NIH Data Management and Sharing Policy

This section will be dependent on your study. For NIAGADS to help you prepare your DMS Plan, we need to know the type and the estimated size of the data.

NIAGADS will cover the costs to transfer and store smaller datasets. If you plan to submit a dataset over 50TB or >1K short-read raw WGS samples, please reach out to help@niagads.org to discuss storage and transfer options.

Example:

We will be generating whole genome sequencing from participants with South American ancestry who are suspected to have Alzheimer’s disease or who are cognitively normal. We estimate this data will be about 100TB and have consulted with NIAGADS on the cost needed to store this data. NIAGADS has quoted us $X for the transfer, curation, and storage of this data.

Specify the types of data that will be submitted.
X data will be submitted to NIAGADS in alignment with their submission checklist for X data type. (See Data Submission Checklist for submission checklist)

List the file types that you plan to submit using the submission checklist as a guide.

Example:

Whole Genome Sequencing data be submitted to NIAGADS once the data is cleaned (QC/QA) and de-identified. Data will be submitted to NIAGADS in alignment with their submission checklist for WGS data. FASTQs, relevant sequencing information, Phenotype Data File in tab delimited format, APOE and other genotypes in PLINK or VCF file format will be shared with NIAGADS.

Specify the types of files that will be submitted.
X will be shared with NIAGADS. (See Data Submission Checklist for submission checklist)

List the file types that you plan to submit using the submission checklist as a guide.

Example:

A data dictionary, README, consent level as specified in the Institutional Certification form for each subject, NIA sharing plan, list of cohorts included and a description for each, any relevant clinical phenotypic information, and any other pertinent information will be shared with NIAGADS.

Specify the tools, software or code that will be needed to use the files or reproduce results submitted to NIAGADS.

Example:

GATK version 4.1.1 was used to generate sequencing results.

You can find the standards that NIAGADS adheres to below.

Data will be deposited in NIAGADS, an NIA designated repository.

All data submitted to NIAGADS is assigned a unique dataset accession number (NGXXXXX) in addition to a DOI, which will link back the dataset page on the NIAGADS DSS site. Each dataset will appear on the DSS site as its own dataset page and will be searchable on the NIAGADS DSS site. NIAGADS will make the dataset available to users in alignment with the institutional certification provided for the dataset/s.

Data will be deposited to NIAGADS and released at publication or when the funding period ends, whichever comes first. NIAGADS will store this data and make it accessible to qualified users indefinitely. NIAGADS can release updated versions of the dataset if needed, but there is no mechanism to retire or delete datasets at this time.

NIAGADS recommends submitting data for deposition 3 months in advance of when it need to be released.

Work with your institutional review board and NIH funding source to determine what restrictions apply to your data. For reasons why data may be limited, check out the FAQs the NIH has put together on justifiable reasons for limiting data sharing.

NIAGADS follow NIH Genomics Data Sharing Policy and will distribute data in alignment with the institutional certification researchers provide to NIAGADS.

NIAGADS will distribute data to qualified researchers in accordance with the institutional certification for subjects.
If data requires controlled access: The NIAGADS Data Access Committee will review and approve request in accordance with the NIAGADS DSS data access request process.

Data deposited in NIAGADS is de-identified in accordance with HIPAA and the common rule. NIAGADS will share data with qualified researchers in compliance with the data use limitations provided by the depositing researcher.

Data deposited will be shared with qualified researchers, as determined by the NIAGADS Data Access Request process. Data Access Requests submitted by interested researchers are reviewed by the NIAGADS ADRD Data Use Committee (NADAC) to ensure the data request aligns with data use limitations for the data and have plans in place to return derivative data.

NIAGADS collects meta-data for reproducibility and data provenance.

NIAGADS follows the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) by ODHSI.

NIAGADS uses standard ontologies such as Ontology for Biomedical Investigations (OBI) and related OBO Foundry ontologies. Phenotypes are labeled using Human Phenotype Ontology (HP)35, Disease Ontology (DO), OBI and other related OBO ontologies; these ontologies can incorporate other standard terminologies such as OMIM, CADRO (Common Alzheimer Disease Research Ontology, and PhenX (consensus measures for Phenotypes and eXposures). Genomic features are labeled using OBI and Sequence Ontology.

