BME100 s2015:Group7 9amL6

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BME 100 Spring 2015 Home
Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
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Name: Brandon Hansen
Name: Harris Tran
Name: Luke Shaffer
Name: Jaid Coronel


Bayesian Statistics

Overview of the Original Diagnosis System

In this setting, multiply teams of brilliant scientists work similarly to develop data necessary to conclude a disease-associated SNP allele in a collective sample group of patients. There are eight groups, with four-five scientists each with the knowledge and skill necessary to successfully complete the diagnostic, assigned with two patients each. Separately, each group were given different patients to diagnose. However, each group proceed through a similar set of steps and techniques to diagnose the patients for a disease-SNP. Meaning both the process and the result are kept as close as possible to each other, as to not deviate too much collectively.

First, small sample-size taken from a patient of unknown condition are further divided into plastic tubing, to be primed for the PCR machine and procedure. After the PCR cycle, each group takes their respective sample and proceed with the fluriometer testing. Around this time, the newly replicated samples are primed with a color-indicator solution, and the machine is correctly calibrated for use. This allows the laser of the fluriometer to pick up any DNA that are linked with the disease-SNP. However, this dilutes the sample to half its initial concentration after the PCR replication.

By using ImageJ and the pictures taken from the fluriometer testing, each group were able to calculate the area of colored concentration in each sample. An average assumption can be made about the patient assigned to each grouped. After the all the data are collected, each group collectively input their final result. Those that shows large gradient of the color-indicator in the DNA sample designates the patient to be carrying the disease-SNP. However the exact opposite cannot be said for certain. They're patients that shows a noticeable level of the SNP; however when compared to a calibrated sample that acts as a threshold, the sample became conclusively negative.

What Bayes Statistics Imply about This Diagnostic Approach

For the most portion, multiple data-sample correctly correspond to the concentration of the calibrated positive control, signafying that the patient is a likely candidate to be carrying the target SNP. Analyzing the collective data, it can be concluded the frequency of the negative tests are more than half of the sample gathered--excluding the data that are inconclusive. And calculating for the Bayes value, the end results in a high percentage of which each sample are tested positive in a positive PCR reaction. Similarly, the negative instances of a negative PCR reaction are also close to 1.00 in their Bayes value.

However, there are matters that could greatly alter the statistical Bayes value. For example, if there are cases that affects the Bayes value in a negative direction, then the frequency of the result will deviate collectively. One possible explanation is contamination before, during, or after prepping the sample for either machine usage. This affects the concentration of DNA present in the solution sample. Or another circumstances where the calibration of the controlled samples are tested incorrectly. If not done correctly, then the images that appears and are compared to the controlled will not be consistent. And there are instances where the the final result is inconclusive from the calculation, where the value for calculation are nonexistent.

Similar to the individual PCR replicates, there is a high probability of receiving the disease if the final conclusion is tested positive for the SNP. And vice versa for those tested negative for the disease. The Bayes numerical values for each instances concludes in a high percentage, close to 1.00.

Computer-Aided Design


Our Design

Name: New and improved PCR machine

Often than most time, medical processes requires extensive amount of time in order to properly replicate, manipulate, and analyze. Given the circumstances where all other work are finished, and waiting leaves certain individuals anxious, the machine itself can be used to both stimulate the users muscle and movement coordination, and prevent boredom. In this way, it benefits the users immensely, keeping both the mind and body sharp and awake to perform more tedious work. Through using electricity and hollow-based technology, the improved PCR machine comes equipped with customizable lighting and sound-bass MP3 amplifier, respectively. In this way, it allows the users to be active and de-stressed without leaving the laboratory. Along the same time, the more powerful PCR machine will perform its initial function and process the chain-reaction at an increased rate. Depending on the make and model, each machine could produce more amount in the same given time as its predecessors.

Feature 1: Consumables Kit

Giving considered amount of thoughts to the packaging schematics for the kit, the group decided to model the packaging methods after more popular choices: bubble-warps. In this way, both the machine and the consumables will be protected during the handling and shipping process of the product. The liquid solution will be kept cooled at a specific temperature in a separate insulated container; while the dry materials and hardware will be warped within multiple layers of bubble-warp for protection alongside the liquid-package. With the plastic tubing be kept inside a sturdy box for convenient storage. Although the weakness in this scheme is that there will be two separate packages to specially handle, it will prevent the cooling agents for the liquid mixture to condense and damage the machine's hardware. Furthermore, it will be easier and economically efficient for the company to ship or sell additional units of the kit.

Within each Consumable Kit:

  • Liquid reagent container and solution (specially marked)
  • Small plastic tubing
  • Plastic micropipettor tips
  • Instruction for proper equipment usage and storage
  • Instructions for customizing lighting
  • Emergency hotline for quick supply/assistance

Feature 2: Hardware - PCR Machine & Fluorimeter

THe finished product is a PCR machine with a built in fluorimeter. The fluorimeter will be contained in a little tray table compartment that extends out of the PCR machine.

One of the key weaknesses we identified in the previous versions of the previous PCR machine is that it takes ages for the machine to work, and it does not even provide an interesting sight while its work is in progress. To eliminate this hassle, we have decided that the new and imporved PCR machine will not increase the DNA by a factor of two, but a factor of four, and additionally will be a portable rave machine to provide the busy researchers with a much needed dance break from their busy lives. The machine has the lights built in (cylinders built on top) and a massive sound system to meet these needs. Last but not least, the PCR machine will feature an adjustable timer so that one may set the length of the dance party in advance, because everyone has a busy schedule, and we as designers tried to be midful of that.