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Evolution of Sequencing Technology for Genomics Applications

Evolution of Sequencing Technology for Genomics Applications

By: Vijay Walia June 05 2019

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Evolution of Sequencing Technology for Genomics Applications

Sequencing is the process of decoding deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). DNA is constantly replicated in all living cells as cell prepares for cell division, and is copied to transcribe RNA. These strategies are enabling researchers to understand how changes in DNA sequence regulate diseases and phenotypes. Since 2003, after the completion of the Human Genome project, significant progress has been made in sequencing. Sequencing technologies have revealed astonishing data over the last ten years for multiple species.

Fred Sanger published the dideoxy method that revolutionized the whole sequencing industry [2], after nearly 20 years of DNA structure discovery [1]. This method involves copying single strand DNA using dideoxynucleotides, which are chemically altered bases, allowing chain termination to occur as bases are incorporated, followed by resolving using capillary electrophoresis. During mid-1980, a number of improvements in Sanger sequencing, such as fluorometry-based detection and capillary-based electrophoresis, led to automated DNA sequencing machines. During the 1990’s, DNA sequencers were used in many laboratories for sequencing and played a significant role in Human Genome project, which was an international effort to decode the human genome over a 10 year period with billions of dollars of investment [3][4]. Since then many laboratories routinely use Sanger sequencers for identifying genetic variations. Although, the throughput of these sequencers is not sufficient for large-scale genomic studies, they still are a popular tool for denovo applications and smaller genomics studies.

Around 2005, a new sequencing technology based on “sequencing by synthesis” started gaining attention as it would allow massive parallel sequencing. This is now known as “next-generation sequencing,” (NGS), a term given to methodology that enables researchers to rapidly sequence millions of base pairs of RNA or DNA molecules [5]. This approach is different from Sanger sequencing as NGS does not use chain termination chemistry, but instead records nucleotide addition to the polymerized strand. In 2008, Dr. Jonathan Rothberg published the first human genome sequence of Dr. James D. Watson, who elucidated DNA structure in 1950s. Rothberg group achieved this in two months using massive parallel sequencing for less than $1 million [6]. Currently, both Sanger sequencing and NGS technologies are used throughout the world for many genomics applications for research and clinical use.

At Fisher Clinical Services, a part of Thermo Fisher Scientific, we offer NGS not only to detect key cancer-associated mutations but for a broad range of applications, which include; expression profile of genes, chromosomal counting, epigenetic changes, whole genome analysis, and whole exome analysis, which is driving field of personalized medicine ahead every day. NGS has reshaped the way we study genetics, by reducing time, cost, and increasing scale of genomic investigations. Various NGS technologies are now available with the same fundamental feature of parallel sequencing of millions of individual DNA molecules [7]. We provide semiconductor based Ion Torrent NGS services to our clients for fast and flexible workflow that is scalable for a broad range of NGS applications, unlike optics or modified nucleotides based NGS technologies.

Thermo Fisher’s Ion Torrent technology reads DNA sequence by sequential addition of A, T, G, C to the DNA chain allowing release of a hydrogen ion. This causes a change in pH, which is captured by semiconductor chip (0, 1). Millions of such changes determine the sequence of DNA fragments, and when this occurs in parallel, we get millions of reads sequenced at the same time.We currently provide services for multiple research applications including; oncology, human leukocyte antigen, infectious diseases, targeted disease panels, whole exome, microbiome, agrigenomics, or even denovo sequencing.

Targeted sequencing using Thermo Fisher’s AmpliSeq technology is very popular among biobanking customers as this uses a multiplexed PCR based sequence enrichment step, which allows detection of a panel of genes in a sample. Tumor samples or FFPE blocks from patients can easily be sequenced for targeted oncogenes / tumor suppressor genes or any specific alteration in genome in no time and at very low cost. Download our overview brochure to learn more about how you can maximize the value of your samples.

Bibliography

  1. Watson J, Crick F (1953) Molecular structure of nucleic acids. Nature 171:737–738.
  2. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci 74:5463–5467. doi: 10.1073/pnas.74.12.5463
  3. International Human Sequencing Genome (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921.
  4. The Celera Genomics Sequencing Team (2001) The sequence of the human genome. Science (80- ) 291:1304–1351.
  5. Margulies M, Egholm M, Altman WE, et al (2005) Genome Sequencing in Open Microfabricated High Density Picolitre Reactors. Nature 437:376–380. doi: 10.1038/nature03959
  6. Wheeler DA, Srinivasan M, Egholm M, et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872–876. doi: 10.1038/nature06884
  7. Heather JM, Chain B (2016) The sequence of sequencers: The history of sequencing DNA. Genomics 107:1–8. doi: 10.1016/j.ygeno.2015.11.003
Evolution of Sequencing Technology for Genomics Applications