BME100 s2015:Group3 12pmL6

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OUR COMPANY

Name: Abraham Rosengard
Name: Juan Patterson
Name: Gabriella Leiva-Hidalgo
Name: Jessica Resendiz
Name: Raghad Tamim


LAB 6 WRITE-UP

Bayesian Statistics

Overview of the Original Diagnosis System

The experiment encompassed 34 teams made up of 6 students each which analyzed patient data from 68 patients. Each group performed a PCR test on 2 patient samples. Each sample was tested using a PCR technique and was primed with SYBR Green in order to make the final result of the exam more accurate. Photos were taken an the imageJ software was used to analyze set photos which would yield values that would be compiled from all 34 groups. Potential errors in examining the DNA can be attributed to human error when actually performing the experiment, along with not properly analyzing the images taken while using the imageJ software. Potential sources of error also include the light sensitivity of the samples and how they may have been damaged during the experiment if the cover was not placed on them while the samples were not needed.In order to avoid errors during the performance of the lab, several pictures were taken, a total of 3, for each sample in question in order to collect the best photo that would be prime to be analyzed on imageJ. The data was then compiled using the data from imageJ, all groups would run a statistical analysis on the data. In order to compensate for error some of the data that seemed incredibly off was omitted, so it is important to keep in mind that not all data was used when statistics were performed on the data collected from the PCR lab. Most of the data presented in the spreadsheet was reliable which made it possible to calculate values for this lab. Considering this particular analysis; the frequencies of testing positive, having the condition, development for condition, and having DNA sequence for condition; were all calculated and compared to one another in order to find the probabilities of different potential instances a patient may have. In conclusion the data made available by all the groups allowed for an accurate Bayesian Statistical analysis. The DNA sequence that was tested for during this PCR lab was the one for Coronary Heart Disease, using the data provided along with a Bayesian interpretation of the data, it can be said that a positive PCR lab result indicates that a patient has the disease or is at risk of development since it is present in the pateint's DNA.

What Bayes Statistics Imply about This Diagnostic Approach


The probability that the patient will have a positive result about is half of 1.00 and the positive PCR reaction is about half of 1.00 as well. The probability of the patient having a positive PCR reaction given the probability that a patient will get a positive result is very high. The probability that the patient will get a positive result given a positive PCR reaction is also very high. That means that the patient does have the disease.

The probability that the patient sample contains a negative result is relatively close to being half. The negative diagnostic signal is in the middle of the spectrum as well. The frequency of a positive PCR, which is very high. The probability that a patient will get a negative final test conclusion, given a negative diagnostic signal extremely high, as a matter of fact it's OFF THE CHARTS.

The probability the patient will develop disease is relatively low. The chances that the DNA sequence matches that of CHD (Coronary Heart Disease) is a little less than half, still relatively low. The probability that a patient will develop the disease, given a positive final test is about a 50% chance. The probability that a sample with the coronary heart disease sequence present given the probability of the patient developing the disease is slightly more than half. The probability that the patient does not have CHD is slightly more than half. The given a non- CDH DNA sequence is also slightly more than half. The probability that the patient will not have the disease given the fact that the DNA sequence for CHD is not present is about half. The probability that a patient will not develop the disease, given a negative final test conclusion is also half.

Pipetting can cause error because often enough the sample can burst when it is being released or extracted causing the sample to spread throughout the glass slide which could potentially cause cross contamination of samples. The apparatus itself could also cause errors due to the fact that the system is not one but a consisting of very movable parts that can easily shift and change final results that image j calculates e.g. the phone holder can be accidentally moved, when it should be static. Other errors could be attributed to attributed to the design of the system and how the 'trap door' must be fully closed before the picture is actually taken. The door does not always close all the way causing extra light to come into the box which can skew the results once analyzed on image j. The samples were also sitting out the whole time and they were left uncovered for a time, being light sensitive, the samples have the potential to be damaged.

The first set of calculations dealt with whether a sample will test positive if the DNA of CHD is present in the sample. The probability of the sample having the DNA sequence in question, Coronary Heart Disease, is 0.437/1.00. The probability of the sample testing positive in the lab is 0.417/1.00. Given the fact that a patient sample dose have CHD within the DNA there is a 0.90/1.00 chance that the sample will test positive, meaning that there is 90% that the patient has the disease. Given the fact that the lab test was positive there is a 0.943/1.00 percent chance that the patient does have the condition's DNA sequence within their own genome, which means that they have a very high possibility of having or developing the disease.

The second calculation focused on the probabilities that given a negative test result, he DNA sequence does not contain the sequence for Coronary Heart Disease. The probability that the CHD sequence is not present in the DNA is about 0.562/1.00. The chances that there will be a negative signal in the lab is 0.541/1.00. Now if the patient indeed does have not have the CHD sequence the there is a 0.981/1.00 chance that the lab test will yield a negative test result. If a negative test result is proven than there is a 1.019/1.00 percent probability that the patient does not have the CHD DNA sequence, so there chances of currently having the condition is zero.

