BME103:W930 Group9: Difference between revisions
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| [[Image:Daniella.jpeg|100px|thumb|Name: Daniela<br>Data Compiler and Analyzer]] | | [[Image:Daniella.jpeg|100px|thumb|Name: Daniela<br>Data Compiler and Analyzer]] | ||
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'''Everyone has contributed to this project even though there are only two usernames. Every person used these two users to make edits to the wiki. Dr. Haynes said that this would be sufficient enough to give each member full participation credit for this project''' | |||
=LAB 1 WRITE-UP= | =LAB 1 WRITE-UP= | ||
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==Research and Development== | ==Research and Development== | ||
<br> | |||
'''What Does PCR Do?''' | '''What Does PCR Do?'''<br> | ||
DNA strands across human beings are very similar, but there is a correlation between the discrepancies between DNA sequences and phenotypic conditions such as cancer or heart disease. Because DNA is so small, and has so many components, it is not reasonable to simply look through the entire strand for the sequence of interest. This report used a technique that amplified specific DNA strands which is called Polymerase Chain Reaction or PCR. This technique uses a primer that identifies and replicates a specific Single Nuleotide Polymorphism(SNP), if present. For this to work, the DNA strand and primer need to go through a cycle of temperature shifts that allow the DNA to replicate. The steps are denaturing, annealing and extension. The denaturing process happens when the system is heated to the point where the DNA strands are changed into single strands. After this the annealing step involved cooling the DNA strand and reconstructing of the double stranded DNA. Extension then takes place which is exactly as it sounds, the primer extends or builds a DNA strand that has the gene sequence the primer is looking for, if it is in the DNA. This is where amplification occurs and how we can measure if the DNA at test holds the sequence in question. For measuring purposes, a fluorescent is added, in tandem with the primer. | |||
'''Looking at rs17879961(CHEK2)'''<br> | |||
As mentioned above, there are single nucleotide polymorphisms that are consistently found in the population that can indicate phenotypic behaviors in the person. To explain how this method is used, we will consider the sequence, rs17879961. This specific sequence is found on chromosome 22, has been named CHEK2, and is associated with colorectal and breast cancer. Below are the sequences of the "normal" sequence and the cancer associated sequence. Notice that the only difference is marked in brackets and is only a change from a T base to a C base pair. By adding a primer to this strand that attached only to the cancer sequence we knew if the tested DNA has the strand if the sequence was amplified by the primer after a denaturing, annealing, extension cycle. The primer sequence is also shown below in the forward and backward direction. | |||
Normal | |||
GGAAGTGGGTCCTAAAAACTCTTACA[T]TGCATACATAGAAGATCACAGTGGC | |||
Cancer | |||
GGAAGTGGGTCCTAAAAACTCTTACA[C]TGCATACATAGAAGATCACAGTGGC <br> | |||
Forward | |||
CCTTCACCCAGGATTTTTGAG | |||
Backward | |||
ATGTATCTTCTAGTGTCACCG<br> | |||
'''Baye's Rule'''<br> | |||
To interpret the results into something that is meaningful we used Baye's rule which basically gives a number value of the predicative reliability of the test. SO, for instance, if somebody tested positive for a specific allele that was associated with freckles, there will still be a chance that they do not have freckles. THis is true for people that test negative, they may still have freckles. In the bayesian parameters there are four numbers to look at; the positive predictive value(ppc) which is the probability that somebody testing positive will display the associated phenotype, the negative predicative value(npv) which is the probability that somebody testing negative will not display the associated phenotype, false positive which is the probability of somebody testing positive that doesn't display the phenotype, and false negative which is the probility of somebody testing negative that actually has the phenotype. Below is the formula. <br><br> | |||
'''p(CIT)=_9TIC)/(P(CIT+p(TI~C)*(~C)'''<br><br> | |||
To put this in words we can use an example of positive predictive value. It will the number of patients that test positive that have the phenotype divided by the total number patients that tested postive. High PPV and NPV are ideal. <br> | |||
In this lab we considered the Bayesian values of the CHEK2 SNP and its association with breast cancer as tested by Vahteristo in Finland. | |||
He noted that 2% of people with cancer associated gene had the breast cancer and 1.4% of people without the gene mutation had breast cancer. This means the allele presence has a PPV of 2.0% and a NPV of 98.6%. This doesn't seem very high but when a doctor can look at other associations like breast cancer in family history the PPV grows to as high as 3.1%. It doesn't exactly indicate whether somebody has the cancer but it can let them know they need to be careful and get regular screenings. | |||
Latest revision as of 10:14, 14 November 2012
BME 103 Fall 2012 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
OUR TEAMEveryone has contributed to this project even though there are only two usernames. Every person used these two users to make edits to the wiki. Dr. Haynes said that this would be sufficient enough to give each member full participation credit for this project LAB 1 WRITE-UPInitial Machine TestingThe Original Design The open PCR is a device that enables the splitting of DNA. It is run through many cycles of heating and cooling that enables the splitting and recombination with polomers. It connects to a computer program to run the cycles. The temperature change is controled by the heating lid and than the information is fed to the LED screen. The heating lid heats tubes that are held in the heat tube holder to the appropriate temperature and then cools them as needed in each cycle. Experimenting With the Connections When we unplugged part 3, the LCD, from part 6, the Open PCR Brains Board, the LCD on the machine stopped working and did not show anything on it. When we unplugged the white wire that connects part 6, the Open PCR Brains Board, to part 2, the heat tube, the machine no longer measures the temperature of the plate and sends it to the LCD.
First test run: 24 Oct. 2012
ProtocolsPolymerase Chain Reaction Procedure for amplifying a person’s DNA
The Samples
Flourimeter procedure 1. Place the flourimeter on the table and turn on the blue light. Instructions for opening images in imageJ
Research and Development
Looking at rs17879961(CHEK2) Normal GGAAGTGGGTCCTAAAAACTCTTACA[T]TGCATACATAGAAGATCACAGTGGC Cancer GGAAGTGGGTCCTAAAAACTCTTACA[C]TGCATACATAGAAGATCACAGTGGC Forward CCTTCACCCAGGATTTTTGAG Backward ATGTATCTTCTAGTGTCACCG To put this in words we can use an example of positive predictive value. It will the number of patients that test positive that have the phenotype divided by the total number patients that tested postive. High PPV and NPV are ideal.
Results
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