Pacific Biosciences of California Inc (PACB)

[Paulieme]

November 12th, 2013- PacBio Posts Slides from User Group Meeting
-Lance Hepler, Center for AIDS Research, UC San Diego

Hepler used the PacBio RS to study intra-host diversity in HIV-1. He compared PacBio’s performance to that of 454®, the platform he and his team previously used. Hepler noted that in general, there was strong agreement between the platforms; where results differed, he said that PacBio data had significantly better reproducibility and accuracy.
George Weinstock, Washington University St. Louis

Weinstock discussed his overall approach to human microbiome projects, including both targeted 16S sequencing with PacBio, as well as shotgun sequencing of the whole sample. In a pilot project, Weinstock’s team created a mock microbiome of 24 samples with a 300-fold range of concentration; PacBio sequencing was able to accurately identify the taxa for all 22 species where 16S amplification succeeded, yielding highly accurate full-length 16S consensus sequences.
John Huddleston, University of Washington

Huddleston is looking at challenging regions in the human genome, noting
that assembly accuracy needs to be quite high to resolve breakpoints and
reconstruct duplication architectures. His team is working with BACs to
validate the use of the PacBio platform as a faster, more cost-effective
alternative to Sanger. In one study, his team found that PacBio results
had 99.994% identity with Sanger results and showed uniform coverage
across the clone.
Lisbeth Guethlein, Stanford University School of Medicine

Guethlein looked at highly repetitive and variable regions of the
orangutan genome. Guethlein reported that “PacBio managed to accomplish
in a week what I have been working on for a couple years,” (with
Sanger) and the results were concordant.
Alisha K. Holloway, Gladstone Institute

Holloway presented data from transcript identification work in chicken.
Because she uses chicken to model human heart development, she needs good
annotations of RNA produced at various developmental stages to figure out
where problems arise. Unlike short-read technologies, PacBio provided
reads long enough to span entire transcripts and dramatically improved
gene annotation.
Chongyuan Luo, Salk Institute for Biological Studies

Luo from the Ecker lab spoke about studying the genome and epigenome of several Arabidopsis thaliana strains using SMRT® Sequencing. PacBio sequence data detected 40 percent more SNPs than short-read technology, indicating that some regions may not have been covered well enough with short reads to find all SNPs.
(LOTS MORE)!!! http://www.homolog.us/blogs/blog/2013/11/12/pacbio-posts-slides-user-group-meeting/