NIAGADS is committed to key principles and industry standards in human genetics/genomics and data science. (1) FAIR and TRUST. All data are accessible through user-friendly web interface with documentation/metadata; production and quality control are fully documented, using industry standards and open-source software for transparency, interoperability, reusability.  Furthermore, NIAGADS constantly evaluates and incorporates latest advances in genomics data science and technology for data production and management.

All NIAGADS datasets can be identified using the NIAGADS Data Sharing Service website.  The DSS website lists all datasets with Subject/Sample manifest, Cohort summary, Consent and Research Use Limitations, Language for acknowledging study and funding, and approved data requests.  Researchers can identify relevant datasets by Data Type, Disease, Platform and Imputation Panel.  Once a researcher receives permission to access the data, the researcher can browse through available data with the web-based DSS Data Portal at individual files and genomic data at sample level by Sex, Phenotype, Self-reported Race/Ethnicity, APOE Genotype, Assay.  NIAGADS provides detailed documentation on the study in the form of READMEs prepared by the data submitter, and available data including data dictionary, file list summary with file size, data type and MD5 checksum.

Except for the case that data need to be removed (i.e. a participant withdraws from a study and requests their data be destroyed), NIAGADS data are managed indefinitely and available for data request.  If NIAGADS funding is discontinued, NIAGADS will host the data and website for one more year before arranging for the data to be hosted at other qualified access repositories such as dbGaP.

For data that require controlled access, such data will be deposited in NIAGADS Data Sharing Service (DSS), a qualified access data sharing process that is compliant with the NIH Genome Data Sharing (GDS) policy.  Qualified researchers from accredited institutions (having privilege to access other sensitive human genetics data at NIH) can submit Data Access Requests (DARs) to request available data.  The DAR is then reviewed by the NIAGADS ADRD Data Access Committee (NADAC) to determine if the DAR is compliant with data use restrictions. 

Data access restrictions are determined by the IRB of the submitting institution following NIH GDS policy to ensure data access uses do not violate the original informed consent(s) signed by the study participants.

All data obtained from these sources and all genetic data generated will be stored on secure servers at NIAGADS. NIAGADS DSS implements security controls compliant with FISMA Moderate level to preserve authorized restrictions on information access and disclosure. Information security risk management process and continuous monitoring process required by the FISMA regulation are integrated to keep the data confidentiality within DSS.

All data deposition and qualified data sharing are covered by data transfer agreements between University of Pennsylvania and the submitter/recipient institutions, as well as two other policy documents developed by NIA. Data submitters and recipients are required to submit NIA AD Genomic Sharing Policy (https://www.nia.nih.gov/research/dn/alzheimers-disease-genomics-sharing-plan ) with institutional signature and comply with requirements.  Recipients of qualified data are required to submit NIAGADS Data Distribution Agreement (https://www.niagads.org/sites/all/public_files/NIAGADS-DDA.pdf) with institutional signature and comply with requirements. 

Effective March 15, 2017, the Certificate of Confidentiality (Certificate) issued for the NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) is subject to the requirements of section 301(d) of the Public Health Service Act (42 U.S.C. 241(d)). Moreover, as of October 1, 2017 NIAGADS is required to adhere to the NIH Policy for Issuing Certificates of Confidentiality (NOT-OD-17-109). Therefore, Approved Users of NIAGADS, whether funded by the NIH or not, who access a copy of information protected by a Certificate held by NIAGADS, are also subject to the requirements of the Certificate of Confidentiality and subsection 301(d) of the Public Health Service Act.

NIAGADS is supported by a cooperative agreement between University of Pennsylvania and National Institute on Aging, and all data management and sharing activities are monitored by both institutions.  NIAGADS provides annual progress report to NIA including data sharing activities and publications that acknowledge NIAGADS.  Qualified data sharing all data deposition and qualified data sharing are covered by data transfer agreements between University of Pennsylvania and the submitter/recipient institutions, executive by the University of Pennsylvania Office of Research Services.