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A New Chapter

On August 16, Edge BioServ LLC, the Services Division of EdgeBio, entered into agreement to be acquired and become part of GeneDx (www.genedx.com), a division of BioReference Laboratories, Inc. (http://www.genomeweb.com/sequencing/bioreference-laboratories-acquire-edge-bioserv). GeneDx specializes in genetic testing for rare hereditary disorders.

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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.

The Pilgrimage to Marco Island

 

It’s February on the calendar and it is pretty cold here in the Mid-Atlantic so that means it must be time for our annual trek to Marco Island, FL for the AGBT meeting. The conference is a highlight on an increasingly crowded meeting calendar in the genomics community. This will be the 14th installment of the AGBT Meeting and I am happy to say I have been to all except for the very first one. The meeting organizer, Rita Dunton of G Corp, has done an amazing job over the years of keeping everyone happy while running a top-flight scientific retreat. This year the organizers implemented a new registration system to try and make sure industry, academic, and government had equal representation after the registration the two previous years was sold-out within the first ten minutes of being open.

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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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CLIA Inspection: A highly anticipated day

As many of you know, we received our CLIA designation back in March of this year for our first CLIA test, the Clinical Exome Test. While this is not a catchy name with a clever acronym, it does a pretty good job of conveying exactly what the test is, I believe. What you may not know is that you do not get inspected by State regulators before you receive your CLIA and State certificates, you get audited afterwards. So, while highly confident in our data submission package for CLIA application, until you get audited, there is still a bit of doubt as to whether you are truly good enough. Similar to asking someone to marry you, when proposing, generally you are pretty confident in the response. But there is always that little bit of doubt…

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