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HRS adds Genetic data to NIH database

With financial support from the American Reinvestment and Recovery Act (ARRA, RC2 AG036495-01), the HRS has genotyped 12,507 respondents who provided DNA samples and signed consent forms in 2006 and 2008. In 2006, saliva was collected using a mouthwash collection method. In 2008, saliva was collected using the Oragene DNA collection kit (OGR-250). Saliva completion rates were 83% in 2006 and 84% in 2008. Based on prior rates of consent and completion, we expect approximately 6,000 additional Oragene samples to be added by 2013, including a substantial expansion of the minority sample.

The genotyping was performed by the NIH Center for Inherited Disease Research (CIDR, X01HG005770-01, http://www.cidr.jhmi.edu/), using the Illumina Human Omni-2.5 Quad beadchip, with coverage of approximately 2.5 million single nucleotide polymorphisms (SNPs). For more information about the specific SNPs included on the Illumina Human Omni-2.5 Quad beadchip, please refer to/download the files in the links below. Genotyping Quality Control was performed by the Genetics Coordinating Center at the University of Washington, Seattle, WA. A copy of the QC report is available here.

"The addition of genetic data provides a major new dimension for the study and is expected to result in much deeper insights into how we age," said Richard Hodes, director of the National Institute on Aging. "With detailed information on genetic background, combined with the wealth of data on important aspects of the lives of older people, researchers will be better able to describe the spectrum of behavioral and environmental risk factors for disease and disability, as well as those that may protect our health."

The initial data product is available through dbGaP. Specific information on the data can be found at www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000428.v1.p1

How to Apply

HRS Public Data

Researchers can view the HRS public data (phenotypes) at any time by registering as an HRS data user. The concordance tool is a convenient way to search for survey content by topic/keyword.

Genotype Data

The genotype data and a limited set of phenotype measures have been deposited in the NIH GWAS repository (dbGaP), which provides a convenient method of distribution to researchers who meet NIH requirements for access. Researchers wishing to use the HRS genetic data must first apply to dbGaP for access to the genotyped data. The process to request access to any dbGaP study is done via the dbGaP authorized access system. Please see the YouTube video dbGaP: Apply for Controlled Access Data for a step-by-step demonstration of how the process works.

Imputations

Current dbGaP data products also include imputation of approximately 21 million DNA variants from the 1000Genomes Project (http://www.1000genomes.org/). Imputation will increase the number of available markers and will make possible comparisons across platforms that do not assay the same genome-wide SNP panel. These imputation analyses were performed and documented by the Genetics Coordinating Center at the University of Washington, Seattle, WA. A copy of the imputation report is available here.

Cross-Reference File

Once access to dbGaP has been granted, researchers who wish to link to HRS phenotype measures not in dbGaP may apply for access to the HRS-dbGaP Cross-Reference File by submitting a Genetic Data Access Use Agreement.

  1. Visit the HRS User Registration/File Download Web site. Note: If you do not already have a username and password, you must register in order to enter the site and download HRS public (phenotype) data.
  2. Look for the Genetic Data Access Use Agreement under the Requesting HRS Special Access Files heading on the right-hand side of the Data Downloads page. Click here to see a sample version)
  3. There is now one form for all the sensitive health data sets. Download and complete the Sensitive Data Access Use Agreement in hardcopy format. (Click here to see a sample DUA)
  4. Send a signed copy of the agreement...
    1. via email (PDF) to:
      HRS Data Requests (hrsdatareq@umich.edu)
    2. via surface mail to:
      Health and Retirement Study
      DUA Review Committee
      426 Thompson Street
      Ann Arbor, Michigan 48104-2321

    Restricted Data Linkages

    Users wishing to link to HRS restricted data products must submit a restricted data application.

    Upcoming Products

    By the end of 2012, an additional 3,200 samples, collected during the HRS 2010 field period, will be genotyped and added to dbGaP. By the end of 2013, data from samples collected during the HRS 2012 field period will be available through dbGaP. The 2010 and 2012 data will include a significant expansion of the minority sample.

    Exonic variants are also currently being measured using the Illumina Human Exome BeadChip v1 on the approximately 16,000 samples collected to date (2006-2010 samples). These exome data will be available through dbGaP in 2012.

    Training

    The online course Six Weeks to Genomic Awareness is now available. This free, self-paced online course is designed to provide a foundation for understanding genomic advances and identifying the relevance of genomics to public health. The course units focus on:

    1. Introduction to Genomics
    2. Genes in Populations
    3. Genetic Testing
    4. Gene-Environment Interactions
    5. Ethical, Legal and Social Issues
    6. An Overview of State and National Resources

    This course is offered by the Michigan Public Health Training Center.

    Additional Information:

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