Clinical Chemistry Case Study (7103406) PDF

Clinical Chemistry Case Study (7103406, 2CHs) Introduction Introduction to the course Concept of health and disease Health Disease; Etiology, Pathogenesis, Morphology and Histology, Clinical Manifestations, Diagnosis, and Clinical Course Introduction to the course...

Clinical Chemistry Case Study (7103406, 2CHs) Introduction Introduction to the course Concept of health and disease Health Disease; Etiology, Pathogenesis, Morphology and Histology, Clinical Manifestations, Diagnosis, and Clinical Course Introduction to the course COURSE DESCRIPTION This course discusses the biochemical and molecular basis of some human diseases in a case-study approach. The clinical findings and the diagnostic investigations of the selected cases will be presented in addition to a thorough discussion of the underlying pathophysiological process. The diagnostic and therapeutic approaches undertaken by the authors of the presented cases, especially the clinical chemistry laboratory investigations, will Introduction to the course Teaching Week Topic Hours 1st and 2nd Introduction to the course week Concept of health and disease  Health  Disease; Etiology, Pathogenesis, Morphology and Histology, Clinical Manifestations, Diagnosis, and Clinical Course The clinical chemistry laboratory 4 hours  Organization of the laboratory, different stages of analysis, and specialized laboratory procedures.  Test parameters  Specificity, sensitivity, positive predictive value, negative predictive, and the efficiency of the test. 3 , 4 and  rd th History and Examination: General 5 weeks  th Cardiovascular history and examination  Cardiac markers and a case study titled “Cardiac Troponin: Clinical Role in the 6 hours Diagnosis of Myocardial Infarction”  We may start with the next topic  A self study case 1st hour exam Introduction to the course Teaching Week Topic Hours 6th and 7th  Lipoprotein metabolism and a case study on: weeks  “Low-Density Lipoprotein Receptors and Familial Hypercholesterolemia”  A case study on “Abetalipoproteinemia” 4 hours  A case study on “Tangier disease: A disorder in the reverse cholesterol transport pathway” 8th week Serum protein electrophoresis Respiratory system History and Examination 2 hours A case study on “a1-antitrypsin deficiency” 9th and 10th  GI history and physical examination 4 hours week  Bilirubin metabolism and a case study on “Neonatal Hyperbilirubinemia”  A self study case 2nd hour exam 1 hour  Introduction to the course Teaching Week Topic Hours 11th and  CBC and Anemias 12 weeks  th b thalassemia, Iron deficiency anemia, A case study titled “G6PD Deficiency and 4 hours (+/-) Oxidative Hemolysis” (+/-)  A case study titled “sickle cell anemia” 13 week  th Genitourinary history and examination 2 hours  Diabetes mellitus and a case study on “Type I Diabetes Mellitus” 14 and th  Neonatal examination 15 week  th A case study on “Pyruvate Dehydrogenase Complex Deficiency” 2 hours  A case study on “Neonatal Hypoglycemia and the Importance of Gluconeogenesis” 16 week Final exam (2 hours) th 2 hours Concept of Health WHO (1948) defined health as a “state of complete physical, mental, and social well-being and not merely the absence of disease and infirmity,” a definition that has not been amended since that time. Concept of Disease A disease is considered an acute or chronic illness that one acquires or is born with that causes physiological dysfunction in one or more body system. Each disease generally has specific signs and symptoms that characterize its pathology and identifiable etiology. The aspects of the disease process include etiology, pathogenesis, morphologic changes, clinical manifestations, diagnosis, and clinical course. Etiology The causes of disease are known as etiologic factors. Among the recognized etiologic agents are: 1. biologic agents (e.g., bacteria, viruses) 2. physical forces (e.g., trauma, burns, radiation), 3. chemical agents (e.g., poisons, alcohol) 4. one’s genetic inheritance, Etiology Most disease-causing agents are nonspecific, and many different agents can cause disease of a single organ. On the other hand, a single agent or traumatic event can lead to disease of a number of organs or systems (i.e., produces widespread pathology) For example, cystic fibrosis, defective transporter molecule sickle cell anemia: a single amino acid resulting in a defective protein familial hypercholesterolemia: a defective Etiology Most disease states do not have a single cause. Instead, the majority of diseases are multifactorial in origin. This is particularly true of diseases such as cancer, heart disease, and diabetes. The multiple factors that predispose to a particular disease often are referred to as risk