# BME103 s2013:T900 Group3 L3

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# OUR TEAM

 Name: Jonus ReynaResearch and Development Name: Amnah AlkhanRole(s) Name: Haifa Role(s) Name: StudentRole(s) Name: StudentRole(s)

# LAB 3 WRITE-UP

## Original System: PCR Results

PCR Test Results

 Sample Name Ave. INTDEN* Calculated μg/mL Conclusion (pos/neg) Positive Control 620903.7 0.4332 N/A Negative Control 53882.67 0.08821 N/A Tube Label:-1 Patient ID: 92307 rep 1 218793.3 0.13226 POS Tube Label:-2 Patient ID: 92307 rep 2 224585 0.136599 POS Tube Label:-3 Patient ID: 92307 rep 3 152779.3 0.0828495 NEG Tube Label:+1 Patient ID: 76893 rep 1 157484.3 0.0863714 NEG Tube Label:+2 Patient ID: 76893 rep 2 113996.3 0.05381881 NEG Tube Label:+3 Patient ID: 76893 rep 3 137177.7 0.0711711 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:

• [Must have #1 For what we must have in our new design of the open PCR machine , we decided to make simple soft ware. The reason for this is to illustrate information of the devise for the users and give in simple explanation of using the product. Therefore, we don’t want the system to be users friendly.
• [Must have #2 Small sample volume this is directly to the PCR size; having small sample may lead us to have accurate data ;because with this small sample volume we can indicate quick measurement to get results. ]

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

• [Want #1 In our new design we want to make it easy to fix, because the PCR is a sensitive device which mean it can be easy to damage.Therefore,we design the new PCR for limiting down time for using the PCR ,and to make as much as able to do its work. ]
• [Want #2 also in this design we want to make our PCR Hard ware modifiable which mean that be can update our original design]

We concluded that a good system Must Not Have:

1- troublesome USB connectivity: our group faced this problem in first and second lab. Our USB was not working. So, we think it is important to use any thing else than USB to send the data and orders from the computer/laptop to the PCR machine such as blue-tooth.

2- Casing fire hazard: PCR machine goes through different high temperatures, more than 90 C, this high temperature may causes fire. Also it’s connected to electricity and USB to the computer/laptop may cause also fire. In addition, the case of the machine is made of wood, which is easy to fire. However, we use the PCR inside labs, which has too many chemicals and several electricity resources.

We concluded that a good system Should Avoid:

1- OpenPCR is fragile: the PCR machine is covered by a wood case. Wood is not strong enough to keep the PCR machine safe. It is easy to break. PCR cycles go through different very high temperatures and it is also connected to electricity, these two things may cause fire and woody case helps to huge the fire.

2- slow analysis: the PCR works 1 at each time the machine started. for example, we can not add extra tubes to the PCR while it's working, so we have to wait for hours. this is wasting of time.

## 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
1. Step 1
2. Step 2
3. Etc.

• DNA Measurement and Analysis Protocol
1. Step 1
2. Step 2
3. Etc.

## New System: Research and Development

BACKGROUND

Humans need certain cells to reproduce or replenish such a skin cells. Skin can be damaged from falling on rough pavement or other similar circumstances. However, certain cells need to stop rebuilding or growing when necessary otherwise it can grow out of control. This problem may include the consumption of excessive nutrients which could starve surrounding organs and damage it, thus cancer develops. CHEK2 is a gene that stands for Checkpoint Kinase 2. When DNA is damaged, a protein called Checkpoint Kinase 2 (which is made by CHEK2) is activated and stops the overgrowth of cells, otherwise it will lead to cancer. SNP stands for single nucleotide polymorphism and it is a DNA sequence. If the base pair sequence of the SNP is paired incorrectly, it could inhibit cell death which could cause cancer.

DESIGN

A specific sequence of cancer nucleotides is chosen to amplify. The cancerous sequence forward would be C-T-A-A-C forward and G-T-T-A-C in the reverse. A forward and reverse primer is ordered to complement the cancerous template DNA. Adenine only attaches to thymine and cytosine only attaches to guanine. The DNA is mixed with the primers, dNTPs, Taq DNA polymerase, and magnesium chloride. The cancerous allele will give a product because the ordered primers will be a sequence that is base paired to the template. The non-disease allele will not be base paired and will not match the template so it will not produce a PCR product.

Our primers address the following design needs

• Design specification 1 - The software needs to be user friendly. The user simply orders the primers, places it in the mix, then puts it in the PCR machine and presses the start button.
• Design specification 2 - The ordered primers will be documented on the software. If the PCR software recognizes down time with the PCR machine which could cause the PCR mix to be unusable, it would automatically order more of the same PCR mix as per preset authorized settings.

## 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.]