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Personal Genome Project Sees Whole-Genome Sequencing as 'Increasingly a Viable Option'


By Julia Karow

This article was originally published Oct. 14.

Organizers of Harvard Medical School's Personal Genome Project said that as the cost of DNA sequencing declines, they are considering whole-genome sequencing rather than exome sequencing for the second phase of the study, PGP-100.

The project has already added results from the genome of its founder and principal investigator, George Church, to its website, whose genome was recently sequenced by Complete Genomics.

Launched in 2007 with 10 participants, the PGP aims to sequence the genomes of 100,000 people and to correlate their genotypes with trait information. In April, the project said that it plans to scale up to 100 participants for its second phase (see In Sequence 5/5/2009).

In a newsletter e-mailed last week to individuals interested in the study, PGP organizers said that they have been closely monitoring the decrease in cost of whole human genome sequencing "because it will impact our sequencing strategy for the PGP-100."

The cost has already fallen to less than $50,000 per genome, PGP said, "with some speculating that the arrival of $5,000 genomes is imminent," a reference to Complete Genomics' $5,000 human genome sequencing service, which is scheduled to launch in January.

The project's initial strategy, according to the organizers, was to focus on the exome, since it is "information rich" and seemed "a more economical alternative" to whole-genome sequencing.

"However, the cost of exome sequencing has not fallen as rapidly as whole-genome sequencing," they noted, and as a result, for the PGP-100, "the decision to pursue whole genome is increasingly a viable option."

It will depend, though, on factors such as the project's ability to raise funding as well as "the willingness of sequencing companies to publicly showcase their technologies through sponsorship of PGP-100 genomes."

According to its website, the PGP is funded by donations from individuals, Google, Orbimed, the COUQ Foundation, a grant from the Broad Institute, technology development grants from the Department of Energy and NIH, and in-kind support from various organizations., a 501(c)3 charitable organization, seeks to raise $1.5 million in donations for the project this year from foundations, private companies, and individuals.

The project has already posted results from an analysis of Church's genome, which was recently sequenced by Complete Genomics. Church told In Sequence last month that the company has committed to sequencing nine additional PGP genomes, though it was unclear whether it will charge the PGP for its services (see In Sequence 9/15/2009).

For the interpretation of the genomic information, the PGP is using Trait-o-matic, an open-source tool developed in house, which automatically identifies, filters, and annotates genetic variants. The project plans to use the software to generate research reports that contain variants "that may be of potential significance" and has already generated prototypes of such reports for its first 10 participants, based for nine of them on partial exome sequence data.

Future releases of Trait-o-matic will "enable a community of volunteers to annotate and interpret integrated genomic and trait datasets from the PGP."