Team:Grenoble/Human Practice/Cost

From 2012.igem.org

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<section>
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<h2>Specifications</h2>
<h2>Specifications</h2>
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Based on the requirements of the medical field (see the section <a href="https://2012.igem.org/Team:Grenoble/Human_Practice/Meeting">meeting</a> for further details), we set our pathogen detection specifications. So, sEnsiColi should be:
Based on the requirements of the medical field (see the section <a href="https://2012.igem.org/Team:Grenoble/Human_Practice/Meeting">meeting</a> for further details), we set our pathogen detection specifications. So, sEnsiColi should be:
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<section>
<section>
<h2>Design of sEnsiColi</h2>
<h2>Design of sEnsiColi</h2>
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</br>
 
</br>
</br>
Regarding the specifications above, we set two possible designs for sEnsiColi.  
Regarding the specifications above, we set two possible designs for sEnsiColi.  
</br>
</br>
</br>
</br>
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The first one is intended for prevention purposes such as assessing the contamination level of hospital’s rooms. The design of this detection-kit is given by the picture below:
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The first one is intended for prevention purposes such as assessing the contamination level of hospital’s rooms. The design of this detection-kit is given by the picture below:<br/>
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<center><img src="https://static.igem.org/mediawiki/2012/6/6f/Table.PNG"></center>
<center><img src="https://static.igem.org/mediawiki/2012/6/6f/Table.PNG"></center>
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</br>
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This first prototype is easy to use:  a sample of the surface to test can be taken by a swab and then put in the test tube containing the bacterial solution. After about 5 hours we can check the tube.  If we have a fluorescent response then the tested surface is contaminated by <i>Staphylococcus Aureus</i> (see <a href="https://2012.igem.org/Team:Grenoble/Modeling/Conclusion">modeling section</a> for an assessment of time response).
</br>
</br>
-
This first prototype is easy to use:  A sample of the surface to test can be taken by a swab and then put in the test tube containing the bacterial solution. After about 5 hours we can check the tube.  If we have a fluorescent response then the tested surface is contaminated by Staphylococcus Aureus. (see <a href="https://2012.igem.org/Team:Grenoble/Modeling/Conclusion">modeling section entire system</a> for an assessment of time response)
 
</br>
</br>
 +
So, sEnsiColi average response time is at about 5 hours which is twice the response time of a PCR (PCR needs between 2 and 3 hours to deliver the result). Then in term of rapidity sEnsiColi is not really competitive compared to a PCR method.
</br>
</br>
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Then, sEnsiColi average response time is at about 5 hours which is twice the response time of a PCR (PCR needs between 2 and 3 hours to deliver the result). Then in term of rapidity sEnsiColi isn’t really competitive compared to a PCR method.
 
</br>
</br>
 +
However, if we examine the reliability of the kit (see <a href="https://2012.igem.org/wiki/index.php?title=Team:Grenoble/Modeling/Amplification/Stochastic">modeling stochastic section</a>) it appears that, thanks to the feed-forward loop in the amplification module, the probability of having a false positive response is very low. Moreover, our device is composed of millions of bacteria that will each act as a sensor and each be capable of propagating a response in the whole population. Therefore the probability of false negatives is expected to be extremely low ! A PCR-based pathogen detection method achieves a perfect specificity (0% <a href="https://2012.igem.org/Team:Grenoble/Human_Practice/Cost#ref">[1]</a>) but is prone to false negatives (93% <a href="https://2012.igem.org/Team:Grenoble/Human_Practice/Cost#ref">[1]</a>). While false positives only have financial costs, false negatives can be deadly for the patient and should be avoided.
</br>
</br>
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However, if we examine the reliability of the kit (see <a href="https://2012.igem.org/wiki/index.php?title=Team:Grenoble/Modeling/Amplification/Stochastic">modeling stochastic section</a>) it appears that thanks to the designed And Gate in the amplification module, the probability of having a false positive response doesn’t exceed 0.43%. Compared to the reliability of a PCR (93% <a href="https://2012.igem.org/Team:Grenoble/Human_Practice/Cost#ref">[1]</a>) this value is highly satisfying.
 
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In order to enhance even more the reliability of our system, we decided to set a second design based on a 96-well plate. Thus, the probability that a false occurs diminishes significantly: If no Golden staph has to be detected, no more than one sample out of 96 gets a visible output signal.
 
