Tag Archives: 454

Is China breaking the dominance of Illumina?

BIGIS-4 is the name of an independently developed next generation sequencer made in China. The sequencer shall challenge the dominance of Illumina. On 18 April, scientists from the Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences and partner company Zixin Pharmaceutical Industrial Co Ltd demonstrated their BIGIS-4 sequencing machine in Changchun, Jilin province.

The Chinese machine has a longer read length than dominant sequencers like those made by Illumina in the US. Its manufacturing cost will be one third cheaper than imported machines, and operation costs about one fifth lower, according to Yu Jun of BIG, chief scientist of the project. Yu was also a co-founder of Shenzhen-based BGI, a spin-off of BIG and now the world’s largest sequencing service provider.

Yu’s sequencer differs from Illumina’s in that the fluorescent tag is cleaved from the newly synthesised DNA as it is incorporated, so that the reading speed is much quicker. This is similar to the pyrosequencing technology employed by Roche Diagnostics’ subsidiary 454 Life Sciences.

A publication about the complete genome sequencing and assembly of a Glaciecola mesophila spec. with BIGIS-4 is published here.

Do You Still Remember Which NGS Sequencer Was The First On The Market?

gs-20It was 2005, when Roche launched the first NGS sequencer called the Genome Sequencer 20 (GS 20). This device was able to achieve read length of approx. 100 bp, with a total data output of approx. 20 Mbp per run.
As a consequence, sequencing of a bacterial genome of 5 Mbp (e.g. E. coli) with 20-fold coverage required 5 individual runs on the GS 20. Sequencing costs were in the range of several tens of thousands Euros, bringing the cost compared to Sanger sequencing down 10-fold.

Looking back it’s also difficult to imagine for me, that the GS 20 software at that time could handle genomes of a max size of 50 Mbp only.

Since then, 5 major leaps in the Roche/454 sequencer’s development took place:

  • GS 20 to GS FLX
  • GS FLX to GS FLX with Titanium chemistry
  • Launch of the desktop sequencer GS Junior
  • GS FLX Titanium to FLX+
  • FLX + to FLX++ sequencing (new GS FLX software v2.8)

This all happened in only 7 years.

The current Roche/454 FLX++ chemistry enables read length up to 1100 bp and read outputs of up to 1.2 Gbp per run. As a consequence, today, 8 years later, sequencing of a 5 Mbp bacterial strain can be done on a ¼ plate of a full run. The 9-10-fold longer reads make a great difference in respect to contig length and contig number of the genome assembly.

Meanwhile other NGS sequencers dominate the market. Nevertheless the Roche /454 technology is still of superior quality for de-novo sequencing of genomes of any size and for amplicon sequencing.