BME103 s2013:T900 Group1 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 Kristi Norris: Protocol/Procedure Carlos Renteria: Research and Design Specialist Raul Monzolo: Open PCR Machine Engineer Johnny Montez: Open PCR Machine Engineer Robert Sanchez: Research and Design Specialist Group 1 LAB 3 WRITE-UP Original System: PCR Results PCR Test Results Sample Name Ave. INTDEN* Calculated μg/mL Conclusion (pos/neg) Positive Control 4967763 --- N/A Negative Control 472744.6667 --- N/A Tube Label: A1 Patient ID: 29013 rep 1 382980 --- NEG Tube Label: A2 Patient ID: 29013 rep 2 280396.666 --- NEG Tube Label: A3 Patient ID: 29013 rep 3 520011 --- NEG Tube Label: B1 Patient ID: 13146 rep 1 5257810.667 --- POS Tube Label: B2 Patient ID: 13146 rep 2 5240422.333 --- POS Tube Label: B3 Patient ID: 13146 rep 3 5286556.333 --- POS * 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: [Results which are easily determined - When doing any kind of diagnostic test, having a clear result is imperative. A system which only distinguishes a positive from a negative result by a narrow margin is not nearly as clear as a system that has a clear distinction between the two. This is even more critical when testing for serious conditions such as cancer because an unclear result may cause a patient to not undergo necessary treatment or to live in fear unnecessarily. Neither option is beneficial.] [Small Sample volume - We need our system to be able to use small volumes of sample material. A system which requires large volumes of sample necessitates large volumes to be collected from a patient. This may result in several issues, the first being the toll on the patient of having it removed. The second problem becomes that of storing and processing a large volume. Smaller samples allow for higher volumes of tests to be done on a single patient's sample as well as multiple patients' samples to be tested in a high throughput method.] We concluded that we would Want a good system to have: [Fewer steps - Each step allows another opportunity for error. Additional steps also require more hands-on time for processing, reducing the efficiency of the over-all process.] [High volume throughput - In a practical setting, multiple samples are likely to be in line for processing. Even when only doing 3 repetitions of 2 patients, the ability to do more of the process simultaneously would increase the number of readings which could be done per hour or per day. This would allow for more responsive diagnosis and treatment of the patients.] We concluded that a good system Must Not Have: [Easy to mix samples during imaging - This is a source of error that can very easily be eliminated. Contamination of the samples in the very last step in which they are used is an unnecessary and unwanted source of potential incorrect readings.] [Fire Hazard - Safety issues take precedence. A slightly increased cost to raise the safety quality of an electric item which intentionally produces heat is a cost worth accepting.] We concluded that a good system Should Avoid: [Minute adjustments of the phone - Adjustment and careful placement of the phone with each picture is a very time-consuming step in this process. Elimination of this procedure would aid in our other goals of higher volume and more streamlined processing.] [Manual processing of the images - Manual image processing is very time consuming. The processing step alone takes significant amounts of time. Additionally, because the processing is manual, there is more room for error. The area selected is unlikely to be always consistent; the variations in reflections might be improperly included or excluded. An automatic image processing system would eliminate time and error from this procedure.] 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 DESIGN Primers for PCR 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.]