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Illumina MiSeq: TruSeq Amplicon - Cancer Panel

In a previous post we explored some of the fixed AmpliSeq panels available for use on the Ion Torrent PGM.  The TruSeq Amplicon Cancer Panel is a similar panel available for the MiSeq.  In this post we’ll explore the similarities and differences between the TruSeq Amplicon Cancer Panel and the Ion Torrent AmpliSeq panels and describe our efforts to call the highest confidence SNPs possible with the TruSeq panel.  Since the throughput of the MiSeq is quite high, we tested the TruSeq Amplicon Cancer Panel on three well characterized cancer cell lines and barcoded two replicates of each over one MiSeq 2x150 run.  We tested the MiSeq default alignment (bwa) and variant calling (Illumina Somatic Variant Caller) pipeline as well as novoalign and several variant calling tools that we leverage in our exome sequencing pipeline and compared the results.  If you are interested in sequencing any of the panels mentioned in this post, please contact us.

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Miseq 2x250 Does Length Really Matter?

At EdgeBio, we are always on the lookout for improving efficiencies, reducing costs, and providing an overall higher quality service to our clients.  With this comes an immense amount of R&D and New Technology Development (NTD).  A great example of this is a series of five technical white papers we recently released on targeted resequencing applications, including exomes.  You can find them here.  Today I will share some of our experience with longer reads (2 x 250 bp) on the Illumina MiSeq instrument.  In theory, y

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Ion AmpliSeq Fixed Panels on HCT-15 Colon Carcinoma Cell Line

One of the more powerful and exciting applications for benchtop sequencing platforms is targeted sequencing panels.  These panels allow sequencing of targeted regions of the genome amplified by multiplexed PCR amplicon pools.  This allows for rapid, sensitive, and specific amplification of targets and rapid sequencing of samples.  These panels allow us to deliver results to customers with our standard ten business day turnaround time for benchtop sequencers.  To check the performance of these panels we tested three of the Ion Torrent AmpliSeq Ready-to-use Panels with DNA isolated from a well characterized colon cancer cell line, CCL-225 (HCT-15).  The Inherited Disease Panel was also run on Craig Venter HuRef (NS12911) DNA.

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While You Were Waiting...The $1,000 Exome.

It’s been quite some time since my last blog post. We’ve been rather busy over the summer, so let me fill you in on what has happened. At Edge, we have been diligently working on our CLIA certification and offering, with our latest test offering a CLIA exome on our Illumina HiSeq2000 platform using either the Agilent SureSelect capture or Roche Nimblegen capture. Over the coming weeks the staff at Edge will be releasing a series of blog posts relating to targeted resequencing methodologies. They will relate specifically to Project Design, Research & Clinical applications, “Tools of the Trade”, Data Delivery and then a summary “Cheat Sheet”. They will be information heavy, with lots of tables and data to digest, so try not to read them right after a large meal.

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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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