The range of diagnostic tools available to the clinician now is possible due to the completion of the human genome project that lead to human genome sequencing. We are at the threshold of seeing an exponential rise in molecular diagnostics, which is revolutionizing the concept of personalized medicine as depicted below.
Personalized medicine is the practice of providing the right medicine for the right patient at the right dose, saving lives and preventing dangerous side effects. However, to practice this concept is predicated on the development and availability of genetic tests that accurately and reliably predicts a patient's response to a drug. Genetic testing helps in discovering potential abnormalities and tailoring treatment. Today, genetic tests are available clinically for more than 900 diseases.
Promise of Personalized Medicine
- Shift emphasis from reaction to prevention
- Select optimal therapy (trial-and-error)
- Avoid adverse drug reactions (drug safety)
- Increase patient compliance
- Reduce time and cost of clinical trials
- Revive drugs that are failing in clinical trials or were withdrawn from the market
- Reduce the overall cost of healthcare
Biomarkers are employed across the entire healthcare spectrum from the biological research laboratory to patient monitoring in the clinic.
- DNA and/or mRNA expression profiles
- Tissue proteins and blood based tests to detect:
- Predisposition for disease
- Confirm diagnosis
- Assess its severity
- Predict response to therapy
- Monitor clinical course.
- For establishing disease predisposition, early detection, cancer staging, therapy selection, identifying whether or not a cancer is metastatic, therapy monitoring, assessing prognosis, and advances in the adjuvant setting.
- Help improve cost-efficiency
- Avoid late stage attrition
- Help make better and more informed decisions
- Help predict and minimize risk
- The predictive power of molecular diagnostics is reshaping how diseases including cancers are treated
- By determining which sets of genes and gene interactions affect different subsets of cancers, our tests will give doctors the information needed to prescribe the right treatment, for the right person at the right time.
- In the fight against cancer, molecular diagnostics are disease management tools.
- Molecular diagnostics will permanently transform the way diseases are managed at every stage of the disease continuum.
Cancer Diagnosis/ Prognosis
Cancer is a priority because targeted drugs like Herceptin (trastuzumab), Gleevec (imatinib), and Iressa (gefitinib) are already on the market and can benefit from a more targeted therapy utilizing biomarkers. There are three diagnostic tests for breast cancer that are currently available to predict tumor recurrence. For example, American Diagnostica's PAI-1/uPA tumor tissue biomarker test (Femtelle®) costs $250, which is performed on fresh frozen tissue, and can indicate a low risk of recurrence. Mammaprint from Agendia is a gene signature test from 70 related genes in a breast tumor. It is an FDA-approved oligonucleotide array that can also be performed on fresh frozen tissue. It costs about $3,000 and can reportedly identify which early-stage breast cancer patients are at risk of distant recurrence following surgery. The Oncotype DX breast cancer test from Genomic Health predicts chemotherapy response from estrogen receptor (ER)+ tumors from formalin-fixed paraffin-embedded (FFPE) tissue and recommends a treatment regimen. The test costs about $3,200. A number of promising biomarkers including the ErbB2 receptor for Her-2 could be used to rule out chemotherapy for those individuals who do not respond to trastuzumab. Another noteworthy biomarker is P13k; it controls important cellular pathways and several drugs are currently in development. In addition, the KRAS mutation predicts response to EGFR receptor drugs such as cetuximab and is a good predictive biomarker. Scintilla seeks to offer the above tests in India at an affordable level to all patients.
Universal Genetic Testing (UGT)
UGT encompasses a wide net that includes carrier screening to predict one's risk of having a child with a genetic disease, prenatal diagnosis to assess fetal risk of genetic disease, preimplantation genetic diagnosis to select embryos with which to start a pregnancy, and pre-dispositional testing to assess an individual's risk for developing disease in the future, choosing the right dose and drug for the disease.
Genetic Diagnostic tests fall under 3 applications:
- Pharmacogenomic testing
- Prenatal Newborn testing
- Predisposition and Diagnostic testing
Quality genetic testing requires good tests and competent laboratories. Tests must reliably be able to detect a particular genetic variation that in turn is correlated with health status or disease risk, and laboratories must reliably be able to ascertain its presence or absence and to communicate results appropriately to health care providers.
Genetic predisposition to certain chronic diseases are well documented, including, Bladder Cancer, Breast Cancer, Coeliac Disease ,Colorectal Cancer, Coronary Heart Disease, Gastric Cancer ,Graves' Disease, Lung Cancer, Lupus, Migraine, Multiple Sclerosis, Obesity, Osteoarthritis, Peripheral Vascular Disease, Prostate Cancer , Psoriasis, Rheumatoid Arthritis, Skin Cancer, Type 1 Diabetes, Venous Thromboembolism.
Diagnostic testing is used to confirm or rule out a known or suspected genetic disorder in a symptomatic individual.
