BME100 s2014:T Group15 L6

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
OUR COMPANY Name: Ariana L. Shults Name: Samantha J Hatley Name: Megan Mendieta Name: Heston Scott Hamilton Name: Mohammed A. Tamim Name: Brenda Cardenas [Instructions: add the name of your team's company and/or product here] LAB 6 WRITE-UP Computer-Aided Design TinkerCAD [Instructions: A short summary (up to five sentences) of the TinkerCAD tool and how you used it in lab on November 20th] TinkerCAD is a tool to help easily create a design that can be used to create a model for a 3D printer. The program can be used as a way to manipulate objects into the shape that you want. Our Design [Instructions: A short paragraph describing your design. Why did you choose this design? How is it different from the original OpenPCR design?] 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 [Instructions: Summarize how the consumables will be packaged in your kit. You may add a schematic image. An image is OPTIONAL and will not get bonus points, but it will make your report look awesome and easy to score.] The consumables will be packaged in a very similar way to the previous design. The plastics will still be packaged the same way in the container holding [Instructions: IF your consumables packaging plan addresses any major weakness(es), explain how in an additional paragraph.] Feature 3: Hardware - PCR Machine & Fluorimeter [Instructions: Summarize how you will include the PCR machine and fluorimeter in your system. You may add a schematic image. An image is OPTIONAL and will not get bonus points, but it will make your report look really awesome and easy to score.] [Instructions: IF your group has decided to redesign the PCR machine and/or Fluorimeter to address any major weakness(es), explain how in an additional paragraph.] 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.