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PGP Tests Saliva Collection, Telomere Analysis, Medical Record Privacy Technology


By Julia Karow

Harvard Medical School's Personal Genome Project is currently testing saliva collection processes in preparation for collecting samples from all participants, Clinical Sequencing News has learned. The project has also teamed up with a company to measure participants' telomeres and is testing medical record privacy technology with a grant from Google.

Last month, PGP participants received a letter asking for 100 volunteers to provide saliva samples through a mail-in collection kit by Aug. 15. Preference for this pilot project was to be given to those who had already uploaded existing genetic data to their public profile, completed an online survey, and reside in the continental US.

According to the letter, the saliva samples will be used for several research projects, including telomere measurement, whole-genome sequencing, and epigenetic profiling, as well as to evaluate low-cost saliva collection kits and protocols. Any results will be shared with participants and made publicly available, in accordance with the study's consent form.

For the telomere analysis, the PGP has teamed up with TeloMe, a company based in the Boston area that is "interested in performing telomere analysis on PGP participants." The firm's CEO and CSO, Preston Estep, is a former graduate student of PGP principal investigator George Church at Harvard Medical School.

The letter cautioned that the analysis of the samples could take months "or possibly a year or more," and that participants are not guaranteed to receive results.

Following the pilot study, the plan is to collect saliva from all study subjects "as soon as we evaluate our performance with processing these 100 samples," according to the letter. Currently, almost 1,400 participants are enrolled in the PGP, of which only 14 have had their entire genomes sequenced.

According to Jason Bobe, director of community for the PGP, the project hopes to complete at least 500 DNA extractions by the end of the year.

Bobe said the main goal of the pilot is to evaluate low-cost saliva collections kits, although the samples may also be used for research, such as telomere measurements, genotyping validation, evaluating "the possibility of using saliva for whole-genome sequencing," and, "down the road a bit," epigenetic profiling and microbiome studies.

"As with all research projects, we can't guarantee that all these potential uses will be performed on all samples, but we hope that the samples will be useful for a variety of purposes," Bobe told Clinical Sequencing News in an e-mail message.

While DNA will be extracted from all saliva samples, they might not all be sequenced, for example, at least not initially. "Saliva is much cheaper and easier to work with compared to blood, but blood is currently preferred for whole-genome sequencing," Bobe explained. "Because of this we may first perform whole-genome sequencing on a trial set of matched blood and saliva samples before choosing to use our saliva samples for this purpose." Instead, the saliva samples might be genotyped "as an important validation step for blood-based whole genome sequencing."

Also, sequencing resources will be allocated based on phenotype and not on the order the samples were received, he said. Family trios, participants with diseases of interest, older participants, and participants from underrepresented groups may get sequenced first.

TeloMe, on the other hand, is expected to start its telomere analyses "more or less immediately," he said.

Funding for the pilot comes from "in-kind services," proceeds from the annual Genomes Environments Traits conference, and donations, including a "significant" contribution from Church, who donated prize money from the Bower Award and Prize for Achievement in Science, which he received this year, to scale up the PGP's tissue collection and analyses. The award comes with a cash prize of $250,000.

In addition, the PGP recently won a grant worth under $100,000 from Google for evaluating privacy-enhancing technologies for medical records. "The idea is that the PGP's public dataset is an ideal sandbox for researchers and engineers to evaluate various privacy tools on real medical data," Bobe said. Because many PGP participants already made their records public, engineers need not worry about accidental data leaks due to software bugs. The project will include about 1,000 "Continuity of Care Records" that participant have shared with the PGP through Google Health.

Google said recently that it will discontinue Google Health at the end of 2011, and according to Bobe, the PGP is currently looking for other services to collect participants' baseline health and medical data and share it with the PGP.

Last October, the PGP announced several projects and collaborations (IS 10/12/2011), some of which have progressed. In a partnership with Peter Gregerson at the Feinstein Institute for Medical Research in Manhasset, NY, PGP researchers plan to study the genetics of absolute pitch. About 20 individuals are currently undergoing further screening for this trait, and those who demonstrate it will be selected for whole-genome sequencing, Bobe said. This collaboration serves as a model the PGP hopes to expand in which "researchers can sponsor PGP participants with specific traits," he added.

Also, with funding from the Alan and Priscilla Oppenheimer Foundation, the PGP has selected a 90-year-old man, one of its oldest participants, for whole-genome sequencing, which is expected to be completed "in the next couple of months." Older participants are "particularly valuable" for the project because of their long medical history that might provide insights into what genetic variants contribute to health and longevity, he said.

A microbiome study of PGP participants, on the other hand — a collaboration with Rob Knight and Noah Fierer at the Howard Hughes Medical Institute and the University of Colorado — is "just getting started."

Have topics you'd like to see covered in Clinical Sequencing News? Contact the editor at jkarow [at] genomeweb [.] com.