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Principles of diagnostic sampling – the “ bead game” Pilot training school in PRRS diagnostics, 2012 Zagreb, Croatia Dr. Derald Holtkamp September 25, 2012 Iowa State University College of Veterinary Medicine Exercises 1. Detecting one or more positive pigs in an expected NEGATIVE population – Role of sample size and target prevalence 2. False positive test results in a truly negative population 3. Estimating Sensitivity (SE) & Specificity (SP) by testing "known status" samples (if time permits) Iowa State University College of Veterinary Medicine Exercises 1. Detecting one or more positive pigs in an expected NEGATIVE population – Role of sample size and target prevalence 2. False positive test results in a truly negative population 3. Estimating Sensitivity (SE) & Specificity (SP) by testing "known status" samples Iowa State University College of Veterinary Medicine What you need to know to determine the sample size needed to find at least one positive animal in a herd 1. Target prevalence (TP) 2. Confidence level (CL) 3. Population size (PS) Sample size needed = f(TP, CL, PS) – Cannon RM, Roe RT. Livestock disease surveys: A field manual for veterinarians. AGPS, Canberra, 1982. Iowa State University College of Veterinary Medicine Table of sample sizes needed based on Cannon and Roe Population Size (Detecting One or More Positives) Prevalence Confidence Estimate Level >1% 70% 80% 90% 95% 99% >10% 70% 80% 90% 95% 99% >25% 70% 80% 90% 95% 99% >50% 70% 80% 90% 95% 99% 100 71 81 91 96 100 12 16 21 26 37 6 7 9 11 16 3 4 5 6 8 Iowa State University College of Veterinary Medicine 1000 114 149 206 259 369 13 17 23 30 44 6 7 10 12 17 3 4 5 6 8 4000 120 158 224 289 434 13 17 23 30 45 6 7 10 12 18 3 4 5 6 8 10000 121 160 228 295 449 13 17 23 30 45 6 7 10 12 18 3 4 5 6 8 Exercises 1. Detecting one or more positive pigs in an expected NEGATIVE population – Role of sample size and target prevalence 2. False positive test results in a truly negative population 3. Estimating Sensitivity (SE) & Specificity (SP) by testing "known status" samples Iowa State University College of Veterinary Medicine Slide courtesy of D. Polson Iowa State University College of Veterinary Medicine Exercises 1. Detecting one or more positive pigs in an expected NEGATIVE population – Role of sample size and target prevalence 2. False positive test results in a truly negative population 3. Estimating Sensitivity (SE) & Specificity (SP) by testing "known status" samples Iowa State University College of Veterinary Medicine Properties and Definitions of Diagnostic Tests Test Positive Test Negative TRUE Positive TRUE Negative a (true positive) c (false negative) b (false positive) d (true negative) Sensitivity = a / ( a + c ) False Negatives = c / ( a + c ) Specificity = d / ( b + d ) False Positives = b / ( b + d ) Positive Predictive Value = a / ( a + b ) Negative Predictive Value = d / ( c + d ) Accuracy = ( a + d ) / ( a + b + c + d ) True Prevalence = ( a + c ) / ( a + b + c + d ) Assay Prevalence = ( a + b ) / ( a + b + c + d ) Prevalence Estimate = a / ( a + b + c + d ) Likelihood Ratio of a Positive Test = Sensitivity / ( 1 - Specificity ) Likelihood Ratio of a Negative Test = ( 1 - Sensitivity ) / Specificity Sensitivity is the percent of TRUE positives that are TEST positives. Specificity is the percent of TRUE negatives that are TEST negatives. False Positive Rate is the percent of FALSE positives that are TEST positives. False Negative Rate is the percent of FALSE negatives that are TEST negatives. Positive predictive value (PPV) is the probability of a test positive being a true positive. Negative predictive value (NPV) is the probability of a test negative being a true negative. Accuracy is the percent of all test results that agree with the true status of the sample. True Prevalence is the percent of all samples that are true positives. Prevalence Estimate is the percent of all samples that are tested positive. Likelihood Ratio of a Positive Test is the odds of a positive test result in a true positive sample. Likelihood Ratio of a Negative Test is the odds of a negative test result in a true negative sample. Sensitivity and specificity are absolute properties of a test. PPV and NPV are relative, and vary depending on the true prevalence of positive samples. As the prevalence decreases, PPV decreases and NPV increases. Iowa State University College of Veterinary Medicine Acknowledgements • Dale Polson, Boehringer Ingelheim Vetmedica Inc., U.S Iowa State University College of Veterinary Medicine