factors. The five causes of cancer and the pathophysiology that evolves from the disease mechanisms triggered by Etiology Etiologic factors that cause disease can be grouped into categories according to whether they were present at birth or acquired later in life. Congenital conditions are defects that are present at birth, although they may not be evident until later in life or may never manifest. Congenital conditions may be caused by genetic influences, environmental factors (e.g., viral infections in the mother, maternal drug use, irradiation, or Etiology Genetic disease: a genetic disorder or disease is caused by one or more genetic mutations. It is often inherited, but some mutations are random and de novo. Hereditary or inherited disease: is a type of genetic disease caused by genetic mutations that are hereditary (and can run in families) Etiology Acquired defects are those that are caused by events that occur after birth. These include injury, exposure to infectious agents, inadequate nutrition, lack of oxygen, inappropriate immune responses, and neoplasia. Many diseases are thought to be the result of a genetic predisposition and an environmental event or events that serve as a trigger to initiate disease development. Etiology Iatrogenic disease: is a disease that is caused by medical intervention, whether as a side effect of a treatment or as an inadvertent outcome. Idiopathic disease: an idiopathic disease has an unknown cause or source. Etiology Primary disease: a disease that is due to a root cause of illness, as opposed to secondary disease, which is a sequela, or complication that is caused by the primary disease. A secondary disease is a disease that is a sequela or complication of a prior, causal disease, which is referred to as the primary disease or simply the underlying cause (root cause) Etiology For example, a bacterial infection can be primary, wherein a healthy person is exposed to a bacteria and becomes infected, or it can be secondary to a primary cause, that predisposes the body to infection. For example, a primary viral infection that weakens the immune system could lead to a secondary bacterial infection. Similarly, a primary burn that creates an open wound could provide an entry point for bacteria, and lead to a secondary Pathogenesis Pathogenesis: the sequence of cellular and tissue events that take place from the time of initial contact with an etiologic agent until the ultimate expression of a disease. Pathogenesis explains how the disease process evolves. Pathogenesis Although etiology and pathogenesis are two terms often used interchangeably, their meanings are quite different. For example, atherosclerosis often is cited as the etiology (or cause) of coronary artery disease. In reality, the progression of the inflammatory process from a fatty streak to the occlusive vessel lesion seen in people with coronary artery disease represents the pathogenesis of the disorder. The true etiology of atherosclerosis remains Morphology Morphology refers to the fundamental structure or form of cells or tissues. Morphologic changes are concerned with both the gross anatomic and microscopic changes that are characteristic of a disease. A lesion represents a pathologic or traumatic discontinuity of a body organ or tissue. Morphology Descriptions of lesion size and characteristics often can be obtained through the use of radiographs, ultrasonography, and other imaging methods. Lesions also may be sampled by biopsy and the tissue samples subjected to histologic study. Clinical Manifestations Diseases can manifest in a number of ways. Sometimes the condition produces manifestations, such as fever, that make it evident that the person is sick. In other cases, the condition is silent at the onset and is detected during examination for other purposes or after the disease is far advanced. Signs and symptoms are terms used to describe the structural and functional changes that accompany a disease. Clinical Manifestations A symptom is a subjective complaint that is noted by the person with a disorder, Pain, difficulty in breathing, and dizziness are symptoms of a disease. A sign is a manifestation that is noted by an observer. An elevated temperature, a swollen extremity, and changes in pupil size are objective signs that can be observed by someone other than the person with the disease. Clinical Manifestations Signs and symptoms may be related to: the primary disorder: example jaundice in liver disease, or they may represent the body’s attempt to compensate for the altered function caused by the pathologic condition (example kussmaul’s respirations in DKA). Clinical Manifestations Many pathologic states are not observed directly. For example, one cannot see that a