Lecture 2 Flashcards
What are the criteria for an ideal biosensor?
(1) Clinical performance of biomarker
(2) analytical performance of biosensor
What defines the clinical performance of the biomarker
Sensitivity and Specificity
In the clinical performance of the biomarker, what are the four outcomes of a test?
(1) True positive (Sensitivity)
(2) True negative (Specificity)
(3) False negative
(4) False positive
What is clinical sensitivity?
True positive rate (TPR): the probability that the biomarker will be detected positive in the diseased patient.
Write an equation describing clinical sensitivit of a biosensor.
TP/(TP+FN)
Write an equation describing clinical specificity of a biosensor.
TN/(TN+FP)
What is clinical specificity?
true negative rate (TNR): the probability that the biomarker will be absent or below a given threshold in a “non-disease” control.
What does it mean to have a biomarker with 100% sensitivity?
all individuals with confirmed disease test positive for the biomarker
What does it mean to have a biomarker with 100% specificity?
all individuals without disease test negative for the biomarker
What does the Receiver Operating Characteristic (ROC) curve describe?
a graphical representation of the relationship between sensitivity (y) and specificity (x=1-specificity)
How to plot ROC?
true positive rate (y=sensitivity) against false negative rate (x=1-specificity)
Why do we use the ROC curve?
to assess the efficacy of a biomarker for every possible cutoff point (i.e., for every chosen threshold value that distinguishes healthy from sick)
A change in cutoff value that leads to an increase in sensitivity will typically be at the expense of lowering specificity, and vice versa.
What does the area under the ROC curve measures?
the biomarker (or test) ability to discriminate between “healthy” and “sick” states
How can you increase the clinical performance of biomarkers? give an example.
Combination of different biomarkers (multiplexing). For example, using PSA along Age to diagnose prostate cancer is a better test/ indicator that using PSA alone.
What are the requirements for high analytical performance if biosensors?
(1) Sensitivity
(2) Specificity
(3) precision
What does sensitivity measure in high analytical performance? how is it done?
Measures the ability to detect the lowest concentration of the target biomarker
by using: the calibration curve and limit of detection (LOD)
What does specificity measure in high analytical performance? how is it done?
Measures the sensor’s ability to differentiate between target and non-targeted biological entities in a sample by using a complex matrix or a negative control or adding competitor.
What does specificity depends on biosensor analytical preformance?
(1) the affinity of the target/bioreceptor pair,
(2) the functionalization method,
(3) the implemented assay protocol
What is precision in analytical performance of a biosensor?
evaluation of the degree of agreement between a number of measurements obtained for the same sample
How to measure Biosensor Precision?
(1) repeatability:
the degree of agreement between results taken under identical conditions
(2) reproducibility
the degree of agreement between results conducted by different individuals, at different locations, with different instruments.
How many types of biosensors is there? what are they?
- Research based and point of care (POC)
What are the basic elements of all biosensors?
(1) sensing
(2) transduction
(3) signal processing
What additional element is required for POC devices?
a sample processing element to enable purification or separation of the analyte of interest of the biological matrix.
What are the advantages and features of research-based biosensors?
Advantages: rapid and accurate analysis of complex biological components and interactions
Features:
(1) usually bulky and expensive
(2) often accommodate liquid handling elements (for multistep sensing processes) and temperature controllers (for thermocycling applications).
(3) a trained professional is required to: (i) safely and efficiently operate such large and costly devices. (ii) process, analyze, and interpret the generated data.
Explain PCR as an example of research-based biosensor.
PCR is an elegant enzymatic assay that enables amplification of a specific DNA fragment among a pool of DNA.
What are the main types of PCR
(1) qualitative PCR: determines the presence or absence of a particular DNA product
(2) Real-Time quantitative PCR (qPCR) can additionally determine how much of that DNA is present
What are the main types of PCR
(1) qualitative PCR: determines the presence or absence of a particular DNA product
(2) Real-Time quantitative PCR (qPCR) can additionally determine how much of that DNA is present
What are the advantages of PCR?
(1) Amplfying DNA from trace amounts of analyte.
(2) High sensitivity and specificity
(3) Well-established, gold-standard
What are the limitations of PCR?
(1) Contamination
(2) Specificity may be compromised by unspecific binding of primers to DNA fragments sharing high sequence homology with the DNA target of interest.
(3) Errors may arise from DNA polymerase incorporating incorrect nucleotides
(4) Costly and time-intensive
(5) Requires trained personnel
What is POC?
Rapid clinical tests that are conducted outside the
laboratory, including:
(1) at the patient’s bedside,
(2) in the operating theatre,
(3) clinical care unit,
(4) or in remote areas with limited resources.
What are the features of POC biosensors?
(1) Portable
(2) Easy-to-use
(3) Non-expert use
(4) Out of the lab
(5) In the home or field environment
What is the aim of POC?
To provide access of critical laboratory-based tests to patients, in order to provide rapid, reliable and cost-effective tools to improve disease management and facilitate real time or pseudo-real time clinical decision making
What are the world health organization (WHO) requirements for POC?
ASSURED; Affordable, Sensitive, Specific, User-friendly, Rapid, Equipment free, Deliverable.
give examples of POC devices
(1) Lateral Flow Assay (LFA); pregnancy tests
(2) Glucose monitoring
What are the advantages of POC?
(1) fewer manual steps
(2) minimal contamination
(3) reduction in the volume of expensive reagents
(3) time reduction
name three strategies to develop POC devices?
(i) Miniaturisation to reduce reagent and sample volumes, assay times and cost
(ii) Integration of additional sample processing capabilities.
(iii) Simplification of readouts for ease of interpretation
Explain some strategies to take PCR to POC.
(1) Design the space domain of a chip as the sample flows through a microfluidic channel, its temperature is controlled by integrated heating blocks in a location-dependent manner.
(2) Exploit symmetry to reduce the number of heaters: serpentine and radial channels
(3) Miniaturize: microfluidics is a suitable platform to perform digital PCR
(4)Control temperature, keep sample solution stationary: heating by a tungsten lamp or a laser, while cooling can be achieved by a fan
What materials are exploited in POC biosensors?
(1) Polymers in microfluidics
(2) Paper and fibrous substrates for lateral flow assay
(3) Nanomaterials for readouts
