Name: Alexander Oropel Research and Development Scientist
Name: Student Role(s)
Name: Student Role(s)
Name: Student Role(s)
LAB 3 WRITE-UP
Original System: PCR Results
PCR Test Results
Sample Name
Ave. INTDEN*
Calculated μg/mL
Conclusion (pos/neg)
Positive Control
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N/A
Negative Control
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N/A
Tube Label:___ Patient ID: ____ rep 1
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Tube Label:___ Patient ID: ____ rep 2
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Tube Label:___ Patient ID: ____ rep 3
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Tube Label:___ Patient ID: ____ rep 1
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Tube Label:___ Patient ID: ____ rep 2
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Tube Label:___ Patient ID: ____ rep 3
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* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images
Bayesian Statistics
These following conditional statistics are based upon all of the DNA detection system results that were obtained in the PCR lab for 20 hypothetical patients who were diagnosed as either having cancer or not having cancer.
Bayes Theorem is an equation in probability theory and statistics that relates inverse representations of probabilities concerning two events, or rather, it expresses a degree of change when accounting for evidence. Bayes Theorem is represented as follows:
P(A|B) = P(B|A) * P(A) / P(B)
Which can be read as
the probability of A given B = (the probability of B given A * the probability of A) / the probability of B
This information will be utilized to determine various probabilities listed below when accounting for the positive/negative values determined by the entire class as well as an outside document listing the actual yes/no cancer diagnosis
Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal.
A = Cancer-Positive Conclustion = 9/20 = .45
B = Positive PCR Reactions = 26/60 = .433
P (B|A) = Positive PCR given cancer Positive conclustion = 11/13 = .846
P(A|B) = .879=88%
Calculation 2: The probability that the sample actually has a non-cancer DNA sequence, given a negative diagnostic signal.
A = Cancer negative conclustion = 11/20 = .55
B = Negative PCR reactions = 17/30 = .567
P (B|A) = Negative PCR given cancer-negative conclustion = 16/17 = .94
P(A|B) = .911 = 91%
Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.
A = "yes" cancer diagnosis = 7/20 = .35
B = "positive" test conclusion = 9/20 = .45
P (B|A) = Positive given yes = 6/20 = .3
P(A|B) = .233 = 23%
Calculation 4: The probability that the patient will not develop cancer, given a non-cancer DNA sequence.
A = "no" cancer diagnosis = 13/20 = .65
B = "negative" test conclusion = 11/20 = .55
P (B|A) = Negative given no = 1/2 = .5
P(A|B) = .591 = 59%
New System: Design Strategy
We concluded that a good system Must Have:
[Must have #1 - why? short, ~4 or 5 sentences]
[Must have #2 - why? short, ~4 or 5 sentences]
We concluded that we would Want a good system to have:
[Want #1 - why? short, ~4 or 5 sentences]
[Want #2 - why? short, ~4 or 5 sentences]
We concluded that a good system Must Not Have:
[Must Not Have #1 - why? short, ~4 or 5 sentences]
[Must Not Have #2 - why? short, ~4 or 5 sentences]
We concluded that a good system Should Avoid:
[Should Avoid #1 - why? short, ~4 or 5 sentences]
[Should Avoid #2 - why? short, ~4 or 5 sentences]
New System: Machine/ Device Engineering
SYSTEM DESIGN
KEY FEATURES
We chose to include these new features
Feature 1 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
Feature 2 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
Etc.
[OR]
We chose keep the devices the same as the original system
Feature 1 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section
Feature 2 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section
Etc.
INSTRUCTIONS
New System: Protocols
DESIGN
We chose to include these new approaches/ features
Feature 1 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
Feature 2 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
Etc.
[OR]
We chose keep the protocols the same as the original system
Feature 1 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section
Feature 2 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section
Etc.
MATERIALS
PROTOCOLS
PCR Protocol
Step 1
Step 2
Etc.
DNA Measurement and Analysis Protocol
Step 1
Step 2
Etc.
New System: Research and Development
BACKGROUND
DESIGN
Primers for PCR
Our primers address the following design needs
Design specification 1 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section
Design specification 2 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section
Etc.
New System: Software
[THIS SECTION IS OPTIONAL. If your team has creative ideas for new software, and new software is a key component included in your new protocols, R&D, or machine design, you may describe it here. You will not receive bonus points, but a solid effort may raise your overall page layout points. If you decide not to propose new software, please delete this entire section, including the ==New System: Software== header.]
BME 103 Spring 2013
