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 Freezing is undoubtedly the best way to preserve any biosp

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mona alshaikh

on 26 January 2015

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Transcript of  Freezing is undoubtedly the best way to preserve any biosp



:E/ Use of recycled DNA in Downstream molecular applications :
1)-PCR efficiency and PCR product size assessment Sequencing of some candidate genes (if possible)
 
2)-Epigenetic analysis: DNA Methylation profile
Methylation analysis will be achieved as follows:
Bisulfate modification
 
Clean up of bisulfate converted DNA
Methylight analysis
Percentage of Methylated Reference (PMR)

Proposal Abstracts :

In order to overcome the shortage of high-quality and fully annotated biological samples, it is necessary to best use the available biospecimens stored in the biobanks in downstream molecular analysis to develop new drugs, markers or diagnostic tools for several diseases mainly cancer.

The current study explores a new DNA extraction approach to reuse these already stained FFPE slides again in studying cancer molecular biology.





Using the DNA fixed on the already stained IHC slides, its DNA extraction
protocol of DNA is not common practice worldwide and
represents the novelty of this project.


Therefore, using these used IHC slides to get pure DNA and assess
its use in further downstream molecular analysis and profiling (at both
genetic and epigenetic levels) will be a promising approach to increase
the value of samples and expand their use in medical and research
applications.






 Freezing is undoubtedly the best way to preserve any biospecimen; it’s the only way to keep cells viable for future expansion, and it is also the best method for preserving intact DNA, RNA, protein, and even Peptides

 or cryopreservation in liquid nitrogen, is now widely preferred, particularly for long term storage. Cell lines, protein, and DNA remain stable for years at -80oC, though RNA does begin to degrade after 5 years. Cryopreservation also provides excellent sample stability, and may protect samples from desiccation and from temperature fluctuations
related to repeated freezer door

 For decades the process of formalin-fixing, paraffin embedding (FFPE) has been the method of choice for tissue preservation, because this technique best maintains the morphology of the original tissue.


Reuse of DNA Extracted from Already Immunostained Formalin Fixed Paraffin Embedded (FFPE) Slides:
Technique Refinement and Use in Downstream Molecular Analysis to study Cancer Biology


A/ Patient consent
B/ Type of biospecimen used
C/ Extraction of DNA from IHC
stained slides .
D/ Concentration Measurement
and Quality Assessment of
Genomic DNA .





Proposal Plan:


 

1)- A proof of concept that the DNA extracted from already stained IHC is still useful for other molecular analysis

2)- Establish and refine the reused DNA extraction
protocols

3)- Determine the type of downstream molecular analysis in which such recycled DNA can be used.


Proposal Aims:


So far, the conventional FFPE technique considered as the gold standard for preserving
histomorphology, while cryopreservation of tissue is the gold standard for biomolecule preservation

In this context, once a cancer sample is freshly collected by surgeon, part or this entire sample is stored as a Formalin Fixed Paraffin Embedded (FFPE) block for further use in diagnosis, prognosis and prediction of disease or for further research in order to customize and improve the healthcare service offered to this patient and other patients in Saudi Arabia and worldwide .


In this context, once a cancer sample is freshly collected by surgeon, part or this entire sample is stored as a Formalin Fixed Paraffin Embedded (FFPE) block for further use in diagnosis, prognosis and prediction of disease or for further research in order to customize and improve the healthcare service offered to this patient and other patients in Saudi Arabia and worldwide .

.

Literature review:
Nowadays, the medical field is the site of huge milestones to improve the quality of the healthcare delivered to patients .

Several diseases (e.g. cancer) are now threatening the human welfare mainly because of their mutagenic and
In this context, once a cancer sample is freshly collected by surgeon, part or this entire sample is stored as a Formalin Fixed Paraffin Embedded (FFPE) block for further use in diagnosis, prognosis and prediction of disease or for further research in order to customize and improve the healthcare service offered to this patient and other patients in Saudi Arabia and worldwide
complicate way of progression and treatment.





A Resereach proposal for master defree in
Biotechnoloogh and genmic
submitted by :
Muna Salem Al-shaikh.
Supervised by
D.Mona Al-sharaif
phD. Abdelbaset buhmeida
1436 -2015
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