BME100 s2015:Group15 12pmL6

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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: Tyler McCluskey: Team Leader
Name: Kelsie Hermanson: Driver
Name: Matt Birkholz: Negotiator
Name: Alexzandra Rico
Name: Jasilynn Cox


Bayesian Statistics

Overview of the Original Diagnosis System BME100 tested patients for the disease-associated SNP by utilizing PCR reactions and ImageJ to measure the phosphorescence of the samples. By measuring the phosphorescence of samples, it could be determined through utilization of positive and negative controls whether a patient was at an increased risk for the disease. Through division of labor, 68 patients were tested for the disease, but 20 patient's tests were inconclusive or were rejected for lack of data. Within each team, 2 sub-groups were created, those who captured data and those who examined and interpreted the data. Error in data was prevented by the creation of positive and negative controls for every group so that each data set could be compared against it. The separate controls effectively created individual ranges for which the data could be compared to. The number of replicates ensured that the average of the data would heed a value close to expected. The ImageJ calibration tools and color splitting tools allowed for the stripping of colors other than green that may have added to the amount of phosphorescence. By stripping all photos of blue and red pigment, the green is better measured. In addition, the calibration creates unity among all groups in measurement technique. While twenty of the patients' tests must be discarded, the patients whose data was not significantly skewed showed a high reliability as the Bayes values were nearly 1.00.

What Bayes Statistics Imply about This Diagnostic Approach

The results of calculations 1 and 2 imply that the reliability of the individual PCR replicates for concluding that a person has the disease or not is very credible as the Bayes values are very close to 1.00. Possible sources of error, be both human or machine, include but are not limited to: human error in data input, mis-measurement of data, rounding error, and machine malfunction. The data that was discarded led to a smaller pool of available data but positively-impacted the overall reliability of results.

Computer-Aided Design

TinkerCAD is a child's version of CAD and is used to manipulate 3D objects just as CAD is except without the complexity ad ease of use. It is not as complex and has far fewer manipulation tools.

Our Design

We used the pre-made parts of the PCR machine and altered them so that they would actually fit together. We altered the shapes of the pieces so that the tabs would fit flush in the slots.

Feature 1: Consumables Kit

The Consumables Kit will include the following items:

1. PCR Reaction Mix

2. Empty PCR Tubes

3. Disposable pipette tips

4. Micropipettor

5. SYBR Green I

6. DNA Primer Mix

Some major weakness of the consumables in the PCR kit:

–SYBR Green I is light sensitive

–Tubes containing Chemicals look similar (Easily confused with each other)

–A lot of Pipette tips required (non-reusable)

In order to best address these minor issues we have decided upon the following alterations:

SYBR Green will be packaged separately in special packaging and will be clearly marked "Light Sensitive". Additionally, the tubes the SYBR Green I is contained in will be dark colored to minimize light exposure and help the customer to be aware of the importance of this. The tubes containing chemicals such as the Primer Mix or the Taq Polymerase will also be labeled clearly on their exterior to avoid misuse. The pipette tips will be packaged at a limited number, if the consumer should need more they are available as an additional purchase or the consumer also has the option to include extra tips with their order because each tip must be disposed after use to avoid cross contamination. Other than those minor deviations there will be no additional changes made to standard consumables kit packaging.

Feature 2: Hardware - PCR Machine & Fluorimeter

The PCR machine and fluorimeter will be included within the system so that only one machine is needed to process and analyze the results. By placing two machines into a closed system, not only are the samples not exposed to outside conditions but ease of storage as well as transportation is achieved. A cradle for a phone (not pictured) works in similarity to phone mounts for automobile use: rubber clamps/arms holding the phone in a designated position as to not allow for shift in position.

The box is remade as to allow for the dis-assembly and reassembly with ease by designing the individual sides to come apart but snap into place, much like Lego pieces. The pieces will audibly click together once solid contact is made so that the user knows the sides are stable.

The Fluorimeter was redesigned so that light would not be continually be an obstacle as the sides were difficult to close in time for the flash to go off for the camera as well as difficult to close without shifting or knocking the camera causing blurriness and lack of focus.