* 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.
Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal.
A = frequency of cancer-positive conclusions = 9 / 20 = 0.45
B = frequency of positive PCR reactions = 26 / 60 = 0.43
P (B|A) = frequency of positive PCR given cancer-positive conclusion = 24 / 26 = 0.92
P(A|B) = 0.96 = 96%
Calculation 2: The probability that the sample actually has a non-cancer DNA sequence, given a negative diagnostic signal.
A = frequency of cancer-negative conclusions = 11 / 20 = 0.55
B = frequency of negative PCR reactions = 34 / 60 = 0.57
P (B|A) = frequency of negative PCR given cancer-negative conclusion = 31 / 34 = 0.91
P(A|B) = 0.88 = 88%
Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.
A = frequency of "yes" cancer diagnosis = 9 / 20 = 0.45
B = frequency of "pos" test conclusion = 26 / 60 = 0.43
P (B|A) = frequency of pos given yes = 24 / 26 = 0.92
P(A|B) = 0.96 = 96%
Calculation 4: The probability that the patient will not develop cancer, given a non-cancer DNA sequence.
A = frequency of "no" cancer diagnosis = 11 / 20 = 0.55
B = frequency of "neg" test conclusion = 34 / 60 = 0.57
P (B|A) = frequency of neg given no = 31 / 34 = 0.91
P(A|B) = 0.88 = 88%
New System: Design Strategy
We concluded that a good system Must Have:
- easily determined results: The easier the results are to read accurately, the less likely a misdiagnosis in either direction. It is undesirable both to give a false negative, where a patient is not treated when care is needed, or to give a false positive, wasting time and resources on those who do not need them. This aspect is central to any diagnostic tool.
- Simple OpenPCR Software: Simplicity increases ease and efficiency in lab experiments and hopefully leads to faster diagnoses. It also makes troubleshooting easier should problems arise. The more straightforward the system, the more quickly users can learn to use the machine.
We concluded that we would Want a good system to have:
- Low cost: Currently an OpenPCR machine costs $599 and a Fluorimeter costs $300. An inexpensive material would help reduce cost and increase accessibility, since there is always a limited budget for new equipment. This would not only allow users to increase the amount of tests that can be run at the same time, but also boost sales, which is important for marketing any device.
- integrated camera: phone cameras are easily moveable and vary in size and quality, leading to differing results. Smartphone camera settings can be time consuming or nonexistent. Having a built-in camera increases cost, but it is worth it to increase speed and accuracy. Furthermore, the program is simpler because it does not have to adjust to different cameras and phone sizes and shapes vary enough to make building a cradle to fit them difficult.
We concluded that a good system Must Not Have:
- Troublesome USB Connectivity. USB connectivity should function well in order for OpenPCR machine to work.
- Casing = fire hazard. High temperature with PCR can be dangerous.
We concluded that a good system Should Avoid:
- Avoid slow amplification.
- Hard to adjust phone/ fluorimeter. The phone can be easily moved by accident, which requires readjustment between the phone and the fluorimeter.
New System: Machine/ Device Engineering
SYSTEM DESIGN
We decided to have some addition of the fluorimeter to allow easy adjustment and positioning of the phone. The benefit of this addition is that it will help save time to try to readjust the phone in the correct position, and that photos can be taken better and more accurate, which give better and accurate data results.
KEY FEATURES
This new device will hold the camera phone in place. It will be able to connect temporarily to the fluorimeter, allowing the phone to be held in place. The device will also have an adjustable distance from the phone to the fluorimeter, as well as the height for more compability of other different phones, without trying to adding more heights to the phone or the fluorimeter.
INSTRUCTIONS
Step 1: Connect the base to the fluorimeter.
Step 2: Set the camera phone into the base.
Step 3: Set the height and distance.
Step 4: Take Photo.
New System: Protocols
DESIGN
We chose to add an extra device to the fluorimeter. However, protocols should remain the same.
MATERIALS
Supplied in the Kit
Amount
Smart phone
1
Reaction mix
given more for more reactions
Battery
Software
Supplied in the User
Amount
Filter water
SYBR Green
Primers
DNA sample (negative and positive)
PROTOCOLS
PCR Protocol
Step 1: Reaction mix
Step 2: Add 2.5 μL of negative and positive DNA sample
Step 3: Fluorometer gave the sample result
DNA Measurement and Analysis Protocol
Step 1: Set up the equipment
Step 2: Put the smart phone and fluorometer in the dark box
Step 3: Major the distance between the fluorometer and phone.
Step 4: Run the samples
Step 5: Take a picture of the experiment
Step 6: Repeat this trial with different samples
Step 7: Use Image J and make a circle around the drop.
New System: Research and Development
BACKGROUND
CHEK2 is a gene located at chromosome 22. It provides instructions for making protein call checkpoint kinase 2. The checkpoint kinase acts as a tumor suppressor. Mutations of CHEK2 gene can lead to breast cancer, Li-Fraumeni syndrome, and other type cancers and diseases.
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