person that has decreased pulmonary gas exchange. Instead, what can be observed is the body’s attempt to compensate for changes in function brought about by the disease, such as the increased respiratory rate that occurs with pneumonia. Another example the examiner can’t usually observe upper GI hemorrhage in his patient but he may observe tachycardia as a sign of compensation for Clinical Manifestations A syndrome is a compilation of signs and symptoms (e.g., Cushing’s syndrome) that are characteristic of a specific disease state. Complications are possible adverse extensions of a disease or outcomes from treatment. Clinical Course The clinical course describes the evolution of a disease. A disease can have an acute, subacute, or chronic course. An acute disorder is one that is relatively severe, but self-limiting. Chronic disease implies a continuous, long-term process. A chronic disease can run a continuous course or can present with exacerbations (aggravation of symptoms and severity Clinical Course Subacute disease is intermediate or between acute and chronic. It is not as severe as an acute disease and not as prolonged as a chronic disease. Clinical disease is manifested by signs and symptoms. Subclinical disease is not clinically apparent and is not destined to become clinically apparent. It is diagnosed with antibody or culture tests. Most cases of tuberculosis are not clinically apparent, and evidence of Clinical Course The preclinical stage of a disease, the disease is not clinically evident but is destined to progress to clinical disease. Example: Prediabetes, prehypertension Hepatitis B: possible to transmit a virus during the preclinical stage of hepatitis B infection. A persistent chronic infectious disease persists for years, sometimes for life. Clinical Course Carrier status refers to a person who harbors an organism but is not infected, as evidenced by antibody response or clinical manifestations. This person still can infect others. Carrier status may be of limited duration or it may be chronic, lasting for months or years. Diagnosis A diagnosis is the designation as to the nature or cause of a health problem (e.g., bacterial pneumonia or hemorrhagic stroke). The diagnostic process requires: 1. careful history, used to obtain a person’s account of his or her symptoms and their progression, and the factors that contribute to a diagnosis. 2. careful physical examination, done to observe for signs of altered Diagnosis 3. diagnostic tests: which are ordered to: validate what is thought to be the problem to determine other possible health problems that were not obtained from the history and physical examination, but may be present given the signs and symptoms identified. Diagnostic tests and test parameters will be discussed further in next lecture Diagnosis The development of a diagnosis involves weighing competing possibilities and selecting the most likely one from among the conditions that might be responsible for the person’s clinical presentation. The clinical probability of a given disease in a person of a given age, gender, race, lifestyle, genetic background, and locality often is influential in arrival at a presumptive diagnosis. Laboratory tests and imaging are used to confirm a diagnosis.  Clinical Chemistry Case Study (7103406, 2CHs) Clinical Chemistry laboratory and test performance parameters Introduction A laboratory is a facility that provides controlled conditions in which scientific or technological research experiments, and measurement can be performed. A medical laboratory or clinical laboratory is a laboratory where tests are done on clinical specimens in order to get information about the health of a patient with regard to the diagnosis, treatment, and prevention of disease. What Is Clinical laboratory test?? Clinical laboratory tests are medical procedures that involve testing and analyzing a sample of blood, urine, or other substance from the body. The information provided by those tests is then used by the medical team to make decisions regarding a patient's medical care. 85% of all medical decisions are based on the results of clinical laboratory testing. Reasons for Ordering a Laboratory Test There are 4 major legitimate reasons for ordering a laboratory test: Screening (eg, for congenital hypothyroidism via neonatal thyroxine testing). Diagnosis (to rule in or rule out a diagnosis). Monitoring (eg, the effect of drug therapy). Research (to understand the pathophysiology of a particular disease process). The place of clinical biochemist ry in medicine Diagnosis of any disease is done by a physician who collects information from the patient history and clinical examination and then confirms the diagnosis by other diagnostic The clinical