Pacific Biosciences of California Inc (PACB)

[Paulieme]

Tuesday, June 18, 2013Back from SFAF, and Eager for More Finished Genomes

Last month’s Sequencing, Finishing, Analysis in the Future (SFAF) meeting in Santa Fe, New Mexico, hosted by Los Alamos National Laboratory, attracted terrific scientists and we really enjoyed hearing about their work as well as sharing our own technology advances. It was great to be at a meeting where genome finishing and analysis were key themes; it was an environment where our customers’ experience with HGAP and Quiver resonated, particularly around the automated finishing of microbial genomes.



SFAF had a number of keynote speakers, including Mark Adams from the J. Craig Venter Institute, who spoke about antibiotic resistance in microbes. He noted that lateral transfer of multidrug resistance genes is creating new drug-resistant pathogens in our hospitals. A key theme in his talk was the need for comprehensive information about the genomes of these drug-resistant microbes, including the difficult-to-assemble regions such as duplications, repetitive sequence, plasmids, and so on. He said that standard strain typing does not provide enough information to distinguish the particular form of resistance between bugs. For example, plasmids and phages play a critical role in horizontal gene transfer of drug resistance genes, yet these elements are notoriously difficult to assemble with short-read NGS methods. Adams commented that PacBio’s HGAP assemblies provide both finished genomes and plasmids, which offer important clues about drug resistance mechanisms and microbial adaptation.


Throughout the conference, many speakers mentioned the challenge of reference-based sequencing when there are errors in the reference, or when the reference is not a good enough representation of the genome being sequenced and compared to it. It was apparent that the trend is shifting back to de novo sequencing, which provides more information about the organism under investigation and is more likely to pick up unexpected differences that are not included in a reference genome. This idea is especially compelling in the microbial world, where pan-genomes and horizontal gene transfer have turned the whole idea of a single reference genome on its head.


Finishing genomes — how to generate them and how much they cost — was another common thread. It was impressive to see how many conference attendees were using the HGAP/Quiver method to finish all sorts of microbial genomes. Ken Dewar from McGill University gave a presentation based on a simple question: Can we sequence one full bacterium in one day for less than $1,000? We were thrilled to see that PacBio’s technology is meeting his goal. In another talk, Adam Phillippy from the National Biodefense Analysis and Countermeasures Center said that with PacBio® technology, it’s now cheaper to finish a microbial genome than it is to publish one. Phillippy noted that once reads exceed 7 kb for microbial genomes, assembly complexity is drastically reduced; using the XL chemistry, 40 percent of their PacBio reads have been at least that long. He and other speakers noted that they have been getting Q60 scores from their PacBio data with the latest hardware and software upgrades.


Most of all, we were inspired by so much compelling science and the community’s renewed commitment to finished genomes. Many attendees talked about their motivation to go back to their labs and try out these new methods for finishing microbial genomes, especially since the whole process can now be automated. http://blog.pacificbiosciences.com/2013/06/back-from-sfaf-and-eager-for-more.html