BME100 s2018:Group5 W1030 L6

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 Name: Amelia Ikuta Name: Kyle Williams Name: Luke Roy Name: Elena Gomez

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LAB 6 WRITE-UP

Bayesian Statistics

Overview of the Original Diagnosis System

The number of four-person teams diagnosing the 14 patients was 7, with two patients per team. In order to prevent error, three PCR tests were done per patient and three images were taken and analyzed per tests. A positive and negative control tests were performed (with three images taken of each). Also, Three images of a no-concentration solution (water droplet) were taken as a controls for imageJ results. The number of conclusive results was 9 out of 14, and the remaining 5 were inconclusive.

In calculation 1, the probability that a patient will have a positive PCR reaction given a positive final test conclusion is about 80%. The probability that a patient will get a positive final test conclusion given a positive PCR reaction is close to 50%. This implies that the PCR replicates are not very reliable in determining positive correlations.

In calculation 2, the probability that a patient will have a negative diagnostic signal given a negative final test conclusion is about 80%. The probability that a patient will get a negative final test conclusion given a negative diagnostic signal is also about 80%. This implies that the individual PCR replicates for concluding that a person has the disease or not is more reliable when both are negative.

In calculation 3, the probability that a patient will have a positive test conclusion given the patient develops the disease is close to 50%. The probability that a patient develops the disease, given a positive test conclusion is more than 100%. This implies that the PCR is reliable in predicting the disease from a positive test conclusion but is not reliable in diagnosing the disease once it is already present.

In calculation 4, the probability that a patient will get a negative final test conduction given the patient did not develop the disease is around 80%. The probability that a patient will not develop the disease given a negative final test conclusion is more than 100%. This implies that the PCR is reliable in predicting the disease from a negative test conclusion but is only partially reliable in diagnosing the disease once it is already present.

One possible source of error was the camera quality and inconsistent positioning of the camera while it was taking pictures in the fluorimeter. This would result in differing image qualities that imageJ would not be able to accurately test. Another source of error is the micropipettor not receiving and releasing all of the solution every time. This would result in different measurements of solution than expected. Another error is the SYBR green not being properly handled by being given overexposure to light. This chemical is supposed to be kept in a dark place for it to work at its highest capacity but exposing it to light weakens it.

Intro to Computer-Aided Design

3D Modeling
Solidworks was used to design the modification to the fluorimeter. It was a good choice since there had already been some prior experience with that software. The parts were drawn independently of any previously given files, the dimensions being based on primarily the average measurements of the group members' smart phones as well as the measurement for the width of the fluorimeter. The time spent designing was appropriate for the complexity of the design. This is due to the intuitive interface of solidworks and the easily definable dimensions of the design. All of the features necessary, like filet, sketch, boss extrude, cut extrude, and rotate, were easily manipulated to design the product the way intended.

Our Design

Our design is an adjustable and fixable phone stand that will be included in the kit with the fluorimeter. It has two clamps and an adjustable arm. The clamps are spring powered and can fit around almost all smart phone models and different sizes of fluorimeter bases, so our design is compatible with various brands and products often used. The arm is also adjustable so that the phone can be raised or lowered to optimum height for imaging. The arm can also be tightened, allowing for a set distance between the phone and the LED light of the fluorimeter.

In the original fluorimeter design, the distance between the phone camera and the LED light/ drop to be imaged could vary wildly between pictures. Each time the phone is picked up and replaced between trials, its position could be different from the last trial. This causes errors in imaging and image analysis because the distance affects the intensity of green light detected by the phone camera. Because this is the most important part of the imaging step in this lab, it is very important to minimize the possible error in this step.

Feature 1: Consumables

A "very important" component of an experiment means that these ingredients/items are vital to the experiment. Essentially, the experiment could not be constructed nor conclude to accurate results without these consumables. If in fact, we did redesign the PCR machine with shorter more efficient tubes, not many accommodations would have to be made in relevance to the consumables included. Nonetheless, our kit would include everything needed to complete the PCR reaction as well as the fluorimeter function. This would include the PCR mix, the SYBR Green Solution, and the primer and buffer mixes. Along with the vital chemical components needed to complete the PCR reaction, our kit will also include disposable pipette tips and glass slides. Through our kit, the consumer will be covered through RegEnergy with all of the consumable aspects of the experiment, and will only be responsible for already being equipped with a micropipette and lab protective gear, such as lab coats and gloves. And of course, the RegEnergy PCR Kit we will include a standard PCR machine and our edited Fluorimeter.

Our kit includes all the major consumables in order to edge out our competition. As said before, many companies only include certain components in the kit and might sell the other parts separately or might not offer them at all. We see this as an opportunity to be more appealing to consumers as we offer a more economical and inclusive option to PCR experimenting. Another component of our approach stems from our improved fluorimeter design.

Feature 2: Hardware - PCR Machine & Fluorimeter

We will not alter any parts of the PCR machine in our design. As it is, the Open PCR machine has may advantages, including being open source, being fairly inexpensive, having a clear and straightforward interface, and being easy to use. In this lab, we did not conclude that any errors or inaccuracies were due to this machine or this step in the lab. For these reasons, we will keep the Open PCR machine in our redesign without changes.

For the fluorimeter part of the design, we will add an adjustable phone stand to the original design. The major problem with the fluorometer is that the distance between the LED light and the phone (camera) may vary each time the phone is picked up and replaced. This can introduce error because the distance affects the amount of green light the camera picks up, so there may be differences in green light observed between samples that is not due to SYBR green or the presence of specific DNA. Our phone stand will solve this problem. It will clamp to the fluorimeter and to the phone and tighten to each, allowing a set position for the phone. The phone can be taken in and out of its clamp without disturbing the distance between itself and the LED light.