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A Virtual Technique Will Make It Possible to Predict Genetic Diseases

By: Gimena Ruiz Pérez, Unimedios

Using knowledge of the genome to anticipate diseases that a person will suffer is close to being a reality. A technique developed by researchers at the University of Wisconsin—Madison and the Universidad Nacional de Colombia, based on tiny structures known as nanochannels, is helping to decipher the genetic code with greater detail and speed.

What if a medical consultation could tell you that in 10 years time you will suffer from cancer, Parkinson's, arthritis or other afflictions, but that treatment to prevent the onset of the disease could begin now? Surprising isn't it? Researchers from the University of Wisconsin-Madison in the United States and from the Universidad Nacional de Colombia in Medellín are working jointly to achieve this important scientific advance.

Over the course of several decades, professor David C. Schwartz developed an optical map in microchannels (set of “tubes” or “tanks” created on a microscopic scale using lithography methods, 1 million times smaller than normal tubing), which makes it possible to completely sequence and extract the human genome in high-resolution.

This technique is based on the organized presentation of DNA molecules that are then analyzed using visual tools such as the optical microscope.

Predictions in a short time

Although the procedure was created years ago, the complete analysis of a genome – from its preparation until its interpretation – takes months. That is why, based on this first advance, professors at both institutions developed a methodology to optimize and reduce the time for the procedure to just hours, through the use of nanochannels (1 billion times smaller than microchannels ).

“This is the only method that currently exists in the world to analyze the genome at a resolution of various nucleotides (the basic unit of DNA). There are latest generation techniques that create sequences, but none have the quality, simplicity and low cost of optical nanomapping. This means that in a few years we will be able to have a clinical tool that will enable us to compare good and bad genes to predict whether a person will suffer from diabetes or if their offspring will have malformations”, says Juan Pablo Hernández Ortiz, a professor at the Mining Faculty at the UN in Medellín.

"In optical nanomapping we mark the DNA at various points and then pass it through a nanochannel, where we stretch it and read it optically as though it were a barcode. This reading enables us to extract the genome”, he reports.

Thus, using a computational model (developed at the UN), a digital experiment is carried out into which all of the physical elements of the process are incorporated.

The researchers have performed experiments with sequences and genomes of animals and humans using the procedure. According to professor Hernández, “in the physical experiment, the virtual simulation process is replicated. A DNA solution is taken, in other words, from a chromosome, it is separated and the DNA molecules are extracted. They are then placed in a saline medium and enzymes are added that adhere to determined parts of the molecules, creating a fluorescent point. Using a syringe, this substance is then injected into a microchannel, and in an electrical field, the molecules are forced to pass through the nanochannels. By combining this information, the genetic code is extracted one by one.”

State-of-the-art in medicine

He affirms that perfecting this technique would make it possible to advance in other hitherto unexplored fields. “There are diseases whose origins have not been determined and it is not known how to prevent them. They are aberrations of our genetic code that could be clarified through this procedure”.

For professor David C. Schwartz, “the project is discovering ways of obtaining data from the so-called ‘individual genetic profile’, fostering medical advances through the development of new computer programs and machines that rapidly and economically read the biological information of each individual”.

"When medical science is able to gain access to this technique, complications from these illnesses will decrease. In the economic sphere, people will spend less on medications, more will be known about conditions such as cancer and diabetes and many new diseases will be preventable”, reconstructive plastic surgeon Claudia Mora acknowledges from her perspective.

Catalina López Correa, vice president for Scientific Affairs at Genome Québec, stresses the way in which microfluids technology and nanotechnology applied to the study of DNA and genomics in general (DNA, RNA, study of proteins) is accelerating and facilitating research such as optical mapping. “Its impact on the development and validation of new genetic tests and the way of diagnosing and treating diseases such as cancer and other cardiometabolic conditions is huge”.

“Seeing and reading the complete book of life”. That is how professor Hernández views the process that can be carried out using this technology: “DNA is simply a language of four letters that tells us all of the functions of living things. Using the high-resolution genome, we will also be able to study the way to create vaccines and treatments. In this way, a field of research will also open up for other disciplines such as pharmaceuticals and bioengineering”.

The project entitled ‘Study of DNA in Nanochannels for High–resolution Genome Studies (Estudio de ADN en nano–canales para estudios de genoma de alta resolución) is financed by the National Institute of Health (NIH) and the National Science Foundation (NSF) of the USA through the Nanoscale and Engineering Center (NSEC) of the University of Wisconsin–Madison.

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