BME100 f2014:Group6 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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Name: Prakriti Shukla
Name: Galt Goettl
Name: Laura Stokes
Name: Gavin White
Name: Yamilex Bustamante
Name: Paul Chua


Bayesian Statistics

Overview of the Original Diagnosis System

In order to calculate the Bayes statistics, 34 groups perform the diagnostics in order to perform the DNA analysis. The groups were given 3 DNA samples from 2 patients. The overall data was then made public to the rest of the groups. In order to prevent error and ruining the rest of the data, each of the groups only performed tests on 2 of the patients. The same procedure was followed throughout all the groups in order to limit human error. This includes how the samples were analyzed in the PCR machine and how the images were taken in the flourimeter. While taking the images, 3 different drops were used also in order to prevent error. Furthermore, the camera used to take the images was approximately the same distance away from the flourimeter for each of the groups. (4-5 cm). The majority of the class had valid data, however there was some groups that did not fill in the data and some data that was inconclusive.

What Bayes Statistics Imply about This Diagnostic Approach

Calculations 1 and 2 show that the results were very reliable in seeing that the patients had the diseased gene or not. Both the calculations were very small or close to 1.00 (100%) thereby showing the accuracy of the calculations. Possible sources of error include human error, sample contamination or using the machine incorrectly. These errors would cause many changes in the calculations. Contamination could ruin the patient sample and the incorrect strand may be replicated. Finally, using the machine incorrectly and setting the incorrect values on the OpenPCR machine could have provided for error.

Calculations 3 and 4 imply that the results were not reliable as the Bayes was not close to 1.00 (100%) and was very small.

Computer-Aided Design


TinkerCAD is a building software that has preprogrammed shapes. The group imported the original shapes from the OpenPCR machine and built the original PCR machine. The tools on TinkerCAD were used to ensure that the machine was the correct size.

Our Design

New PCR Design (back).PNG

New PCR Design (front).PNG

This design is different from the original PCR machine because it limits the amount of equipment needed for analysis. The fluorimeter is attached to the bottom portion of the PCR machine. The fluorimeter also has a camera attached so errors in analysis can be limited.

Feature 1: Consumables Kit

The PCR machine will come with a consumables kit that includes the following:

  • Gloves
  • SYBR Green
  • Taq Polymerase
  • dNTPs
  • Buffer Solution
  • Micropipetter
  • Primer

The consumables kit will come in a box along with the PCR machine. There will be detailed instructions in what each of the materials do and how to use them.

Feature 2: Hardware - PCR Machine & Fluorimeter

The flourimeter and the PCR machine in the new design are combined in one but do not use the same hardware. The purpose of combing the machines is to limit error and hassle. The flourimeter uses completely different hardware and also has a camera attached to prevent error from analysis.

The fluorimeter uses a camera to analyze the pictures through ImageJ. However, there can be some discrepancies from the camera accidentally moving. We implanted a camera in the flourimeter to limit these discrepancies.