BME103:T130 Group 15: Difference between revisions
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| [[Image:KaolaGP15.jpg|100px|thumb|Name: Nehal Jolly<br>Role: Experimental Protocol Planner]] | | [[Image:KaolaGP15.jpg|100px|thumb|Name: Nehal Jolly<br>Role: Experimental Protocol Planner]] | ||
| [[Image:Snoop-Dogg-008.jpg|100px|thumb|Name: Ben Reising<br>Role: Open PCR machine Engineer]] | | [[Image:Snoop-Dogg-008.jpg|100px|thumb|Name: Ben Reising<br>Role: Open PCR machine Engineer]] | ||
| [[Image: | | [[Image:Glenbeckcrying.jpg|100px|thumb|Name: Mayuri Gupta<br>Role: Open PCR machine Engineer]] | ||
|} | |} | ||
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'''Flourimeter Measurements'''<br> | '''Flourimeter Measurements'''<br> | ||
[[Image:Screen Shot 2012-11-08 at 3.41.08 PM.png|400px]] | [[Image:Screen Shot 2012-11-08 at 3.41.08 PM.png|400px]] | ||
<br> | <br>Image above shows the set up of the flourimeter measurments | ||
<br><br> | |||
'''Flourimeter Assembly Procedure'''<br> | |||
#First, the glass side of the slide was placed faced down onto the device.<br> | |||
#A different pipette was used for transferring each content from the small tubes to the bigger ones.<br> | |||
#After labeling the tubes and pipettes,gloves were worn to ensure a contamination free procedure.<br> | |||
#Using the specific pipette for each component, one drop of buffer was put onto the first and second centered holes of the slide and two water drops were placed on the gathered buffer drops.<br> | |||
#The device was then put under the black box provided and the phone was placed into the holder inside the box.<br> | |||
#After customizing the photo settings in the phone according to the instruction sheet, a shot of the drop sample was taken and saved.<br> | |||
#The number of the photo was recorded in a table to keep track of the photos.<br> | |||
#The photo was sent to the e-mail of the group member who was responsible for analyzing the photo.<br> | |||
#The previous steps were repeated for each sample with the exception of<br> | |||
#* Replacing the water drops with the rest of the samples<br> | |||
#* using a different row on the glass slide each time a sample was used.<br> | |||
'''Sample Flourimeter Image - Patient 1, Rep 2''' | |||
[[Image:BME103_Group15_Patient_1_Rep_2.JPG|200px]] | |||
'''Sample Flourimeter Image - Patient 2, Rep 1''' | |||
[[Image:BME103_Group15_Patient_2_Rep_1.JPG|200px]] | |||
'''Open ImageJ'''<br> | |||
1. By using a USB cable, connect the camera phone to the desired computer that has already ImageJ installed<br> | |||
2. Under my computer, choose portable devices where you could find the smartphone listed; double-click on it<br> | |||
3. After localizing the DCIM folder and opening it, you should select camera<br> | |||
4. The desired photos can then be transferred by simply putting them into the created folder<br> | |||
5. Open ImageJ and go to file; click on it and choose open<br> | |||
6. Select browse then pick the desired picture from the same folder created earlier<br> | |||
7. To continue opening different pictures, you should only repeat steps 5 and 6<br> | |||
[[Image:BME103_Group15_1455Green.jpg|200px]] | |||
'''Sample ImageJ Green - Patient 1, Rep 2''' | |||
[[Image:BME103_Group15_1462Green.jpg|200px]] | |||
'''Sample ImageJ Green - Patient 2, Rep 1''' | |||
<br><br> | <br><br> | ||
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==Results== | ==Results== | ||
'''Image Analysis Data Table''' | |||
[[Image:BME103_Group15_Data_Table.jpg|800px]] | [[Image:BME103_Group15_Data_Table.jpg|800px]] | ||
[[Image:BME103_Group15_WaterGreen.jpg|200px]] | [[Image:BME103_Group15_WaterGreen.jpg|200px]] | ||
'''Water and SYBR Green I Solution'''<br> | '''Water and SYBR Green I Solution'''<br> | ||
<br> | |||
'''SYBR Green I Solution and DNA Calf Thymus ''' [[Image:BME103_Group15_DNA_Calf_Thymus_Green.jpg|200px]] | |||
<!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. ---> | <!--- Enter the values from your group's Data Analyzer table below. E6, F6, etc. are the excel cells from which you should copy your data. ---> | ||
