BME100 f2014:Group2 L6

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Owwnotebook icon.png BME 100 Fall 2014 Home
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: Jordan Shinn
Name: Victoria Bowman
Name: Chandler Heaton
Name: Abigail Weiss
Name: Alena Zapata


Bayesian Statistics

Overview of the Original Diagnosis System

To test the patients for the disease-associated SNP, the labor was divided between thirty-four teams of six students each. These teams worked together to diagnose sixty-eight patients total. Each team diagnosed two patients. There were many precautions taken to prevent error. One precaution was each team tested three replicates per patient. For the PCR controls, SYBR Green I Dye was used for each replication. The same volume of SYBR Green I Dye and DNA in µl was used. For the ImageJ calibration controls, the color channels were separated, and only the green channel was measured. The images were compared to the previously established positive and negative controls. Three images were used for the each unique PCR sample in the ImageJ analysis. After compiling the class data, there were eight inconclusive results. There were six blank tests. There were thirty positive tests and twenty-four negative tests.

What Bayes Statistics Imply about This Diagnostic Approach

The PCR values for calculations one and two are close to 1.00, therefore the PCR replicates are reliable in concluding if a patient has the disease SNP or not. There are many sources of error that could have occurred that could have affected the Bayes values in a negative way. One possible source of human error is the sample preparer contaminating the patient’s PCR sample with their own DNA. Another possible human error is the mislabeling of the positive and negative PCR controls which would have negatively affected all the ImageJ analysis. A possible source of machine error is the PCR machine getting stuck which would prevent the tester from knowing if the PCR reaction was properly completed.

The PCR values for calculations three and four are not close to 1.00. Thus, the PCR is not reliable in the predicting of the development of the specific disease SNP, also referred to as diagnosis.

Computer-Aided Design


Tinkercad is a web-based 3D design application. Tinkercad let's you design products with all the work done and saved on the lab. A Tinkercad account is not needed to design these products. This software was used to design a 3D representation of an improved PCR machine. Using Tinkercad, the different pieces of the PCR machine were assembled into a single 3D design.

Our Design


Our design has the same foundational mechanics as the original PCR machine, but has a single light added to it. When completeing the PCR lab a PCR machine can get stuck on a cycle and go un-noticed for extedned periods of time. The new design incorporates a light system so that if the thermocycler gets stuck a single light at the top of the machine will turn red and notify the user of the problem.

Feature 1: Consumables Kit

The reagents will be packaged in small cuvettes and then placed into a plastic box which holds them all in place similar to the box that contained all the micro-pipette tips. This box will be placed in a Styrofoam block that has a space cut out for this box to be placed in as well as spaces cut out for the small plastics, and fluorimeter. This block of Styrofoam will slide into a larger cardboard box.

This design gives every part of the kit its own specific place to be stored when not in use so that nothing can be lost or damaged.

Feature 2: Hardware - PCR Machine & Fluorimeter

The PCR machine and fluorimeter will remain separate pieces as they are currently. The only change made was the addition of a problem detection system involving a warning light, which was previously mentioned. Significantly changing the mechanics of the current system could potentially stop the system from working properly. The fluorimeter will be packaged into the same Styrofoam piece as the reagents and small plastics and then slide into a larger cardboard box along side the Styrofoam piece that holds the PCR machine. So even though they are technically separate pieces they are compatible to one another and used in the same overall system.

Adding a light that turns on when the PCR machine is stuck saves users from wasting time and notifies them that the results could be wrong or inconclusive. This is a problem that was experienced first hand during a previous lab. The users were not aware that the system was stuck, it was just assumed that the machine was running slowly. By adding this feature it makes PCR machines more user friendly and leaves less room for bad data.