Next Generation Sequencing (NGS) and Bioinformatics Technology

By: David Agustriawan, Ph.D.

Bioinformatics Technology

Deoxyribonucleic acid (DNA) sequencing is a process to identify the composition of the nucleotide base sequence in a DNA molecule of an organism. The DNA sequencing process is carried out using biochemical methods to determine the right DNA sequence using a machine or sequencing technology. A DNA sequencing machine can produce data consisting of DNA sequences in the form of reads, which include five letters, adenine (A), thymine (T), cytosine (C), guanine (G), and Not known/Ambiguous (N). The first sequencing technology was developed in 1977 by Frederick Sanger from the University of Cambridge, who received a Nobel Prize in Chemistry in 1980. The discovery opened up space for studying the genetic code of organisms and inspired researchers to develop sequencing technologies that were more efficient, fast, and cheap. The sequencing technology that was first developed by Sanger was a sequencing technology era that provided a new perspective for exploring and determining the entire sequence of DNA or genome in organisms.

In 2005, a new sequencing technology called Roche’s 454 was commercialized as a technology capable of producing large amounts of DNA sequences at a much lower cost than the first sequencing technology. This technology is commonly known as the first generation Next Generation Sequencing (NGS) technology. NGS technology has the ability to perform parallel processing of DNA sequences in large numbers from multiple samples and at a much lower cost. This technology can generate millions to billions of reads in a single process with a gigabase size (1 billion nucleotides) in just a few days or a few hours. For example, the human genome consisting of 3 billion DNA nucleotides varying in length from 33 to 247 million nucleotides distributed on 23 chromosomes in the cell nucleus. Human genome sequencing uses Sanger sequencing technology can take about 15 years which requires cooperation from many laboratories in the world and costs around 100 million US Dollars (USD). Meanwhile, sequencing using NGS Roche’s 454 technology only took two months at a total cost of around 1 million USD, although it has not been able to read the genome. The technology is still limited to sequencing small numbers of fragments and producing millions of reads. Then, NGS sequencing technology evolved to the third generation which offers much cheaper costs with shorter processing times than the previous generation. So that in this third generation of NGS technology, we can do the sequencing for one human genome in just one day at a price of around 1,000 USD or around 15 million rupiahs. Examples of NGS technology are as follows: (1) Second-generation NGS technologies include: 454 GS Junior +, HiSeqx illumine, SOLID 5500xl W, and Ion Torrent Ion S5 / S5XL 540; (2) Third generation NGS technologies include: Pacbio Sequel and Oxford Nanopore PromethION.

According to an article published in PRNewswire New York, on August 7, 2019, informs that: globally, the market for NGS technology is USD 4.533 million in 2018 and is predicted to reach USD 18.565 million in 2026. Based on the mapping of the purchasing area of ​​technology NGS is located in North America (United States, Canada, Mexico), Europe (Germany, France, England, Italy, Spain, and so on), Asia-Pacific (Japan, China, Australia, India, South Korea, Taiwan, and others). -Other), LAMEA (Brazil, Turkey, Saudi Arabia, South Africa, and others). North America was the largest buyer of NGS technology in 2015. The Indonesian government has also become a consumer of NGS technology. The Indonesian government has known the benefits of NGS technology so that the Ministry of Research, Technology and Higher Education (Kemristekdikti) in the era of Mr. Mohamad Nasir, through the Directorate General of Strengthening Research and Development (Dirjen Risbang) built a National Genome Center at the Institute of Molecular Biology (LBM Eijkman) on June April 26, 2017. This aims to encourage national research in the field of Molecular Biology, especially in the health sector. With the existence of the Genome Center, it is hoped that it can catch up with Molecular Biology research in Indonesia from other nations so that it can help increase the nation’s competitiveness.

The results of DNA sequencing of an organism can be used in many fields of Molecular Biology, such as in the fields of health, forensics, agriculture, fisheries, and so on. For example, in the health sector for cases of cancer, reads obtained from NGS sequencing results from cancer patient data and normal can be processed and analyzed by Bioinformatics experts. By comparing the two data, it will be able to identify potential biomarkers (mutations in DNA, genes / microRNA / DNA methylation whose expression is not normal) in the cancer cells studied. By knowing these potential biomarkers, a therapy or treatment that targets these potential biomarkers can be created. In the forensic field, reads from the sequencing results can be used to identify the perpetrators of murder, the spread of the HIV / AIDS virus, and so on by comparing the HIV / AIDS virus DNA found in victims with the HIV / AIDS virus DNA found in the suspected perpetrator. In agriculture, we can identify biomarkers in superior seed plants. In the world of health, sequencing technology also makes it possible to create personalized medicine where the treatment will be adjusted to the patient’s genome so that drug administration can be more precise and effective. In the field of fisheries in Indonesia, sequencing technology makes it possible to create superior seeds from fish varieties in Indonesia. Making a vaccine to deal with the Covid-19 pandemic which has an impact throughout the world at this time can be done in a short time, less than a year cannot be separated from the contribution of bioinformatics in analyzing SARS-CoV-2 genome data to search for conserved regions and drug planning. And many other sectors of life can be optimized through sequencing technology. Thus, the benefits of Molecular Biology research with NGS technology are enormous.

Indonesia has a very abundant wealth of biodiversity which can be sorted to examine its uses and benefits. So that we need more NGS machines, along with human resources to accelerate the mapping and sequencing process of all biodiversity in Indonesia. It would be even better if there were research clusters for research topics that made use of the NGS engine. Many research clusters can be created, such as research on the benefits of herbal plants, research for infectious diseases, research for cancer, phylogenetic research, epigenetic research, personalized medicine, research in agriculture, and so on. From there it can be seen that the scope of research that utilizes NGS technology is very broad and the contribution of Bioinformatics is very large for the advancement of molecular biology research from the design stage of research methods, analyzing data to the stage of interpreting data.

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