BME103 s2013:T900 Group8 L3
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(→Original System: PCR Results) 
Current revision (22:02, 16 April 2013) (view source) (→New System: Machine/ Device Engineering) 

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* P (BA) = P of positive signal, given cancerpositive conclusion = 21 / 24 = 0.875  * P (BA) = P of positive signal, given cancerpositive conclusion = 21 / 24 = 0.875  
* '''P(AB) = 0.92 = 92%'''  * '''P(AB) = 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  This means that if there is one positive diagnostic signal, there is a probability of .92 that the test conclusion will be positive  
  <br>  +  <br><br> 
Calculation 2: The probability that the sample has a noncancer DNA sequence, given a negative diagnostic signal.<br>  Calculation 2: The probability that the sample has a noncancer DNA sequence, given a negative diagnostic signal.<br>  
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* P (BA) = P of Negative PCR reaction, given cancernegative conclusion = 29/31 = .935  * P (BA) = P of Negative PCR reaction, given cancernegative conclusion = 29/31 = .935  
* '''P(AB) = .907 = 91%'''  * '''P(AB) = .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  
+  <br><br>  
Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence (positive conclusion).<br>  Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence (positive conclusion).<br>  
* A = P of positive cancer diagnosis = 7/20 = .35  * A = P of positive cancer diagnosis = 7/20 = .35  
  * B = P of  +  * B = P of positive conclusion = 9/20 = .45 
  * P (BA) = P of  +  * P (BA) = P of positive conclusion, given positive cancer diagnosis = 6/7 = .857 
* '''P(AB) = .667 = 67%'''  * '''P(AB) = .667 = 67%'''  
  
+  This means that if a test concludes in a positive signal, the probability of the patient developing cancer is .67  
+  <br><br>  
Calculation 4: The probability that the patient will not develop cancer, given a noncancer DNA sequence (negative conclusion).<br>  Calculation 4: The probability that the patient will not develop cancer, given a noncancer DNA sequence (negative conclusion).<br>  
* A = P of negative cancer diagnosis = 13/20 = .65  * A = P of negative cancer diagnosis = 13/20 = .65  
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* P (BA) = P of negative conclusion, given negative cancer diagnosis = 10/13 = .769  * P (BA) = P of negative conclusion, given negative cancer diagnosis = 10/13 = .769  
* '''P(AB) = .909 = 91%'''  * '''P(AB) = .909 = 91%'''  
  +  
+  This means that if a test concludes in a negative signal, the probability of the patient not developing cancer is .91.  
<br>  <br>  
+  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.  
+  <br><br>  
==New System: Design Strategy==  ==New System: Design Strategy==  
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'''SYSTEM DESIGN'''<br>  '''SYSTEM DESIGN'''<br>  
  +  [[Image:ASU BME 103 group 8 highlighted PCR.jpg100px]]  
+  <br>  
+  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.  
+  <br><br>  
+  [[Image:ASUBME103 group 8 PCR plug.jpg50px]]  
+  <br><br>  
<! If your design goals include modifying the Open PCR machine, include an image or images from the Open PCR Solid Works 3D rendering exercise. Write a short paragraph that summarizes what your team is going to modify >  <! If your design goals include modifying the Open PCR machine, include an image or images from the Open PCR Solid Works 3D rendering exercise. Write a short paragraph that summarizes what your team is going to modify >  
<! If your goal includes modifying the Fluorimeter, include a labeled image or images of the Fluorimeter. There is no Solid Works file for the Fluorimeter. Write a short paragraph that summarizes what your team is going to modify >  <! If your goal includes modifying the Fluorimeter, include a labeled image or images of the Fluorimeter. There is no Solid Works file for the Fluorimeter. Write a short paragraph that summarizes what your team is going to modify >  
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'''INSTRUCTIONS''' <br>  '''INSTRUCTIONS''' <br>  
+  
+  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.  
<! Changing the machine will require new instructions for using the machine. Write a short stepbystep list of instructions on how to set up and use the new machine. The instructions must be specific to your new design. >  <! Changing the machine will require new instructions for using the machine. Write a short stepbystep list of instructions on how to set up and use the new machine. The instructions must be specific to your new design. > 
Current revision
BME 103 Spring 2013  Home People Lab WriteUp 1 Lab WriteUp 2 Lab WriteUp 3 Course Logistics For Instructors Photos Wiki Editing Help  
OUR TEAMLAB 3 WRITEUPOriginal System: PCR ResultsPCR Test Results
* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images
Bayes Theorem equation: P(AB) = P(BA) * P(A) / P(B)
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 noncancer DNA sequence, given a negative diagnostic signal.
This means that if there is one negative diagnostic signal, there is a probability of .91 that the test conclusion will be negative
This means that if a test concludes in a positive signal, the probability of the patient developing cancer is .67
This means that if a test concludes in a negative signal, the probability of the patient not developing cancer is .91.
New System: Design StrategyWe concluded that a good system Must Have:
We concluded that we would Want a good system to have:
We concluded that a good system Must Not Have:
We concluded that a good system Should Avoid:
New System: Machine/ Device EngineeringSYSTEM DESIGN
We chose to include these new features
INSTRUCTIONS 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: ProtocolsDESIGN We chose to include these new approaches/ features
Part of our problems were that on the very end when all the results were collected from all the groups that were involved in this BME is that we were not 100% on the results on each patient. Also we had trouble matching numbers with positive and negative results. to increase the accuracy of our results it would be good to place tow more tubes into the PCR machine that can serve as extra controls.
each group in the BME lab have used different smart phone, which means different types of cameras were used. each of those cameras have setting on that can not be changed. i think standarizing and raising the the cameras in the class would greatly improve the confidence that our results are correct.
Reagents supplied by the user :
3.Sample mixed should contain sample of two patient each containg 3 replicates. As well as
3.place two rows of four tubes into PCR that were prepared before, using PC click start and
3.take each sample and place one drop on perforated and hydrophobic glass. calibrate the camera and then
New System: Research and DevelopmentBACKGROUND
To amplify the cancer associated sequence a primer pair that has a change in the normal allele forward primer needs to be designed; the "cancer allele forward primer". Vice versa, thr "cancer allele reverse primer" will stay the same. Normal allele forward primer:CCCAGGATTTTTGAGAATGTA
Cancer allele forward primer:CCCAGGATTTTGAGACTGTA The cancerous gene will produce a positive result, while the noncancer gene will give a negative result, because the primers are designed to amplify cancerous DNA. Therefore, the cancerous mutation cannot bind to normal DNA, ultimately meaning that amplification cannot occur.(http://openwetware.org/wiki/BME103_s2013:T900_Group8)
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"
With a primer that has more mutations,the positive results will amplify more, makes it easier to identify the green in the fluorimeter.
