|Genome-Wide Association Study on Parkinson's
Disease Finds Public Home at NIH
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), 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 confidentiality. In order to protect
the volunteers' confidentiality, 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 appropriate protections.
"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 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. dbGaP 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 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 the National
Institute of Neurological Disorders and Stroke (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 David Lipman, M.D., Director of NCBI.
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 dbGaPfirstname.lastname@example.org.
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 (NIH) — 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 information about NIH and
its programs, visit www.nih.gov.