BME103 s2013:T900 Group8 L3

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BME 103 Spring 2013 Home
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
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Name: Anthony ZingaleRole:Experimental Protocol Planner
Name: Anthony Zingale
Role:Experimental Protocol Planner
Name: Josh SnyderRole:Machine Tester
Name: Josh Snyder
Role:Machine Tester
Name: Adam PakRole: Experimental Protocol Planner
Name: Adam Pak
Role: Experimental Protocol Planner
Name: Sunshine SilvasRole:Machine Tester
Name: Sunshine Silvas
Role:Machine Tester
Name: Renee TranRole:Research and Development scientist
Name: Renee Tran
Role:Research and Development scientist


Original System: PCR Results

PCR Test Results

Positive Control (+) --- N/A
Negative Control (-) --- N/A


Bayesian Statistics



  • A = P of positive conclusion = 9 / 20 = 0.45
  • B = P of positive PCR reaction = 26 / 60 = 0.43
  • P (B|A) = P of positive signal, given cancer-positive conclusion = 21 / 24 = 0.875
  • P(A|B) = 0.92 = 92%

This means that if there is one positive diagnostic signal, there is a probability of .92 that the test conclusion will be positive

Calculation 2: The probability that the sample has a non-cancer DNA sequence, given a negative diagnostic signal.

  • A = P of negative conclusion = 11/20 = .55
  • B = P of negative PCR reaction = 34/60 = .567
  • P (B|A) = P of Negative PCR reaction, given cancer-negative conclusion = 29/31 = .935
  • P(A|B) = .907 = 91%

This means that if there is one negative diagnostic signal, there is a probability of .91 that the test conclusion will be negative

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

  • A = P of positive cancer diagnosis = 7/20 = .35
  • B = P of positive conclusion = 9/20 = .45
  • P (B|A) = P of positive conclusion, given positive cancer diagnosis = 6/7 = .857
  • P(A|B) = .667 = 67%

This means that if a test concludes in a positive signal, the probability of the patient developing cancer is .67

Calculation 4: The probability that the patient will not develop cancer, given a non-cancer DNA sequence (negative conclusion).

  • A = P of negative cancer diagnosis = 13/20 = .65
  • B = P of negative conclusion = 11/20 = .55
  • P (B|A) = P of negative conclusion, given negative cancer diagnosis = 10/13 = .769
  • P(A|B) = .909 = 91%

This means that if a test concludes in a negative signal, the probability of the patient not developing cancer is .91.
Neither resulting probability is especially encouraging as treatment for a life threatening disease may rely on this data. Calculation 3 represents cancer growth probability based on a positive conclusion and 1 minus Calc 3, 1-.67 = .33 is the probability of a false positive. Calculation 4 represents no cancer growth probability based on a negative conclusion and 1 minus Calc 4, 1-.91 = .09 is the probability of a false negative. This means that roughly 9 patients out of every 100 will be given a negative conclusion yet will still develop cancer. This could be due to other factors such as starting to develop cancer after the DNA was taken for the PCR test. A second or third test would have to be run automatically independent of the results in order to make sure that an incorrect conclusion is not reached.

New System: Design Strategy

We concluded that a good system Must Have:

  • [Must have #2 - A "must have" for our new device is easily replaceable parts. The reason for this would be that it can allow a wider range or people to use the product because if the parts are easier to replace then it will drop the price of the device. It will also allow for quick and easy repairs, that can save time and prevent results from being delayed.

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

  • [Want #2 - Another thing that we wanted was for the PCR machine to be durable. The reason why we would want the device to be durable is because of the fact that it would take off the stress of breaking the machine. Humans will make mistakes so the more durable it is the less of an impact those mistakes will have.

We concluded that a good system Must Not Have:

  • [Must Not Have #2 - It is important that the machine does not have any complicated instructions on how to handle and use the device. If the device is so complicated that it takes lots of time to understand how to use then it defeats the purpose of having the device in the first place.

We concluded that a good system Should Avoid:

  • [Should Avoid #2 - Since we are wanting a durable machine we should avoid using non-reliable parts. This is important because of the fact that if the parts only a few trials and then need to be replaced. The device needs to be able to repeat the same results over and not have any strain on the devices. If we are able to have a device that is constant then we will have a marketable device.

New System: Machine/ Device Engineering


The primary modification from the first OpenPCR machine will be the USB connection. In order to ensure a better connection, a more durable cable with rubber around the leads, similar to the one pictured below will be implemented. This includes adjusting the port on the PCR machine itself in order to make the new cable fit.


We chose to include these new features



Instructions for the new machine do not need to be altered as the new cable and connection serves the same purpose and are used in the same way as the previous version.

New System: Protocols


We chose to include these new approaches/ features



  • Feature 2 = improving Fluorimeter imaging standards -


Standard Application

Reagents supplied by the user :

  • Template DNA
  • Primer
  • DNA polymerase

make following mixes.

2.prepare following reaction mix :

Component Volume
Master mix 10μL
patient sample 10μL

then can be instserted into PCR machine


General Guidelines for Amplification by PCR

go through appropriated cycles


Stage Cycles Heat (Celsius) time
1 1 95 3 minutes
2 35 95 to 52 to 72 each 30 seconds

Using SYBR Green Dye

Reagents supplied by the user :

  • SYBR Green I
  • DNA being tested


was run previously.

Solution Concetration of SYBR green
1 None (Water)
2 0.25 micrograms per ml
3 0.05 micrograms per ml
4 1.0 micrograms per ml
5 2.0 micrograms per ml
6 5.0 micrograms per ml

repeat this process for all 6 samples.

Materials summery

Supplied in the kit Supplied by User
  • Water
  • pipette
  • Superhydrophobic surface
  • cradle
  • Smart phone
  • Box
  • plastic base
  • small box to set up the phone
  • software
  • PCR
  • Pipette and tips
  • two rows of empty test tubes
  • Water
  • Set of read SYBR green(5 samples)
  • master mix
  • Smartphone

New System: Research and Development





Normal allele forward primer:CCCAGGATTTTTGAGAATGTA
Cancer allele reverse primer:GGGTCCTAAAAACTCTTACAT

Primers for PCR

Cancer allele forward primer:CCCAGGATTTTGAGACTGTA
Cancer allele reverse primer:GGGTCCTAAAAACTCTTACAT


Our primers address the following design needs

  • Design specification 1 - "Use one more positive and one more negative control"

Design cancer positive primers with more than one mutation. Rather than just switching the "ATT" to "ACT", the primer can also switch out a larger stran like "TTTTTT" to "TATAT"

  • Design specification 2 - "Improving Fluorimeter imaging standards"

With a primer that has more mutations,the positive results will amplify more, makes it easier to identify the green in the fluorimeter.

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