BME100 f2013:W900 Group13 L6: Difference between revisions
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==Feature 1: Cancer SNP-Specific Primers== | ==Feature 1: Cancer SNP-Specific Primers== | ||
'''Background on the cancer-associated mutation'''<br> | '''Background on the cancer-associated mutation'''<br> | ||
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''[Instructions: Use the answers from questions 3, 4, 5, and 7 to compose, in your own words, a paragraph about rs17879961]'' | ''[Instructions: Use the answers from questions 3, 4, 5, and 7 to compose, in your own words, a paragraph about rs17879961]'' | ||
A nucleotide is a compound consisting of a nucleotide linked to a phosphate group and is the basic structural unit of nucleic acids. A polymorphism is where there is one or more variants of a particular DNA sequence. The species in this variation is rs17879961 is homo sapiens (humans). The clinical significance of this SNP is that is so pathogenic. This SNP (rs17879961) occurs on chromosome 22 out of the typical 23 pairs of chromosomes that humans have. | |||
'''Primer design'''<br> | '''Primer design'''<br> |
Revision as of 23:40, 25 November 2013
BME 100 Fall 2013 | 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[Instructions: add the name of your team's company and/or product here]
LAB 6 WRITE-UPComputer-Aided DesignTinkerCAD Implications of Using TinkerCAD for Design
Feature 1: Cancer SNP-Specific PrimersBackground on the cancer-associated mutation [Instructions: Use the answers from questions 3, 4, 5, and 7 to compose, in your own words, a paragraph about rs17879961] A nucleotide is a compound consisting of a nucleotide linked to a phosphate group and is the basic structural unit of nucleic acids. A polymorphism is where there is one or more variants of a particular DNA sequence. The species in this variation is rs17879961 is homo sapiens (humans). The clinical significance of this SNP is that is so pathogenic. This SNP (rs17879961) occurs on chromosome 22 out of the typical 23 pairs of chromosomes that humans have. Primer design
In a PCR reaction, primers are one of the most important components in amplifying DNA. Both of the primers are designed to bind only to a specific sequence of the DNA that contains the SNP. When the primers bind to the DNA, it will take nucleotides that are complementary to the sequence of the DNA from the reaction mix and bind them together. This happens in both the forward and reverse directions in order to incorporate both strands of the DNA.If the sequence does not correlate 100% to template of the forward or reverse primer, then the complementary DNA strand will not be formed. This way, the primers will exclude DNA with non-cancer alleles and amplify DNA with the cancer-associated SNP rs17879961. Feature 2: Consumables KitIn our kit, the consumables will be clearly labeled to differentiate between the primers, PCR Mix, and the sample DNA. The tubes in which these materials are packaged will be color-coded and labeled to avoid any confusion that could lead to mistakes in the lab. We will maintain the current micropipettor design and will not be changing the PCR tubes themselves outside of the aforementioned labeling. We will also be making the packaging tubes have a hydrophobic surface on the inside so that the materials do not stick to the inside of the tube. These changes will help prevent human error and will also help prevent excess waste from being left over. [Instructions: IF your consumables packaging plan addresses any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) explain how in an additional paragraph.]
Feature 3: PCR Machine Hardware[Instructions: Summarize how you will include the PCR machine 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.] This kit will include a redesigned PCR machine that features a latch to seal the PCR lid tight, a durable and heat-proof plastic design, and a removable plate for easy transport of PCR tubes. [Instructions: IF your group has decided to redesign the PCR machine to address any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) explain how in an additional paragraph.] The redesigned PCR machine incorporates a latch in order to keep the heat inside the PCR machine. This will keep the temperature constant to facilitate the PCR reaction in the three processes of denaturing, annealing, and extending. This prevents susceptibility for error, allowing consistent performance. A durable, heat-proof plastic design will minimize cost to allow maximum profit. The addition of the removable plate will allow for easy transport as well as facilitate loading/unloading of the samples.
Feature 4: Fluorimeter Hardware[Instructions: Summarize how you will include the 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 REALLY awesome and easy to score.] [Instructions: IF your group has decided to redesign the fluorimeter to address any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) 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 CHEK2 PCR for predicting cancer. Please do NOT type the actual numerical values here. Just refer to them as being "less than one" or "very small." The instructors will ask you to submit your actual calculations via e-mail. We are doing so for the sake of academic integrity and to curb any temptation to cheat.] |