BME100 f2013:W1200 Group3 L6

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BME 100 Fall 2013 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
Course Logistics For Instructors
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Name: Samuel Mokdad
Role(s) TinkerCAD & Design
Name: Morgan Jameson
Role(s) Design & Improvements
Name: Tony Facchini
Role(s) Data Analysis
Name: Cameron Ghods
Role(s) Design & Improvements
Name: Evan Epperson
Role(s) Design & Improvements

All contributions on lab work is equal throughout the group though it may not appear in the open wetware history of contributions due to the way our group has structured our execution of lab work. All members of the group perform equal duties and contribute to the completion of all lab work.


Computer-Aided Design


TinkerCAD is a simplified version of AutoCAD that is used to create 3D objects and designs. The program is pretty straight forward and is an introductory program for people going into design. In this program I created a 96 well plate which I used to hold the micro test tubes. I designed a PCR machine that was capable of holding up to 96 samples as opposed to the previous 16. Additionally, I color coated them (-=red, +=blue) which can help with identification of the positive and negative controls as well as adding tags that loop around the top which can also help with labeling. This way it is easier to see which test tube is which and doesn't require writing on the actual tube. This program saves designs as .stl files so they are capable of being 3D printed.

Implications of Using TinkerCAD for Design

A possible way of redesigning the OpenPCR machine is to make it faster, hold more samples, and more compact. We cannot show how to make it faster using TinkerCAD since that is based on the internal functions, but it would be a good improvement. What we can do is make is more efficient by increasing the number of samples it can fit. By adding a 96 well plate inside this machine will only need to be used a few times for an entire class because of the drastic increase in capacity while saving time, power, and money. When we opened up the OpenPCR machine a few classes ago we notices there was a lot of empty space inside so we could redesign it to become more compact while still being able to hold more samples be making into this shape as opposed to the taller version. This way the samples can all fit while still maintaining the components and rearranging them into shorter, but wider manner. This will then reduce the amount of material needed and save money in production costs. If you look at the image below you can see the wasted space as well as the lack of room for samples in the current openPCR model.

Feature 1: Cancer SNP-Specific Primers

Background on the cancer-associated mutation

rs17879961 is a pathogenic mutation that is found in homo sapiens on the 22nd of the 23 chromosomes. This mutation affects the single nucleotide polymorphisms in the CHEK 2 gene which has been found in both hereditary and non-hereditary cancers. This gene's primary function is to produce checkpoint kinase which is a protein that works to repress tumors. Nucleotides are the building blocks or sub-unites of nucleic acids that are also organic molecules that serve as monomers. Polymorphism is two or more clearly different phenotypes that exist within the same population of a species.

Primer design

  • Forward Primer: 5'-A C T C A C T T A A A C C A T A T T C T
  • Cancer-specific Reverse Primer: 5'- G G T C C T A A A A A C T C T T A C A C

How the primers work:
Primers are specifically sequenced DNA that work to produce specific genetic material.Primers do this by attaching to a specific area of the gene on two strands. These strands are not exactly the same and compliment each other. The primer then works to extend only the specific area of the gene it attached to. If the primer is not an exact compliment to the other strand the DNA will not replicate. When this happens only the cancer containing DNA will be replicated. In our lab the DNA containing the cancer SNP rs17879961 will be amplified by the primers.

Feature 2: Consumables Kit

The small tubes are typically placed all together in a plastic bag. Instead the tubes would be placed in a holder similar to the one the micro-pipette tips are in. This makes for a more convenient set-up and organization. As well the tubes would be perforated so that the there could be any amount in a set, not just four. Lastly, to secure all of the tubes there would be lid to go over the container to help prevent spillage.

Feature 3: PCR Machine Hardware

The PCR machine will be redesigned to address a few small issues that were found with the original version. Using the original version of the PCR machine was a large time consuming processes, so we are redesigning our PCR machine to reduce the run time. Another problem we saw with the PCR machine was that the performance was not reliable. Our redesigned machine aims to be accurate 100% of the time. We did not see a problem with the PC software; most people interested in using a PCR machine will have access to a computer. By putting the software on the computer, we are able to minimize the size of the machine. The last change that we are going to make to the machine is the size of the sample tray. Originally the PCR machine was only able to use 16 samples, but we thought this number was much too low. The improved PCR machine will be able to run 96 samples in each run."

Feature 4: Fluorimeter Hardware

After using the fluorimeter hardware in another system, we have decided to make several changes that we see necessary. These changes will mainly be concerning the amount of variables in operation. The original fluorimeter hardware was very difficult to set up because of the large quantity of variables. We place on creating a more effective camera stand that is adjustable for different cellular phones that may be used by the consumers. The camera stand will also be attached to the device so that the distance from the camera to the lights will become constant. We hope to improve the results of the machine by making the product more user-friendly and by reducing the chance of user error.

Media:Instruction manual for PCR.docx==Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach==

The results from calculation 3 give the probability of a person with cancerous DNA receiving a positive PCR diagnosis. This calculation has very low percentage meaning that the cancerous DNA will most likely not return a positive result from the PCR machine. The PCR instrument may not be the best device to use for this experiment. Calculation 4 tests specificity, giving the probability that a non-cancerous DNA sample will test negative using the PCR test. The calculated percentage for calculation 4 was also very small meaning that the PCR diagnosis test will likely return a positive result for a non-cancerous DNA sample. This suggests that the PCR machine would not be a good instrument to use to test for a non-cancerous negative result.