Targeted resequencing - open source

stanford_genome_tech

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Targeted resequencing - open source

09-24-2011, 09:56 PM

Hi all,

Stanford Genome Technology has published a 2nd generation "open source" capture technology using in solution oligonucleotides.

We have an in silico design covering the CCDS genes (most of the exome) release and will have one covering the majority of the genome out soon (under review). You can download oligo sequences and create your own capture assays.

http://oligoexome.stanford.edu

A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021088

We have developed an integrated strategy for targeted resequencing and analysis of gene subsets from the human exome for variants. Our capture technology is geared towards resequencing gene subsets substantially larger than can be done efficiently with simplex or multiplex PCR but smaller in scale than exome sequencing. We describe all the steps from the initial capture assay to single nucleotide variant (SNV) discovery. The capture methodology uses in-solution 80-mer oligonucleotides. To provide optimal flexibility in choosing human gene targets, we designed an in silico set of oligonucleotides, the Human OligoExome, that covers the gene exons annotated by the Consensus Coding Sequencing Project (CCDS). This resource is openly available as an Internet accessible database where one can download capture oligonucleotides sequences for any CCDS gene and design custom capture assays. Using this resource, we demonstrated the flexibility of this assay by custom designing capture assays ranging from 10 to over 100 gene targets with total capture sizes from over 100 Kilobases to nearly one Megabase. We established a method to reduce capture variability and incorporated indexing schemes to increase sample throughput. Our approach has multiple applications that include but are not limited to population targeted resequencing studies of specific gene subsets, validation of variants discovered in whole genome sequencing surveys and possible diagnostic analysis of disease gene subsets. We also present a cost analysis demonstrating its cost-effectiveness for large population studies.

More completely new third generation targeting technologies coming soon in a Nature journal. Be on the look out for it shortly.

SGTC sequencing techies
Tags: cancer genomes, gene sequencing, mutations, targeted resequencing, targeting
ECO

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Join Date: Oct 2007

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#2

09-27-2011, 08:19 AM

Very cool paper. Making no friends at Agilent.

Is your "TargetedOligoDesign" program available for designing oligos for different genomes/targets? I can't seem to find it.

Also, your zip file download is broken.
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stanford_genome_tech

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#3

09-27-2011, 03:22 PM

The zip file download is fixed. The oligo design program isn't "polished" enough for release, but we are releasing an in-silico set that covers the majority of the human genome.
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ECO

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#4

09-27-2011, 03:27 PM

Excellent, thanks!
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