BME103 s2013:T900 Group2 L3

BME 103 Spring 2013	Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help
OUR TEAM Name: Joe Sansone Role(R&D Scientist) Name: Shang Ruan Open PCR Machine Engineer Name: Student Role(s)]] Name: Student Role(s) Name: Student Role(s) LAB 3 WRITE-UP Original System: PCR Results PCR Test Results Sample Name Ave. INTDEN* Calculated μg/mL Conclusion (pos/neg) Positive Control --- --- N/A Negative Control --- --- N/A Tube Label:___ Patient ID: ____ rep 1 --- --- --- Tube Label:___ Patient ID: ____ rep 2 --- --- --- Tube Label:___ Patient ID: ____ rep 3 --- --- --- Tube Label:___ Patient ID: ____ rep 1 --- --- --- Tube Label:___ Patient ID: ____ rep 2 --- --- --- Tube Label:___ Patient ID: ____ rep 3 --- --- --- * 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. Bayes Theorem equation: P(A|B) = P(B|A) * P(A) / P(B) Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal. 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] 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 - why? short, ~4 or 5 sentences] [Must have #2 - why? short, ~4 or 5 sentences] 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] We concluded that a good system Should Avoid: [Should Avoid #1 - why? short, ~4 or 5 sentences] [Should Avoid #2 - why? short, ~4 or 5 sentences] New System: Machine/ Device Engineering SYSTEM DESIGN KEY FEATURES We chose to include these new 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 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). Sources: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=17879961 http://hmg.oxfordjournals.org/content/16/15/1794.full.pdf http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechPCR.shtml Our primers address the following design needs 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.]