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How Much Exome Coverage Do I Need?

If I had a nickel for every time we answered the “How much coverage is that?” question in relation to our exome sequencing services, I wouldn’t need to be writing this article.  I’d be on a boat in the Caribbean.  But, I’m not on a boat anywhere, so with all my non-boating free time I thought I would try and collect information that would help people understand which important factors to consider when doing exome sequencing.

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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Genomics X Prize public phase: reference genome preparation and comparisons to Illumina and Complete Genomics

This is a guest post contributed by Dr. Brad Chapman from the Harvard School of Public Health. Original post can be found here.

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