BME100 s2015:Group11 12pmL6

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BME 100 Spring 2015 Home
Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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Miranda Kaml
Framarz Alam
Joe Florio
Name: student
Name: student


Bayesian Statistics

Overview of the Original Diagnosis System There were 68 patients tested for the disease-associated SNP. 34 teams of 6 students each were assigned two patients to diagnose. Each patient provided two DNA samples to prevent error in the diagnosis. The samples were tested against a positive and negative control for the disease. Three images were taken for each sample to rule out error. The three photos for each sample were each measured in ImageJ and the numbers were averaged for each sample calculation. Inconclusive results and blank data were ruled out so that the Bayesian statistics for the entire group were accurate and valid.

What Bayes Statistics Imply about This Diagnostic Approach
Calculation 1

Variable Description Value
A frequency of cancer positive conclusion .375
B frequency of positive PCR reaction .4375
P(B/A) frequency of positive PCR reaction for cancer positive conclusion .6667
P(A/B) probability cancer DNA sequence .5714

Calculation 2

Variable Description Value
A frequency of cancer negative conclusion .625
B frequency of negative PCR reaction .5625
P(B/A) frequency of negative PCR reaction for cancer negative conclusion .9
P(A/B) probability cancer DNA sequence 1

Calculation 3

Variable Description Value
A frequency of cancer yes diagnoses .4375
B frequency of positive DNA test conclusion .375
P(B/A) probability positive given cancer - yes .6667
P(A/B) probability devolve cancer .778

Calculation 4

Variable Description Value
A frequency of cancer no diagnoses .5625
B frequency of negative DNA test conclusion .625
P(B/A) probability negative given cancer - no .9
P(A/B) probability not devolve cancer .81

Calculations 1 and 2 were proven reliable as the number was close to .5. The PCR replicates were reliable for a correct diagnosis of the disease SNP being present or not. Calculations 3 and 4 were closer to 1 and proved that the ability for PCR to predict the diagnosis is low because of the high calculations. Many errors could have occurred during these PCR and detection steps. The students could have mixed up the PCR samples to get an incorrect result. The students could have added the wrong amount of PRC solution during the PCR step or the SYBR Green during the imaging step. The students could have also mixed up the order of the images when analyzing them in ImageJ.

Computer-Aided Design


Our Design

PolymerEase Self-Cleaning Fluorimeter Slide

The improved fluorimeter slide tackles the problematic cleaning of previously used test samples. Rather than using a pipettor which may fail to collect the entire volume of waste fluid from the slide and possibly leave residue that may interfere with the placement of future samples due to the cohesiveness of water, this fluorimeter slide is coated in a highly hydrophobic coating that will deter any liquid from remaining on its surface. The circular indentations will assist in keeping samples in place during testing. Afterwards, clean-up is a breeze with the simple tilting mechanism that easily disposes of any liquid on the slide into a conveniently positioned and removable waste collection container.

PolymerEase Self-Cleaning Fluorimeter Handle

Part 1

Assess the original design

Consumables Open PCR Fluorimeter system
Strength Pipettor-cheap Portable and small Compatible with multiple phone types and cheap
Weakness Pipettor-disposable tips Reaction time Drops of PCR solution can leave residue on slides

Part 2

Design a new system

Our Brand Name:


Branding Positioning Target Markets Messaging Place
Efficient easy to use fluorimeter Fluorimeter cleans itself Bio-Chemical and Dairy market Making your life easier, it's in our DNA Online website

Feature 1: Consumables Kit

The consumable portions of the kit will be separated between the disposable plastics and pipettor, and the liquid reagents. Sterile pipettor tips will be kept in their own closed containers to prevent contamination from contacting any other materials. The same will be done to any unused test tubes. The pipettor will be kept on a rack to enhance organization and keep track of kit materials. The liquid reagents, such as the PCR DNA samples and PCR products, will be packaged separately in a refrigerated rack in order to prevent their degradation. Dyes such as SYBR Green will also be packaged here.

Feature 2: Hardware - PCR Machine & Fluorimeter

The fluorimeter's slide will be hydrophobic. Once the camera is done taking the picture the slide will move up at an angle in order for the drop to travel off the slide. This fix will have the fluorimeter clean itself after each trial.

The flourimeter will have a handle on the side that will tilt the slide back so that the drop of PCR mixture rolls off and does not have to be removed with a micropipettor. This will speed up the PCR imaging process.