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| '''Sample''' || '''Integrated Density''' || '''DNA μg/mL''' || '''Conclusion''' | | '''Sample''' || '''Integrated Density''' || '''DNA μg/mL''' || '''Conclusion''' | ||
|- | |- | ||
| PCR: Negative Control || 790480 || 0 || Negative | | PCR: Negative Control || 790480 || 0.888 || Negative | ||
|- | |- | ||
| PCR: Positive Control || 2614324 || | | PCR: Positive Control || 2614324 || 3.994|| Positive | ||
|- | |- | ||
| PCR: Patient 1 ID 27762, rep 1 || 2597111|| | | PCR: Patient 1 ID 27762, rep 1 || 2597111|| 3.966 || Positive | ||
|- | |- | ||
| PCR: Patient 1 ID 27762, rep 2 || | | PCR: Patient 1 ID 27762, rep 2 || 3654456|| 5.673 || Positive | ||
|- | |- | ||
| PCR: Patient 1 ID 27762, rep 3 || | | PCR: Patient 1 ID 27762, rep 3 || 2620690 || 4.004|| Positive | ||
|- | |- | ||
| PCR: Patient 2 ID 59448, rep 1 || | | PCR: Patient 2 ID 59448, rep 1 || 700607 || 0.905 || Negative | ||
|- | |- | ||
| PCR: Patient 2 ID 59448, rep 2 || | | PCR: Patient 2 ID 59448, rep 2 || 444410 || 0.491 || Negative | ||
|- | |- | ||
| PCR: Patient 2 ID 59448, rep 3 || | | PCR: Patient 2 ID 59448, rep 3 || 331748 || 0.309 || Negative | ||
|} | |} | ||
KEY | KEY | ||
* '''Sample''' = The samples were different sources of DNA that were analyzed.<br> | * '''Sample''' = The samples were different sources of DNA that were analyzed.<br> | ||
* '''Integrated Density''' = | * '''Integrated Density''' = The integrated density was calculated by subtracting the measured integrated density of the drop from the measured integrated density analyzed from the background. This calculation takes into account the background noise in the sample. | ||
* '''DNA μg/mL''' = | * '''DNA μg/mL''' = This was calculated by taking the integrated density of the sample divided by the integrated density of the drop and multiplying that by two. | ||
* '''Conclusion''' = | * '''Conclusion''' = If the sample is considered "positive" then it will glow green and the cancerous mutation is said to be present. However; if the sample is considered to have "no signal" then it will just be clear and the cancerous mutation is said to be not present. | ||
Latest revision as of 15:11, 15 November 2012
BME 103 Fall 2012 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
OUR TEAMLAB 1 WRITE-UPInitial Machine TestingThe Original Design Experimenting With the Connections
ProtocolsPolymerase Chain Reaction
The Components of the GoTaq® Colorless Master Mix
DNA Samples (8)
Flourimeter Measurements
Sample Flourimeter Image - Patient 1, Rep 2 Sample Flourimeter Image - Patient 2, Rep 1 Open ImageJ Sample ImageJ Green - Patient 1, Rep 2 Sample ImageJ Green - Patient 2, Rep 1
Research and DevelopmentSpecific Cancer Marker Detection - The Underlying Technology There is a genetic relation to having cancer or not when an individual is over the age of 40. The specific gene, in this case, is located on chromosome 22, r17879961. To test an human's DNA for this cancer gene, we have go through a series of reactions called PCR on the DNA for replication and amplification of the patient's DNA strand.
Based on Bayesian reasoning, the probability that someone will test positive that will actually have the disease has approximately 7.8 percent. However, the chance that someone does not test positive, and doesn't have cancer is about 99.8%.
These percentages generally mean that the test itself is generally in favor of testing negative, which means there are less chances to have false diagnosis and/or treatments.
[math]\displaystyle{ Negative Predictive Value = (True Negative)/(True Negative + False Negative) }[/math] The values for these above equations are gathered from Bayesian's reasoning.
Baye's Theorem: [math]\displaystyle{ p(C/T) = (p(T/C)*p(C))/(p(T/C)*p(C)+p(T/nC)*p(nC)) }[/math] where p(C/T) is the probability of a person with positive results will have cancer out of the entire patients participating. p(C) is the probability of having cancer present, p(T/C) is the percent of patients who tested positive with have cancer and had it. n = not
Results
Water and SYBR Green I Solution SYBR Green I Solution and DNA Calf Thymus
KEY
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