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Total Volume 175.0 µL<br>
Total Volume 175.0 µL<br>
'''Patient ID''' 72537 74083<br>
'''Sex''' Male Female<br>
'''Age''' 54 49<br>
Revision as of 00:28, 14 November 2012
|BME 103 Fall 2012|| Home |
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
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LAB 1 WRITE-UP
Initial Machine Testing
The Original Design
(Write a paragraph description for visitors who have no idea what this is)
Experimenting With the Connections
When we unplugged the LCD screen (part 3) from the Open PCR circuit board (part 6), the screen went blank the machine had no visual output.
(Write the date you first tested Open PCR and your experience(s) with the machine)
Polymerase Chain Reaction
1. A Polymerase Chain Reaction(PCR) is used to amplify a single piece of DNA. The steps that lead up to the replication of a DNA sequence are denaturation, annealing, and extension which involve several different cycles ranging in terms of length of time and temperature. This results in the exponential replication of a certain sequence of DNA.
Patient ID 72537 74083
Research and Development
Specific Cancer Marker Detection - The Underlying Technology
A single nucleotide polymorphism is a variation in a single DNA nucleotide. The four DNA nucleotides are represented using the letters A, T, C and G. These variations occur normally throughout DNA and represent the most common form of genetic variation among people. They occur at a rate of 1 per every 100 to 300 bases along the 3-billion-base human genome. SNPs are point mutations that have been evolutionarily successful enough to recur in a significant proportion of the population of a species. In other words, SNPs are evolutionarily stable, meaning they do not change much from generation to generation. This allows SNPs to be considered highly conserved within the population and therefore serve as ideal biological markers for genetic research. In order for a sequence variation to be classified as a SNP it must occur in at least 1% of the population. Millions of SNPs have been identified in the human genome and cataloged in accessible databases.
SNPs can occur with a gene, which is the coding region of DNA, or in a non-coding region. Because only about 3-5% of DNA actually codes for the production of proteins, most SNPs are found within non-coding regions. Since SNPs can be located near a gene associated with a certain disease, or occasionally within that gene, researchers have been able to pinpoint various diseases on the genome map. SNPs found within a gene, or somewhere in the regulatory region of a gene, are of particular interest because they are more likely to alter the biological function of the gene and therefore, the function of the protein.
It is important to remember that SNPs do not cause or identify a disease state directly, but allow for the possible diagnosis or assists in determining the likelihood that someone will develop a particular illness. They also have the ability to help predict an individual’s response to certain drugs, environmental factors, chemicals, toxins, etc. In fact, since SNPs occur most frequently in the non-coding regions of DNA, they do not produce physical changes in people and have no effect on health or development. (Written by Kim L, Posted by William L).
Polymerase Chain Reaction and SNPs
A polymerase chain reaction experiment uses a set of nucleotide primers to amplify a specific section of DNA. Specifically, this diagnostic is testing for the presence of the cancer-linked rs17879961 SNP mutation. Since this SNP creates a new DNA sequence, primers can be made to only bind to the mutated DNA sequence. As a result, the PCR test can be run with a unique primer that will only bind if the target DNA shows rs17879961 mutation, allowing the test to identify the presence or absence this cancer-linked SNP. In rs17879961, there is an anomalous A-T pair that creates a new and unique DNA sequence specific to this cancer-linked mutation. Thus, only a specific primer will bind to the targeted sequence and, as a result, the PCR will only react if the specific mutation is present.
(BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)