BME103:W930 Group7 - Revision history

Seong Song: /* Protocols */

Seong Song — Wed, 14 Nov 2012 16:30:25 GMT

Protocols

←Older revision		Revision as of 16:30, 14 November 2012
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	5. Sample Description:		5. Sample Description:

-	Patient 1 ID: 91562	+	Patient 1 ID: 91562 Male

-	Patient 2 ID: 25235	+	Patient 2 ID: 25235 Male

	(see table above for listed volumes of each reagent)		(see table above for listed volumes of each reagent)

Frea Mehta: /* OUR TEAM */

Frea Mehta — Wed, 14 Nov 2012 14:58:52 GMT

OUR TEAM

←Older revision		Revision as of 14:58, 14 November 2012
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-		+	http://www.youtube.com/embed/x5yPkxCLads?rel=0
-	~~<gflash>560 315~~ http://www.youtube.com/embed/x5yPkxCLads?rel=0~~</gflash>~~	+

	=LAB 1 WRITE-UP=		=LAB 1 WRITE-UP=

Frea Mehta: /* Results */

Frea Mehta — Wed, 14 Nov 2012 14:58:12 GMT

Results

←Older revision		Revision as of 14:58, 14 November 2012
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	KEY		KEY
	* '''Sample''' = Sample denotes the sample of DNA used in a given trial. Each sample represents one extraction of DNA from one of two patients. The multiple trials per patient guarantee accurate results that a single trial could not, for example false positives and false negatives can impact the results and multiple trials will somewhat eliminate the error of one trial.		* '''Sample''' = Sample denotes the sample of DNA used in a given trial. Each sample represents one extraction of DNA from one of two patients. The multiple trials per patient guarantee accurate results that a single trial could not, for example false positives and false negatives can impact the results and multiple trials will somewhat eliminate the error of one trial.
-	* '''Integrated Density''' = ~~<!--- explain what "integrated~~ density~~" means and how you did background subtraction~~ to ~~get this~~ value ~~--->~~	+	* '''Integrated Density''' = Integrated density is the sum of the values of the pixels in a given area, which is equivalent to the product of the area of the selection and the mean gray value.
	* '''DNA μg/mL''' = To calculate the concentration of DNA, we created a calibration curve using the given concentrations of DNA for the negative and positive control samples - 0 μg/mL and 2 μg/mL, respectively. This yielded the equation y = (X-267793)/(13571087.5) where y = the concentration of DNA in μg/mL and X = the integrated density for a given sample.		* '''DNA μg/mL''' = To calculate the concentration of DNA, we created a calibration curve using the given concentrations of DNA for the negative and positive control samples - 0 μg/mL and 2 μg/mL, respectively. This yielded the equation y = (X-267793)/(13571087.5) where y = the concentration of DNA in μg/mL and X = the integrated density for a given sample.
	* '''Conclusion''' = DNA concentrations of over 1 μg/mL yielded positive results; if the concentration was less than 1 μg/mL, the sample yielded negative results		* '''Conclusion''' = DNA concentrations of over 1 μg/mL yielded positive results; if the concentration was less than 1 μg/mL, the sample yielded negative results

Tyler Shea Allen: /* Protocols */

Tyler Shea Allen — Wed, 14 Nov 2012 11:43:08 GMT

Protocols

←Older revision		Revision as of 11:43, 14 November 2012
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	'''Flourimeter Measurements'''<br>		'''Flourimeter Measurements'''<br>

-	[[Image:~~Bme_103_group7_setup_diagram~~.png‎‎\|500px\|Flourimeter Setup]]	+	[[Image:Bme_103_group7_setup_diagram2.png‎‎\|500px\|Flourimeter Setup]]

Seong Song: /* Protocols */

Seong Song — Wed, 14 Nov 2012 11:20:51 GMT

Protocols

←Older revision		Revision as of 11:20, 14 November 2012
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	5. Sample Description:		5. Sample Description:

-	Patient 1 ID: 91562	+	Patient 1 ID: 91562

	Patient 2 ID: 25235		Patient 2 ID: 25235

Tyler Shea Allen: /* Initial Machine Testing */

Tyler Shea Allen — Wed, 14 Nov 2012 11:10:54 GMT

Initial Machine Testing

←Older revision		Revision as of 11:10, 14 November 2012
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	'''Test Run'''		'''Test Run'''

