BME100 s2014:T Group15 L6: Difference between revisions
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* Reverse Primer: ''5’ AGTTTTCTAATGAAATCA'' | * Reverse Primer: ''5’ AGTTTTCTAATGAAATCA'' | ||
How the primers work: | 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. | |||
Revision as of 11:31, 17 April 2014
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
LAB 6 WRITE-UPComputer-Aided DesignTinkerCAD [Instructions: A short summary (up to five sentences) of the TinkerCAD tool and how you used it in lab on November 20th]
[Instructions: Show an image of your TinkerCAD design here] [Instructions: A short paragraph describing your design. Why did you choose this design? How is it different from the original OpenPCR design?]
Feature 1: Disease SNP-Specific Primers[Instructions: This information will come from the exercises you did in PCR Lab B.] 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
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.] [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[Instructions: This section is OPTIONAL, and will get bonus points if answered thoroughly and correctly. Here is a chance to flex some intellectual muscle. In your own words, discuss what the results for calculations 3 and 4 imply about the reliability of PCR for predicting the disease. Please do NOT type the actual numerical values here. Just refer to them as being "close to one" or "very small." The instructors will ask you to submit your actual calculations via a Blackboard quiz. We are doing so for the sake of academic integrity and to curb any temptation to cheat.]
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