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By Kevin Davies

March 29, 2011
| After its exciting debut at ABGT last year, Ion Torrent (now part of Life Technologies) received some timely validation for its benchtop Personal Genome Machine from the Broad Institute’s Chad Nusbaum. Over past 12 months, the Broad has pushed the machine’s run output up to Megabases (Mb), with one use being DNA quality control for Illumina runs (probably not the market niche Ion is looking for). Ion says it is currently getting 300,000 reads of more than 100 bases/run, while the Broad is typically about two weeks behind them. Improving the quality of the reads while halving the sample prep time are two key priorities for Ion this year.

Life Technology is pushing cancer genome applications as one of the most promising applications for the SOLiD platform. The Translational Genome Research Institute’s David Craig spoke about SOLiD’s “sweet spot” in analyzing cancer genomes because of its accuracy, approaching 99.9%.

Opening Pacific Biosciences’ commercial workshop, co-founder Steve Turner creditably addressed the accuracy rate, which is hovering at 85% (c.f. 99%+ for more established 2nd-gen platforms). While there is clearly room for improvement, some of which may come from incorporating data from the kinetics of nucleotide incorporation, there is impressive uniformity of sequence accuracy across a wide spectrum of GC content.

In the closing talk, CSO Eric Schadt discussed PacBio’s recent cholera genome paper in the New England Journal and “connecting molecular biology to clinical medicine.” There were also early signs of the value of integrating PacBio’s long reads with the more abundant short-read coverage of an Illumina for de novo genome assemblies.

Illumina CSO David Bentley said the HiSeq 2000 (which had a launch spec of 200 Gb/run) has surpassed 1 Terabase/run in house. There was also some promising early data on the genetic changes in the evolution of chronic lymphocytic leukemia (CLL). “This technology has the potential to direct future clinical trials and therapeutic decisions,” said Bentley.

Oxford Nanopore unveiled its GridION “box” just days before AGBT. ONT’s scientific collaborator, Mark Akeson (University of California Santa Cruz) demonstrated some recent significant progress in single-strand DNA sequencing using nanopores coupled to DNA polymerase, which ratchets the strand through the pore. Akeson said that the system should be working for short reads, at least in an academic setting, later this year.

Steve Salzberg (U Maryland) presented impressive benchmarking of Ben Langmead’s Bowtie DNA alignment software, which seems to outperform BGI’s SOAPdenovo and other established tools by a considerable margin. Bowtie 2 is on tap for release this spring, Salzberg said.

Rob Knight (HHMI/U Colorado), with a quaint kiwi accent and sense of humor, presented an excellent talk on ‘the human microbiome’: the results of metagenomic profiling of bacteria living in—and on—people, including detailed analyses of the different species living on different parts of our face, hands etc.
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