BME100 f2014:Group25 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
Course Logistics For Instructors
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Angus Cheung
Brandon Dorr
Daniel Gentry
Beniamin Drotar
Srekar Nagishetty Ravi
Diana Tran


Bayesian Statistics

Overview of the Original Diagnosis System - The 68 patients were split between the 34 teams of 6 students. Each team got assigned 2 patients each and given DNA samples to analyze for disease associated SNPs. In order to prevent errors 3 samples from each patient were tested and a positive and negative control were given to each group. Each group also had to do a pipette challenge to ensure that the micro-pipette is used correctly and each group had to calibrate the fluorimeter using known controls. Three pictures were used for the ImageJ calculations and the average of the three were used for the final results. Finally each teams results were compiled into one spreadsheet to be used by the entire class.

Calculation 1

Variable/Calculation Meaning Value
A Probability of a Positive Conclusion 0.48
B Probability of a Positive PCR Reaction 0.49
P (B l A) Probability of Positive PCR given a Positive Conclusion 0.89
P (A l B) Probability of a Positive Conclusion given a Positive PCR Reaction 0.87

Calculation 2

Variable/Calculation Meaning Value
A Probability of a Negative Conclusion 0.39
B Probability of a Negative PCR Reaction 0.39
P (B l A) Probability of Negative PCR given a Negative Conclusion 0.77
P (A l B) Probability of a Negative Conclusion given a Negative PCR Reaction 0.77

Calculation 3

Variable/Calculation Meaning Value
A Probability of a Conclusive Positive Diagnosis 0.34
B Probability of a Positive PCR Test Conclusion 0.48
P (B l A) Probability of Positive PCR Test Conclusion given a Conclusive Positive Diagnosis 0.43
P (A l B) Probability of Conclusive Positive Diagnosis given a Positive PCR Test Conclusion 0.30

Calculation 4

Variable/Calculation Meaning Value
A Probability of Conclusive Negative Diagnosis 0.66
B Probability of a Negative PCR Test Conclusion 0.39
P (B l A) Probability of Negative PCR Test Conclusion given a Conclusive Negative Diagnosis 0.27
P (A l B) Probability of Conclusive Negative Diagnosis given a Negative PCR Test Conclusion 0.46

What Bayes Statistics Imply about This Diagnostic Approach

The probability for making a positive conclusion based upon a positve PCR reaciton were close to 100%, therefore they were reliable in that sense. The same was true for the negative, but they were slightly lower. This means the tests were definitive, but these calculations do not address weather or not they were accurate. There are many sources for human error while conducting the PCR and fluorometry tests. Some many include: contamination of the DNA sample due accidently reusing a pipette tip, inaccurate amounts of the samples and components of the reaciton when improperly pippetting, light contamination of the SYBR green which could lead to varying results, and differing pictures when doing the fluorimetry which could case varying values and inconclusive data.

Calculations 3 and 4 show the inaccuracy of the tests, as the values were below 0.50, they were very small. Flipping a coin could possibly have a better chance of making a correct diagnosis. The tests were not accurate very much at all, as they are not even accurate for predicting the direct opposite. The sources of error could have had a significant impact of the class's results, due to pippette contamination, improper amounts, variable camera lighting and position, and light contamination when taking the photos.

Computer-Aided Design


TinkerCAD is a browser based computer aided design program that allows you to create 3-dimensional models and images. The program sacrifices many of the specialized and customizable features that similar programs like SolidWorks offer in exchange for being highly intuitive and user friendly. Various STL files containing basic components for the basic OpenPCR machine were downloaded off of Thingiverse, a website that shares 3-dimensional designs that can be printed using a 3D printer. These components were used to create an new OpenPCR machine that addressed the shortcoming of the original. Our Design

Consumables Open PCR Machine Fluorimeter system
Strengths - Accurate and Precise Pippette, Endurance, Limited Cross Contamination Strengths - Portable, Self-run, Cheap Strengths - Simple applicaiton, Fast
Weakness - Wasteful, Long Process, Expensive Weakness - Time consuming Process, Limited number of Samples Weakness - Light leakage, Height Adjustment Problems, Not Consistent Phone Mount, Requires outside analysis

There are several weaknesses with the Fluorimeter:

  • Non-fixed Phone Position
  • Unequal Drop Sizes
  • Height Adjustment

The new design will have a mounted camera which is fixed to the device. The device will have software which will automatically process the images and controls to output values on a screen. The device will be fitted inside a box, which is efficient for blocking out outside light. It will have automated slide adjustment.

PCR Machine

Original PCR Top-View


Original PCR Side-View


Modified PCR Top-View


Shows the addition of the led-light as well as an increased size of slot for the reagent tray.

Modified PCR Fan-View


Shows the addition of the fan which is used for cooling.

Modified PCR Side-View


Shows the overall larger size of the PCR machine as well as highlights the color customizability.

Fluorimeter Flu1.jpg Flu2.jpg Flu3.jpg Flu4.jpg

Feature 2: Consumables Kit

Currently, the Consumables Kit used for PCR is wasteful and expensive. To reduce the amount of resources and supplies being wasted, our company has designed a new micropipettor. Everything is the same, except, the tips will be stored in a circular cartridge that can hold up to ten 500μL tips. The tips will come sterilized, via autoclave, and wrapped in an aluminum foil seal. When the cartridge is put into the revolving chamber inside of the base of the micropipettor, the pressure will push through the aluminum foil seal, keeping the tips sterile, while also reducing the amount of waste used in packaging.

Feature 3: Hardware - PCR Machine & Fluorimeter

The new PCR machine and fluorimeter will operate in the same fashion as the old ones except with the new modifications.

Changes to Open PCR Machine

The new design for the Open PCR machine includes the addition of a light indicator on the top of the machine, a cooling fan, an overall larger machine, a slot for a bigger tray to hold PCR reactants, as well as color customization. The light indicator at the top of the PCR machine would light up blue when the PCR machine is finished, or red if the PCR machine has encountered problems. This is necessary as, sometimes, the thermocycler could fail thus ruining the PCR reactants, the light would indicate to the user if the PCR machine has encountered this problem. Also in order for the PCR machine to be able to cool off much more efficiently a fan has been added; the fan would turn off when the PCR machine is trying to warm up. This is necessary as if often takes a longer time to cool down then to heat the PCR machine up, the fan would help save time. Furthermore with a bigger PCR machine and a bigger slot at the top of the PCR machine (the slot which holds the tray with the PCR reactangs), it is possible to be more efficient as the PCR machine is able to process more reactants with a bigger tray. Finally, we have given the user the option of color customization when buying the PCR machine in order to make the product more personal and memorable.


  • LED Screen: Placed on the outside of the fluorimeter to allow the user to see inside the box and observe the dropper for any potential malfunctions whilst a box covering or other material cover is placed on top to restrict the passage of light.
  • Automated Drop Dispenser: This will ensure that an even amount of liquid is dispensed onto the hydrophobic slide for more accurate ImageJ analyses.
  • Hydrophobic slide: Installed on top of the base to keep the drop in proper positioning for the picture to be taken.
  • Mold: An outline placed on top of the hydrophobic slide to guide the drop of liquid from the automated dispenser to remain in the proper positioning in accordance to distance and shape for more standardized ImageJ processing.
  • Blue LED light: Permeates the liquid drop to allow for the ImageJ computer to properly analyze the pictures.
  • ImageJ Computer: Directly and immediately processes the picture taken by the Built-In Camera
  • Built-in Camera: Located onto the side of the ImageJ computer to maintain an equal distance from the drop each time as well as having pre-installed settings such as an automated timer and camera qualities for optimal picture capturing.