BME100 s2014:T Group6 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: Nicole D. Fisk Name: Doan-Nhi T. Tran Name: Mark A. Keppler Name: Rayan S. Altayyar Name: Brittani M. Ogden [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] Our Design [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 [Instructions: Use the answers from questions 3 - 7 to compose, in your own words, a paragraph about rs237025] Primer design Disease SNP-specific Forward Primer: [Instructions: type the sequence of the forward primer] Reverse Primer: [Instructions: type the sequence of the reverse primer] How the primers work: [Instructions: explain what makes the primers disease-sequence specific. In other words, explain why the primers will amplify DNA that contains the disease-associated SNP, and will not exponentially amplify DNA that has the non-disease allele.] Feature 2: Consumables Kit [Included in our complete consumables kit: -buffer tubes -micropipette -micropipette tips -glass slides -PCR tubes -tube rack -calf thymus ] [SYBR Green I is a light sensitive dye that binds to DNA. In our experiment, foil was placed on top of the tube(s) containing SYBR Green I. The foil failed to cover the entirety of the tube. In our new designed kit, the color of the tubes containing SYBR Green I are colored black in order to avoid any light hitting the dye. The rack containing all the test tubes will come a bit bigger in order to hold more of the tubes. All items listed will come in one complete kit instead of having to buy or grab all parts separately. It will contain the right amount of slides, tubes, and tips needed.] 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.] "Calculations 3 and 4 measured the positive predictive value and the negative predictive value of the PCR process, respectively. The positive predictive value (PPV), or the probability that the person that receives a positive result actually has the disease is supposed to be as close to 100% as possible (IS THIS GOLD STANDARD???). However, for calculation 3, the calculated value for the PCR results was more than 30% away from 100%. This means that the machine is not an effective predictor, and therefore there is a rather high probability that a patient given a positive result does not actually have the disease. For calculation 4, the negative predictive value (NPV) was found. This value is the probability that someone who receives a negative test result does not have the disease. This calculated value for the PCR sumo4 gene existence test was somewhat closer to 100% than calculation 3. For calculation 4, the value was slightly over 20% below the 100% golden standard. This means that it has a relatively high NPV, meaning it does not offer as many false negatives as it does false positives, and one can be fairly confident that their negative result is accurate???(IS THIS RIGHT?). __________???? ADD MORE???? INCLUDE PREVALENCE???"