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Microarray
​Applications and Limitations of Microarray
Microarrays versus Sequencing

- Arrays only detect known organisms.
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- Allows greater replication and has greater diversity in environmental samples.
How to solve the problem?
Sequencing can detect unknown organisms.
Arrays versus Real-Time PCR
- Offers a bigger capacity for multiplexing purpose.
- Concurrently screen for higher number of potential pathogens.
- Problem in detecting femtogram quantities, detection limit of 1fg has been reported.
How to solve the problem?
Detection limit can be solved by increasing the sample size or centrifugation to concentrate the genetic material.
Microarrays versus Macroarrays

- Needs more specialised equipment than macroarrays.
- Better control on the binding of oligonucleotides.
- Less sensitive than macroarrays.
How to solve the problem?
Sensitivity improved by using high copy number target DNA regions and a PCR labelling step that amplifies the query region of the target molecule.
Limitations of microarray

- Time consuming in designing and testing discriminatory genetic regions that distinguishes one species from another.
- Difficult to handle DNA when working on microarrays. This problem is overcome by using smaller chips together with higher densities of sample.
- Needs specialised and more advanced equipment.
- Resolution of scanner used limits the technique.
- Development of software to process the databases.
- Raise a number of ethical issues: potential genetic discrimination.
This figure shows the example of applications for DNA microarray.
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