Difference between revisions of "BME103 s2013:T900 Group4 L3"

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OUR TEAM

 Name: Kinjal Ahir Role:Protocol Name: Zach Young Initial Machine Testing Name: Anna Essex Initial Machine Testing Name: Tuan Phan Research and Design Name: Amelia Lax Research and Design

LAB 3 WRITE-UP

Original System: PCR Results

PCR Test Results

 Sample Name Ave. INTDEN* Calculated (μg/mL) Conclusion (pos/neg) Positive Control 1,450,385 1.60 N/A Negative Control 488,789 0.18 N/A Tube Label: B2 Patient ID: 17818 rep 1 709,603 0.51 pos Tube Label: C2 Patient ID: 17818 rep 2 642,405 0.41 pos Tube Label: D2 Patient ID: 17818 rep 3 417,721 0.07 neg Tube Label: B1 Patient ID: 85158 rep 1 450,174 0.12 neg Tube Label: C1 Patient ID: 85158 rep 2 387,850 0.03 neg Tube Label: D1 Patient ID: 85158 rep 3 376,360 0.01 neg

* 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 equation: P(A|B) = P(B|A) * P(A) / P(B)

Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal.

• A = [text description] = [frequency shown as a fraction] = [final numerical value]
• B = [text description] = [frequency shown as a fraction] = [final numerical value]
• P (B|A) = [text description] = [frequency shown as a fraction] = [final numerical value]

Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.

• A = [text description] = [frequency shown as a fraction] = [final numerical value]
• B = [text description] = [frequency shown as a fraction] = [final numerical value]
• P (B|A) = [text description] = [frequency shown as a fraction] = [final numerical value]

New System: Design Strategy

We concluded that a good system Must Have:

- Result easy to determine.

- Simple OpenPCR Software: The OpenPCR Software shoulder be simple and easy to use and that would help lab experiments done faster, rather than the need to spend extra time to figure out how the software works.

We concluded that we would Want a good system to have:

- Low cost: OpenPCR \$599 Fluorimeter \$300. A low cost material would help since there is always a limited budget for the research experiment. This would allow us to buy more OpenPCR and fluorimeter and create more data results in the same amount of time.

Phone camera should not be easily moveable when played in front of the fluorimeter. Phone camera adjustment can be time consuming and not setting it in the correct position/distance results data error.

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
1. Step 1: Reaction mix
2. Step 2: Add 2.5 μL of negative and positive DNA sample
3. Step 3: Fluorometer gave the sample result

• DNA Measurement and Analysis Protocol
1. Step 1: Set up the equipment
2. Step 2: Put the smart phone and fluorometer in the dark box
3. Step 3: Major the distance between the fluorometer and phone.
4. Step 4: Run the samples
5. Step 5: Take a picture of the experiment
6. Step 6: Repeat this trial with different samples
7. 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

Primers for PCR

GGAAGTGGGTCCTAAAAACTCTTACA[C/T]TGCATACATAGAAGATCACAGTGGC

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.]