BME100 f2014:Group12 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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Peter Hillebrand
Darci Botsch
Devon Rusk
Krishnaa Pradhan
Sebastian Fonseca
Jorge Espinoza


Bayesian Statistics

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Overview of the Original Diagnosis System

The BME 100 labs tested for disease associated SNP using DNA samples of patients that are amplified through PCR using the PCR machine. 34 teams of 6 students tested 2 patients for disease associated SNP, resulting in 68 patients being tested total. Several things were done to prevent error. The same PCR controls were used to compare the results of the 68 patients. Three replicates per patient were used to compare the control results to. This reduced any misdiagnosis in the disease associated SNP. All groups also used ImageJ calibration controls. ImageJ was calibrated by each group to measure the amount of SYBR Green I in the pictures of the DNA drops. Three drops were used for each patient, again, reducing any misdiagnosis. The results conclude that out of 186 patients, 92 patients tested positive and 73 negative for the disease associated SNP. 21 were inconclusive. Out of the 68 patients, 30 tested positive, 24 negative, 6 with no results, and 8 inconclusive for the disease associated SNP. Looking at the patients that actually were positive, 89% tested positive and looking at the patients who were actually negative, 77% tested negative.

What Bayes Statistics Imply about This Diagnostic Approach

The Bayes values for calculations 1 and 2 were close to 100. From these values it can be inferred that the device is reliable. Based on these values a patient with a positive PCR result will most likely receive a positive final test conclusion, and a patient with a negative PCR result will most likely receive a negative final test conclusion. Sources of human error that could negatively effect the PCR include miscalculation and inaccurate measuring of the samples placed i the PCR machine. Machine error could include the failure of the machine to properly heat itself or track time, which would result in an error in the results used in calculating the Bayes Statistics.

For calculations 3 and 4 the Bayes values were very small. These results imply that the PCR machine is reliable in predicting the development of the disease, or diagnosis. In other words, patients will most likely not receive a diagnosis prior to showing symptoms of the disease.

Computer-Aided Design

The TinkerCad Tool is an online 3D design tool made for anyone to use in order to create designs. After learning how to use TinkerCAD, the provided PCR parts were imported into TinkerCAD and were placed together using the grouping tool. When each new part was imported, the piece was modified using the rotation tool in order for the parts to fit together correctly. The TinkerCAD tool made assembling the PCR parts together easy and allowed for modifications to the original PCR machine to be made because the parts were able to be modified in TinkerCAD.

Our Design

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This design is similar to the original OpenPCR machine, but minor details have been made in order to improve the device and its functions. This PCR machine will be used in the same functional manner as the original, by testing samples and determining whether a patient is positive or negative for a particular disease. The new design, on the other hand, will provide the machine with improvements that will allow for the machine to be able to function at its full potential. The previous design did not always function properly, giving unreliable data which caused many issues including a great consumption of time. The new design has a larger area for test samples in order to be able to run more samples at once. Also, the machine will decrease the total run time by having a precise way of entering in the desired number of trials. The time that it takes a PCR machine to execute its function is now limited to two hours or less. This design was chosen because the PCR device is a good design, with minor flaws. By modifying the original device, the PCR will be able to function at its full potential of determining whether a patient is positive or negative for a disease in less time and by testing more samples at once.

Feature 1: Consumables Kit

The consumables were, for the most part, very well designed; they will be used similarly and packaged the same as they were in the PCR lab completed above.

Although they worked very well, the consumables were not all flawless. For example, the fact that the primers were exclusive to specific nucleotides made them far less efficient than the ideal. A multi-platform primer is introduced in our design. Also addressed is the meticulous nature of the pipettor. The pipettes used necessitated extreme care and caution, and this made for an extremely slowed process. The improved pipettor is simpler and more refined for quick adjustment and use. One of the advantages of this new pipettor is that the amount of liquid it extracts can be modified and monitored through an electronic display window, and therefore the values can be entered by pressing the buttons with the digits that correspond to the desired value.

Another of the improvements done in the consumable kits is the introduction of a mechanism to unload completely the substances that are taken in the pipettor. In several occasions this last device did not deliver 100% of the amount of the substance that it contained. Although the amount of liquid that remained is very small it could possibly contribute for errors in future experimental practices.

Feature 2: Hardware - PCR Machine & Fluorimeter

PCR Machine Our PCR Machine will be used in the same functional manner; it will test the samples and determine whether the patient is positive or negative in regards to the disease.

There will, however, be improvements upon the previous design. The previous design was often defective, and this unreliability caused many issues including a great consumption of time as well as the losing of data. This must be rectified; every machine should work equally well, and every machine should be efficient in what it does. The time that is takes a PCR machine to execute its function has now been completely limited to two hours or less.

Fluorimeter The fluorimeter's function will also remain unchanged. It will be used to measure the fluorescence in proportion to the total amount of substance measured.

The fluorimeter used was not perfect; for example, one attribute that needs to be improved was the camera stand; whether a phone is used as the official camera or another more precise camera, the intended camera must be able to stay firmly in place; the picture should be taken from the same place every time to ensure consistency. This issue is addressed in our design; the camera stand is placed such that it does not have to be moved for any reason throughout the experiment. Another issue encountered was the precision aspect: a great deal of precision was necessary to complete the experiment, but the utensils given were not necessarily conducive to such results. What the fluorimeter needed was more instruments that allowed for precision; a set place to balance the pipette will be added to our fluorimeter to establish further consistency.