Predictive testing is offered to asymptomatic individuals with a family history of a genetic disorder. Predictive testing is of two types: presymptomatic (eventual development of symptoms is certain when the gene mutation is present, e.g., Huntington disease) and predispositional (eventual development of symptoms is likely but not certain when the gene mutation is present, e.g., breast cancer).
Specific Genetic Diseases
There are many diseases that are now thought to be caused by alterations in DNA. These alterations can either be inherited or can occur spontaneously. Some diseases that have a genetic component to them include.
Genetic Variation and Mutation
An example of a disease caused by a genetic variation and mutation is Huntington disease, a severe disorder of a part of the brain that is marked by dementia, hydrocephalus, and unusual movements.
There have been several cases regarding individuals who are given a certain therapeutic drug to treat symptoms or to keep symptoms from occurring in which the individual has a serious side effect to the drug or feels no affect whatsoever. Many times this happens because of the genetic makeup of the individual. The study of this phenomenon is called "pharmacogenomics" or "pharmacogenetics."
The lack of the enzyme to metabolize drugs like codeine was directly related to a variation in the gene that produced it. This genetic variation is a polymorphism that can cause a very serious reaction in an individual and could lead to death due to drug overdose.
In some cases, individuals "hypermetabolize" drugs. This occurs when there is too much of an enzyme present that breaks down the helpful drug too quickly, leading to a lack of response to the drug. This can happen when too many copies of the gene are made and too much enzyme is produced. In other cases, the special receptor that the drug binds to on cells or tissues is missing, again because of a variation in the gene that makes the receptor protein. When there is no receptor to bind the drug, the drug may not have any effect on the cells or tissues that it should.
Genetic testing to determine the polymorphisms that play a role in our response to a drug is typical of basic genetic analyses. DNA is removed from cells, manipulated to find a specific area on a specific chromosome, and compared to "normal" DNA. In this way, genetic variations can be seen that may play a role in the over- or under-responsiveness to a therapeutic drug. This testing can also determine an individual's resistance or sensitivity to the effectiveness of certain drugs used in viral therapy (HIV or hepatitis C drugs, for example).
Tissue Typing for Transplantation
In the past, it was difficult to tell exactly whether an organ or tissue, such as a kidney, lung or bone marrow, was an exact match for the transplant between a donor and recipient. If it was not, a serious rejection reaction could sometimes occur between the recipient patient and the transplanted organ."
Basic laboratory testing for tissue transplantation involves mixing the white blood cells (leukocytes) from the donor (or the donor tissue) and the recipient together and observing whether an immune response occurs. Proliferation of a specific population of leukocytes signals the onset of an immune response and the likely rejection of the tissue by the recipient's body. Although this technique is still commonly used, analysis of the DNA in both the donor and the recipient (tissue typing) is used to diminish the likelihood of rejection in the case of tissue transplantation. In bone marrow transplants, DNA testing is done to determine whether the leukocytes and their precursors repopulating a recipient's bone marrow are his own or those of the donor.
A very specific set of genes is examined when DNA testing is used for tissue typing. On chromosome 6, a large set of genes called the "Major Histocompability Complex," or MHC, resides. These genes are very polymorphic (different) between individuals, and they code for the production of specific glycoprotein antigens located on the surface of many cells. It is these antigens that "recognize" our own organs and tissues from those of another individual. These antigens have the ability to begin an immune system response that results in organ or tissue rejection if the tissue looks foreign.
DNA is extracted from donor and recipient cells, then manipulated and fragmented in such a way as to isolate a specific region on a chromosome and within a gene. The fragments are subjected to further analysis that allows for comparison of the polymorphisms in the HLA-DP between the donor's tissue and the recipient's blood. This careful analysis of genetic material results in fewer rejection reactions and the chance for a successful transplant.
Infectious Disease Testing
Infectious diseases remain among the leading causes of death and disability worldwide. About 15 million (>25%) of 57 million annual deaths are estimated to be related directly to infectious diseases. Biomarkers, molecules that can be sensitively measured in the human body, are by definition potentially diagnostic. The efficacy of biomarkers to infectious diseases lies in their capability to provide early detection, establish highly specific diagnosis, determine accurate prognosis, direct molecular-based therapy and monitor disease progression. They are increasingly important in both therapeutic and diagnostic processes, with high potential to guide preventive interventions. The development of effective strategies for the assessment and control of infectious diseases requires a better understanding of pathogen biology, host immune response, and diseases pathogenesis as well as the identification of the associated biomarkers. Therefore, characterizing and identifying host and pathogen determinants of protection or progression to disease in exposed subjects are the necessary first steps toward disease control.
BDisease-causing bacteria and viruses are known as infectious agents, and some of them can be quickly identified by using genetic testing techniques; however, common infectious agents, such as certain bacteria and viruses, are much less expensive to identify using standard laboratory methods that don't involve genetic testing techniques.
