Calibration
The camera was placed in the cradle at a right angle, and the height was adjusted so that the camera was able to get a straight shot on the picture. The distance from camera to slide was carefully measured, and the cradle was placed inside the lightbox properly.
Distance between the smart phone cradle and drop = 11 cm
Solutions Used for Calibration
Amount of Calf Thymus DNA solution(micrograms/mL)
Volume of the DNA solution (μL)
Volume of the SYBR GREEN I Dye Solution (μL)
Final DNA concentration in SYBR Green I solution (µg/mL)
5
80
80
2.5
2
80
80
1
1
80
80
0.5
.5
80
80
0.25
0.25
80
80
0.125
0
80
80
0
Placing Samples onto the Fluorimeter
Place the slide on the Flourimeter with the rough side facing up
Place 80 micro-liters of SYBR green solution on the slide on the two circles in the middle
Following that, place an additional 80 micro-liters of the calibration solution in with the SYBR green solution
Then, light the drop with the blue light from the Flourimeter by adjusting the position of the slide
Using the phone camera, take a covered picture of the sample
Using the ImageJ software, collect the data
Repeat each of the previous steps for each subsequent sample
Data Analysis
Representative Images of Negative and Positive Samples
This doesn't have DNA:
This has DNA:
Image J Values for All Calibrator Samples
G2023(Mg/mL)
Area
Mean
RawIntDen Drop
RawIntDenBackground
Drop-Background
0
112704
37.029
4173330
4173330
80486
0.125
115052
115.304
132565969
13265969
355717
0.25
76220
42.315
3225427
3225247
211612
0.5
108269
84.101
9105547
9105547
237419
1
99946
125.025
12475765
12475765
46683
2.5
104836
183.136
19199198
19199198
108537
0.125
104976
114.33
12001882
12001882
509621
0.25
74493
40.904
3042076
3042076
65389
0.5
112648
81.69
9202174
9202174
240454
1
90873
126.962
11537375
11537375
53851
2.5
106250
177.936
18905736
18905736
107969
0.125
117716
145.994
17185841
17185841
17037984
0.25
72426
39.731
2877591
2877591
48997
0.5
113313
81.15
9195343
9195343
241627
1
98512
126.812
12492486
12492486
58334
2.5
105285
168.462
17736545
17736545
91600
0
116198
36.957
4294334
4294334
285141
0
109924
35.248
3874568
3874568
76169
Calibration curve
PCR Results Summary
Our positive control PCR result was .34 μg/mL
Our negative control PCR result was 0 μg/mL
Observed results
Patient 58272: .35 μg/mL
Patient 80239 : .68 μg/mL
Conclusions
Patient 58272 : This patient seems to be negative, despite values that are awfully close to the positive control, they are significantly lower than the 2nd patient, which implies a negative outcome.
Patient 80239 :This patient seems to be positive, as the estimated values are far above what is to be expected of a positive sample
SNP Information & Primer Design
Background: About the Disease SNP
SNP stands for Single-nucleotide polymorphism; it is a disease in which a single nucleotide in a DNA sequence differs from that of the other chromosome in the pair or from other individuals of the species. There are 4 nucleotides used in a DNA sequence: two purines called adenine and guanine and two pyrimidines called cytosine and thymine. In a SNP, adenine may be changed out for a guanine to create a singe-nucleotide change in the DNA code. There are 10 million SNPs in the human genome where a single SNP occurs within roughly every 300 nucleotides. Most SNPs will have no affect on an organism in its environment but certain SNPs can have outstanding effects. Some of there effects include resistance to certain drugs and toxins. Scientists often use SNPs as "biological markers" where they use the singe alternate nucleotide as an indicator for the location of a certain gene. They can also be used to track genes and determine if a given gene is inherited by the offspring of two individuals.
Primer Design and Testing
The results of our primer test were conclusive. Each trial ran produced the expected results, our positive control gave off bright green light and our negative control along with the water trial was clear. As we ran the two different patient samples three times each we observed that both were consistent to themselves, meaning our results were not only accurate but repeatable as well.