biochemistry repertoire Core biochemistry: common and frequently requested tests Specialized tests: less common tests, sometimes for rare diseases, large labs as referral centers Types of samples that are used in testing Types of samples that are used in testing: Body fluids: blood, serum, plasma, urine, cerebrospinal fluid (CSF), feces, and other body fluids or tissues. Clinical biochemical tests comprise over one third of all hospital laboratory investigations. Test request priorities Lab tests should be ordered according to the critical need for the result based on the patient’s clinical condition. Following these guidelines will ensure that lab tests are available to each individual according to their needs. Test request priorities STAT: Collect and process results immediately after order received. Reserved for those situations of life- threatening (life and limb) medical emergency Priority must be determined by the attending physician STAT orders will be given priority over all other test requests Results will be available within 60 minutes of ordering Test request priorities Urgent: (ASAP – (As Soon As Possible)) Collection as soon as possible after order received. Requests are processed as soon as possible upon receipt of the order in the lab Results will be available within 3 hours of ordering does not have to be done immediately and requires that laboratory personnel hasten its completion, but NOT to the Test request priorities Timed: Collect at time indicated (at a specific time). This specimen will be collected at the time indicated and analyzed with the next routine batch (unless ordered STAT). This type of procedure is one used to monitor treatment or therapy at timed intervals. Test request priorities Routine: Collect at regular collection times. Orders without any indication of priority No collection time is required Inpatient specimens will be collected during a regular collection round Most results will be available within 8-24 hours of receipt of the specimen in the lab Laboratory testing cycle: The Laboratory testing cycle includes the entire steps of laboratory test, starting from test ordering by a doctor until reporting the results. Three phases of laboratory testing: Pre-analytical: test ordering, specimen collection, transport and processing Analytical: specimen analysis and testing in the lab Post-analytical: testing results transmission, interpretation, follow-up, retesting. Errors can occur at age stage of the laboratory cycle Types and Rates of Error in the 3 Stages of the Laboratory Testing Process Pre-analytical: inappropriate test request, entry errors, patient misidentification, inappropriate container, insufficient sample volume, transport mistakes. Analytical: equipment malfunction, sample mix-ups, interference, quality control failures, incorrect procedures Post-analytical: reporting failure, mistakes in data validation, improper data entry Specimen collection Blood specimens: Blood is the bridge between patient and laboratory. One of three different blood specimens may be used: whole blood serum plasma Whole-blood specimen: Must be analyzed within limited time: Over time, cells will lyse in whole-blood which will change the conc. of some analytes as potassium, phosphate and lactate dehydrogenase. Also, some cellular metabolic processes will continuo which will alter Blood specimens: Serum: If blood is collected into a plain tube and allowed to clot, after centrifugation a serum specimen is obtained For many biochemical analyses this will be the specimen recommended Blood specimens: Plasma: If blood is collected into a tube that have an anti- coagulant then centrifuged, a plasma specimen is obtained Difference between Serum and plasma Serum is the same as plasma except it doesn't contain clotting factors (as fibrin). Plasma contains all clotting factors. So, serum and plasma all has the same contents of electrolytes, enzymes proteins, hormones except clotting factors Serum is mainly use in chemistry lab & serology.  Blood collection tubes: Two major types of blood collecting tubes: 1. Serum separating tubes (SST) Top Color Additives Principle Uses Red containing a clot Enhancing the formation of Serology activator but no blood clot -Antibodies anticoagulants, -Hormones preservatives, or -Drugs separator material Virology Chemistry Gold clot activator and Serum separating from the Serology serum gel separator blood through the gel in Chemistry the tube  Blood collection tubes: Two major types of blood collecting tubes: 2. Plasma separating tubes (PST) examples Top Additives Principle Uses Color Lavender EDTA - The strongest anti- - Hematology coagulant - Blood bank (ABO) - Ca+2 chelating agent - CBC - To preserve blood cells - HbA1C components