Genomes II

 Genomes II


In blue, real price per Mb of DNA;
in white, expected price following Moore’s law.
From: National Human Research Institute

During the last decade, DNA sequencing technology has advanced at an astonishing rate. 

The price per megabase of DNA has diminished from 5,292.39 USD on January 2001, to 0.09 USD (nine cents) on October 2011, which means a price 58,800 times less than what was charged almost ten years ago.

Here we present a brief timeline about the Next Generation Sequencing technologies.


1970s


F. Sanger

On February 1977, in the Proceedings of the National Academy of Sciences, Dr. Walter Gilbert and his student, Allan Maxam, from Harvard University, published a paper titled: “A new method for sequencing DNA”. This particular method made use of radioactive markers and chemical degradation of DNA, with a maximum sequencing capacity at least 100 nucleotides, as the authors believed that the main cause for this limitation was the resolution limitation of polyacrylamide gels. 


W. Gilbert

However, due to the technical difficulties of the realization of this method, it would be quickly displaced by other chain-termination sequencing technologies. The technology developed by Sanger would soon displace the Maxam-Gilbert procedure.


Since 1975, Sanger had already published a sequencing method based on extension using DNA polymerase, but the process had to be adapted for it to displace Maxam and Gilbert’s technique.

For their contributions to DNA sequencing, Sanger and Gilbert (along with Paul Berg, for his contributions to recombinant DNA technology) received the 1980 Nobel Prize in Chemistry.


1980s


Dr. Leroy Hood currently leads
a research group at the
Institute for Systems Biology

However, both Maxam-Gilbert’s method as well as Sanger chain-termination method by then had the disadvantage of using radioactive markers. 


The solution to this would be proposed in a 1985 publication by the research group of  Leroy Hood  in Caltech: using nucleotides tagged with fluorescent probes. At the beginning, the development involved the use of fluorescent primers, but that would soon evolve to the use of fluorescent dideoxynucleotides (ddNTPs). 

Dr. Hood’s group also worked on the first semiautomatic sequencing mechanisms; at the end of the decade, the first commercial sequencing platforms were made available and started to gain popularity, mainly Applied Biosystems and Pharmacy. 

1990s


During the 90s, the race to complete the sequencing of the human genome attracted public attention towards genomics. The evolution of the systems used in chain-termination sequencing kept its course with the introduction of new, sophisticated capillary systems, while other technologies remained only in white papers.


2000-present

The first functional draft of the human genome was published in 2001, and by 2003 the project was declared completed.

The evolution of sequencing systems took an interesting turn with the introduction of high-throughput, parallel sequencing technologies, giving birth to the so-called “deep sequencing” or “next generation sequencing” technologies.


A polony sequencing illustration.

A polony (PO-lymerase co-LONY) is a DNA colony that has been amplified upon a particular site.


Among the first methodologies to create polonys are the ones developed by Church and Mitra from the MIT, published in 1999, and the method developed by the Serono Institute, published in 2000. These techniques would soon be adapted for many applications, such as the quantification of the relative effect on gene expression of allelic variants of human genes, genotyping and haplotyping and DNA sequencing, among others.

Changes to this sequencing method were made mainly in Harvard University’s School of Medicine, thanks to Dr. Church’s group, who worked with the Dover Coorporation in the development of the Polonator Genome Analyzer.

One of the distinctive characteristics of polony sequencing is the existence of free online resources like instructions for the construction of equipment and software for the analysis of the obtained data, making this particular sequencing method a more open access alternative.

Pyrosequencing
In a winter afternoon in 1986, Pål Nyré, a Swedish researcher, got out his laboratory and headed towards Fulbourn on his bike. Any other person would have mindlessly continued with their evening routine, but not Dr.Nyré: he came up with the idea for a new DNA sequencing method. 

Sample preparation for 454 sequencing
from Margulies et al., (2005)

This idea was based on the pyrophosphate liberation made by the polymerase as it adds nucleotides to a DNA chain. A decade later, Dr.Nyré founded Pyrosequencing AB (later called Biotage AB), who would sell in 1999 the first automated pyrosequencing system with a parallel 96 sample capacity. QIAGEN acquired Biotage AB’s Biosystems section in 2000 and currently distributes a platform for 96 samples, the PyroMark Q96 series.


But the definitive step towards making pyrosequencing a truly high-throughput technology came a few years later, with the introduction of a massively parallelized version of pyrosequencing: the 454 method, which uses reactors of extremely small size, in the range of picolitres. This technology is based on two main innovations: the PCR amplification of framgents of the sample DNA in a liquid-lipid emulsion and the fiber optic technology to transmit the luminescence signal.

In 2000, 454 Life Sciences was founded and in 2005 the GS20 next-generation sequencing platform was launched, which was used by Margulies and collaborators to obtain the genomic sequence of Mycoplasma genitallum.

Finally, in 2007 Roche acquired 454 Life Sciences, and a new GS20 sequencing platform was developed: the GS FLX. With this methodology, in 2008 James Watson’s genome was successfully sequenced: the process took two months at 1/100 of the cost compared to sequencing the same genome using Sanger’s method.





To be continued with:
-Solexa/Illumina
-IonTorrent
-Nanopore

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