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ClinGen Adds Portal for Patients to Contribute their De-identified Data for Research


NEW YORK (GenomeWeb) – The Clinical Genome Resource, a National Institutes of Health-funded program to provide access to clinically annotated genes and variants, has launched GenomeConnect, an online portal for patients to voluntarily contribute their de-identified genotypic and phenotypic information to publicly available genomic databases such as the National Center for Biotechnology Information's ClinVar and to connect with other patients.

GenomeConnect, which officially launched this past October, is hosted by PatientCrossroads, a company that provides FISMA-compliant secure online patient registries. It initially seeks to collect data from patients with rare diseases who have had or are considering genetic testing, as well as family members who've had genetic tests or a disease diagnosis. However, the effort could be expanded to include data from other disease conditions as well, Heidi Rehm, director of the Laboratory for Molecular Medicine at the Partners Healthcare Center for Personalized Genetic Medicine and one of ClinGen's principal investigators, told GenomeWeb.

It's an attempt, she said, to engage directly with patients and not only access their genetic results but also to collect data that could help better define their disease phenotypes. Data from these patients could help researchers and clinicians studying rare diseases identify novel variants associated with these conditions, gain new insights into the mechanisms and effects of these variants, and identify therapies that could potentially be used to treat the associated conditions.

This initial version of the system only offers capabilities for patients to upload their information to the registry. Later iterations will offer features that let participants connect with individuals with similar health conditions and disorders, as well as mechanisms for notifying patients of opportunities to be part of research studies that are relevant to their respective conditions, Rehm said. In principle, the effort is not unlike PatientsLikeMe, a network founded in 2004 that enables patients and family members to share information about diseases.

To contribute to GenomeConnect, participants create accounts, complete an online consent process —parents' permission is required if the participant is between the ages of 10 and 17, fill out a detailed initial health history survey, and then they can upload a copy of their genetic test report, which will be curated by a certified genetic counselor to ensure that results are based on the most current genomic information available. Depending on their responses to the initial survey, patients can complete additional surveys that dig deeper and ask more specific questions. So far about 10 patients have set up accounts and completed the initial health survey, Brianne Kirkpatrick, a genetic counselor at Geisinger Health System and research coordinator for GenomeConnect, told GenomeWeb. A few other patients have registered but have yet to fill out the survey, she said.

Before data is shared externally, patients' personal information is replaced with a unique number code stored in a password protected and secure location accessible by only authorized GenomeConnect staff. De-identified information will be deposited in three partner databases, according to the ClinGen project, including ClinGenDB, the National Center for Biotechnology Information's Database of Genotypes and Phenotypes (dbGAP), and ClinVar.

Access to data in ClinGenDB and dbGAP is controlled, but ClinVar's information is accessible to anyone.  In order to reduce the risk of re-identifying participants, variants shared in ClinVar are listed singly instead of linked to each other. Patients have to give permission before more detailed phenotypic information and genomic data files can be shared with trusted partners. They also have the option not to engage with other participants and researchers.

ClinGen researchers have begun spreading the word about GenomeConnect. William Andrew Faucett, the principal investigator on the project and director of policy and education at the Geisinger Health System, told GenomeWeb that he and his colleagues have adopted a multi-pronged strategy to get the word out to genetic counselors and other clinicians, as well as patient advocacy groups. In reaching out to advocacy groups, ClinGen's aim is twofold, Faucett said. It is offering GenomeConnect as a place for patients plugged into these groups to provide third-party access to their data in a secure fashion, but it is also willing to work with advocacy groups that have established their own registries to help them better capture and curate genotype and detailed phenotype information. Ultimately, "the goal is for everyone with a genetic test result to join a registry where genetic variant information can be captured, de-identified, and shared so that the information is available for study rather than being hidden away in proprietary databases or medical charts," he said.

GenomeConnect's developers also plan to reach out to the National Society of Genetic Counselors and the American College of Medical Genetics to encourage them to get their members on board with the resource. The registry site includes resources that clinicians and healthcare provides can use to inform their patients about the registry. Physicians don't enter their patients' information into GenomeConnect because past experience with running other registries indicates that collecting information directly from the patients themselves results in more detailed data on phenotypes, according to Faucett. However, physicians can help patients set up accounts and ensure that they have access to copies of their genetic tests results, he said.

Also, the group is reaching out to testing laboratories and asking them to include information about GenomeConnect in the resource section of the reports they return to clinicians, Faucett said.

Comparisons with 23andMe

GenomeConnect's strategy for accessing and sharing individual's data may raise comparisons among industry observers between this effort and consumer genomics firm 23andMe's use of customers' data for research. Although 23andMe has stopped reporting health-related genetic data interpretation services to new customers, in compliance with the US Food and Drug Administration's directive, it continues to collect and use data for research purposes with many of the same safeguards adopted by ClinGen in place to protect customers. 

After the FDA's warning letter to 23andMe pointed out the company's lapses in working with the agency to garner market clearance for its tests, some in the life sciences community criticized the direct-to-consumer model as putting patients at risk. Meanwhile, others in the field accused the FDA of paternalism and of restricting consumers from accessing their own genomic data. 

Faucett, though, was quick to distance GenomeConnect's efforts from those of a consumer focused genetic testing firm, such as 23andMe.

"I think the major complaint is that some people feel they have not been transparent about how the information collected is being used and the types of research 23andMe will be performing," said  Faucett adding that that is troubling to some people. They argue, he said, that since they pay for 23andMe's service they should have control over their information being used in research.

According to 23andMe's privacy statement, people can choose not to participate in additional research if they don't want to and those who have given consent can withdraw it at any time. But the company retains access to their genetic and self-reported information and notes in its statement that the data may still be used "by us and shared with our third-party service providers to provide and improve our services … and shared as aggregate Information that does not identify you as an individual."

As a 23andMe customer, Faucett believes the company has been upfront about its activities although he concedes that there is room for misunderstanding. "I'm not critical of what [they] are doing but I understand where the criticism is coming from."

In contrast, GenomeConnect "is transparent and clear that our goal is to share their de-identified genetic and phenotypic information with clinical laboratories and researchers," he maintained. "We are not a commercial entity and are an opt-in registry. We also promise to never share participants' identity or contact information without their permission." Moreover, GenomeConnect has approval from the Geisinger Health System's Institutional Review Board. "We worked closely with the IRB staff to make sure our consent and assent contents are transparent, so that patients know what they are agreeing to when they join," he said. A 23andMe blog post from 2010 states that the company does have IRB approval for its research protocol and consent document but does not explicity state where the approval comes from.

Faucett also pointed out that while 23andMe's chip examines largely common genetic variants found in the genome with some unique mutations — mutations associated with breast cancer and Alzheimer's disease, for example — GenomeConnect targets people with specific conditions and seeks to capture the variants that are associated with their particular disease.

GenomeWeb editor Turna Ray contributed to this story

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