BME100 f2015:Group14 8amL6

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BME 100 Fall 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: Johnathon Talos
Name: Jared Johns
Name: Zachary Smith
Name: Ryan Bartholomew
Name: Morgan Cobban
Name: Cara Beauvais


Bayesian Statistics

Overview of the Original Diagnosis System

DNA samples were collected from patients and distributed amongst 17 teams of 6 students each to diagnose a total of 34 patients with disease-associated SNP. The DNA samples were diluted with a buffer solution and SYBR Green, then a drop of this solution was placed inside the fluorimeter, and three images were taken of each sample. These three images acted as our repeated trials. To further reduce error, we compared the DNA samples to a positive and negative control, made sure to keep light out of the fluorimeter, and tested our patient DNA after calibrating the machine. Our data could have been affected by the quality of the camera (many images were slightly blurry), light leaking into the system, and there was a lot of room for human error with the pipetting system, and everything had to be completed one at a time. The material the fluorimeter was made of was a flimsy cardboard, and this could have had an effect on the validity of our results. There was also a lot of waste involved with the process, including numerous slides and even more pipette tips. However, image J worked well as a software to distinguish between the positive and negative samples. The class data displayed 6 blank sets, 16 negative results, 8 positive, and 4 inconclusive.

What Bayes Statistics Imply about This Diagnostic Approach

In Calculations 1 and 2 we calculated Bayes values very close to 1.00. This means that there is a close to 100% probability that a patient will get a positive final test conclusion given a positive PCR reaction, or a negative final test conclusion given a negative PCR reaction. This indicates good reliability of the individual PCR replicates for concluding if a person has the SNP disease or not.

Our Bayes values for calculations 3 and 4 were quite low, close to 0.5, which indicates a 50% probability of a final test result correctly diagnosing a patient with the disease. A 50% chance of a correct diagnosis means that PCR was not reliable at all for predicting the development of the disease.

Three possible sources of error that our data could have been affected by are the quality of the camera which in turn effects the quality of the image produced, the possibility of light leaking into the system as we where taking our image due to the lack of a reliable flap, and the possibility of human error while pipetting the reagents and DNA.

Intro to Computer-Aided Design

During this lab, TinkerCAD was used to recreate an Open PCR device like the one used in previous labs. However, this new device will be altered to propose a potentially more effective and higher quality device based on what we as a group felt the strengths and weaknesses were of the original PCR device. Using TinkerCAD, we were tasked with adding or removing components of the PCR device that we feel will make it a more effective product. Given a pre-made template for the body of the device we will add theoretical components to increase the efficacy and reliability of the product and the data it provides. TinkerCAD is a highly simplified computer aided design program similar to that of SolidWorks or CAAD. This simplicity can make this program more accessible to more people but can also limit the detail and precision of designs made in the program as there are not as many variables and values to be considered like in the more complex SolidWorks or CADD.

Our Design

In our design PCR machine, we chose to focus on altering the lid and increase the ease with which it can be used and sealed, and the size of the machine itself. By adding additional sealant around the entire lid, we where able to improve upon the seal created without requiring additional operator effort. In addition to this, we included latches to ensure that the seal remains intact and the device insulated as the measurements are taken, and included a convenient handle to allow for easier manipulation of the lid. In addition to altering the lid, we nearly doubled the size of the device itself to allow for the machine to accommodate more samples.

Feature 1: Consumables

  • Pre-measured reagent dispensers (PCR mix, primer, SYBR green, etc)
  • Multichannel micropipette and tips
  • Glass slides

Example of the Multichannel Micropipette

The new product will no longer include a single micropipettor and unmeasured quantities of reagents like we were provided in the lab. Due to the unreliability of the common consumer this new product will instead include pre-measured amounts of reagents, such as the PCR mix and DNA primer, pre-packaged and pre-loaded in a multichannel micropipette. Inexperienced consumers, unable to achieve proper measurement using a micropipettor, will be able to accurately dispense the reagents needed to conduct PCR testing without worrying about the proper measurements of these reagents as the proper amounts will be provided to them. The same glass slides will be used with the fluorimeter system and provided in packages containing multiple slides. In order to dispense the prepackaged reagents on to the glass slides, the consumer will layout the glass slides provided and dispense the reagent mixture directly onto the individual slides.

Feature 2: Hardware - PCR Machine & Fluorimeter

The major weakness associated with the PCR machine used to replicate the patient DNA included the inability of the machine to replicate multiple sets patient DNA at a time and the difficulty of the lid to manipulate and seal. To remedy this we will increase the size of the machine in general so it can accommodate more samples. In addition to this we will alter the lid to include a seal that lines the outside so that when closed, the seal is immediate and the operator doesn't have to worry about spinning a cumbersome knob to ensure a proper seal. Also to ensure that the seal remain intact as the measurements are taken, we will include a latch that will ensure to integrity of the seal.

The major weakness of the fluorimeter used in the previous lab was the camera system. Due to varying sizes of cell phones and the placement of their cameras it was difficult to properly align the lens with the edge of the test slides. Also, since the phone was loosely placed inside the fluorimeter box, maintaining the position of the camera was difficult. To remedy this, the new product's fluorimeter system will be equipped with a way to align and hold a cell phone camera in place outside of the fluorimeter box so that it is aimed properly at the edge of the test slides through a hole in the side of the box. A seal will made between the edge of the camera lens and the edge of the box to prevent light from entering the system.