A LIMS Case Study with EdgeBio and Genologics

Recently, we participated in a case study with Genologics.  The focus was on us, EdgeBio, a growing sequencing and bioinformatics services business. Given we work in an expanding lab environment that includes three different sequencing platforms and associated, highly configurable workflows - we needed something to solidify project management and organize sample data and metadata.


Ion Torrent PGM, Miseq, PacBio RS Comparison

As a provider of next generation sequencing services, our laboratory and bioinformatics teams must keep abreast of a rapidly expanding range of new technologies.  From the latest library prep protocols and capture kits, to emerging sequencing platforms and latest analysis software, we need to be able to provide technological expertise to our clients.  As we continue to monitor the latest developments, we are always interested in hearing from other groups about their experiences with technology comparison and development.

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Exome Data Analysis Pipeline

The most important step in confident downstream variant analysis of next generation sequencing data is aligning the massive number of short input reads accurately to the reference.  Today there are numerous aligners that do a fairly good job of that, but it is always a challenging task to detect true biological variants from those arising due to sequencing errors and unspecific mappings, especially in the repeat regions.  To address these issues, the bioinformatics team here at Edge evaluated multiple aligners and zeroed in on Novoalign for all of our re-sequening alignments.  Novoalign was chosen after careful consideration of various factors such as its ability to provide sensitive alignments which are very important for accurate SNP and INDEL detection, accuracy, speed, scalability and convenience of use. Several of these tools are already being used as components of diagnostic workflows in the CLIA setting. Scientific findings demonstrate the widely varying abilities of common read alignment tools and their impact on downstream variant calling, which begs for careful and thorough evaluation. We have found Novoalign provides exceptional results while finding SNPs and even Indels where most other aligners lack accuracy.  Several recent publications have reinforced our confidence in building out our exome analysis pipeline based on the combination of Novoalign and the GATK.

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Free Webinar: Towards A medically Actionable Whole Genome Sequence

Please join us on June 20, 2012 from 10am-11am PT for "Towards A Medically Actionable Whole Genome Sequence" a free webinar with:

  • Grant Campany - Senior Director, Archon Genomics X Prize presented by Express Scripts
  • Justin H. Johnson - PhD Director of Bioionformatics, EdgeBio
  • Marc Salit - PhD Group Leader, Biochemical Science Multiplexed Bimolecular Science, National Institute of Standards and Technology (NIST)
  • Moderated by Kevin Davies - PhD editor in chief of Bio-IT World

Ion Torrent Hits 400bp Read Length Mark...Why we're excited.

It’s been a while since I have blogged on Ion Torrent data.  There are several reasons for this.

First and foremost is that my head has been buried in The Archon Genomics XPrize Validation Protocol in which we were contracted to execute staring at the end of last year.  The AGXP is an ambitious, incentivized prize competition that will award $10 million to the first team to rapidly, accurately, and economically sequence 100 whole human genomes to a level of accuracy never before achieved.  The VP provides an opportunity to test and score current WGS technologies, assist the scientific community in establishing the reference genome(s) for this Competition and the means for analyzing the results of the Competition.

Second, it was with great anticipation and excitement that we received our Certificate of Compliance recently from the US Dept. of Health and Human Services Centers for Medicare and Medicaid Services. This means we have been deemed a CLIA lab and can begin to offer our Clinical Exome test under CLIA guidelines.  No small feat.

But, here I am, again, knocking the dust off the blogging boots, and wading into another data set Ion Torrent has publically released. 

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