Association study of promoter region SNP rs2275913 of IL-17A in brain cancer in Pakistani Population

Project Title

Association study of promoter region SNP rs2275913 of IL-17A in brain cancer in Pakistani Population

Project Area of Specialization Biomedical EngineeringProject Summary

This is a Genome-wide association study of promoter region SNP rs2275913 of IL 17A involved in the progression and worsening of brain cancer in Pakistan.

Brain cancer is a disruptive neurological condition that leads to the formation of masses referred to as tumors. They are quick and can affect the functioning of the body. There are a number of different factors involved in the formation and progression of the tumor but the core factor on which this research is focused are the genetic polymorphisms. 

IL 17A is a proinflammatory molecule that mediates and amplifies the inflammation response. IL 17A is a double-sided sword because if its quantity passes a threshold limit it potentially leads to cancer formation and progression by incorporating various other factors like suppression of tumor necrosis factor, formation of IL 6 and Th 17 , formation of myeloid-derived suppressor cells, and release of VEGF.

During inflammation, a transcription factor NFAT is released that binds to promoter region  and causes differentiation of IL 17A. So hypothetically if there is a mutation present in that site it can potentially interfere with the production and maintenance of the interleukin leading to the destruction of normal homeostasis.

Our main goal is to identify the SNP and its role in brain cancer, for this we will first design primers necessary for PCR amplification and allele specific mutation identification using bioinformatic and IT-driven tools and software. Then DNA isolation and quantification will be done through the use of DNA kits. 

Moving onwards, the DNA isolated from the blood samples would then be run through allele specific PCR protocols for the identification of mutations. 

The data would then be cross-checked using linear regression analysis performed using biostatistical and bioinformatic driven software. The findings and Data would then be compiled and published.

Project Objectives

Brain cancer causes about 2,081 deaths in males and 1,259
deaths in females annually which roughly translates into 2.4
and 1.4 percent respectively per 100,000 cancer deaths. An
annual increase of 0.4% is expected each year which is
mainly due to the lesser understandings of genetic factors,
lack of preventative measures and late diagnosis.

Studies of genetic markers and SNPs may help predict a
person's predisposition to cancer which could enable
scientists and medical practitioners to come up with better
diagnosing protocols and management strategies.

So our main objective is to identify and illuminate the causative factor that is SNP rs2275913 involved in Brain Cancer which would save lives , money and would lead to better overall health and economy.

Project Implementation Method

The basic methodology follows the designing of primers which are an integral first step to kickoff the research using bioinformatic, Big Data and IT driven tool.

Primer designing is followed by DNA isolation using commercially available DNA kits from blood samples of the affected population that would make our experimental group and also from healthy individuals that would make up our control and reference group. 

The DNA isolated would then be subjected to allele specific PCR protocols that require a master mix and customized PCR conditions. This is followed by visualization of the data through gel electrophoresis analysis.

Afterwards the data obtained is crosschecked and verified using biostatistical, bioinformatic, IT and Big Data tools and softwares. 

The verified Data would then be compiled , analyzed and studied and extrapolated.

The results obtained would then be documented and published.

Benefits of the Project

Each year, roughly 8.8 million people die from cancer, mostly in low- and middle-income countries like Pakistan, according to WHO official statistical reports. 

Studies that involve genetic markers and SNPs may help predict a person's predisposition to cancer which could enable scientists and medical practitioners to come up with better diagnosing protocols and management strategies, these in turn would mean that cancers are identified before they even begin. This would lead to better lives, less burden on hospitals and medical sector and better economy.

Technical Details of Final Deliverable

Our major Goal is to identify the role of SNP rs2275913 in the proliferation, progression and worsening condition of tumors in the brain. 

Using the protocols to assess the involvement we hope to identify some sort of relationship between the two ; the SNP and Brain Cancer.

If our findings support our initial hypothesis we greatly hope that the Data generated through our research would enable doctors and scientists to collaborate and come up with strategies to detect cancer as early as possible even before its inception. This translates to the fact that this research could lead to better diagnosing and management protocols that could eventually save countless lives , save many people from the stress , tensions and turmoil of cancer treatment , save people a lot of money , decrease the load on hospitals and driving the finances to the sectors of economy that really need it.

Final Deliverable of the Project Software SystemCore Industry HealthOther Industries IT , Medical , Others Core Technology OthersOther Technologies NeuroTech, Shared Economy, Big DataSustainable Development Goals Good Health and Well-Being for People, Partnerships to achieve the GoalRequired Resources

Item Name	Type	No. of Units	Per Unit Cost (in Rs)	Total (in Rs)
			Total in (Rs)	75000
PCR master mix + Taq Polymerase+Dntps+gel Ladder	Equipment	01	028000	28000
PCR Primers	Equipment	2	7500	15000
DNA isolation kits	Equipment	01	025000	25000
Travelling and transportation	Miscellaneous	04	500	2000
Thesis Binding , printing and stationary	Miscellaneous	01	5000	5000