PacBio Aims to Reach Average Read of Lengths of 7000-9000 Bases in 2013

PacBio, the next-gen sequencing technology company, announced that PacBio is looking to improve upon on read length, accuracy, and throughput in 2013. Revealing its goals in a blog post describing its technology roadmap, PacBio said it has many improvements coming to the PacBio RS starting from the first half of 2013 and it can eliminate the limit on read length to produce read lengths of 7000-9000 bases.

PacBio Aims Reados Length 7000-9000 and Increase Throughput Drastically (Image: PacBio)

PacBio Aims Reados Length 7000-9000 and Increase Throughput Drastically

PacBio RS to Double the Throughput in the First Half of 2013

First, PacBio is looking to implement a hardware update on current machines that will double the throughput from a sequencing run. The throughput improvement is due to doubling “the number of zero-mode waveguides (ZMWs) that can be interrogated” during a sequencing run.

In addition, PacBio has implemented a new loading procedure that uses magnetic bead loading technology instead diffusion based approach used currently. The diffusion based loading requires higher concentration of DNA and it is kind of biased towards producing small DNA fragments.  The new magbead technology eliminates the small DNA problem and can sequence long DNA fragments successfully with smaller amount of input sample.

PacBio to Produce Sequence Reads of length 7000-9000

PacBio also added that it is making a good progress on techniques to eliminate the limit on read lengths produced by PacBio RS. A main factor affecting the read length is that often polymerases die and stop the sequencing reactions because of the energy transfer from the flouresecnt dye that is excited by the laser. PacBio is developing technique that protects polymerase from the dye using photo-protective scaffold between the enzyme and dye. PacBio hopes that it will eliminate this photodamaging effect on read length and produce average read lengths of 7,000 to 9,000 bases. This is almost double the read lengths of what PacBIO RS can do with the new XL polymerase.

PacBio RS SMRT sequencing system with current chemistry C2 runs for 90 mins producing about 30k-50k reads of length (average) 3,000 bases. (95th percentile: 8k and max: 14.8k bases). Recently, PacBio announced a new chemistry called XL (eXtreme Length reads) that uses new polymerase. The new XL chemistry and the run time extension from 90 mins to 120 mins enables sequencing of reads of length 5,000 bases on an average.

PacBio’s Roadmap for 2013

Here is the list of improvements that is expected from PacBio
  • 125 mega bases per SMRT cell: C2 Polymerase:
  • 250 megabases per SMRT cell: XL Polymerase + magBead loading
  • 500 megabases  per SMRT cell: Hardware upgrade (Zero-mode waveguides (ZMWs)) expected at 1st half of 2012
  • 1 Gigabases per SMRT Cell: Photo protected nucleotides expected at the end 2013
  • 2 Gigabases per SMRT Cell: with more advances in the future

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