BME100 f2017:Group2 W0800 L6

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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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Name: Zachery Camacho
Name: Briana Bailey
Name: Jordan Harris
Name: Che Jimenez
Name: Julia Murphy
Name: Sofia Salazar-Banquicio



Bayesian Statistics

Overview of the Original Diagnosis System

Calculation 1: What​ ​is​ ​the​ ​probability​ ​that​ ​a​ ​patient​ ​will​ ​get​ ​a​ ​positive​ ​final​ ​test​ ​conclusion,​ ​given​ ​a positive​ ​PCR​ ​reaction?

Variable Description Numerical Value
A Positive final test conclusion 0.24138
B Positive PCR test 0.27381
P(B A) Positive PCR given test conclusion 0.86957
P(A B) Positive test conclusion given a positive PCR .76657

Calculation 2: What​ ​is​ ​the​ ​probability​ ​that​ ​a​ ​patient​ ​will​ ​get​ ​a​ ​negative​ ​final​ ​test​ ​conclusion,​ ​given​ ​a negative​ ​diagnostic​ ​signal?

Variable Description Numeric value
A Negative Final Test Conclusion 0.75862
B Negative PCR reaction 0.63095
P(B|A) Negative PCR given negative conclusion 0.90566
P(A|B) Negative test conclusion given negative PCR 1.08891

Calculation 3: What​ ​is​ ​the​ ​probability​ ​that​ ​a​ ​patient​ ​will​ ​develop​ ​the​ ​disease,​ ​given​ ​a​ ​positive​ ​final​ ​test conclusion?

Variable Description Numeric Value
A Patient will develop Disease 0.24138
B Positive Final test conclusion 0.24138
P(B|A) Positive final test conclusion given patient will develop the disease
P(A|B) Patient will develop the disease given positive final test conclusion

Calculation 4: What​ ​is​ ​the​ ​probability​ ​that​ ​a​ ​patient​ ​will​ ​not​ ​develop​ ​the​ ​disease,​ ​given​ ​a​ ​negative​ ​final test​ ​conclusion?

Variable Description Numeric Value
A Patient will not develop the disease
B Negative final test conclusion 0.75862
P(B|A) Negative Final test Conclusion given the patient will not develop the disease.
P(A|B) Patient will not develop the disease given a negative final test conclusion.

BME100 tested patients for the disease-associated SNP by dividing up into 17 teams of 6 students. Each team diagnosed 34 patients total in order to determine whether or not the patients' genetic codes contained the disease-associated SNP. Determining the presence of the SNP required a PCR. This was used to amplify the desired portion of the genetic code. SYBR GREEN 1 was used to provide visible and measurable results. Once the desired portion of the patient's DNA had been amplified as well as the fluorescence that had been measured, the results were compared with a positive control and a negative control. This was done to determine whether the patient had the disease-associated SNP.

What Bayes Statistics Imply about This Diagnostic Approach

Which calculation describes the sensitivity​ of the system regarding the ability to​ ​detect​ ​the disease​ ​SNP ? Calculation 1
Which calculation describes the sensitivity​ of the system regarding the ability to predict​ ​the disease​? Calculation 3
Which calculation describes the specificity​ of the system regarding the ability to detect​ ​the disease​ ​SNP​? Calculation 2
Which calculation describes the specificity​ of the system regarding the ability to predict​ ​the disease​? Calculations 4

For calculations 1 and 2 the effectiveness according to our calculations are around 80% for positive readings, and around 100% for reading the negative results. this implies that the results are fairly accurate. however more so when testing negative readings. These results could also be errors.

Several ways human and machine error could have occurred. Labelings could have been mixed up and PCR solutions may have crated wrong readings and numbers. The ImageJ analysis process was not entirely consistent, when an oval was drawn over a droplet, it may not have been over the proper area size over the droplet. The initial pictures taken would have caused these errors as the image sizes were inconsistent, as having to change out what droplets were taken required moving the entire set up including the camera making similar copies impossible. As a result of this initial blunder, the Image J process was also affected. These messed up numbers may have lead to the varied numbers for the Bayes Values. Causing many more to actually have tested positive or negative

Intro to Computer-Aided Design

3D Modeling
Our group used TinkerCAD for the computer-aided design lab; TinkerCAD is the software we have used before for this lab, and we figured this would be beneficial for us in the future. TinkerCAD is pretty easy to navigate and with all possibilities with this software we were able to create multiple concepts easily and quickly. Which is another reason why we chose this software. As long as we could picture our design, with a little bit of trial and error this could be accomplished with TinkerCAD. TinkerCAD is "battle tested" when it comes to making thoughts into 3D objects, as it is used in industry all of the time. During the Computer-Aided Design Lab we often found ourselves frustrated, with how TinkerCAD perceived what we were doing versus what we were actually trying to do. After a little bit of practice, trial and error, and countless YouTube videos, we figured out how to turn our thoughts into a design. The design was rough at first, but with learning new skills came more precision in turning our design to exactly what we wanted. This design is everything we wanted, and with all of the finishing touches we are proud to show it off.

Our Design

TinkerCAD123456.png TinkerCAD78910.png

Our design integrates both the PCR and flourimeter into one machine. It has an opening for microliter tubes, a camera, SYBER green dye dispenser, advanced software for storing data, and USB ports so that data can be transferred to any flash drive or computer. Our design is different from the original openPCR design, because it introduces new features that make both the PCR and flourimeter process user friendly, quick, and simplified.

Feature 1: Consumables

Consumables used will be of the same type as a standard PCR machine, this includes the reagents(PCR mix, primer, SYBR Green, and buffer)and plastic tubes however the PCR Fluorimeter hybrid will not need glass slides as one will be present within the machine. Most consumables used are standard for most PCR machines however the "built in" consumables such as glass sliders and plastic tubes are easy to remove for cleaning and sterilization. The PCR/Fluorimeter has standard sized plastic tubes allowing for heating to appropriate temperatures. 4 tubes are in the machine at a single time however due to the way the PCR machine works heating then recording the Fluorimeters image post heating. Consumables that will be packed are the product specific tubes, and glass sliders along side replacements for both the glass slider and plastic tubes.

Feature 2: Hardware - PCR Machine & Fluorimeter

Our design will incorporate an open PCR and fluorimeter into one machine. It will have a 6 inch touchscreen for easy navigation and selections for running PCR or measuring fluorescence with the fluorimeter. There will be a blue light of specific wavelength to excite fluorescence of the molecule. Software will quickly and accurately quantify DNA and RNA in under 5 seconds. SYBER green dye will be stored in a small storage compartment so that it can be easily dispensed onto the slide. This will also allow the SYBER green dye to be kept away from light and will minimize the chance of contamination. Built in software will calculate mean pixel value and RAWitden that will quantify length of DNA segments. A camera will be incorporated into the machine and will be used for taking photos of the SYBER green dye and DNA mixture for measuring fluorescence. The camera will also have a sensor so that when multiple photos are taken, you can have the option of storing the best reading, or the one with the least amount of brightness. High resolution and auto focus feature will be available. the software will allow up to 500 photos to be stored and a USB port will allow the transfer of data to any flash drive or computer. For the open PCR feature, there will be an opening to accommodate up to 4 microliter PCR tubes at a time for a quicker process. There will also be options to set timer or monitor progress for the PCR. Software will record data and store up to 500 results.