AGBT 2014 – Digest of Days 2 – 4

AGBT 2014 Summary

Days 2 – 4 of the Advances in Genome Biology and Technology meeting (AGBT) meeting were packed with great talks and insightful comments #AGBT14. For a summary of day 1 check out our earlier post. We’re just going to give a brief digest of the talks we attended and will update this blog post as we fill in more details.

Day 2 at the Advances in Genome Biology and Technology meeting (AGBT) started off with a cancellation of the much-anticipated talk by Evan Eichler on “Advances in Sequencing Technology Identify New Mutations, Genes and Pathways Related to Autism”. Dr. Eichler studies gene duplication and DNA transposition within the human genome. We’re assuming that what he was going to present was just published this month, “de novo convergence of autism genetics and molecular neuroscience”. Let us know if you know otherwise or when Dr. Eichler is speaking again!

Stephen Fodor, founder of Affymetrix announced a new approach for quantitation of mRNA transcripts in single cells. The method utilizes a single tube endpoint assay and allows for precise measurements of transcripts without the need for cycle to cycle real time measurements or physical partitioning (digital PCR). The procedure works by encoding all mRNA molecules with molecular barcodes allowing the user to amplify their samples and not worry about duplication rates. Pixel™, the name of their device is described in more detail in their white paper.

Hiroyuki Aburtani presented a lecture on applying epigenome profiling and single cell transcriptome analysis and demonstrated that Wnt / B-catenin signaling switches transcriptional networks and re-organizes the epigenome into specific pluripotent lineages. Their analysis is designed to improve the understanding of cell fate during differentiation.

David Jaffe’s much anticipated talk on the assembly of bacterial genomes using long nanopore reads generated a significant amount of interest. David presented data on two bacterial genomes, methylation negative E. coli and Scardovia. His conclusion was that the data was not useful by itself for de novo assembly, but he speculated on applications that would benefit from data where 84% of reads had at least a perfect 50-mer. This talk was nicely summarized by two other blog posts: The one and only Oxford Nanopore talk at AGBT 2014 – with real data and Oxford Nanopore Data and MinION: Valentines Day’s Gift to Genome Enthusiasts.

William McCombie’s talk demonstrated his group’s ability to generate 10 kilobase reads to assemble the Saccharoyces W303 genome using HGAP and the Celera Assembler. Their resulting contig N50 approached 1 million bases. Their hybrid assembly made it possible to generate whole genome, eukaryotic genomes that exceed BAC assemblies with Sanger sequencing.

Gene Myers discussed a new assembler called the “Dazzler” (the Dresden Azzembler) that can assemble 1-10 Gb genomes from PacBio RSII data. The advantages for the new assembler are that it can scale to Gb genomes 100 fold faster than current assemblers and it has a “scrubbing phase” that detects and corrects read artifacts that can cause problems with long contiguous assemblies. A nice summary of this talk is described in Dale Yuzuki’s blog post: http://www.yuzuki.org/favorite-talk-agbt-2014-gene-myers-max-planck-dresden/

 Hessam Esfandyarpour from Genapsys, presented on what they call a “truly cost-disruptive sequencing platform”, the GENIUS 110 System. Backed with just under $50 million in venture funds from Yuri Milner, DeChang Capital and IPV Capital, the GENIUS system uses nano-electronic technology (clonal amplification as opposed single molecule sequencing) combined with unmodified nucleotides and polymerase to generate “long reads”. They announced the Genius Club, an early access program, to test the instrument. While he did talk about consumables, three chips with 1Gb, 10Gb and 100Gb, he didn’t show much data. We’ll have to wait to hear more.

Jeffery Schloss, director of the division of Genome Sciences at the National Human Genome Research Institute gave a talk on “Ambitious Goals, Concerted Efforts, Conscientious Collaborations – 10 Years Hence”. His talk began with a graph measuring the cost per base on the y-axis and the years from 1990-2005 on the x-axis. He reiterated their strategic plan of Base pairs to Bedsides: http://www.genome.gov/Pages/About/Planning/2011NHGRIStrategicPlan.pdf. Schloss’s talk was nicely summarized in a recent Dale Yuzuki’s post.

We’re in the process of updating and adding summaries of talks from AGBT 2014. Check in again !

 

 

 

 

 

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