Monthly Archives: October 2013

ASHG 2013 Poster Buzz

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This year’s ASHG 2013 meeting did not disappoint. As expected, while most talks weighed heavily on understanding genome variation, there was certainly a trend in discussion related to the transcriptome. This was nicely summarized by Tuuli Lappalainen, “almost nothing in the genome makes sense, except in the light of the transcriptome.” While the plenary and platform talks were excellent, I’ve found the poster sessions to be the most valuable. They give you an opportunity to really understand the basis for a particular study and usually talk with the person who has designed the experiment or actually held the pipette (or keyboard). This year there were 3,095 posters. While sitting in my hotel room sifting through the abstracts I wanted to attend, I hit Ctrl-F for a few keywords and the results were interesting. There were several graphical depictions of Twitter buzz during the whole meeting and specifically the plenary talks, below are examples of ASHG poster abstract buzz:

Platforms:

ASHG Poster Sequencing Sequencing Platform Mentions

Library Preparation Types:

barchart_libprep_mentions

Other Keywords:

As an intelligent marketplace that connects researchers with NGS sequencing service providers, understanding what researchers are looking for when choosing services is a critical component to our business. Having the opportunity to attend the poster sessions at ASHG and learn about the latest eQTL and epigenetic changes, GWAS or SNV study keeps us up to date with the latest genome research, ensuring our consultation services on Genohub stays fresh.  Thanks to all those poster presenters who spent time with us at ASHG!

Bioinformatic Analysis: A New Option On the Genohub NGS Market

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The ability to list and purchase bioinformatic analysis services along with next-gen sequencing comes to Genohub. This additional feature set will further simplify the NGS project experience by offering capabilities for the bioinformatics project step, all in one roof. By launching this service, researchers on Genohub are now able to shop from full-service sequencing providers who offer the three main services required in every NGS project with options for Illumina, Ion, SOLiD, PacBio, and Roche454 platforms:

  1. Library prep
  2. Next generation sequencing
  3. Bioinformatic analysis

The addition of this service alleviates the burden many researchers face of shopping for three separate sequencing related services from multiple providers and efficiently managing the entire process.

The benefits of this feature for researchers includes:

  • Researchers save time and money purchasing sequencing and bioinformatic services simultaneously
  • By enabling next gen sequencing providers to list bioinformatic services, it becomes easier and faster for researchers to compare and select a provider for their project
  • Risk is mitigated, as researchers are able to purchase bioinformatic services along with NGS services by providers that have gone through the Genohub vetting process

Providers also benefit:

  • Providers are now able to better highlight their unique services by listing specific bioinformatic services. These include basic primary analysis that may be included with every sequencing order, as well as more complex secondary and custom bioinformatics services that can be ordered as add-ons to NGS projects.
  • The bioinformatics platform enables providers to more succinctly communicate bioinformatic services to researchers, cutting down on back and forth communication prior to the researcher opting to move forward with the services listed by the provider

Providers may now list bioinformatic analysis services on the familiar “Manage Services Offerings” page:

New manage services page includes bioinformatics analysis services

New Manage Services Page

Researchers will be able to view these services once they select to view details about a sequencing package found when shopping by project or technology.

At Genohub we constantly strive to improve the service we offer to the NGS community through the development of new features and functionality. When we launched Genohub in August, 2013 our goal was to launch a service that was useful to researchers and sequencing providers, and continue to enhance and improve our service based directly on feedback from our clients.

The bioinformatic analysis listing feature come as a direct result of our development methodology. Researchers asked for a one-stop-shop for all of their sequencing needs, and sequencing providers asked for more ways to highlight and differentiate their services on Genohub. You asked, we listened!

Please visit Genohub often as we are constantly adding new useful features to improve the next-gen sequencing shopping experience including upcoming features to further enable providers to differentiate themselves and mitigate risk in decision making for researchers. If you have any feedback on additional features you would like to see, please send us feedback by shooting us an email at info@genohub.com.

Library Preparation Guide

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One of the most important steps in the sequencing process is library construction. With the rapid expansion of Next Generation Sequencing into a growing number of labs, the number of techniques to create libraries has grown. Heard or Gro-Seq, HITS-CLIP or GBS? These are just a few examples of established techniques that took on a sequencing twist (genomic run-on, cross-linking immunoprecipitation and genotyping respectively). You could say that the growing throughput of sequencing has enabled these methods and that these methods are enabling the growth of sequencing into more labs. Our aim is to keep track of these techniques, offer brief descriptions of each, along with comparison metrics. We’ve started by writing the Guide to Library Preparation, describing the techniques and kits used by our service providers on Genohub. When searching for library preparation services on Genohub, researchers will be able to see the type of kit a provider uses and click on its name for a more detailed description of the technology behind the construction of libraries.

As of today, there are a little more than 200 different techniques to construct libraries. Our guide is certainly a work in progress. If you’ve recently developed a new technique and would like it described in our guide, please contact us with a description of the library protocol. We’re also looking for feedback on the guide’s content and what you think we should add.