BME100 f2013:W900 Group1 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
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EZ Diagnosis

Neema Jamali
Name: Riddhi Rohit
Name: Carter Hill
Kaitlyn Allen
Crawford Pederson


Computer-Aided Design


TinkerCAD is a free online 3D design software that allows you to create designs for prototyping which can be saved and 3D printed. We used this software to redesign PCR tubes in our lab. Many problems that were experienced from the original PCR tubes was fixed. We redesigned our tubes by connecting them and adding a place to slide a lid in. We made the lid separate so it makes it easier to label. Also, our design would be the standard distance apart so you can use them with most PCR machines as well as they have the ability of being cut to whatever number of tubes you need.

Implications of Using TinkerCAD for Design

TinkerCAD could be a very practical tool and has many applications in multiple fields of study. It could be used in this lab to design a camera holder that make it a fixed, known, distance between the beam of light and the camera lens, effectively eliminating some of the error in the data. If you wanted to, you could then mount the fluorimeter to the camera holder and mount that entire assembly directly into the enclosure. The beneficial part of the software is that you can put all your thoughts and concepts together and figure out ways of making them all work together before spending time and money fabricating it. You can quickly download the stl. file and get printing right away. Depending on how large and complex your design is, you can have a working prototype within a few hours.

Feature 1: Cancer SNP-Specific Primers

Background on the cancer-associated mutation

Nucleotides are the basic building blocks of DNA. When a nucleotide differs between the same species it is called a single nucleotide polymorphism(SNP), in other words it is a certain little section that can differ between two organism within the same species. Certain SNPs can have harmful effects. For example, rs17879961 is a pathogenic SNP that can be found on the 22nd chromosome of the species Homo Sapiens. If a person has it, it can be found on the CHEK2 gene. This SNP has been linked to inheritable cancer because the CHEK2 gene deals with tumor suppression and SNP hinders this function.

Primer design

  • Forward Primer: A C T C A C T T A A A C C A T A T T C T
  • Cancer-specific Reverse Primer: 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 a complimentary DNA sequence for the specific allele selected. They bond to that allele and the DNA polymerase replicates that specific allele, but only that allele because the polymerase can only synthesize the molecules with the primer. This is why only the cancer SNP is duplicated and amplified. The PCR cycle is a processes that changes the temperature of the sample causing the amplification of the certain gene. The growth rate for the amount of that allele is exponential (2^n), resulting in a large enough population of the SNP rs17879961 to accurately measured.

Feature 2: Consumables Kit

All the consumables will come in durable containers like the ones we had in class. The PCR tubes will, micropipette tips, and glass slides will all have their own separate containers. The fluorimeter and camera mount will be placed at the bottom of the box with a styrofoam layer covering it, in order to protect it and keep it from moving around. Next all the consumable containers will be placed in the box with another piece of styrofoam over top. The box will be closed up and placed in another box for shipping.

Feature 3: PCR Machine Hardware

The PCR machine will come pre-assembled in order to avoid the possible inconveniences that may likely result from human error in assembly. A peltier device will replace the resistor used for heating and cooling. This peltier device will far more efficient and will be able to adjust temperatures more rapidly and accurately. The software's user interface will be simple and effective, with certain PCR protocols already built in to the system. All of the protocols can be edited and saved for future use.

Feature 4: Fluorimeter Hardware

The fluorimeter will also come pre-assembled in a compact, self-contained unit. The slides will be able to slide outside of the fluorimeter so that they can be cleaned. At the top of the fluorimeter will be a lid that covers a hole just large enough to fit a micropipette tip. This fixed hole will allow for consistent droplet placement. There will also be a camera inside of the fluorimeter in order to stop extra light from entering the system and skewing data. Software included inside of the fluorimeter will be able to perform the same type of analysis as ImageJ, removing the problems posed by human inconsistency. Finally, a USB port will allow users to upload both the images and the data onto a computer for interpretation.

Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach

Bayesian Statistics can help understand the limitations of diagnostic tests. In this particular lab, Bayesian stats were used to determine whether a patient have cancer or not. By getting really small value for calculation 3, it can be determined that CHECK2 PCR has a low sensitivity. Low sensitivity mentions the probability that a person with the disease being tested for will result in positive. On the other hand, the CHECK2 PCR also has a high specificity in the prediction of cancer because the Bayesian statistics delivered a number of more than one for calculation 4. High Specificity means that the probability that a person who does not have the disease being test for will result in a negative diagnosis.