Matthew Scotch, PhD, MPH

Decision Analysis
BMI 201

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Diagnostic Problem
Patient presents with symptoms and is
suspected of having a disease.
Physician orders a diagnostic test to
assist in making a diagnosis.
Test result is either positive (indicating
disease) or negative (indicating no
disease).
In truth, the patient either has the disease
or does not have the disease.
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2 X 2 tables
To characterize (and/or evaluate) a
diagnostic (or screening) test, we use a 2
X 2 table

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Definitions
True Positive (TP): Diseased person
correctly receives a positive test result.
False Positive (FP): Non-diseased person
incorrectly receives a positive test result.
True Negative (TN): Non-diseased person
correctly receives a negative test result.
False Negative (FN): Diseased person
incorrectly receives a negative test result.
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2 x 2 Table
TRUTH
Disease

TRUTH
No Disease

Test
Positive

True
Positive

False
Positive

Test
Negative

False
True
Negative Negative

Total

Total

Grand
Total
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2 x 2 Table
Test for Hyperparathyroidism

TRUTH
Disease

TRUTH
No Disease

Total

Test
Positive

90

95

Test
Negative

10

895

905

100

900

1000

Total

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Definitions
Sensitivity: Proportion of those with true
disease who test positive.
Specificity: Proportion of those who truly do not
have disease who test negative.
NOTE: Sensitivity and specificity are also often
expressed as a percentage and not a proportion;
proportion is preferred; to convert a percentage to a
proportion, divide by 100
82% = 0.82

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 Positive Predictive Value (PPV)

Probability that disease exists given that the test is
positive
PPV = P (D+ | T+)
Negative Predictive Value (NPV)
Probability that disease does not exist given that the
test is negative
NPV = P (D- | T-)
Prevalence
Rate of true disease in the group being tested
Prevalence = P (disease+)
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Calculating Sensitivity and

Specificity
TRUTH

Test
Result

Disease

No
Disease

Positive

a+b

Negative

c+d

a+c

b+d

a+b+c+d

Total

Total

a / (a + c) d / (b +d)
sensitivity specificity
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Calculating Sensitivity and

Specificity

Sens = TP/TP + FN
Spec = TN/TN+FP

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Test for Hyperparathyroidism

TRUTH
Hyperparathyroidism

TRUTH
No
Hyperparathyroidism

Total

Test
Positive

90

95

Test
Negative

10

895

905

100

900

1000

Total

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Example
Hyperparathyroidism
TRUTH
Disease

Test
Result

No Disease

Total

Pos

90

a+b

Neg

10

895

c+d

Total

100

900

a+b+c+d

a / (a + c)

d / (b +d)

90/100 = .90

895/900 = .994

Sensitivity

Specificity
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Predictive Values
Predictive values help in deciding whether
to believe the results for an individual
patient

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Predictive Values
Positive Predictive Value (PPV):
Likelihood that the patient has the disease
if the test is positive
PPV = TP/TP+FP

Negative Predictive Value (NPV):

Likelihood that the patient does not have
the disease if the test is negative
NPV = TN/TN+FN
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2 x 2 Table
Sensitivity and Specificity
TRUTH
Disease

TRUTH
No Disease

Test
Positive

True
Positive

False
Positive

Test
Negative

False
True
Negative Negative

Total

Grand
Total

Total
Sensitivity

Specificity
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2 x 2 Table
Positive and Negative Predictive Values
TRUTH
Disease

TRUTH
No Disease

Test
Positive

True
Positive

False
Positive

Test
Negative

False
True
Negative Negative

Total

Total
PPV

NPV

Grand
Total
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Example
Hyperparathyroidism
TRUTH
Hyperparathyroidism

Test Positive
Result
Negative
Total

90

No
Hyperparathyroidism

Total
95

90 / 95 = .
957
PPV

10
100

895
900

905
1000

895 / 905 = .
989
NPV

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Using Predictive Values

Critical to the interpretation of test results
Sensitivity and specificity are inherent
characteristics of the test and are constant
Positive and Negative Predictive Values
are affected by the context and the
characteristics of the person being tested
(More on this point later in this lecture)

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PPV and Prevalence

The lower the prevalence, the lower the
PPV and the higher the NPV
Low Prevalence = Higher FP
Screening for a rare disease:
Most will be classified as FPs (b) or TN (d)

What is impact on high FPR?

