BME100 s2014:T Group15 L6

From OpenWetWare

Jump to: navigation, search
BME 100 Spring 2014 Home
People
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
Photos
Wiki Editing Help
Image:BME494_Asu_logo.png


Contents

OUR COMPANY

Name: Ariana L. Shults
Name: Ariana L. Shults
Name: Samantha J Hatley
Name: Samantha J Hatley
Name: Megan Mendieta
Name: Megan Mendieta
Name: Heston Scott Hamilton
Name: Heston Scott Hamilton
Name: Mohammed A. Tamim
Name: Mohammed A. Tamim
Name: Brenda Cardenas
Name: Brenda Cardenas


ASU's High Capacity PCR and Fluorimeter


LAB 6 WRITE-UP

Computer-Aided Design

TinkerCAD


TinkerCAD is a tool used to help easily create designs that can be readily exported to a 3D printer for production. The program can be used as a way to manipulate a design inexpensively and without having to physically create different versions.

Our Design


Image:meganisgod.jpg

This design was chosen in order to increase the effectiveness of the PCR Machine design. By increasing the amount of PCR tubes that can be processed, the cycles will be twice more efficient than the original design. This will in part will cause an increase in the overall size of the machine, as well as in the heating and cooling units. An increase in size is a small sacrifice for double the efficiency, which is called for by consumer need.

Feature 1: Disease SNP-Specific Primers

Background on the disease-associated mutation

SNP stands for single nucleotide polymorphism. This means that two different phenotypes of a base pair of DNA exist within the same population of a species. In the case of rs237025, this species is homo sapiens. This sequence is located on Chromosome six at position 6:149721690. The clinical significance of this SNP is listed on NCBI's website as "other". This SNP is associated with the SUMO4 (SUMO4 stands for small ubiquitin-like modifier 4) and Tab2 genes. Diseases linked to this SNP include Type 1 diabetes and rheumatoid arthritis. The normal non-disease allele contains the base sequence GTG, a change in this allele at the G position is linked to the disease. The disease-associated allele contains the sequence ATG instead.


Primer design

  • Disease SNP-specific Forward Primer: 5’ GTGAACCACGGGATGTCAG
  • Reverse Primer: 5’ AGTTTTCTAATGAAATCA

How the primers work: The forward primer to be used in PCR contains 20 bases and ends with the nucleotide from the disease-associated allele. Based on how the forward primer was designed, the primer will bond only to a complementary disease-SNP-containing template from a patient with the disease containing allele. If either primer can't bind 100% to the template (such as a to a template not containing the disease allele), PCR will not occur.



Feature 2: Consumables Kit

The consumables will be packaged in a very similar way to the previous design. The plastic tips will still be packaged the same way as before, in the plastic container. The regents will be packaged differently. They will also be in a container this time similar to what the plastic tips were held in but black as to have no light coming through. All of the reagents, PCR mix, buffer, primer, and SYBR green dye, can fit into the one container. The glass slides will stil be the same with the easy accesibility. One way that our new packaging addresses a major weakness is by the new container for the reagents. With having a solid black container less light will get through distorting the SYBR Green dye less in the long run. Our new consumables packaging plan still has the accuracy of the micropipeter and easy accesibility of the reagents as the first design as well.



Feature 3: Hardware - PCR Machine & Fluorimeter

The PCR machine was altered in order to represent ASU (colors) and to most importantly increase the cycle efficiency by adding another heating block. The fluorimeter will be packaged with the PCR machine just as it was in the original design. This includes the phone holder, the laser beaming fluorimeter, and the box that is utilized to block out light. There is an included dispossible container for plastics and glass.

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

In calculation three, the frequency of testing positive for the disease, frequency of positive conclusions, the frequency of the probability of a positive conclusion given a positive disease and the frequency of the probability of a positive disease given a positive conclusion were determined. Both the calculated frequencies of positive disease and positive conclusion were closely correlated, as well as being quite small, and suggest accurate results by the PCR testing process. Calculation 4 shows a similar situation, but to an even greater degree. All frequencies in calculation 4, predicted and actual, are identical, strengthening the case for the reliability of the PCR results.

Personal tools