</br>
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In order to enhance the reliability of our system, we decided to set a second design based on a 96-well plate to perform 96 tests simultaneously. This enables to build tests with fewer false positive and false negative rates. According to the results of the stochastic modeling section, if no <i>Staphylococcus aureus</i> has to be detected, no more than one sample out of 96 gets a visible output signal.
</br>
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<center><img src="https://static.igem.org/mediawiki/2012/8/86/Device_gre.PNG"></center>
<center><img src="https://static.igem.org/mediawiki/2012/8/86/Device_gre.PNG"></center>
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<ul>
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     <li>A detection-kit that is absolutely easy to use and needs no qualified staff to use it. This test is      approximately ten times faster than a traditional plate test (48h) and twice slower than a PCR (from 2 to 3 hours) as it needs 5 hours to give a visible output signal. Besides, thanks to this system, the probability of having a false positive response is 0.43%. Its design makes it a competitive candidate for assessing contamination level in medical environment</li>
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     <li>A detection-kit that is absolutely easy to use and needs no qualified staff to use it. This test is      approximately ten times faster than a traditional plate test (48h) and twice slower than a PCR (from 2 to 3 hours) as it needs 5 hours to give a visible output signal. Besides, thanks to this system, the probability of having a false positive response is expected to be low. Its design makes it a competitive candidate for assessing contamination level in medical environment</li>
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     <li>A 96-well plate kit for diagnosis, easy to use, fast enough (5 hours) and above all reliable to 99.99%.</li>
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     <li>A 96-well plate kit for diagnosis, easy to use, fast enough (5 hours) and above all highly reliable.</li>
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<section>
<h2>Comparative study of cost assessment</h2>
<h2>Comparative study of cost assessment</h2>
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</br>
 
</br>
</br>
We wanted to make sure that sEnsiColi would be competitive in term of price. So we conducted a comparative cost analysis between the mostly used detection methods in the CHU and our two possible designs of sEnsiColi.
We wanted to make sure that sEnsiColi would be competitive in term of price. So we conducted a comparative cost analysis between the mostly used detection methods in the CHU and our two possible designs of sEnsiColi.
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You can find <a href="">here </a> the xl-files we created to assess the cost of the PCR and sEnsiColi test in its two forms: test tube and 96-well plate.
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You can find <a href="https://static.igem.org/mediawiki/2012/8/8d/Cost_assessment_gre.pdf" target="_blank">here </a> the files we created to assess the cost of the PCR and sEnsiColi test in its two forms: test tube and 96-well plate.
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       <tr><td>PCR</td><td>21.70</td></tr>
       <tr><td>PCR</td><td>21.70</td></tr>
       <tr><td>sEnsiColi (test tube)</td><td>0.23</td></tr>
       <tr><td>sEnsiColi (test tube)</td><td>0.23</td></tr>
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       <tr><td>sEnsiColi (96-well plate)</td><td>5.69</td></tr>
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       <tr><td>sEnsiColi (96-well plate)</td><td>5.77</td></tr>
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We will contact him again once we have achieved constructing our BioBricks and conducting the necessary experiments concerning sensitivity, rapidity and reliability. We will thus be able to evaluate the effectiveness of device and discuss what further improvements need to be done.
We will contact him again once we have achieved constructing our BioBricks and conducting the necessary experiments concerning sensitivity, rapidity and reliability. We will thus be able to evaluate the effectiveness of device and discuss what further improvements need to be done.
</section>
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<section>
<section>
<h2 id="ref">References</h2>
<h2 id="ref">References</h2>
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<b>[1]</b> <a href="https://www.msu.edu/user/msuhla/mod10_3.pdf" target="_blank">Ralf M. Hagen, Irene Seegmüller ,Jila Navai et al. Development of a real-time PCR assay for rapid identification of methicillin-resistant Staphylococcus aureus from clinical samples. International Journal of Medical Microbiology, 2005, 295, 77–86.</a>
<b>[1]</b> <a href="https://www.msu.edu/user/msuhla/mod10_3.pdf" target="_blank">Ralf M. Hagen, Irene Seegmüller ,Jila Navai et al. Development of a real-time PCR assay for rapid identification of methicillin-resistant Staphylococcus aureus from clinical samples. International Journal of Medical Microbiology, 2005, 295, 77–86.</a>
</section>
</section>

Latest revision as of 00:09, 27 September 2012

iGEM Grenoble 2012

iGEM Grenoble iGEM
iGEM 2012
main page
Project

Design of the device and comparative study of cost

assessment

Specifications


Based on the requirements of the medical field (see the section meeting for further details), we set our pathogen detection specifications. So, sEnsiColi should be:

  • Sensitive
  • Reliable (little false positives)
  • Fast
  • Easy to use
  • Lower in price than the current methods.


