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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Wherefore art thou mouse dbSNP VCF file?

Every once in a while I come across a problem that surprises me. Getting a VCF file for the Mouse genome (mm9) is one of those problems. We use the GATK extensively internally, and it has standardized around the VCF format (rightfully so), so when validating, annotating, and recalibrating variants, one requires a VCF file.

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Resequencing J. Craig Venter w/ SOLiD4 - Part 1

As a follow on to the release of our E. coli Ion Torrent data, over the coming weeks, we will be releasing both Whole Genome and Exome data of J. Craig Venter generated on the SOLiD4 platform.  We use this sample internally for platform and analysis validation/regression testing since it is so well characterized and validated.  The first data set to be released is the 50Mb Exome data using the Agilent's SureSelect Target Enrichment System.  Running a quarter slide produced 12 billion bases of paired end data.

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