Cardiovascular Disease Diagnosis/ Prognosis
Presently, the typical blood lipoprotein analysis (aimed at assessing cardiovascular risk) is confined to total cholesterol, low-density lipoprotein cholesterol (LDL or bad cholesterol), high-density lipoprotein cholesterol (HDL or good cholesterol), and triglycerides. The new lipid analyses, which health providers around the country can make available to patients through the Berkeley HeartLab, consists of the above series plus these six additional tests:
- LDL Particle Size
- Lp(a) -Elevated Lp(a) levels increase the risk of heart disease three-fold and are not detected in routine blood work.
- HDL Subclassification
- Apolipoprotein A-1- It may be a better predictor of heart disease risk than HDL levels.
- Apolipoprotein E — Apo E exists in normal and abnormal genetic forms. By identifying the form, this test indicates whether an individual is prone to develop excess blood lipids or has inherited an increased risk of heart disease independent of other know factors.
- Apolipoprotein B-100 — Apo B is a single protein attached to the LDL particle. This assay provides a more accurate indication of the relative number of LDL particles than does a standard LDL cholesterol blood test.
Anticoagulant Therapy Monitoring
- Warfarin (Coumadin®) is used for treatment of arterial and venous thrombosis to prevent clot propagation. Prevention of thromboembolic disease in thrombophilia, atrial fibrillation, mechanical heart valves, and high-risk surgery
- Standard Unfractionated Heparin (UFH) for treatment of arterial and venous thrombosis to prevent clot propagation.
- Heparin-induced Thrombocytopenia with Thrombosis (HIT) for prevention or treatment of thromboembolic disease
- Low Molecular Weight Heparin (LMWH)
- Fondaparinux (Arixtra®, pentasaccharide)
- Direct Thrombin Inhibitors (DTIs)
Test for CYP2C9 before initiating anticoagulant therapy in patients with atrial fibrillation is critical. We should also test for other risk factors predisposing to anticoagulant-related intracerebral haemorrhage (ICH), including the ApoE genotype, which is a marker for cerebral amyloid angiopathy, and, hence, increased risk of warfarin-related ICH. Our PCR-based assay is capable of measuring CYP2C9 levels for accurate anticoagulant therapy.
Lupus anticoagulant testing is used to help determine the cause of an unexplained thrombosis, recurrent fetal loss, or a prolonged Prothrombine Time (PTT) test. It is ordered to help determine whether a prolonged PTT is due to a specific inhibitor (an antibody against a specific coagulation factor) or to a nonspecific inhibitor like the lupus anticoagulant. It may be ordered along with anticardiolipin antibody and the anti-beta2-glycoprotein I assay to check for antiphospholipid syndrome. If someone tests positive for the lupus anticoagulant, the test may be done again in several weeks to see if the antibody was transient. Occasionally lupus anticoagulant testing may be ordered to help determine the cause of a positive VDRL/RPR test for syphilis (both anticardiolipin antibodies and lupus anticoagulant may produce a false positive result with these tests).
Because there are other inhibitors and analytical variables that can cause abnormal test results, several different tests are used to confirm the presence of a lupus anticoagulant. Typically these may include: PTT, prothrombin time (PT), dilute or modified Russell viper venom screen (dRVVT or MRVVT), and a hexagonal (II) phase phospholipid assay (Staclot-LA test) or kaolin clotting time. A thrombin time test may also be done to rule out heparin contamination (a drug used for anticoagulant therapy), and a fibrinogen test may be done to rule out abnormal deficiency in fibrinogen. These two conditions can cause prolongations in the test results and interfere with lupus anticoagulant detection.
Metabolic Disease Diagnosis/ Prognosis
Metabolic disorders are illnesses occur when the body is unable to process fats (lipids), proteins, sugars (carbohydrates), or nucleic acids properly. Most metabolic disorders are caused by genetic mutations that result in missing or dysfunctional enzymes that are needed for the cell to perform metabolic processes.
Most metabolic disorders are inherited, which means they are passed down through families. Examples of metabolic disorders include adrenoleukodystrophy (ALD), alkaptonuria, cystinosis, DIDMOAD syndrome (diabetes insipidus, diabetes mellitus, optic atrophy, and deafness syndrome), glucose 6-phosphage dehydrogenase (G6PD) deficiency, hyperornithinemia-hyperammonemia-homocitrullinuria (HHH), inborn errors of urea synthesis, Kearns-Sayre, maple syrup urine disease, McArdle's disease, MELAS (mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes) syndrome, metabolic syndrome, phenylketonuria (PKU), pyruvate carboxylase deficiency, subacute necrotizing encephalopathy, Tay-Sachs disease, and trimethylaminuria.
Clinical research-Biomarker identification and validation in pharmacology and Toxicology Biomarkers reduce the attrition rate of late-stage clinical trials by assessing drug potential in terms of efficacy and toxicity at the early stages of clinical development. Thus, biomarkers significantly increase productivity, lower the cost and duration of clinical trials, and help researchers complete the drug development process at a faster pace.
Preclinical Biomarker identification, validation and development : Scintilla also offers services in this important area of drug development.