BME103 s2013:TEMPwu3

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(Protocols)
(New System: Protocols)
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==New System: Protocols==
==New System: Protocols==
'''DESIGN AND MATERIALS'''
'''DESIGN AND MATERIALS'''
-
<!-- Design a new protocol based on your group's new PCR design. Things to consider:
+
 
-
How should the PCR machine be set up? Does it need to be plugged in?
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<!-- If your team decided to change the PCR and/or the Fluorimeter imaging protocols, summarize the new approaches/ features here and delete the '''We chose keep the protocols the same as the original system''' section. -->
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How many samples will fit into a single 2-hour run?
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'''We chose to include these new approaches/ features'''
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How many replicates should be created per patient?
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* Feature 1 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
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What should the final volume of the reaction be?
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* Feature 2 - explanation of how this addresses any of the specifications in the "New System: Design Strategy" section
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Will signal reading be integrated into the PCR machine or remain separate?
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* Etc.
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If it is separate, you will need to include instructions on how to use the fluorimeter.
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How should the user calculate the about of signal amplified?
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[OR]
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etc. -->
+
 
 +
<!-- If your team decided NOT to change any of the machinery/ devices, explain why here and delete the '''We chose to include these new features''' section above-->
 +
'''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'''
'''MATERIALS'''
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'''PCR PROTOCOL'''
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'''PROTOCOLS'''
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<!-- Create a step-by-step procedure for setting up and running PCR reactions. Your instructions should include everything from adding reagents to the tubes, to programming the PCR machine and running the reaction.
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-
 
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 +
* '''PCR Protocol'''
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<!-- Create a step-by-step procedure for setting up and running PCR reactions. Your instructions should include everything from adding reagents to the tubes, to programming the PCR machine and running the reaction.-->
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* '''DNA Measurement and Analysis Protocol'''
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<!-- Create a step-by-step procedure for measuring DNA amplification in the PCR reactions. Your instructions should include everything from diluting the samples in SYBR Green, to placing the drops onto the fluorimeter (if your group is using the fluorimeter), to collecting and processing images in Image J. Don't forget to provide instructions on how to set up the calf thymus DNA samples for calibration, and how to convert INTDEN values into concentrations.--->
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'''DNA Measurement Protocol'''
 
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==Research and Development==
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==New System: Research and Development==
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<!--- Bonus: explain how Bayesian statistics can be used to assess the reliability of your team's method. Just write the equation using variables that are relevant to your team's new test. You do not need actual numbers --->
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'''BACKGROUND'''
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<!--- A description of the CHEK2 gene, it's associated SNP, and the cancer-related function of the gene. Use the information from your Week 13 worksheet. --->
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'''Background on Disease Markers'''
 
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<!--- A description of the diseases and their associated SNP's (include the database reference number and web link) --->
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'''DESIGN'''
 +
<!-- If your team decided to only amplify cancer-associated DNA, list the Cancer allele forward primer and the Cancer allele reverse primer. Include a paragraph that explains why a disease allele will give a PCR product and the non-disease allele will not.-->
 +
<!-- If your team chose an alternative approach to amplify the DNA, list all relevant primers. Include a paragraph that explains how your system works.-->
 +
'''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.
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'''Primer Design'''
 
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<!--- Include the sequences of your forward and reverse primers. Explain why a disease allele will give a PCR product and the non-disease allele will not. --->
 

Revision as of 21:01, 9 April 2013

BME 103 Spring 2013 Home
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Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
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Image:BME494_Asu_logo.png

Contents

OUR TEAM

Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(s)
Name: StudentRole(s)
Name: Student
Role(s)

LAB 3 WRITE-UP

Original System: PCR Results

PCR Test Results

Sample Name ng/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 ---


Bayesian Statistics
These statistics are based upon all of the DNA detection system results that were obtained in the PCR lab for 34 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 AND MATERIALS

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
  • DNA Measurement and Analysis Protocol


New System: Research and Development

BACKGROUND


DESIGN


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.




Illustration




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