GenomeQuest: Difference between revisions
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The purpose of this pilot is to demonstrate the feasibility of a working relationship between the PGP team and the GQ team, and to demonstrate the ability of the GQ platform. It is encouraged that the participants interested in this pilot interact through OpenWetWare wiki, in order to communicate with the entire teams and also to log our progress. With this first pilot, GQ and PGP groups will work out the best combination of sensitivity and specificity parameters to be used in the alignment, assembly and SNP detection. For this, we will focus on PGP2 only, and extend to the rest of PGP10 later as the PGP pipeline becomes finalized for valid comparison. | The purpose of this pilot is to demonstrate the feasibility of a working relationship between the PGP team and the GQ team, and to demonstrate the ability of the GQ platform. It is encouraged that the participants interested in this pilot interact through OpenWetWare wiki, in order to communicate with the entire teams and also to log our progress. With this first pilot, GQ and PGP groups will work out the best combination of sensitivity and specificity parameters to be used in the alignment, assembly and SNP detection. For this, we will focus on PGP2 only, and extend to the rest of PGP10 later as the PGP pipeline becomes finalized for valid comparison. | ||
# PGP | # PGP Deliverables: Illumina files containing the sequence information, and PGP MAQ pipeline-generated results are here for download. ([http://boinc-dev.freelogy.org/~awz/pgp2/feefebcb0587d1f8093d17e0343a0bf9/ here]). | ||
# Publications on exon capture and supplementary information regarding sequencing library preparation, oligo sequences and analysis methods. [[Media:Porrecca07.pdf|Nature Methods 2007]], [[Media:Porrecca07Suppl.pdf|Supplementary Information]], [[Media:Porreca07Table1.xlsx|Probe Table]] | # Publications on exon capture and supplementary information regarding sequencing library preparation, oligo sequences and analysis methods. [[Media:Porrecca07.pdf|Nature Methods 2007]], [[Media:Porrecca07Suppl.pdf|Supplementary Information]], [[Media:Porreca07Table1.xlsx|Probe Table]] | ||
Revision as of 17:43, 18 December 2008
Background
With the anticipated deluge of data from various personal genome projects over a large human population, it is not practical for a single institution or a company to deal with all the data at the bioinformatics, pre-consumption level. One of the models that Personal Genome Project (PGP) has embraced is the open source model, in which various interested parties, whether they be interested individuals, academic labs, or for profit entities, contribute to laying down an integrated, yet highly flexible and independent infrastructure for collecting, analyzing, and distributing genomics data to end-users (i.e. patients, researchers, pharmaceutical companies).
While the main aim of PGP is not to dictate or advocate a specific model of open genomics information distribution to patients, researchers and biotech industries, we are currently exploring ways for different groups and entities, both non-profit and for-profit, to collaborate on incentivizing the release, the sharing and the consumption of such data in order to facilitate personalized health & medicine and any derivative markets.
GenomeQuest (http://www.genomequest.com/) has established itself as one of the leading commercial solutions for bioinformatics, especially in the field of Next Gen sequencing. As PGP scales up to beyond 10 volunteers, it will be important to find out how various established and commercial entities such as GenomeQuest can contribute to the laying down the genomics information highway among researchers and beyond. While the contribution from the open source community will be invaluable, a highly integrated and somewhat selective use of the information derived from PGP and other initiatives like it may also be valuable for biotech industry and medicine.
People
- Jay Lee -- Church lab
- Alexander Wait Zaranek -- Church lab
- John Aach -- Church lab/PGP
- Jason Bobe -- PGP
- Phil Robidoux -- GenomeQuest
Aims
- Assess the GQ platform and compare it to PGP-generated sequence assemblies and annotations using publicly released PGP exome data.
- Assess the GQ platform for scalability and data management solutions pending Step 1.
- Assess the GQ platform for other distribution methods for complementary high-level genomics information, including software and web tools development pending Step 2.
Pilot Study
The purpose of this pilot is to demonstrate the feasibility of a working relationship between the PGP team and the GQ team, and to demonstrate the ability of the GQ platform. It is encouraged that the participants interested in this pilot interact through OpenWetWare wiki, in order to communicate with the entire teams and also to log our progress. With this first pilot, GQ and PGP groups will work out the best combination of sensitivity and specificity parameters to be used in the alignment, assembly and SNP detection. For this, we will focus on PGP2 only, and extend to the rest of PGP10 later as the PGP pipeline becomes finalized for valid comparison.
- PGP Deliverables: Illumina files containing the sequence information, and PGP MAQ pipeline-generated results are here for download. (here).
- Publications on exon capture and supplementary information regarding sequencing library preparation, oligo sequences and analysis methods. Nature Methods 2007, Supplementary Information, Probe Table
