CRUSH COURSE YEAR 3 Semester 1 WORK (Part 1) OmpathStudy

COMPREHENSIVE NOTES — Clinical Chemistry & Cytopathology/Histopathology Source: Dr Lilian Bosire, MKU Lecturer, Pathologist Structure: 3 Sections covering the full 565-page document --- --- SECTION 1: Clinical Chemistry — Fundamentals, Laboratory Tests & Analytical Techniques (Pages 1–83) --- 1. Introduction to Clinical Chemistry Definition: The study of chemical processes and substances in the body — analysing blood, urine, and other fluids to assess health, diagnose disease, and monitor treatment. Key analytical techniques: Spectrophotometry, chromatography, immunoassays, electrophoresis, molecular diagnostics. Key areas of analysis: Blood glucose, cholesterol, kidney function (creatinine, urea), liver function (AST, ALT), electrolytes (Na⁺, K⁺), hormones (thyroid, cortisol), tumour markers. --- 2. Routine Chemistry Panels Panel Key Components Purpose --- --- --- BMP (Basic Metabolic Panel) Glucose, electrolytes, creatinine, BUN, calcium Electrolyte balance, kidney function, acid-base status CMP (Comprehensive Metabolic Panel) BMP + AST, ALT, ALP, bilirubin, total protein, albumin Liver + kidney function, protein status LFTs AST, ALT, ALP, bilirubin (total/direct/indirect), albumin, GGT Liver function, hepatobiliary disease, jaundice Lipid Profile Total cholesterol, LDL, HDL, triglycerides Cardiovascular risk, lipid disorders Thyroid Panel TSH, T4, T3 ± thyroid antibodies Thyroid function, hypo/hyperthyroidism Renal Panel Creatinine, BUN, eGFR ± electrolytes Kidney function, CKD, AKI Electrolyte Panel Na⁺, K⁺, Cl⁻, HCO₃⁻ ± Ca²⁺, Mg²⁺, PO₄³⁻ Electrolyte balance, acid-base disorders --- 3. Specialised Chemistry Tests Hormone Assays Thyroid: TSH, T4, T3 Reproductive: Oestrogen, progesterone, testosterone Adrenal: Cortisol, aldosterone Pituitary: GH, prolactin Purpose: Diagnose endocrine disorders, hormonal imbalances, reproductive issues, monitor HRT Tumour Markers Marker Cancer --- --- PSA Prostate CA-125 Ovarian CA 15-3 Breast AFP Liver/testicular CEA Colorectal CA 19-9 Pancreatic Cardiac Markers Troponin (cTnI, cTnT): Gold standard for myocardial infarction CK-MB: Creatine kinase-MB, cardiac muscle damage Myoglobin: Early but non-specific marker BNP: B-type natriuretic peptide — heart failure severity Other Specialised Markers Autoimmune: ANA, anti-dsDNA, RF, anti-CCP, ANCA — diagnose lupus, RA, vasculitis Infectious disease: HIV antibodies, HBsAg, anti-HCV, VDRL/RPR Allergy/Immunology: Total IgE, specific IgE, allergen panels Genetic/Molecular: PCR, FISH, gene sequencing — diagnose genetic disorders, personalise treatment --- 4. Clinical Utility of Biochemical Tests 1. Diagnosis — Blood glucose → diabetes; creatinine/BUN → kidney disease; ALT/AST → liver damage; lipid panel → hyperlipidaemia 2. Monitoring disease progression — HbA1c (long-term glucose), serial eGFR (CKD), PSA (prostate cancer), BNP (heart failure) 3. Screening — Lipid panels (cardiovascular risk), liver enzymes (asymptomatic patients), metabolic syndrome 4. Risk assessment — Cholesterol for CVD, coagulation tests pre-surgery 5. Preoperative/postoperative — Baseline organ function before surgery 6. Emergency — Troponin for MI, blood gases for respiratory failure, lactate for sepsis --- 5. Specimen Collection & Handling Types of Specimens Blood: Serum (clotted), plasma (anticoagulated), whole blood Urine: Random, first-void, 24-hour collection Other: CSF, sputum, stool, synovial fluid Key Principles of Handling Collection: Correct tube type (e.g., SST, EDTA, heparin), proper order of draw, minimize haemolysis Transport: Timely delivery, maintain temperature (refrigerate if needed, freeze for long storage) Storage: Stability varies — some analytes degrade quickly (e.g., ammonia, lactate) Pre-analytical errors are the most common source of lab errors — lipemia, haemolysis, improper labelling --- 6. Analytical Techniques Technique Principle Applications --- --- --- Spectrophotometry Measures light absorption Glucose, bilirubin, haemoglobin Chromatography Separates components by physical/chemical properties Drug levels, amino acids, hormones Electrophoresis Separates by charge/size in electric field Protein fractions, haemoglobin variants Mass Spectrometry Measures mass-to-charge ratio Toxicology, newborn screening Immunoassays Antigen-antibody reaction Hormones, drugs, tumour markers Electrochemical Measures electrical properties Electrolytes (ISE), blood gases --- 7. Automation in the Lab Key principles: speed, precision/accuracy, integration (with LIS), quality control, cost efficiency, scalability. Autoanalysers process many samples simultaneously with built-in QC checks --- 8. Basic Statistics in Clinical Chemistry Accuracy: How close to the true value Precision: How reproducible the result is (low CV%) Sensitivity: Ability to correctly identify disease (true positives) Specificity: Ability to correctly identify absence of disease (true negatives) Disease prevalence affects positive predictive value (PPV) — high prevalence → higher PPV fo