-	Our first Open PCR test was conducted on Wednesday, October 24, 2012. While running our open PCR test, we experienced nothing but problems. We set the cycles to the appropriate temperatures and time intervals; the Initial cycle on 95°C for 30 seconds, the Denaturing cycle on 95°C for 30 seconds, the Annealing cycle on 55°C for 30 seconds, the Extending cycle on 72°C for 30 seconds, the final cycle on 72°C for 180 seconds, and the final hold at 20°C. Initially, our open PCR appeared to be running correctly for the desired two hour time interval. However, due to a cycling error, our timer extended to nearly three hours. Not only did our test exceed the desired time interval, but our time would not wind down. Our test constantly moved up and down between the times of two hours thirty minutes and two hours and fifty minutes. When our time got close to two thirty, more time would be added to our test. Also, our laptop was experiencing errors. Our laptop received an application error notice multiple times, each time disrupting our process. As a result of these complications, when the two hours elapsed we only reached step seventeen of thirty. We were forced to prematurely end our test. Therefore, we could not receive sufficient results.	+	Our first Open PCR test was conducted on Wednesday, October 24, 2012 on machine number 7. While running our open PCR test, we experienced nothing but problems. We set the cycles to the appropriate temperatures and time intervals; the Initial cycle on 95°C for 30 seconds, the Denaturing cycle on 95°C for 30 seconds, the Annealing cycle on 55°C for 30 seconds, the Extending cycle on 72°C for 30 seconds, the final cycle on 72°C for 180 seconds, and the final hold at 20°C. Initially, our open PCR appeared to be running correctly for the desired two hour time interval. However, due to a cycling error, our timer extended to nearly three hours. Not only did our test exceed the desired time interval, but our time would not wind down. Our test constantly moved up and down between the times of two hours thirty minutes and two hours and fifty minutes. When our time got close to two thirty, more time would be added to our test. Also, our laptop was experiencing errors. Our laptop received an application error notice multiple times, each time disrupting our process. As a result of these complications, when the two hours elapsed we only reached step seventeen of thirty. We were forced to prematurely end our test. Therefore, we could not receive sufficient results.

Seong Song: /* Research and Development */

Seong Song — Wed, 14 Nov 2012 11:05:16 GMT

Research and Development

←Older revision		Revision as of 11:05, 14 November 2012
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	PCR produces amplification in the presence of cancer SNP by creating around 100 billion copies of certain sequences found in the DNA. This process can take only a couple hours. During the process, Primers are added to the extracted DNA, where it attaches to the ends of specific DNA segments. Nucleotides are added so that they can create new copies of the DNA. Finally, DNA polymerase is added and works to make new DNA copies by attaching matching nucleotides. With increased temperatures, the double helix of the target sequence separates. Primers attach onto targeted regions on the separated strands and the polymerase attaches free floating nucleotides on the new strands. The process of separating and reattaching of the targeted sequence is repeated and in the end, around a billion of DNA present will be those of the DNA segments that has been targeted and contains the SNP.		PCR produces amplification in the presence of cancer SNP by creating around 100 billion copies of certain sequences found in the DNA. This process can take only a couple hours. During the process, Primers are added to the extracted DNA, where it attaches to the ends of specific DNA segments. Nucleotides are added so that they can create new copies of the DNA. Finally, DNA polymerase is added and works to make new DNA copies by attaching matching nucleotides. With increased temperatures, the double helix of the target sequence separates. Primers attach onto targeted regions on the separated strands and the polymerase attaches free floating nucleotides on the new strands. The process of separating and reattaching of the targeted sequence is repeated and in the end, around a billion of DNA present will be those of the DNA segments that has been targeted and contains the SNP.
		+

	The gene we are looking at is rs17879961 (CHEK2 gene), a gene that indicates susceptibility to breast and colorectal cancer. It is located on chromosome 22 and codes for a cell-cycle regulatory kinase responsible for DNA repair processes in BRCA1, a gene that is responsible for breast cancer.		The gene we are looking at is rs17879961 (CHEK2 gene), a gene that indicates susceptibility to breast and colorectal cancer. It is located on chromosome 22 and codes for a cell-cycle regulatory kinase responsible for DNA repair processes in BRCA1, a gene that is responsible for breast cancer.
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	The reverse primer:		The reverse primer:
	TGTATCTTCTAGTGTCACCGc		TGTATCTTCTAGTGTCACCGc
		+

	-Bayes Explanation		-Bayes Explanation
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	*p(~C)=0.99		*p(~C)=0.99
	*p(CIT)=0.078 or 7.8%		*p(CIT)=0.078 or 7.8%
-
-
-
-
-

Seong Song: /* Research and Development */

Seong Song — Wed, 14 Nov 2012 11:04:28 GMT

Research and Development

←Older revision		Revision as of 11:04, 14 November 2012
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	TGTATCTTCTAGTGTCACCGc		TGTATCTTCTAGTGTCACCGc

-		+	-Bayes Explanation
	Due to the occurrence of false positives and negatives during testing, not all tests are suitable for a wide-distribution. To enumerate the validity of such tests, Bayes Rule is commonly utilized. Bayes Rule relates the probability of accurate positive and negative results to those of false positive and negative results to determine whether the test is reliable.		Due to the occurrence of false positives and negatives during testing, not all tests are suitable for a wide-distribution. To enumerate the validity of such tests, Bayes Rule is commonly utilized. Bayes Rule relates the probability of accurate positive and negative results to those of false positive and negative results to determine whether the test is reliable.

