacy and toxicity". Cancer Chemother. Pharmacol. 67 (1): 49–56. doi:10.1007/s00280-010-1282-4. PMID 20204365.
- Malhotra AK (2010). "The state of pharmacogenetics". Psychiatr Times 27 (4): 38–41, 62.
- Gardiner SJ, Begg EJ (September 2006). "Pharmacogenetics, drug-metabolizing enzymes, and clinical practice". Pharmacol. Rev. 58 (3): 521–90. doi:10.1124/pr.58.3.6. PMID 16968950.
- Genetic Science Learning Center. "Your Doctor's New Genetic Tools.". Lern.Genetics. Retrieved 15 April 2012.
- "Pharmacogenomics: Personalizing Medicine". Discovery's Edge. Mayo Clinic. Retrieved April 15, 2012.
- Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, Heinzen EL, Qiu P, Bertelsen AH, Muir AJ, Sulkowski M, McHutchison JG, Goldstein DB (September 2009). "Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance". Nature 461 (7262): 399–401. doi:10.1038/nature08309. PMID 19684573.
- Thomas DL, Thio CL, Martin MP, Qi Y, Ge D, O'Huigin C, Kidd J, Kidd K, Khakoo SI, Alexander G, Goedert JJ, Kirk GD, Donfield SM, Rosen HR, Tobler LH, Busch MP, McHutchison JG, Goldstein DB, Carrington M (October 2009). "Genetic variation in IL28B and spontaneous clearance of hepatitis C virus". Nature 461 (7265): 798–801. doi:10.1038/nature08463. PMC 3172006. PMID 19759533.
- Frueh FW, Amur S, Mummaneni P, Epstein RS, Aubert RE, DeLuca TM, Verbrugge RR, Burckart GJ, Lesko LJ (August 2008). "Pharmacogenomic biomarker information in drug labels approved by the United States food and drug administration: prevalence of related drug use". Pharmacotherapy 28 (8): 992–8. doi:10.1592/phco.28.8.992. PMID 18657016.
- Corrigan OP (2011). "Personalized Medicine in a Consumer Age". Current Pharmacogenomics and Personalized Medicine 9: 168–176. doi:10.2174/187569211796957566.
- Paul NW, Fangerau H (December 2006). "Why should we bother? Ethical and social issues in individualized medicine". Curr Drug Targets 7 (12): 1721–7. doi:10.2174/138945006779025428. PMID 17168846.
- Payne K, Shabaruddin FH (May 2010). "Cost-effectiveness analysis in pharmacogenomics". Pharmacogenomics 11 (5): 643–6. doi:10.2217/pgs.10.45. PMID 20415553.
- Oxford Nanopore Technologies. 2012. Press releases - News - Oxford Nanopore Technologies. Available from: http://www.nanoporetech.com/news/press-releases/view/39
- Breckenridge A, Lindpaintner K, Lipton P, McLeod H, Rothstein M, Wallace H (September 2004). "Pharmacogenetics: ethical problems and solutions". Nat. Rev. Genet. 5 (9): 676–80. doi:10.1038/nrg1431. PMID 15372090.
- Corrigan OP (March 2005). "Pharmacogenetics, ethical issues: review of the Nuffield Council on Bioethics Report". J. Med. Ethics 31 (3): 144–8. doi:10.1136/jme.2004.007229. PMC 1734105. PMID 15738433.
- Abbott A (October 2003). "With your genes? Take one of these, three times a day". Nature 425 (6960): 760–2. doi:10.1038/425760a. PMID 14574377.
- Evans WE, McLeod HL (February 2003). "Pharmacogenomics – drug disposition, drug targets, and side effects". N. Engl. J. Med. 348 (6): 538–49. doi:10.1056/NEJMra020526. PMID 12571262.
- Phillips KA, Veenstra DL, Oren E, Lee JK, Sadee W (November 2001). "Potential role of pharmacogenomics in reducing adverse drug reactions: a systematic review". JAMA 286 (18): 2270–9. doi:10.1001/jama.286.18.2270. PMID 11710893.
- Weinshilboum R; Collins, Francis S.; Weinshilboum, Richard (February 2003). "Inheritance and drug response". N. Engl. J. Med. 348 (6): 529–37. doi:10.1056/NEJMra020021. PMID 12571261.
- Pharmacogenomics: Medicine and the new genetics from the Human Genome Project
- Pharmacogenomics in Drug Discovery and Development, a book on pharmacogenomics, diseases, personalized medicine, and therapeutics
- The Pharmacogenomics Journal
- PharmGKB The Pharmacogenetics and Pharmacogenomics Knowledge Base, a free online tool for Pharmacogenetics research
- "Center for Pharmacogenomics and Individualized Therapy". University of North Carolina at Chapel Hill Center for Pharmacogenomics and Individualized Therapy. Retrieved 2014-10-28.