BME100 s2015:Group6 9amL6

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BME 100 Spring 2015 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: Sara Belko
Name: Luc Tieu
Name: Priscilla Delgado
Name: Al Imam
Name: Francisco Campa


Bayesian Statistics

Overview of the Original Diagnosis System

During the experiment, we tested two patients by mixing their DNA samples (3 each) with PCR reaction solution (a mix that contains Taq DNA polymerase, MgCl2, and dNTP’s). Then, the mix was left in a PCR machine to denature the DNA samples. After, the samples were tested to measure different concentrations of the DNA by taking pictures of them mixed with SYBR Green 1. Finally, the pictures were analyzed on ImageJ to measure the internal density of the drop compared to the internal density of the background. To determine if the patients has Coronary Artery Disease, their DNA samples were compared to a positive and negative control. The division of labor was 2 patients per group, so with 8 groups there was 16 patients total. To prevent error, each patient had three separate DNA samples to test. Also, in the ImageJ calibration controls there was a fixed area that allowed us to measure the same amount of area per picture. In the ImageJ calibration controls, five controls were used (0.25, 0.5, 1, 2, and 5) and three pictures of each patient were compared to the controls. For class data, there were 13 successful conclusions (8 negatives and 5 positives), 1 inconclusive results, and 2 blank data.

What Bayes Statistics Imply about This Diagnostic Approach

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 0.357
B positive PCR Reaction 0.381
P(B/A) Positive PCR reaction given positive test conclusions 0.93333
P(A/B) positive test conclusions given Positive PCR reaction 0.875

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

Variable Description Numerical Value
A negative final test conclusion 0.571
B negative diagnostic signal 0.595
P(B/A) negative diagnostic signal given negative test conclusions 0.91666
P(A/B) negative final test conclusion given negative diagnostic signals 0.880

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

Variable Description Numerical Value
A develop disease 0.375
B positive final conclusion 0.357
P(B/A) positive final conclusion given develop disease 0.666667
P(A/B) develop disease given positive final conclusion 0.7002

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

Variable Description Numerical Value
A not develop disease 0.625
B negative final conclusion 0.571
P(B/A) negative final conclusion given not develop disease 0.6
P(A/B) not develop disease given negative final conclusion 0.657

Calculation 1 shows that the chance of positive test conclusions given Positive PCR reaction is above 80.0% likely because the Bayes value was close to 1. Calculation 2 shows that the chance of negative final test conclusions given negative diagnostic signals is 80.0% likely because Bayes number was close to 1 as well. This means that the results are about pretty accurate for both positive and negative conclusions.

Calculation 3 demonstrates that developing the disease given a positive final conclusion was above 70% likely because Bayes number was close to 1. Calculation 4 shows that not developing the disease given a negative final conclusion was above 60% likely because Bayes number was in the mid range from 0 to 1. This means that the results are somewhat accurate in diagnosing a patient; however, they are not 100% accurate.

Computer-Aided Design

During the project, TinkerCAD was useful as it was a important part in accomplishing the objective. It was needed to build and design our description of the box, which would allow less light into the PCR machine which translated to better results. Using TinkerCAD, it was possible to brainstorm potential prototypes for the box's new design

Our Design

Name: Open PCR Machine

In the new box design, limiting the amount of light exposed to the setup within was the primary objective.The more light that comes into the box, the less accurate the pictures will be, because the light interferes with the dark background inside of the box. The new box design includes the standard bottom and back sides, and an additional side with a window cut into it. The side with the window is meant to be open so that a phone camera can take the pictures necessary for analysis. The standard sides are untouched to prevent any unnecessary light from entering. Ideally, this new design will work better than the old OpenPCR design because more light is blocked out.

Feature 1: Consumables Kit

We plan on packing the kit into its compact form for easy shipping and handling. Our kit will include one pair of disposable gloves, 8 tubes of PCR mix 50 milliliters each, 8 empty tubes, micropipettor, 18 disposable micropipettor tips, and a tray to hold the tubes (8 by 3 slots). To package, a row of 8 empty tubes and a row of 8 PCR mix tubes will be placed into the tray. So there will be a row of 8 slots left open. These will be for DNA samples the labs already have. The micropipettor tip will be detached from the base and placed over these 8 open slots. The base of the micropipettor will be placed on top of the rows of empty and PCR mix tubes. Finally, the disposable gloves rolled up and the small bag of micropipettor disposable tips will be placed over the detached micropipettor end. This entire structure will be saran wrapped and an expiration date stamped on the bottom. The kit will be a 2 inch by 4 inch by 4 inch rectangular prism, easy to ship and store at room temperature.

Our packing plan does not address the major weakness of trash. We decided instead to address the weakness of fluorimeter.

Feature 2: Hardware - PCR Machine & Fluorimeter

Include PCR machine to make the whole system more efficient. The Flurometer is included to make our results more accurate, and make analyzing the DNA easier.

PCR Machine

Major Strength: Accurate

Major Weakness: Time for procedure

Heating: extreme pulses of heat

Cooling: extreme pulses of cool air

The group has chosen to redesign the PCR machine to make more time efficient. Instead of taking an hour and half to prepare the sample to analyze the DNA, the PCR machine will take 20 to 30 minutes. This will make the predicted results much easier to approach. This will be possible by applying extreme pulses of heat, and cool air to change the temperature in the machine in a time manageable manner.


Major Strength: Easy to use

Major Weakness: Too much excess light

Redesigning the container to limit the amount of light interfering with the samples

The fluorimeter will be redesigned to eliminate the excess light that hinders accurate analysis of the DNA. This will be done by Flurimeter in a completely enclosed system with a little window that allows the camera to better access the sample for more accurate pictures.