Pacific Biosciences of California Inc (PACB)

[Paulieme]

Three Takeaways from the 3rd Next-Generation Sequencing Conference
Posted on July 29, 2013 by [e-mail]
¦Exciting potential of direct sequencing of modified DNA
¦Small holes with big promise but bigger challenges
¦Paleogenomics: sequencing ancient DNA—how old can you go?
Sometimes small scientific meetings have big impacts on one’s impressions, which was certainly my experience at the 3rd Next-Generation Sequencing (NGS) conference in San Francisco on June 19-21, 2013. Of the many interesting presentations (click here for all speakers and abstracts), three completely different topics struck me the most: Pacific Biosystems’ uniquely powerful single-molecule real-time (SMRT) sequencing of modified DNA, Sequencing-pioneer Prof. David Deamer’s update on Nanopore’s advances and challenges, and the new field of Paleogenomics involving sequencing old DNA. With apologies to all of the other speakers, and admitting personally biased selection, here are my comments about these three topics.

Pacific Biosystems: direct sequencing of modified DNA


—Dr. Jonas Korlach co-invented SMRT technology with Stephen Turner, Ph.D., PacBio Founder and Chief Technology Officer, when the two were graduate students at Cornell University. Dr. Korlach joined PacBio as the company’s eighth employee in 2004. Dr. Korlach was appointed Chief Scientific Officer at PacBio in July, 2012.
Pacific Biosystems (PacBio) deserves a lot of credit for being able to overcome numerous technical challenges facing commercialization of its SMRT sequencing system, which offers some uniquely powerful capabilities. (I’ll save a bit of time and space by refraining from describing how this complex system works, but I encourage you to take advantage of various videos and other technical information available at PacBio’s website.) In addition to providing amazingly long read lengths (up to 20kb) to facilitate genome assembly, SMRT sequencing gives data related to kinetics of nucleotide incorporation. Algorithms for differentiating rate of incorporation of A, G, C or T opposite a cognate nucleotide position in the template strand for various sequence contexts within the “footprint” of a DNA polymerase can also differentiate modified template positions. In other words, the average rate of incorporation of G opposite C is different than that opposite 5-methylcytosine (5-mC). This difference in kinetics allows direct determination of epigenetic methylation patterns in DNA, which was the focus of an excellent presentation by PacBio CSO Jonas Korlach. Direct epigenetic sequencing of 5-mC is completely novel and offers a significant advantage by obviating the need to carrying out so-called ‘bisulfite conversion chemistry’ prior to sequencing. Commercial kits are available for bisulfite conversion but require extra time, can be very tricky, and utilize more sample than may be available—especially for limited amounts of clinical biopsies.

(open link,long story)! http://zon.trilinkbiotech.com/2013/07/29/three-takeaways-from-the-3rd-next-generation-sequencing-conference/