Generation Sequencing

A timeline of next-generation sequencing progress from 1972 to 2019.

Next-generation sequencing (NGS) refers to the application of high-throughput technologies that determine the sequence of a nucleic acid strand (like DNA or RNA) in a matter of days or even hours. These technologies are relatively new to the scene and have transformed genomics research over recent years. The technologies typically involve stepwise cycles of polymerase-based extension or oligonucleotide ligation, which rely on the piecing together of short reads from fragmented DNA.

That said, the newest NGS methods are long-read techniques that produce reads from much larger fragments of DNA. There are two main long-read sequencing methods: nanopore sequencing and single-molecule real-time (SMRT) sequencing. Nanopore sequencing involves measuring changes in electric current while passing strands of DNA through a protein nanopore. Researchers then use a computer to decode the changes and decipher the sequence. On the other hand, SMRT sequencing involves circularizing strands of DNA and using a polymerase to integrate labeled bases that emit light on integration. Researchers detect the light and use this to measure nucleotide incorporation in real time.

As NGS techniques, technologies, and applications continue to evolve, the life sciences journal BioTechniques reflects on how far these techniques and technologies have come since the beginning of DNA sequencing.

The History of Next-Generation Sequencing

Scientists have worked to understand the molecular structures of DNA ever since the discovery of DNA’s basic double-helix structure in the 1950s. Following the completion of the Human Genome Project in 2003, scientists have been dedicating their efforts to developing NGS techniques. Since then, the speed of NGS has accelerated rapidly. Now, researchers can sequence a whole human genome in under one day. Meanwhile, the cost of next generation sequencing techniques has dropped: By 2018, the cost of sequencing a full human genome had fallen to below $1,000.

Here, we’ll delve into the key moments in the history of DNA sequencing.

  •       1972: Paul Berg developed the first technology that enabled the isolation of defined DNA fragments. This triggered the development of modern genetic engineering. Before the advent of this technology, researchers only had access to phages and virus DNA for sequencing.

  •       1973: Walter Gilbert published the first nucleotide sequence, which comprised 24 base pairs of the DNA lac operator.

  •       1977: Frederick Sanger sequenced the first complete DNA genome of a bacteriophage (phi X174). He then developed the method ‘DNA sequencing with chain-terminating inhibitors’. Following this, Walter Gilbert developed a method termed ‘DNA sequencing by chemical degradation’.

  •       1986: Leroy Hood announced an invention at the California Institute of Technology: the first semi-automated DNA sequencing machine. Scientists used this machine to map and sequence genetic material.

  •       1987: Applied Biosystems marketed the first automated sequencing machine: the ABI370. This development marked a major advancement for many research projects.

  •       1990: The Human Genome Project formally launched, involving research teams in the UK, U.S., France, Germany, India, China, and Japan.

  •       1998: Eric Kawashima, Laurent Farinelli and Pascal Mayer developed the ‘Method of nucleic acid amplification’ at the Geneva Biomedical Research Institute. This method was a major milestone in the development of NGS technologies.

  •       2000: As a result of these advances in the genomics field, particularly in sequence analysis, the Human Genome Project completed a ‘rough draft’ of the human genome. Lynx Therapeutics Company then launched the massively parallel signature sequencing (MPSS) technology. (Illumina later bought Lynx Therapeutics.)

The Evolution of Next-Generation Sequencing

NGS techniques became available at the beginning of the 21st century, offering efficient, quick, cost-effective, accurate sequencing methods that vastly improved upon Sanger methods.

These are the key moments in the history of NGS.

  •       2003: International researchers finished the Human Genome Project, which took 13 years to complete, cost approximately $2.7 billion, and pieced together the human genome using Sanger sequencing.

  •       2004: 454 Life Sciences announced a new generation pyrosequencing technology: the Rosche GS20, which was the first NGS platform on the market. This technology revolutionized DNA sequencing by being able to produce up to 20 million base pairs.

  •       2008: The first paper about studying the human genome sequence using NGS was published. Meanwhile, James Watson’s personal genome sequence was estimated to cost $1 million. This was the first example of scientists using NGS to produce a single genome.

  •       2011: Pacific Biosciences’ (PacBio) single-molecule real-time (SMRT) sequencing technology was commercially released. This long-read sequencing technology marked a major development in next-generation sequencing.

  •       2014: Following the release of SMRT sequencing, Oxford Nanopore Technologies’ (ONT) nanopore sequencing was also commercially released. Both SMRT and nanopore sequencing dominate the long-read sequencing space. The technologies are suitable for an increasing number of applications and produce data that differs qualitatively from second-generation sequencing, necessitating tailored analysis tools.

  •       2014: Illumina launched the HiSeq X Ten Sequencer and claimed to have produced the first $1,000 genome. However, it took tens of millions of upfront investments to achieve this milestone. It became apparent that Illumina had monopolized the industry. The company held 70% of the market for DNA sequencers and accounted for more than 90% of all DNA data produced on a global scale.

  •       2018: Veritas Genetics offered whole genome sequencing to 1,000 customers, priced at just $199.

  •       2019: The Nation Human Genome Research Institute noted that the price of sequencing a complete human genome had reached $942, beating Moore’s Law prediction.

The Future of Next-Generation Sequencing

Modern NGS techniques are ideal for a variety of applications, like whole genome sequencing, RNA sequencing, and metagenomics. As these techniques continue to modernize, they will make their way into more and more genomics laboratories as efficient and affordable solutions. For example, the latest NGS technologies use single-cell sequencing techniques to generate more accurate insights into specific cells’ nucleic acids during a particular phase. These technologies avoid ensemble average readings from samples, which can be misleading.

New techniques to sequence directly from a tissue or sample (spatial sequencing) are also emerging. These techniques provide a special resolution to data and enable researchers to examine a cell’s composition and interactions in their natural environments. Such techniques drastically reduce the time and cost of sequencing while improving accuracy, which will open doors for their use across a range of genomics applications.

Explore BioTechniques’ insights into NGS.

About BioTechniques

BioTechniques is the first publication to review lab methodologies and techniques, paving the way for the future of science and medicine. Scientists who specialize in fields like physics, chemistry, computer science, and plant and agricultural science use the open-access, peer-reviewed journal to develop their knowledge of the life sciences and stay up to date with the latest in techniques like chromatography, polymerase chain reaction, western blotting, CRISPR gene editing, and NGS.

Users can also make the most of BioTechniques’ online multimedia website, where a growing community of scientists, lab workers, and other industry experts access webinars, videos, podcasts, eBooks, industry articles, and interviews. They can also share their insights in key conversations that inform medical and scientific practices.

BioTechniques is one of Future Science Group’s journals. The group publishes 34 journals to promote knowledge share in the scientific and medical arena, including titles like Regenerative Medicine, Future Oncology, and Nanomedicine.