		+	-Equation
	p(CIT)= (p(TIC)p(C))/((P(TIC)p(C))+((p(TI~C)*p(~C)))		p(CIT)= (p(TIC)p(C))/((P(TIC)p(C))+((p(TI~C)*p(~C)))
	*C= Cancer Present		*C= Cancer Present
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	*p(TIC)= Conditional Probability		*p(TIC)= Conditional Probability
	*p(TI~C)= Conditional Probability		*p(TI~C)= Conditional Probability
		+	*p(~C)=Prior Probabilities
		+
		+	-Known Variable Values
		+	*p(C)= 0.01
		+	*p(TIC)= 0.8
		+	*p(TI~C)= 0.096
		+	*p(~C)=0.99
		+	*p(CIT)=0.078 or 7.8%
		+

Seong Song: /* Research and Development */

Seong Song — Wed, 14 Nov 2012 10:50:34 GMT

Research and Development

←Older revision		Revision as of 10:50, 14 November 2012
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	PCR produces amplification in the presence of cancer SNP by creating around 100 billion copies of certain sequences found in the DNA. This process can take only a couple hours. During the process, Primers are added to the extracted DNA, where it attaches to the ends of specific DNA segments. Nucleotides are added so that they can create new copies of the DNA. Finally, DNA polymerase is added and works to make new DNA copies by attaching matching nucleotides. With increased temperatures, the double helix of the target sequence separates. Primers attach onto targeted regions on the separated strands and the polymerase attaches free floating nucleotides on the new strands. The process of separating and reattaching of the targeted sequence is repeated and in the end, around a billion of DNA present will be those of the DNA segments that has been targeted and contains the SNP.		PCR produces amplification in the presence of cancer SNP by creating around 100 billion copies of certain sequences found in the DNA. This process can take only a couple hours. During the process, Primers are added to the extracted DNA, where it attaches to the ends of specific DNA segments. Nucleotides are added so that they can create new copies of the DNA. Finally, DNA polymerase is added and works to make new DNA copies by attaching matching nucleotides. With increased temperatures, the double helix of the target sequence separates. Primers attach onto targeted regions on the separated strands and the polymerase attaches free floating nucleotides on the new strands. The process of separating and reattaching of the targeted sequence is repeated and in the end, around a billion of DNA present will be those of the DNA segments that has been targeted and contains the SNP.

-	The gene we are looking at is rs17879961, a gene that indicates susceptibility to breast and colorectal cancer. It is located on chromosome 22 and codes for a cell-cycle regulatory kinase responsible for DNA repair processes in BRCA1, a gene that is responsible for breast cancer.	+	The gene we are looking at is rs17879961 (CHEK2 gene), a gene that indicates susceptibility to breast and colorectal cancer. It is located on chromosome 22 and codes for a cell-cycle regulatory kinase responsible for DNA repair processes in BRCA1, a gene that is responsible for breast cancer.

	In normal patients, the gene sequence is as follows:		In normal patients, the gene sequence is as follows:

Seong Song: /* Research and Development */

Seong Song — Wed, 14 Nov 2012 10:39:25 GMT

Research and Development

←Older revision		Revision as of 10:39, 14 November 2012
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-	~~Bayes Rule attempts~~ to ~~relate~~ the ~~probability~~ of a ~~certain event occurring to~~ the ~~odds~~ of ~~another~~, ~~in terms~~ of ~~that event~~.	+	Due to the occurrence of false positives and negatives during testing, not all tests are suitable for a wide-distribution. To enumerate the validity of such tests, Bayes Rule is commonly utilized. Bayes Rule relates the probability of accurate positive and negative results to those of false positive and negative results to determine whether the test is reliable.

	p(CIT)= (p(TIC)p(C))/((P(TIC)p(C))+((p(TI~C)*p(~C)))		p(CIT)= (p(TIC)p(C))/((P(TIC)p(C))+((p(TI~C)*p(~C)))