Articles

From DNA to bulk sequencing

Geórgia Oliveira

Precision medicine has experienced a remarkable moment of expansion. In this field we often hear about DNA and its sequencing, but have you ever stopped to ask why this has become an increasingly present issue in our lives? A recent example is the importance of sequencing the genetic material of the new coronavirus (COVID-19) for the development of therapies and vaccines. We can also remember the news about the genetic exam of the actress Angelina Jolie, who detected through the sequencing of some genes a greater risk of developing breast cancer. This news shows us that the future of precision medicine is already happening.

We have had many advances in science and especially in understanding diseases since the discovery of the DNA – a molecule composed essentially of nucleotides – and its association with the determination of the characteristics of living beings. The position in which these nucleotides are arranged is what differentiates one DNA molecule from the other, like coordinates on a map. This order is responsible for encoding genetic information for the growth and development of organisms in general, deciphering and ordering it is still a great challenge.

Historic

Illustration 1: Timeline

Subtitle:

  1. Discovery of the DNA shape;
  2. Biological functioning of DNA;
  3. Gel sequencing data;
  4. Sanger sequencing data;
  5. NGS sequencing data.

After the discovery of the three-dimensional structure of the DNA in 1593, we also began the discovery of the central dogma of biology, and what does this mean? It basically means that we find the meaning of life! In other words, the biological sense of reading this great map called DNA. And from then on we were able to advance further in the research because it was possible to decipher this code.

First Generation

It was in the 70s that the first sequencing techniques emerged, and the most popular was the Sanger method (still used today). This method was created by Alan Coulson and Frederick Sanger and consists of determining the sequence of nucleotides through synthesis of a single strand of DNA using DNA polymerase – mimicking the natural process – and dideoxynucleotides (ddNTPs).

In 1986, the biotechnology company Applied Biosystems launched the first automatic sequencing equipment based on the Sanger method, using fluorescent markers for each nucleotide and allowing reactions to be run in a column and read by the color they emitted, this technology capable of reading 96 samples at a time, with an average fragment size of approximately 1,000 bp (1 kb), was used in the human genome project, but for purposes of applicability in mass diagnosis it was still a very time-consuming and costly technique.

Second Generation

In the middle of 2004/2005, the Roche – 454 (which consisted of a Pyrosquencing method) appeared, a precursor of what we call NGS (Next Generation Sequencing) for providing a larger volume of data, at a lower cost, in a faster way and capable of processing a large number of molecules in parallel.

Many other NGS methodologies have emerged year after year (e.g. Illumina MiSeq and Ion Torrent). What they all have in common is the ability to generate information on millions of base pairs from different individuals (DNA libraries) in one single run and redundantly. Finally, all of this information puzzle is processed and organized through bioinformatics.

Third Generation

We consider Third Generation technologies to be capable of Single- Molecule sequencing (SMS) without the need for fragmentation and amplification of DNA shared by all previous technologies. They are long sequences of DNA taking readings on a high performance platform. It is not yet a matter of techniques or equipment widely used for diagnostic purposes, we still have a path of improvement and evolution to go.

Because of the sequencing capacity, today we can compare large stretches of DNA – 1 million bases or more – from different individuals, more quickly and cheaply generating a large amount of information, this opens up more and more space for diagnosis through the analysis of genomes allowing rare changes in genes to be identified, association with phenotypes, predisposition to diseases, response to drugs, among many other clinical applications making the future of personalized medicine real.

Genome sequencing is also used in many other areas of science, such as sequencing of viruses and bacteria, in evolutionary studies, environmental monitoring, validation of raw materials and inputs, genetic improvement of plants and even the study of materials brought from space. And we don’t stop there, there are several possible applications to be discovered!

About the author:

Geórgia Oliveira has a degree in Biomedicine and a postgraduate degree in Molecular Diagnosis. She is a specialist in Lean Six Sigma – Green Belt and is currently a Master’s student in Genetics and a full analyst at Genomika Diagnósticos.

  • Manish Roy

    July 28, 2020

    Sir 🧬 sorry

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