NINDS Interpretation of the NIH GDS Policy

NINDS Interpretation of the NIH GDS Policy

NINDS Expectations for Genomic Data Sharing

The NIH Genomic Data Sharing (GDS) Policy applies to competing grant applications submitted on January 25, 2015 or later. The GDS Policy sets forth expectations that ensure the broad and responsible sharing of genomic research data generated from NIH funded studies in a timely manner.

NINDS expects all NINDS-supported investigators to adhere to the NIH GDS Policy, and compliance with this Policy will be a special term and condition in the Notice of Award or the Contract Award for all applicable projects. Annual reporting is required, and restrictions may be placed on future year funding for non-compliance with the GDS policy.

Scope and Applicability

  • The NIH GDS Policy applies to all NIH-funded research generating large-scale human or non-human genomic data and the use of these data for subsequent research
  • All funding mechanisms (grants, cooperative agreements, contracts, and NINDS Intramural research program)
  • No minimum threshold dollar amount for budget/Cost
  •  Does NOT apply to:
    • T32s and other institutional training grants
    •  K12 or KL2s
    •  Individual fellowships (Fs)
    • Resource grants and contracts (Ss)

Examples of Projects that Fall Under the GDS Policy

Large-scale data can include genome-wide association studies (GWAS), single nucleotide polymorphisms (SNP) arrays, genome sequence, transcriptomic, metagenomic, epigenomic, and gene expression data.  

What are examples of “large scale” genomic data? 

NINDS Interpretation

Type of Data Number of Human Specimens  Number of Non-Human Specimens*

SNP Array data from >500K Single Nucleotide Polymorphisms (SNPs) (e.g. GWAS data)

500 250

DNA sequence data from < 100 genes or regions of interest (e.g. targeted sequencing)

500 250

DNA sequence data from > 100 genes or regions of interest (e.g. targeted sequencing)

100 50

Whole-Genome or Whole Exome Sequencing

50 25

Genome-wide RNA sequencing (RNA-Seq) data (e.g. transcriptomic data)

50 25

Genome-wide chromatin immunoprecipitation sequencing (Chip-Seq) data

100 50

Genome-wide DNA methylation data

100 50

* Large-scale non-human genomic data includes data from microbes, microbiomes, and model organisms. The data from microbes and microbiomes are considered non-human, if the human genomic data has been filtered and removed.

NINDS may also require sharing of data from studies that involve a smaller number of specimens that:

  • Examine rare neurological disorders or rare subtypes
  • Focus on under-studied populations
  • Contain sequencing data from human iPSC lines or NINDS supported clinical trials
  • Contain data of high value or urgent need as determined by NINDS program staff  

Genomic Data Sharing Plan (Provided at time of application)

Investigators who seek NINDS funding and propose to generate human or non-human genomic data in their studies are encouraged to contact their Program Official as early as possible to discuss data sharing expectations and timelines that would apply to their proposed studies.  

NINDS expects investigators to include a basic genomic data sharing plan in the Resource Sharing Plan section of the grant application. The basic plan should include the following three elements

  1. What data will be shared; 
  2. How and where data will be shared;
    • All human studies must be registered in dbGaP regardless of where the data will ultimately be shared
  3. Timeframe for sharing.

Data Repositories (Provided at time of application)

Human Genomic Data: Investigators should work with the NINDS Genomic Program Administrator 

(GPA) and register their studies with human genomic data in dbGaP.  Investigators should submit data to the relevant NIH-designated data repository, e.g., dbGaP, the Single Nucleotide Polymorphism Database (dbSNP), GEO - Gene Expression Omnibus, or SRA - Sequence Read Archive, in a timely manner (see below).  Investigators should also submit any information necessary to interpret the submitted genomic data, such as study protocols, data instruments, and survey tools.  

Non-Human Genomic Data: can be submitted to any widely used data repository (e.g., WormBase, Zebrafish Information Network (ZFIN), or Mouse Genome Informatics).

Data Submission and Release Timeline (Can be provided prior to award)

Under the GDS Policy, human genomic data submission is generally expected within 3 months of data generation, and data cleaning and quality control should occur during these 3 months. Release of human data should generally be within 6 months after data submission is initiated or at the time of acceptance of initial publication, whichever occurs first.  

Data can be shared incrementally if there are several components in the discovery process.

The table below describes levels of expectations for data submission and release with different data types.  Please refer to the Supplemental Information to the NIH GDS Policy for more information.

