AGBT 2015 Starts Today- A Preview

AGBT 2015, one of the biggest genomics conferences starts today. The four-day event at the usual Marco Island covers a variety of genomics topics including Genomic Technologies, Clinical Genomics, Evolutionary Genomics, and Transcriptomics.

It is not an exaggeration to say that the expectations from the last few AGBT years has been mostly about Oxford Nanopore, with loads of lingering questions about its Nanopore sequencer.  It all started in 2012, Oxford Nanopore launching MinIONs at AGBT 2012. And last year at AGBT 2014, David Jefferey’s talk AGBT 2014 offered the glimpse of what Oxford Nanopore data looked like and also Oxford Nanopore separately announced the lucky winners of its early access program.  It has been a year since hundreds of scientists tried out Nanopore MinIon and already a few interesting publications have come out. Now that AGBT has got Oxford Nanopore off its back, one can focus on other technologies and applications.

Here are some interesting talks to look for at AGBT 2015. Follow #AGBT15, if you are on twitter.

  1. Yaniv Erlich, New York Genome/Columbia University
    “Dissecting the Genetic Architecture of Longevity Using Massive-Scale Crowd-Sourced Genealogy”
  2. David Page, Whitehead Institute
    “What SHIMS (Single Haplotype Iterative Mapping and Sequencing) Has Taught Us About Sex Chromosomes”
  3. Elaine Mardis, Washington University School of Medicine “Technical and Informatics-Based Developments in Cancer Genomics”
  4. Neil Weisenfeld, The Broad Institute of MIT and Harvard
    “Personal Genome Assembly”
  5. Wan-Ping Lee, Seven Bridges Genomics
    “Accurate Read Mapping Using a Graph-Based Human Genome”
  6. Richard Leggett, The Genome Analysis Centre
    “Towards Real-Time Surveillance Approaches Using Nanopore Sequencers”
  7. Serafim Batzoglou, Stanford University
    “A Full Diploid Assembly of a Breast Cancer Genome Using Read Clouds”
  8. 10X Genomics, Ben Hindson “Long Range Applications With Short Read Sequencing”
  9. Iain Macaulay, Wellcome Trust Sanger Institute
    “G&T-seq: Separation and Parallel Sequencing of the Genomes and Transcriptomes of Single Cells”
  10. Sara Goodwin, Cold Spring Harbor Laboratory, “An in Depth Evaluation and Optimization of the Oxford MinION Device for de novo and cDNA Sequencing”
  11. Gene Myers, Max Planck Institute – CBG, “Low Coverage, Correction-Free Assembly for Long Reads”
  12. James Gurtowski, Cold Spring Harbor Laboratory, “Error Correction and de novoAssembly of Oxford Nanopore Sequencing”

On the technology side, one of the long-time rumors is that PacBio might unveil a desktop PacBio sequencer to compete/wade off threats from Illumina and Nanopore technologies.  It will be great to see  such PacBio RS-mini, but it is still rumor. OmicsOmics Blog writes that “a baby RS is so technically challenging it is unlikely to be launched”

Another genomic technology getting in the news recently is 10X Genomics. 10X Genomics is a California based startup company and recently raised 55M. 10X Genomics just announced that it is launching GemCode platform.

10X Genomics’ GemCode Platform delivers this additional genetic information by dramatically upgrading the capabilities of existing short read sequencers. We do this through a combination of elegant microfluidics, chemistry and bioinformatics. With the GemCode Platform, researchers can now find structural variants, haplotypes, and other valuable long range information while leveraging existing sequencing workflow.

Here are the links to interesting thoughts on AGBT 2015 and what to expect by Luke Timmerman and OmicsOmicsBlog.

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