Biomarker to launch large scale nanopore sequencing service

Beijing Biomarker Biotechnology Co., Ltd. has started a long-term project working with Oxford Nanopore technology.  Biomarker will develop and apply products based on the Oxford Nanopore platform, to provide users with richer and better services.

The Biomarker and Oxford Nanopore teams: Richard Compton, VP Commercial Operations at Oxford Nanopore, Thomas Bray, China Business Manager together with Eva and Lin from Technical Support.

 

On August 7, 2018, the PromethION, a new high throughput nanopore sequencing device arrived to Beijing Biomarker’s sequencing laboratory. To date, Biomarker has become experienced on nanopore sequencing through use of the handheld MinION and benchtop GridION X5 devices. Biomarker is investing RMB 30 million (US$4.4 million) in expanding its nanopore based service offering.

As the newest and largest product in the nanopore range, PromethION not only offers real-time long read lengths and direct DNA/RNA sequencing, but also has comparable outputs to the highest throughput short read sequencers on the market.  In early 2018, Oxford Nanopore officially announced that the data for a single PromethION flow cell was producing more than 150 Gb internally (the device is designed to run up to 48 flow cells). Nanopore users have sequenced clinical samples, plant samples, and test samples at 100-150 Gb of output per flow cell. As an important partner of Oxford Nanopore, Biomarker will provide customers with commercial sequencing services based on the PromethION/GridION platform.

Nanopore MinION Sequencer

Nanopore GridION X5 Sequencer

Nanopore PromethION Sequencer

Oxford Nanopore sequencing

Nanopore sequencing is based upon translocating DNA or RNA through a nanopore protein, and monitoring the tiny electronic signal produced during this process. Due to differences in the chemical properties of different bases on DNA/RNA, when DNA molecules passes through a nanopore channel, the bases on that molecule causes small changes in the electronic signal. By detecting and analysing these signals, the identity of the corresponding bases can be obtained, and the sequence can be determined. This process is replicated across the entire Nanopore platform.

Oxford Nanopore Sequencing Schematic 1

Nanopore’s base calling algorithm is currently performed through complex algorithms based on “Recurrent Neural Networks”.

Oxford Nanopore Sequencing Schematic 2

Nanopore technical advantage analysis

Compared to other sequencing technologies, it is extremely simple to prepare a sample for nanopore sequencing.  It does not require DNA polymerase or ligase, and does not require dNTPs, so the sequencing cost is very low. PromethION can deliver a 30X human genome for less than $1,000. Nanopores process long DNA or RNA fragments, so the read length can reach above and beyond hundreds of Kb. Currently the longest recorded is 2.3Mb.  Long reads can better solve problems such as complex genome assembly and structural variation. In addition, as the Oxford Nanopore platform allows for direct sequencing of native RNA/DNA strands, base modification information is easily obtained, which in turn provides new methods for the study of gene expression.

Comparison of Oxford Nanopore sequencing platforms

 

Progress in the sequencing of nanoprore sequencing

Biomarker has been developing the Nanopore platform on MinION and GridION X5 for some time now, and has made progress in both sequencing information and output.

Oxford Nanopore platform sequencing data statistics

Nanopore also demonstrated good strength in genome splicing. In addition to the previously published results of tomato, sandalwood and human genome sequencing assembly, Biomarker has assembled some additional species. One plant has a genome size of 1.2 Gb, a Contig N50 of 2.58 Mb, and a longest Contig of 12.72 Mb. After second-generation data correction of the genome, Busco assessed the integrity as 93.54%, Illumina data back efficiency was 98.5%. The HiC heat map evaluation found that the assembly continuity was extremely high, which comprehensively indicated that the genome assembly quality was high.

Biomarker Nanopore services are now available to order!

 

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