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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

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

Preprint posted on 20 February 2020

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

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

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TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Zebrafish immunology

A compilation of cutting-edge research that uses the zebrafish as a model system to elucidate novel immunological mechanisms in health and disease.

 



List by Shikha Nayar

Also in the genomics category:

May in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) Biochemistry/metabolism 2) Cancer cell Biology 3) Cell adhesion, migration and cytoskeleton 4) Cell organelles and organisation 5) Cell signalling and 6) Genetics

 



List by Barbora Knotkova et al.

March in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) cancer biology 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics and genomics 6) other

 



List by Girish Kale et al.

Biologists @ 100 conference preList

This preList aims to capture all preprints being discussed at the Biologists @100 conference in Liverpool, UK, either as part of the poster sessions or the (flash/short/full-length) talks.

 



List by Reinier Prosee, Jonathan Townson

Early 2025 preprints – the genetics & genomics edition

In this community-driven preList, a group of preLighters, with expertise in different areas of genetics and genomics have worked together to create this preprint reading list. Categories include: 1) bioinformatics 2) epigenetics 3) gene regulation 4) genomics 5) transcriptomics

 



List by Chee Kiang Ewe et al.

End-of-year preprints – the genetics & genomics edition

In this community-driven preList, a group of preLighters, with expertise in different areas of genetics and genomics have worked together to create this preprint reading list. Categories include: 1) genomics 2) bioinformatics 3) gene regulation 4) epigenetics

 



List by Chee Kiang Ewe et al.

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Semmelweis Symposium 2022: 40th anniversary of international medical education at Semmelweis University

This preList contains preprints discussed during the 'Semmelweis Symposium 2022' (7-9 November), organised around the 40th anniversary of international medical education at Semmelweis University covering a wide range of topics.

 



List by Nándor Lipták

20th “Genetics Workshops in Hungary”, Szeged (25th, September)

In this annual conference, Hungarian geneticists, biochemists and biotechnologists presented their works. Link: http://group.szbk.u-szeged.hu/minikonf/archive/prg2021.pdf

 



List by Nándor Lipták

EMBL Conference: From functional genomics to systems biology

Preprints presented at the virtual EMBL conference "from functional genomics and systems biology", 16-19 November 2020

 



List by Jesus Victorino

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.