Content from Dubrow, R. CDE 508A: Principles of Epidemiology I.
Yale University. 2007

To individual?
To healthcare system?

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NPV and Prevalence

The higher the prevalence, the higher the
PPV and the lower the NPV
Higher FNs
People remain undetected and can spread
disease

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Bayes Theorem
Quantitative method for calculating
post-test probability using:
Pretest probability
Sensitivity of test
Specificity of test

Derived from definition of conditional

probability and from properties of
probability

Source: Shortliffe EH, Perreault LE. Medical Informatics: Computer Applications in Health Care and Biomedicine. 2 nd Edition.
Springer-Verlag. 2001

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Bayes Theorem
Conditional probability is the
probability that event A will occur
p AB
given event B occurs
Generally, we want probability disease
is present (event A) given a
positive
test (event B)
Source: Shortliffe EH, Perreault LE. Medical Informatics: Computer Applications in Health Care and Biomedicine. 2 nd Edition.
Springer-Verlag. 2001

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Bayes Theorem Notation

TPR = Sensitivity = TP/(TP+FN)

FNR = 1-Sensitivity = 1-(TP/(TP+FN))
TNR = Specificity = TN/(TN+FP)
FPR = 1-Specificty = 1- (TN/(TN+FP))

Source: Shortliffe EH, Perreault LE. Medical Informatics: Computer Applications in Health Care and Biomedicine. 2 nd Edition.
Springer-Verlag. 2001

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Bayes Theorem
p[D]p[R | D]
p[D | R]
( p[D]p[R | D]) ( p[D])x( p[R | D]))

We can reformulate this in terms of a

positive test (PPV)
p[D]xTPR
p[D | ]
p[D]xTPR (1 p[D])xFPR
Source: Shortliffe EH, Perreault LE. Medical Informatics: Computer Applications in Health Care and Biomedicine. 2 nd Edition.
Springer-Verlag. 2001

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Bayes Theorem
We can reformulate this in terms of a
negative test (NPV)
(1 p[D])xTNR
p[D | ]
(1 p[D])xTNR ( p[D])xFNR

Or, NPV = [(1-Prev)(Spec)]/[(1Prev)Spec + Prev(1-Sens)]

Source: Shortliffe EH, Perreault LE. Medical Informatics: Computer Applications in Health Care and Biomedicine. 2 nd Edition.
Springer-Verlag. 2001

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Application of Bayes
Theorem

Pre-test probability of heart disease

= 0.95
TPR = 0.65
FPR = 0.20
Substitute Bayes
0.95x0.65Theorem for a
PPV Test
0.98
Positive
0.95x0.65 0.05 x0.20
Source: Shortliffe EH, Perreault LE. Medical Informatics: Computer Applications in Health Care and Biomedicine. 2 nd Edition.
Springer-Verlag. 2001

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Application of Bayes Theorem

ASSUMPTIONS
5% of women aged 40 with a palpable breast mass
cancer have breast cancer (prevalence)
99% of women with breast cancer and a palpable mass
have positive mammography exam (sensitivity is 0.99)
9.6% of women without breast cancer get positive tests
(specificity is 0.904; false positive rate is 0.096)
EVIDENCE
A woman in this age group with a palpable breast mass
has a positive mammography test
PROBLEM
Whats the probability that she has breast cancer?
Source: Shortliffe EH, Perreault LE. Medical Informatics: Computer Applications in Health Care and Biomedicine. 2 Edition.
nd

Springer-Verlag. 2001

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Example
For the patient 40 with a palpable mass
p(B|A) is tests sensitivity: 0.99
p(B|A) is tests false positive rate: 0.096
p(A) is prevalence of disease: 0.05
Probability of breast cancer given a positive screening
test estimated based on Bayes theorem in a 40 year
women with a palpable breast mass
(0.99)(0.05) / [(0.99)(0.05) + (0.096)(0.95)] = 0.35

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References

Petitti, D. BMI 502: Foundations of Biomedical

Informatics Methods I. Arizona State University. 2012.
Shortliffe EH, Perreault LE. Medical Informatics:
Computer Applications in Health Care and Biomedicine.
2nd Edition. Springer-Verlag. 2001
Dubrow, R. CDE 508A: Principles of Epidemiology I. Yale
University. 2007.

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