* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images
Bayesian Statistics
These following conditional statistics are based upon all of the DNA detection system results that were obtained in the PCR lab for 20 hypothetical patients who were diagnosed as either having cancer or not having cancer.
Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal.
A = [frequency of cancer-positive conclusions] = [frequency shown as a fraction] = [final numerical value]
B = [frequency of positive PCR reactions] = [frequency shown as a fraction] = [final numerical value]
P (B|A) = [frequency of positive PCR given cancer-positive conclusion] = [frequency shown as a fraction] = [final numerical value]
P(A|B) = [answer]
Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.
A = [text description] = [frequency shown as a fraction] = [final numerical value]
B = [text description] = [frequency shown as a fraction] = [final numerical value]
P (B|A) = [text description] = [frequency shown as a fraction] = [final numerical value]
P(A|B) = [answer]
New System: Design Strategy
We concluded that a good system Must Have:
[Must have #1 - Be easy to determine the result. Normally we have bunches of tubes waiting to run the test. Efficiency is important for the test. If it takes sophisticated procedure to determine the result,the test engineer must be highly qualified which is not that common. ]
[Must have #2 - Fast imaging results. Efficiency is essential when the test we are running is based on tons of samples.]
[Must have #3& #4 - Simple OpenPCR software to operate and easy sample loading OpenPCR. Basically the same reason as #1. ]
[Must have #5 - Small sample volume. Operating the whole test is easier with small samples. We don't have to waste time on collecting big amount of sample and then disposing it. ]
We concluded that we would Want a good system to have:
[Want #1 - why? short, ~4 or 5 sentences]
[Want #2 - why? short, ~4 or 5 sentences]
We concluded that a good system Must Not Have:
[Must Not Have #1 - why? short, ~4 or 5 sentences]
[Must Not Have #2 - why? short, ~4 or 5 sentences]
Feature 1 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
Feature 2 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
Etc.
[OR]
We chose keep the devices the same as the original system
Feature 1 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section
Feature 2 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section
Etc.
INSTRUCTIONS
New System: Protocols
DESIGN
We chose to include these new approaches/ features
Feature 1 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
Feature 2 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
Etc.
[OR]
We chose keep the protocols the same as the original system
Feature 1 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section
Feature 2 - explanation of how a pre-existing feature addresses any of the specifications in the "New System: Design Strategy" section
Etc.
MATERIALS
PROTOCOLS
PCR Protocol
Step 1
Step 2
Etc.
DNA Measurement and Analysis Protocol
Step 1
Step 2
Etc.
New System: Research and Development
BACKGROUND
Polymerase Chain Reaction (PCR) is a scientific method that utilizes DNA Polymerase to create a complimentary base strand from a template strand of DNA. Triphosphate nucleotides align with open DNA strands and DNA polymerase works to link the complementary nucleotide bases together growing strands through both condensation and hydroysis reactions. Through these mechanisms it is possible to target specific positions on the template DNA sequence that a scientist intends to amplify(PCR 1). When the PCR process is completed the targeted DNA sequence containing the single-nucleotide polymorphism (SNP) will have manufactured over a billion copies (amplicons). A SNP essentially is a type of gentic variation among organisms which represents a difference in a single nucleotide. For example, a SNP may replace a nucleotide cytosine (C) with a nucleotide thymine (T) in a certain part of an organisms DNA. These SNPs can be utilized as biological markers which in turn can help locate genes that have associative properties that contribute to the formation of harmful diseases.
The targeted SNP for this research was rs17879961. This SNP is found in Humans (Homo sapiens) and represents a variation class SNV, which stands for single nucleotide variation. Furthermore, This SNP is a variant of the CHEK2 gene (Checkpoint kinase 2) which if present in a person's genome may increase their risk of developing breast cancer. This SNV signifies a single base change from a Thymine (T) to a Cytosine (C) located on chromosome 22 and its clinical significance is classified as a pathogenic allele. For example, this mutation would alter the normal alelle ATT and the middle position resulting the cancer associated allele ACT.
DESIGN
Primers for PCR
Cancer allele forward primer: -> TTGAGAATG[TCA]CGTATGTAT Cancer allele reverse primer: -> AACTCTTAC[AGT]GCATACATA
Disease alleles will yield PCR products because the target amplicon is only associated with the cancer DNA sequences. Thus primer annealing will following base pairing rulese when it binds with the template strand. For example, triphosphate nucleotides align with open DNA strands and DNA polymerase works to link the complementary nucleotide bases together growing strands through both condensation and hydroysis reactions. The presence of a primer is required so that polymerase can proceed with directing the new nucleotides in place. Through these mechanisms it is possible to target specific positions on the template DNA sequence that a scientist intends to amplify. When the PCR process is completed the targeted DNA sequence containing the single-nucleotide polymorphism (SNP) will have manufactured over a billion copies (amplicons).
Design specification 1 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section
Design specification 2 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section
Etc.
New System: Software
[THIS SECTION IS OPTIONAL. If your team has creative ideas for new software, and new software is a key component included in your new protocols, R&D, or machine design, you may describe it here. You will not receive bonus points, but a solid effort may raise your overall page layout points. If you decide not to propose new software, please delete this entire section, including the ==New System: Software== header.]