Data from one of the first genome-wide association studies (GWAS), which focused on Parkinson’s diseases and was funded in part by The Michael J. Fox Foundation for Parkinson’s Research (MJFF), is now being made available to researchers through the National Human Genome Research Institute (NHGRI) and the National Center for Biotechnology Information (NCBI), both of the National Institutes of Health (NIH). NHGRI hopes to speed up research by making previously unavailable GWAS data sets publicly available to the research community.
The study, conducted by researchers at Mayo Clinic in Rochester, Minn., in collaboration with scientists at Perlegen Sciences, Inc., in Mountain View, Calif., was the first genome-wide association study applied to Parkinson’s disease. It was funded under MJFF’s Linked Efforts to Accelerate Parkinson’s Solutions (LEAPS) initiative.
“Until now, the individual-level data from this study had been available only to a few researchers,” said Teri Manolio, M.D., Ph.D., director of the NHGRI Office of Population Genomics. “This is the first orphan data set NHGRI is adopting to make public through NCBI, but it certainly will not be the last. We appreciate the willingness of the LEAPS researchers and patients to share their data with the rest of the research community and hope it will increase our understanding of Parkinson’s disease.”
The raw data from a GWAS study is frequently useful to other researchers who may combine it with their own data to improve the analytical power and even make new discoveries. But such information may not be deposited in unregulated public databases because the data typically contain details that could be used to identify study volunteers, potentially violating their privacy. In order to protect the volunteers’ privacy, NIH requires the data submitters to remove identifying information (names, social security numbers, etc.). In addition, researchers who want to use the data must ask for permission and agree to other data use limitations, such as safeguarding participants’ privacy and using the data in ways consistent with consent agreements signed by study subjects. The researcher requests are then reviewed by a data access committee or DAC. Data access committees have been established at several NIH institutes that organize and support GWAS. Because this project was primarily supported by a private foundation, it lacked a DAC to review access requests, so it was considered an “orphan” data set.
NHGRI’s data access committee recently agreed to adopt the study and manage the data access approval process so that the data could be made widely available while ensuring the appropriate protections for confidentiality and privacy.
“It’s wonderful that NHGRI has agreed to facilitate access to this data by researchers around the globe working on Parkinson’s disease,” said Demetrius Maraganore, M.D., a neurologist at Mayo Clinic and the lead principal investigator who provided the Mayo-Perlegen LEAPS data to the dbGaP database on behalf of his collaborators. “Our hope is that these data will be used to make breakthroughs in the prevention and treatment of this devastating disease.”
The Mayo-Perlegen LEAPS Collaboration study will be added to dbGaP, the database of Genotypes and Phenotypes (http://view.ncbi.nlm.nih.gov/dbgap) operated by the National Library of Medicine’s National Center for Biotechnology Information. The dbGaP database contains individual-level data on genotype (an individual’s genetic makeup), and phenotype (observable traits and characteristics). The Mayo-Perlegen LEAPS Collaboration is the second dataset on Parkinson’s disease available through dbGaP. The first was the NINDS-Genome-Wide Genotyping in Parkinson’s Disease: First Stage Analysis and Public Release of Data, which is available through dbGaP at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000089. It was supported by the National Institute of Neurological Disorders and Stroke (NINDS) and conducted by researchers at the National Institute of Aging, another component of NIH.
“The Michael J. Fox Foundation is committed to spurring innovation by creating every possible opportunity for researchers to collaborate and share their knowledge," said Katie Hood, chief executive officer of The Michael J. Fox Foundation. "We are hopeful that NIH's initiative in hosting the Mayo-Perlegen data will accelerate efforts to identify genetic factors underlying Parkinson's disease."
Additional funding for the work was also provided by the National Institute of Environmental Health Sciences (NIEHS) and NINDS, both part of the NIH. The Mayo-Perlegen LEAPS Collaboration study was published online in September 2005 in the American Journal of Human Genetics.
For researchers who want to view the Mayo-Perlegen LEAPS Collaboration data, dbGaP offers two levels of access. The first is open access, where certain data are available without restriction, and the second is controlled access, which requires authorization. The open-access section allows users to view study documents that do not risk identifying individual participants, such as protocols and summaries of genotype and phenotype data. The controlled-access portion of the database allows approved researchers to download individual-level genotype and phenotype data from which the study participants’ personal identifiers, such as names, have been removed.
“Providing the Mayo-Perlegen LEAPS Collaboration data through dbGaP will give researchers new opportunities to investigate genetic factors in Parkinson’s disease,” said Donald A.B. Lindberg, M.D., director of the National Library of Medicine. “By sharing their data, the study investigators and study subjects are not only aiding in the research effort for Parkinson’s disease, but they are helping provide the foundation for researchers to do analyses across multiple studies looking for genetic variations associated with health and disease.”
NHGRI’s DAC has agreed to manage data access for all genome-wide association studies submitted to dbGaP that are not associated with other NIH Institutes, including studies submitted by corporate entities. “Taking on all these orphan studies will result in significantly more data being available through dbGaP and will greatly enhance the discovery opportunities for researchers mining these data,” said NCBI Director David Lipman, M.D.
Researchers interested in accessing the Mayo-Perlegen LEAPS Collaboration study dataset should go to dbGaP’s Web site and complete a request for access to the individual-level data at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000048. Information on data access request procedures is available through the dbGaP “controlled access” Web page, at http://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?login=&page=login.
Although personally identifying information is not included in the database, concern remains that it may someday be possible to identify someone based on their genetic profile. For this reason only researchers agreeing not to attempt to identify individuals in the database will be given access to the data, as outlined in NIH's Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies (GWAS) available at http://grants.nih.gov/grants/guide/notice-files/NOT-OD-07-088.html.
Researchers interested in submitting similar datasets to dbGaP should contact dbGaP staff at dbGaPemail@example.com. The institutional certification that NHGRI will require for submitting datasets is also described in NIH’s Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies (GWAS) at the link above.
The Michael J. Fox Foundation for Parkinson’s Research is dedicated to ensuring the development of a cure for Parkinson’s disease through an aggressively funded research agenda. To date, the Foundation has funded more than $115 million in research.
NHGRI is one of 27 institutes and centers at the NIH, an agency of the Department of Health and Human Services. The NHGRI Division of Extramural Research supports grants for research and for training and career development at sites nationwide. Additional information about NHGRI can be found at its Web site, www.genome.gov.
The National Center for Biotechnology Information (NCBI) was established in 1988 as a national resource for molecular biology information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing molecular and genomic data, and disseminates biomedical information, all for the better understanding of processes affecting human health and disease. NCBI is a division of the National Library of Medicine, the world's largest library of the health sciences. For more information, visit www.nlm.nih.gov.
The National Institutes of Health — "The Nation's Medical Research Agency" — includes 27 institutes and centers, and is a component of the U.S. Department of Health and Human Services. It is the primary federal agency for conducting and supporting basic, clinical and translational medical research, and it investigates the causes, treatments and cures for both common and rare diseases. For more, visit www.nih.gov.
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