The Journey of DNA Sequencing

Every life form has DNA which is woven together by base, sugar and phosphate groups. Determining the order or sequence of the four bases (adenine, guanine, cytosine, and thymine) is termed DNA Sequencing. The earliest known method of DNA sequencing, also called plus-minus sequencing, was developed by Sanger and Coulson. DNA sequencing methods fall into three categories: first, second and third-generation sequencing methods. Contrary to modern sequencing methods, earlier sequencing methods were very accurate, time-consuming and could sequence very small fragments of up to 200-400 base pairs. Examples of the earliest sequencing methods include Sanger sequencing and Maxam–Gilbert sequencing.

Second-generation methods amplify the DNA of interest following which nucleotide incorporation could then be observed by fluorescence tag or electric impulse difference; common examples include pyrosequencing, Illumina, SOLiD, nanoball sequencing and Ion torrent. Pyrosequencing was innovated by 454 Life Sciences in 2005 and further taken over by Roche in 2007. Illumina dye sensing is a very promising technique and already acquired >70% of the sequencing business. SOLiD was developed by Life Technologies and commercialized by Applied Biosystems Instruments in 2008. Nanoball sequencing was developed by Complete Genomics that was further taken over by Chinese genomics service company Beijing Genomics Institute-Shenzhen in 2015. Ion torrent technique was developed in partnership by DNA Electronics Ltd and Roche’s 454 Life Sciences in 2010.

Third generation sequencing is more achievable, appears to reduce the price of sequencing up to a great extent and is still in the developmental stage. The most well-known techniques in this category are Single-molecule real-time sequencing (SMRT), Helicos sequencing, Nanopore sequencing, NGS by electron microscopy. SMRT was developed by Pacific Biosciences. The Helicos sequencing system was marketed by Helicos Biosciences. As this company filed bankruptcy, this service is now provided by SeqLL. The nanopore technology was offered by Oxford Nanopore Technologies. Many scientists tried to visualize DNA in an electron microscope but as the interference of electron beams could damage the DNA structure, this idea was never commercialized [1].

With the advancement of technology, the applications of genome sequencing are increasing on a daily basis. This technology has immensely contributed in medicine, biology and several other closely related fields. The benefits of DNA sequencing could be immeasurable but few mentionable ones could include comparing mutated and healthy sequences in diseases such as cancer, antibody characterization, development of treatment methods, and guide the identification of novel species. Genome sequencing is highly recommended for patients where the cause of the disease is unknown for a long period. Further, the research team from Gastrointestinal (GI) Bacterial Reference Unit, Public Health England are sequencing the isolates from clinical GI patients and food sources on a daily routine basis. Whole-genome sequencing helps in monitoring a wide range of pathogenic bacteria. The team has gathered information on interrelated ancestral strains, strain mutation with time, entry of pathogens in the food chain, improved surveillance and outbreak detection especially in particular geographical locations [2].

Although sequencing techniques are considered prerequisites for some medical conditions, luxury genetic testing has also come into existence now. Many start-up companies, in the market today, are practicing personalized genome sequencing. These companies commercialize curiosity of identifying one’s ancestral history, the probability of inheriting certain diseases, diagnosis of hereditary disease carriers, and other phenotypic traits such as height, skin/hair/ eye color. They hand over data directly to consumers and often, deep sequencing is not performed in these applications. Instead, variant sequencing is carried out as these correspond to the relevant and unique locations in the genome. Accuracy and data interpretation are also questionable in such techniques. In such scenarios, a consumer could choose third party service which could again be prohibitively expensive and will not guarantee certainty. Therefore, genetic screening must be advised by a medical expert [3].

The technology certainly addresses several key health issues but it has also raised many contemporary ethical concerns. Few of them include the real benefit of personal genome sequencing, coverage by insurance, concerns of discrimination due to publicly shared data, misuse of data, genetic screening before conceiving or denial of claims after data exposure.

References:
1. Kulski, J. K. (2016). Next-generation sequencing—an overview of the history, tools, and “Omic” applications. Next Generation Sequencing–Advances, Applications and Challenges, 3-60.
2. ILSI Global (2018, Aug 23) ILSI NA: IAFP 2018: Whole Genome Sequencing Round Table Discussion (Kathie Grant) YouTube. https://youtu.be/F-_bxnvfhxs
3. Tandy-Connor, S., Guiltinan, J., Krempely, K., LaDuca, H., Reineke, P., Gutierrez, S., … & Davis, B. T. (2018). False-positive results released by direct-to-consumer genetic tests highlight the importance of clinical confirmation testing for appropriate patient care. Genetics in Medicine, 20(12), 1515.


Guest post written by Namrata Kumari.

Namrata Kumari is a skilled science communicator with a track record of international high impact publication, conference & workshop presentation, extensive experience as consulting editor, editorial board member of scientific journals and grant management. She has experience in chemical & biotechnology fields resulting in 7 completed team-based projects.

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