Light Blue Sodium Ca+2 chelating agent - PT: Prothrombin Citrate Time - PTT: Partial Thromboplastin Time Green Sodium Heparin binds to Thrombin Enzymes Heparin or and inhibits the second Hormones Lithium step in the coagulation Electrolytes (Na+, K+, Heparin cascade Mg+, Cl- Gray -Sodium Glycolysis inhibitor Glucose, lactate, Blood sampling errors Errors that arise when the clinician first obtains specimens from the patient. Prolonged stasis during venipuncture. Plasma water diffuses into the interstitial space and the serum or plasma sample obtained will be concentrated. Proteins and protein-bound components of plasma, such as calcium or thyroxine, will be falsely elevated. Blood sampling technique. Needle too small, pulling too hard on plunger of syringe or expelling blood vigorously into a tube may lead to hemolysis with consequent release of potassium and other red cell constituents. Blood sampling errors Insufficient specimen. It may prove to be impossible for the laboratory to measure everything requested on a small volume. Inappropriate sampling site. Blood samples should not be taken ‘downstream’ from an intravenous drip. It is not unheard of for the laboratory to receive a blood glucose request on a specimen taken from the same arm into which 5% glucose is being infused. Usually the results are biochemically incredible but it is just possible that they may be acted upon with Blood sampling errors Incorrect specimen container. the blood must be collected into a container with right content (anticoagulant and/or preservative). For example, samples for glucose should be collected into container containing fluoride, which inhibits glycolysis; blood that has been exposed, even briefly, to EDTA will have a markedly reduced calcium concentration, approaching zero, along with an artefactually high K+ concentration. (EDTA chelates Ca2+and is present as its K+ salt. Urine specimens Urine specimen containers may include a preservative to inhibit bacterial growth, or acid to stabilize certain metabolites. They need to be large enough to hold a full 24-hour collection. Random urine samples are collected into small ‘universal’ containers. Other specimen types For some tests, specific body fluids or tissue may be required. There will be specific protocols for the handling and transport of these samples to the laboratory. Consult the local lab for advice Performance of a test Performance of a test In biomedical studies, diagnostic tests are used to determine the presence or absence of diseases in study subjects. For example testing for invasive carcinoma. A diagnostic test is validated by comparing test results against a gold standard that establishes the true status of the subject. Test validation is an evaluation method used to determine the fitness of a test for a particular use and through it, one can Performance of a test Validation involves calculating four objective measures of test performance, namely, sensitivity (Se), specificity (Sp), positive predictive value (PPV) and negative predictive value (NPV). These calculations gives us an answer to the following question: "How well this test discriminates between certain two conditions of interest (health and disease; two stages of a disease etc.)?". The ideal diagnostic test would correctly Performance of a test Calculations of the test performance parameters are based on a four-fold table, where a set of individuals is divided into a group of healthy and diseased individuals based on a definitive method (gold standard), and the individuals have been examined by the tested laboratory test. A gold standard test: The test or procedure necessary to definitively establish to a high level of certainty the presence or absence of a particular Performance of a test The test outcome can be positive (classifying the person as having the disease) or negative (classifying the person as not having the disease). The test results for each subject may or may not match the subject's actual status determined by the gold standard. Performance of a test Depending on the laboratory test result, the individuals can be divided into 4 groups: True positive (TP): Sick people correctly identified as sick False positive (FP): Healthy people incorrectly identified as sick True negative (TN): Healthy people correctly identified as healthy False negative (FN): Sick people incorrectly identified as healthy  Confirme d by the In other words gold standard Actual disease Sickstatus Healthy + TP FP Test result - FN TN Sensitivity of a test Ability of a test to identify correctly affected individuals proportion of people testing positive among affected individuals (i.e true positive rate) Actual disease status Sensitivity (Se) = TP / Sick Healthy ( TP + FN ) + TP FP Test result - FN TN Specificity of a test Ability of test to identify correctly non- affected individuals proportion of people testing negative among non-affected individuals ((i.e true negative rate) Actual disease status Specificity (Sp) = TN / Sick Healthy ( TN + FP ) + TP FP Test result - FN TN Performance of Fecal Occult Blood* (FOT) test in colon cancer (imaginary numbers) Colon cancer (confirmed by biopsy) + - Total FOB + 350 1900 2250 test - 150 7600 7750 Total 500 9500 10000 Sensitivity = 350 / 500 = 0.7= 70 % Specificity = 7600 / 9500 =0.8 = 80 % *Fecal occult blood (FOB) refers to blood in the feces that is not visibly apparent (unlike other types of blood in stool such as melena or hematochezia). A fecal occult blood test (FOBT) checks Data interpretation The previous data means that: FOB test establishes the diagnosis in 70% of the sick individuals (Se = 70%, Error = 30%). FOB test rules out the disease in 80% of the healthy individuals (Sp = 80%, Error = 20%).  Positive and Negative Predictive Values Positive predictive value (PPV) The proportion of patients with positive test results that actually have the disease to the total individuals who tested positive PPV = TP/ (TP + FP) Negative predictive value (NPV) The proportion of individuals with negative test results and actually are free of the disease to the total individuals who tested negative NPP = TN / (TN + FN)  Positive and Negative Predictive Values PPV and NPV are affected by the Prevalence of the disease Prevalence1 is the proportion of persons in a population who have a particular disease at a specified point in time or over a specified period of time. X 100 % Prv = Persons with the disease Total population 1 Prevalence differs from Incidence which refers to the occurrence of new cases of disease or injury in a population over a specified period of time. Although some epidemiologists use incidence to mean the number of new cases in a community, others use incidence to mean the number of new cases per unit of population.  Positive and Negative Predictive Values The sensitivity and specificity are properties of the test. The positive and negative predictive values are properties of both the test and the population you test. If you use a test in two populations with different disease prevalence, the predictive values will be different. PPV and NPV calculation (Community A) Se = 70 % Colon CA Sp = 80 % Prv= 5 % + - Total + 350 1900 2250 FOBT - 150 7600 7750 Total 500 9500 10000 PPV = TP/ (TP + FP) = 350 / 2250 = 0.156= 15.6 % NPV = TN / (TN + FN) = 7600 / 7750 =0.8 = 98.1 % PPV and NPV calculation (Community B) Se = 70 % Colon CA Sp = 80 % Prv= 10 % + - Total + 700 1800 2500 FOBT - 300 7200 7500 Total 1000 9000 10000 PPV = TP/ (TP + FP) = 700 / 2500 = 0.28 = 28 % NPV = TN / (TN + FN) = 7200 / 7500 =0.96 = 96 % When thinking about predictive value of a test…. Understanding Predictive Value A high PPV indicates a strong chance that a person with a positive test has the disease whereas a low PPV is usually found in populations with low prevalence of the condition being examined. A high NPV means that a negative test in effect rules out the disease. Another example: HIV in low risk population ELISA is about 90% sensitive and 99% specific Population HIV New Jersey + - Total (≈ 7 + 94,500 68,950 163,450 ELIS million) A 6,826,0 6,836,55 - 10,500 50 0 Prevalence of 105,00 HIV = 6,895,00 7,000,0 Total PPV = 1.5% 0 0 00 NPP 57.8% = 99.8% But, 10,500 people who are HIV+ think they are disease free Another 68,950 are frightened into believing they If you change to a higher risk population, you get better predictions…. Population HIV IV Drug + - Total Users ELIS + 3,150 35 3,185 A - 350 3,465 3,815 Total 3,500 3,500 7,000 Prevalence of HIV PPV = 50%= 98.9 NPP =90.8% Now 350 people who are HIV+ think they are disease free But only 35 are frightened into believing they have the disease and require more testing Suppose the disease has a Very High Prevalence? HIV seropositivity is 90% (i.e. prevalence) among IV drug users in a state prison. Calculations of PPV and NPV using the same ELISA test (Se = 90%, Sp = 99 %) shows: PPV= 99.9% NPV = 52% Why bother to screen?! Just go for definitive diagnostic tests (i.e. gold standard, in this case Western blot assay for the detection of antibodies to human HIV1 Effect of population prevalence on the values of positive and negative predictive values, using a test with a sensitivity and specificity of 85%. How to remember? PPV: “I just got a positive test result back on my patient. What is the chance that my patient actually has the disease?” NPV: “I just got a negative test result back on my patient. What is the chance that my patient actually doesn't have the disease?”