The modeling part deals with the first three specifications: the deterministic model gives an answer for the sensitivity and the rapidity while the stochastic model gives an answer for reliability.

In this section we will especially deal with the easiness of use and the cost assessment of the device.

Design of sEnsiColi


Regarding the specifications above, we set two possible designs for sEnsiColi.

The first one is intended for prevention purposes such as assessing the contamination level of hospital’s rooms. The design of this detection-kit is given by the picture below:


This first prototype is easy to use: a sample of the surface to test can be taken by a swab and then put in the test tube containing the bacterial solution. After about 5 hours we can check the tube. If we have a fluorescent response then the tested surface is contaminated by Staphylococcus Aureus (see modeling section for an assessment of time response).

So, sEnsiColi average response time is at about 5 hours which is twice the response time of a PCR (PCR needs between 2 and 3 hours to deliver the result). Then in term of rapidity sEnsiColi is not really competitive compared to a PCR method.

However, if we examine the reliability of the kit (see modeling stochastic section) it appears that, thanks to the feed-forward loop in the amplification module, the probability of having a false positive response is very low. Moreover, our device is composed of millions of bacteria that will each act as a sensor and each be capable of propagating a response in the whole population. Therefore the probability of false negatives is expected to be extremely low ! A PCR-based pathogen detection method achieves a perfect specificity (0% [1]) but is prone to false negatives (93% [1]). While false positives only have financial costs, false negatives can be deadly for the patient and should be avoided.

In order to enhance the reliability of our system, we decided to set a second design based on a 96-well plate to perform 96 tests simultaneously. This enables to build tests with fewer false positive and false negative rates. According to the results of the stochastic modeling section, if no Staphylococcus aureus has to be detected, no more than one sample out of 96 gets a visible output signal.


To sum up, we designed two different detector prototypes:

  • A detection-kit that is absolutely easy to use and needs no qualified staff to use it. This test is approximately ten times faster than a traditional plate test (48h) and twice slower than a PCR (from 2 to 3 hours) as it needs 5 hours to give a visible output signal. Besides, thanks to this system, the probability of having a false positive response is expected to be low. Its design makes it a competitive candidate for assessing contamination level in medical environment

  • A 96-well plate kit for diagnosis, easy to use, fast enough (5 hours) and above all highly reliable.


Now that we validated the design of our kit and most of its specifications, you are probably eager to find out if our test is lower in price than the current detection methods. You can have a look at the next section to get the answer.

Comparative study of cost assessment


We wanted to make sure that sEnsiColi would be competitive in term of price. So we conducted a comparative cost analysis between the mostly used detection methods in the CHU and our two possible designs of sEnsiColi.

For the cost assessment, we followed a very specific process in order to have a precise and reliable result.

The first step was to set the protocols of production for each device (for the PCR we followed our PCR protocol available on biological section.)

The next step was to define all the flows including electricity, handworker’s wages, raw materials, consumables…

Finally, we had to search for the cost of each used component and calculate the total cost.

You can find here the files we created to assess the cost of the PCR and sEnsiColi test in its two forms: test tube and 96-well plate.

Method/deviceCost (€)
PCR21.70
sEnsiColi (test tube)0.23
sEnsiColi (96-well plate)5.77


We presented the design of our tests and their prices to MD PhD Max Maurin. He found the design relevant and told us that the prices were interesting as it would reduce the detection costs at least four times. He also seemed to be interested about the developed technique and the new BioBricks.

We will contact him again once we have achieved constructing our BioBricks and conducting the necessary experiments concerning sensitivity, rapidity and reliability. We will thus be able to evaluate the effectiveness of device and discuss what further improvements need to be done.

References

[1] Ralf M. Hagen, Irene Seegmüller ,Jila Navai et al. Development of a real-time PCR assay for rapid identification of methicillin-resistant Staphylococcus aureus from clinical samples. International Journal of Medical Microbiology, 2005, 295, 77–86.

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