The third calculation focused on the probability of the patient developing the condition, given that the DNA sequence for CHD is present in the patient's genome. The probability of developing the disease is 0.375/1.00 percentage chance. The chances of having the DNA sequence present in a patient's genome is 0.437/1.00. If the patient develops the disease the chances of that patient having the sequence in the DNA is 0.667/1.00 percent, which means that the pateint has over a 50% possibility of having the DNA for CHD if the disease is developed. If the patient does indeed have the sequence there is a 0.572/1.00 percentage probability that this person will develop the disease. So if a person has the CHD in his/her DNA than they have over a 57.2% risk of developing the condition.

The fourth calculation focused on the probability of not developing the disease if the sequence is not present in that patient's genome. The probability of not developing the condition is 0.625/1.00. The chances of just not having the DNA sequence of Coronary Heart Disease is 0.562/1.00 percentage. Given the fact that a patient does not currently have condition, there is a 0.55/1.00 percentage chance of that the CHD DNA sequence is not present in the DNA of the patient. If the patient does not have the DNA sequence present, there is a 0.612/1.00 percentage possibility that the patient does currently have the condition.

Computer-Aided Design

TinkerCAD

The TinkerCAD tool was very useful in helping our group design the new product. TinkerCAD allowed group to sketch a virtual model of the original PCR machine and how our custom-made device will look. Our group first produced the original design of the PCR model. Then, we decided to change the simulation according to the weaknesses and flaws that we found in the current design model. TinkerCAD gave our group the ability to transform our product design while we were still designing it.


Our Design


PCR pic 1.jpg PCR pic 2.jpg



This machine is almost completely self-automated. The cybergreen, DNA samples, controls, and pipette cleaning solution are inserted into the slots located on the left box. While user-friendly system controls are typed into the computer to start the process, the machine will take the samples and arrange them accordingly in the PCR machine (center box) using a single pipette, repeatedly cleaning/reusing the same plastic tip. The cybergreen/examination process will take place on the right box and the cybergreen will not be exposed to any light and none of the DNA samples will spill due to human error. The product wastes will appear on the right most side and can be disposed of easily.



Feature 1: Consumables Kit

Our kit will include:

  • SYBR green
  • DNA samples
  • TaqDNA polymerase
  • Forward and reverse primers
  • cleaning fluid for pipette tip and flourimeter glass plate

All the necessary samples come within a seal package. Each substance within the kit will be clearly labeled. After opening the container, the scientist easily places each material and substance into a labeled slot. The machine handles the materials and does all the work after the commands are entered in a user-friendly program. This prevents unnecessary light exposure to the SYBR green and many other possible human error, such as spilling of materials. The machine will take the materials, one at a time, and properly place them inside the PCR unit for experimentation. After each step, the internal pipette system and its plastic tip will be cleaned for multiple usage.

Our device will be more automated so the scientist will have less work to do, and easier time doing his job. After placing the materials in each appropriate slot, the machine will transfer the materials to the PCR unit. After the PCR process is completed, all the products will be moved to the flourimeter section to be photographed. After the entire experiment is completed, the substances are moved to the waste section for easy removal.



Our device will address the some of the original weaknesses of the original design. The internal pipette will have a reusable tip that cleaning fluid will cleanse for multiple uses. The device will also clean and reuse the glass plates used by the fluorimeter. This will produce less waste per experiment. After packaging, the light sensitive materials, such as the SYBR green, has slots for immediate placement. The machine will also handle all the materials within the device, so there will be no exposure to light.

Feature 2: Hardware - PCR Machine & Fluorimeter

Some hardware included/added to our design:

  • pipette with reusable tip
  • reusable glass plate (for flourimeter)
  • HD camera
  • 64 PCR slots
  • metal exterior
  • waste compartment


The basic PCR machine will remain the same. We have added more user-friendly controls to the program so that the PCR stage and the flourimeter process are completed manually. The device cleans and reuses the same pipette tip and flourimeter plate, to be more eco-friendly. Our group has included an internal HD camera so the distance between the camera and the glass plates remain the same. The machine automatically takes the DNA samples from the PCR unit and adds the SYBR green onto the glass plate to be processed and photographed. After the machine takes several necessary pictures of each sample, the samples are discarded for easy removal of materials.

Our group redesigned our machine to be made out of a sturdier substance, such as metal, as opposed to the original wood. The PCR unit also has more slots to save time and allow for more simultaneous experimentation. To prevent human error, our group has included an internal HD camera so the distance between the camera and the glass plates remain the same. The machine automatically takes the DNA samples and adds the SYBR green onto the glass panel to prevent spilling.