COMPUTATIONAL GENOMICS
THE "HOW" OF SCIENCE
PERSONALIZED MEDICINE
WHAT IS PERSONALIZED MEDICINE?
Personalized medicine is an approach to treating a disease that focuses on how every person has a unique risk and reaction to a specific disease. Personalized medicine acknowledges that each person has different disease risks based on their genome.
When a person gets sick, a doctor needs to analyze their genome in order to determine the best possible treatment. For this reason, personalized medicine requires a technological process called a genome-wide association study [1].
This infographic shows the benefits for developing personalized medicine, one of the fields that bioinformatics has a large impact on [1]
WHAT IS A GENOME WIDE
ASSOCIATION STUDY?
The first step in providing personalized medicine to an affected patient is to perform a Genome Wide Association Study.
A genome-wide association study is a process that scientists use to identify the genes that are often involved in a specific human disease. The method searches the genome for single nucleotide polymorphisms (small variations in the genome) that are proven to correlate to the expression of a disease. Researchers use these SNPs to determine if a patient is particularly vulnerable to the disease [2].
This diagram shows the process of performing a GWAS in order to determine whether a patient has a certain disease [2]
HOW DOES A GWAS WORK?
In order to carry out the GWAS, researchers obtain DNA samples from two groups of participants. The first group of participants has the disease and the second contains similar people who are known not to have the disease.
Each set of DNA is purified and placed on a tiny, scannable chip. Machines in the laboratory look specifically for markers of genetic variation in the gene that could correlate with the disease.
If the analysis finds that the diseased people frequently carry a certain genetic variation that the non-diseased people do not, it can be concluded that the variation is "associated" with the disease. This conclusion can point doctors and pharmaceutical researchers to the region of the genome that correlates with the certain disease [2] .
In order to further dissect the problem, scientists often need to sequence DNA base pairs in the associated area to accurately pinpoint the root of the problem [3].
This image shows how a chip can be used to generate the SNPs necessary to perform a GWAS [3]
WHAT TECHNOLOGY IS USED IN A GWAS?
SNPTEST:
SNPTEST is a computer software that is designed to analyze multiple genomes (which are obtained during the GWAS) and find any possible correlations between diseases and gene mutations.
The program implements tests including
-
identifying phenotypes of the sample population
-
calculating probability and frequency of association between two likely factors
-
Study the conditional state of many possible factors [4].
This image shows how SNPTEST analyzes and compares the SNPs that are used in a GWAS [4]
PLINK:
PLINK is a free software that is focused on analyzing the association between whole-genome studies. Like SNPTEST, its goal is to perform the statistical calculations to produce the mathematical results of GWAS.
PLINK was developed by Shaun Purcell while he was working at the Center for Human Genetic Research (CHGR), Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT.
This graph shows the analyzed results of a GWAS that are found using PLINK or another software program [5]