Level

General Description of Data Processing

Example Data Types

Data Submission Expectation

Data Release Timeline

0

Raw data generated directly from the instrument platform

Instrument image data

Human data: Not expected                                         
Non-human data: Not expected

Human data: NA
Non-human data: NA

1

Initial sequence
reads, the most
fundamental form of the data after the
basic translation of
raw input

DNA sequencing reads, ChIP-Seq reads, RNA-Seq
reads, SNP arrays, Array
CGH

Human data: Not expected.
Non-human data: Not expected, except for de novo sequence data (unless it is included with
Level 2 aligned sequence files). Submission of de novo sequence data is expected no later than
the time of initial publication.

Human data: NA.
Non-human data: No later than the time of initial publication; an earlier
release date may be designated for certain data types or NIH projects

2

Data after an initial round of analysis or
computation to clean the data and assess
basic quality
measures

DNA sequence alignments
to a reference sequence or
de novo assembly, RNA
expression profiling

Human data: Project specific; after data cleaning and quality control, which is generally within 3 months after data have been generated.
Non-human data: Data submission is expected
no later than the time of initial publication; an earlier submission date may be designated for certain data types or NIH projects.

Human data: Up to 6 months after data submission is initiated or at the time of acceptance of initial publication, whichever occurs first.
Non-human data: No later than the time of initial publication; an earlier
release date may be designated for certain data types or NIH projects.

3

Analysis to identify
genetic variants, gene
expression patterns,
or other features of
the dataset

SNP or structural variant calls, expression peaks,
epigenomic features

Human data: Project specific; after cleaning and quality control, which is generally within 3 months after data have been generated.
Non-human data: Data submission is expected
no later than the time of initial publication; an earlier release date may be designated for
certain data types or NIH projects.

Human data: Up to 6 months after data submission is initiated or at the time of acceptance of initial publication, whichever occurs first.
Non-human data: No later than the time of initial publication; an earlier
release date may be designated for certain data types or NIH projects.

4

Final analysis that relates the genomic
data to phenotype or
other biological states

Genotype-phenotype
relationships, relationships
of RNA expression or
epigenomic patterns to
biological state

Human data: Data submitted as analyses are completed.
Non-human data: Data submission is expected no later than the time of initial publication.

Human data: Data released with publication.
Non-human data: No later than the time of initial publication.

 

Consent for Future Use and Broad Data Sharing

  • All NINDS-funded studies involving human subjects should seek consent for future research use and broad sharing of participant data via central databases, such as dbGaP during the informed consent process.
  • Studies should seek consent for General Research Use of participant data instead of placing disease-specific or other data use limitations on future use of the data. 
  •  Investigators should discuss with their NINDS Program Officials, prior to receiving the NINDS funding, about any potential issues that prevent them from obtaining consent for future research use and broad data sharing.   
  • NIH has provided Guidance on Consent for Future Research Use and Broad Sharing of Human Genomic and Phenotypic Data Subject to the GDS Policy.

Exceptions to the GDS Policy (Human Studies only)

In cases where data submission to an NIH-designated data repository is not appropriate, investigators should provide a justification for any data submission exceptions requested in the funding application or proposal.  NINDS will consider requests for an exception to data sharing expectations on a case-by-case basis.

Factors that may preclude data sharing include 1) International Laws, 2) concerns about harms to participating individuals or groups, and/or 3) other cases where expectations for data submission cannot be met. Requests for exceptions will be evaluated by NINDS Program staff.  For transparency purposes, if the rationale for the exception is adequate and exceptions are granted, studies will still be registered in dbGaP, the reason for the exception will be included in the registration record, and an alternative data-sharing plan or resource will be provided.

Institutional Certification (Provided prior to award)

The Institutional Certification is the document institutions use to attest that the plans for submitting large-scale human genomic data to NIH meets the expectations of the GDS Policy. 

Extramural investigators: Submit your Institutional Certification with the Principal Investigator and Institutional Signing Officials' signatures to the Program Officer and NINDS GPA by either attaching it in an email, or submitting with Just-in-Time funding material prior to award. 

Intramural investigators: Address compliance with the GDS Policy prior to initiating applicable research.  An Intramural Institutional Certification that is approved by the NINDS Scientific Director is required prior to the start of the research.

GDS Policy Contact Information

The NINDS GPA, Dr. Ran Zhang, will be the point of contact for answering questions about study applicability, GDS Policy requirements and paperwork, and for registering the study in dbGaP.