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CoolMPS: Advanced massively parallel sequencing using antibodies specific to each natural nucleobase

Snezana Drmanac, Matthew Callow, Linsu Chen, Ping Zhou, Leon Eckhardt, Chongjun Xu, Meihua Gong, Scott Gablenz, Jyothi Rajagopal, Qing Yang, Christian Villarosa, Anthony Au, Kyle Davis, Alexander Jorjorian, Jingjing Wang, Ao Chen, Xian Zhang, Adam Borcherding, Xiaofang Wei, Mingxuan Zhang, Yonghui Xie, Nina Barua, Jay Shafto, Yuliang Dong, Yue Zheng, Lin Wang, Lili Zhai, Jiguang Li, Sha Liao, Wenwei Zhang, Jian Liu, Hui Jiang, Jian Wang, Handong Li, Xun Xu, Radoje Drmanac

Preprint posted on 20 February 2020 https://www.biorxiv.org/content/10.1101/2020.02.19.953307v1

A new sequencing method using natural reversible terminator nucleotides and fluorescent antibodies has the potential to reduce the cost of WGS down to $100 whilst increasing sensitivity and decreasing error rates.

Selected by Kerryn Elliott

Background 

The first draft of the human genome sequence took 15 months and cost an estimated $300 million (https://www.genome.gov/about-genomics/fact-sheets/Sequencing-Human-Genome-cost). Since then the price of sequencing whole genomes has decreased dramatically, largely thanks to Next Generation sequencing, which allows the genome to be broken up into small pieces and sequenced in parallel. The decrease in cost continues even now, as 10 years ago it cost around $50,000 to sequence a genome, and today this cost is around $1000. The new CoolMPSTM technology proposed by researchers at BGI has the potential to further reduce the costs down to $100, with the cost decrease coming from the reduced number of expensive reagents required.

Main findings

In this paper the authors describe CoolMPSTM (Massively Parallel Sequencing) a clever adaptation to sequencing by synthesis. In sequencing by synthesis, single stranded templates are used to allow incorporation of one reversible terminator nucleotide at a time. The incorporated nucleotide is then recorded, and the terminator sequence cleaved off to allow the next cycle of nucleotide addition. In CoolMPSTM, instead of using fluorescently labeled reversible terminator nucleotides to image each cycle of sequencing, as seen in Illumina® sequencers, they use natural reversible nucleotides to which they raise antibodies (Figure 1). These antibodies are cheaper to produce than labeled nucleotides, and can themselves be labeled by more than one fluorescent molecule, thereby increasing the detectable signal and increasing sensitivity. The chemistry used to cleave the terminator sequence is also improved, leaving no “scar” on the next incorporated nucleotide.

Figure 1. CoolMPSTM process overview made available under a CC-BY-NC 4.0 International license

In order to achieve the dense signal required for detection, the authors make use of DNA Nanoball sequencing (DNBSEQ) where the DNA fragments generated in library preparation are circularized, allowing production of continuously replicated fragments, creating a ball of DNA which contains many copies of the original fragment. A strand displacing polymerase is also used in the final steps to allow branched DNA nanoballs (Figure 2).

Fig 2. Generation of branched DNA nanoballs made available under a CC-BY-NC 4.0 International license

Through comparison with standardMPS, they show that CoolMPSTM is more accurate and can extend out to 400 base pairs, slightly longer than feasible with current sequencing methods. However, as with other sequencing methods, the later cycles are prone to lag, where the sequencer reads the base -1 to the cycle it should be at, and the intensity decreases over time. Overall CoolMPSTM poses significant advantages over the current sequencing methods in lower costs, longer reads, increased sensitivity, increased signal and decreased error rate.

 

Why I chose this paper:

It has been many years since a large announcement about sequencing methods and this has the ability to change the field and reduce the costs of whole genome sequencing. Being able to reduce the costs of WGS will greatly benefit many researchers including myself, so it was pleasing to see a new technology presented. It is interesting to learn about new technologies, and increasing competition between two big sequencing companies can only be good for science!

 

Questions to the authors:

 

Can I ask about the name of the technology, CoolMPSTM, where “Cool” doesn’t appear to stand for anything. Why did you name it this way?

 

Is it possible to make antibodies for modified bases such as methylated cytosines? I presume this is not possible as this method still uses synthesis and therefore methylated residues would be lost on the original strand.

 

Do you foresee this technology being first choice for the general consumer?

Tags: next gen sequencing, ngs, technology

Posted on: 11 March 2020 , updated on: 12 March 2020

doi: https://doi.org/10.1242/prelights.17514

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