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Old 04-23-2010, 04:30 PM   #1
gendxdoc
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Location: Seattle

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Default Clinical Sequencing Software

Hello All,
Is anyone aware of a group or company developing a next gen sequencing pipeline (AB SOLiD, Illumina GA or Roche 454 platforms) for clinical diagnostics laboratories ?

We're really most interested in the resequencing analysis and variant reporting/annotation aspects and less in the sample management end. We already have an LIS for sample tracking, etc. We would like to accomplish a few basic tasks: 1) Rapidly compare our set of variants with variants in existing databases; 2) Develop our own database as we accumulate variants -- keeping track of pathogenic vs. non-pathogenic variants -- as well as variants of unknown significance; 3) Easily run pipelines such as SIFT or PolyPhen to predict pathogenicity of novel variants.

Once we have a pipeline established -- we're like any good clinical lab -- we want to the same thing over and over again --- and do it well.

Any suggestions you can give or directions you can point me to, would be greatly appreciated !
Thank you !
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Old 04-26-2010, 06:22 AM   #2
NextGenSeq
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Only companies I know of are CLC Bio, NextGene (Softgenetics) and GenomeQuest.

I believe only GenomeQuest helps with custom databases. I personally think they are very expensive.
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