Welcome to NIMH Repository & Genetics Resource

The NRGR provides access to bio-samples, genetic data, and phenotypic data for over 150,000 patient, family, and control subjects across a range of mental disorders.

Allow us to introduce the range of data & samples available, as well as the tools provided to facilitate the use of these resources.

Note You can access summary level info without registering for an account.

The first step for a majority of users will be to create an account with NIMH genetics. Before you receive an account, you can browse summary level data and explore our website to learn what the NRGR has to offer.

If you still have questions, please contact nimhgenetics-admin@isi.edu.

I want to use NRGR summary data to submit a proposal

As a new user of NIMHgenetics.org without log-in credentials or approval for downloading data, you can still browse summary-level data to get an idea of what resources are available via the NRGR. If you are interested in possibly using NRGR data or samples for an upcoming proposal, the Data Explorer and BioQ are two tools that will help you determine how many subjects of a given age, sex, gender, race are available for distribution, along with the type of bio-samples, genetic, and clinical data available.

After perusing summary level data, if you would like to make queries on individual-level data or request access to biosamples, genetic data, or clinical data distributions, you can create an account and request access.

The NRGR receives, processes, and stores biomaterials ready for analysis (DNA, cell lines and other products) from various primary sources (e.g., blood or skin biopsy) submitted by NIMH grantees, and distributes biomaterials to approved investigators. Potential investigators can browse summary-level data for these samples via the following tools:

Bio-Samples and iPSCs

The NRGR receives, processes, and stores biomaterials ready for analysis (DNA, cell lines and other products) from various primary sources (e.g., blood or skin biopsy) submitted by NIMH grantees, and distributes biomaterials to approved investigators.

Potential investigators can browse summary-level data for these samples via the following tools:

  • Data Explorer

    • Data Explorer allows investigators to browse data per disorder, displaying summary counts with customizable order of categorization. "Biomaterial Type" is one searchable category, allowing the user to determine how many specific biomaterials are available (DNA whole blood, LCL, plasma, etc.), and also demographic and/or phenotypic information
    • Queries about iPSC lines can be made through Data Explorer. Summary counts can be displayed in a variety of ways depending upon your primary interest.
      • Summary pie charts are displayed on the first page, allowing quick and intuitive searches with customizable order of categorization (ie Biomaterial type > Gender > Age group > Diagnosis VS Diagnosis > Biomaterial Type > Gender > Age Group)
      • Greater detail about study design (ie Trios, sib pairs, or individuals) can be assessed by clicking "Explore Subject Counts.
      • Data Explorer – Browse iPSC Summary counts
  • BioQ

    • BioQ is a data search tool designed specifically with iPSC & fibroblast data in mind. Currently there is a higher level of diagnostic harmonization across studies in BioQ, as well as greater detail about individual lines available through BioQ than Data Explorer.
    • BioQ

Genetic Data

The NRGR receives, processes, and stores genetic data (GWAS, sequence) submitted by NIMH grantees, and distributes genetic data to approved investigators. In addition to the genetic data stored at the NRGR center, subjects with genetic data stored in other repositories (ie dbGAP) are identified.

Potential investigators can browse summary-level data for these subjects via the Data Explorer.

  • Data Explorer

    • To explore summary counts for individuals with GWAS data, click on the disorder of interest, and then "Explore Subject Counts".
      • GWAS Data Specify platform, SNP rsID’s, Chromosome start & end position, or HGNC Gene Symbol.
      • Data at dbGAP?Check this box if you would like to include individuals with genetic data stored at dbGAP.
    • Data Explorer

Phenotypic Data

The NRGR receives, processes, and stores clinical phenotypic data submitted by NIMH grantees, and distributes genetic data to approved investigators. Phenotypic data is released periodically in distributions per disorder, with a separate distribution for non-family controls.

Within each distribution, there is a main distribution file, which includes demographic information and study-assigned diagnoses, and auxiliary files including DSM codes (or other diagnostic codes), extended race and ethnicity data, and clinical instruments collected by each study (ie ADI-R, DIGS, OP-CRIT, etc.).

Potential investigators can browse summary-level data for these subjects via Data Explorer.

  • Data Explorer

    • Explanation of what phenotypic data is (and is not) available via Data Explorer
    • Data Explorer
I want to download NRGR data

Information available through the website is collected as part of various psychiatric studies and therefore HIPAA protected. To request access and eventually access and download data, the first step is to create an account.

To register for a new account, click here.

Creating a user account gives you

  1. Access to the Access Approval System.
  2. Ability to browse high level summary data in the data explorer.

Eligibility for Access

Applying for Access

In order to download the data distributions, explore the data available using Data Explorer or BioQ, you need to get approval via the access approval system. This system is administered by NIH staff, and is used to grant access.

In order to download the data distributions, explore the data available using Data Explorer or BioQ, you need to get approval via the access approval system. This system is administered by NIH staff, and is used to grant access.

Access Approval Review Process

All requests for access to data and biospecimens from the NIMH RGR will be reviewed by a trans-NIH Data Access Committee consisting of NIH Program Staff from NIDA, NIAAA, and NIMH.

Each access request will be considered based on the following by the Data Access Committee:

  1. The experience and qualifications of the applicant PI and co-investigators.
  2. Ethical considerations.
  3. The applicant PI’s familiarity with the characteristics, limitations, and strengths of the dataset/biospecimens.
  4. The adequacy of the proposed research design.
  5. The adequacy of the research environment.
  6. The adequacy of the applicant PI’s funding resources to support the proposed study
  7. The adequacy of the applicant PI’s agreement on data sharing as stipulated in the data/resource sharing plan.

Greater details about these requirements can be found here.

I want to request delivery of NRGR bio-samples

  1. Create an nimhgenetics.org account. Register for a new account
  2. Request access via the Access Approval System. See Applying for Access above.

Investigators interested in using NRGR bio-materials must request approval via the Access Approval System, the same system that is used to request access to data distributions.

After access certification, login information and pedigree drawings will be sent to the principal investigator via next day FedEx. Shipping information and an Excel file containing an NIMH Repository ID number and NIMH subject ID number for each subject for which biomaterial is requested should be submitted to the Rutgers University Cell and DNA Repository (RUCDR) web portal at http://rucdr.rutgers.edu. The request will then be forwarded for approval to NIMH. Approved projects will be invoiced by RUCDR.

For problems accessing the RUCDR web portal, please contact Ms. Dana Witt at Witt@Biology.Rutgers.Edu

I am a NIMH-funded researcher required to submit data to the center

NIMH-funded studies are required to submit data to the NRGR, based upon the terms described in their Notice of Grant Award and Data Sharing Plans. The NRGR collects, curates, and distributes collected data via a combination of automated Quality Control and human curation to ensure data is submitted in accordance with study-specific requirements.

Data submitted to the center must be formatted in accordance with the Auto-QC System’s requirements. Detailed descriptions and sample files can be found on the QC Help Page.

The Auto-QC system takes in a .zip package of required files. Files are checked for agreement with defined data dictionaries, as well as higher-level checks. These include pedigree checks (are mothers female? Are children younger than parents?), cross-database checks (are RUID’s and PARTID’s accurate according to RUCDR records?), and diagnosis checks (are submitted diagnoses compatible?). Although the error-checking is automated, the Auto-QC system does not automatically correct errors. The investigator must review error logs generated by the QC System, make the necessary changes, and re-submit a corrected .zip package to the system.

After all files pass successfully through the Auto-QC system, the investigator has the option to submit the successful package to expert curators at Washington University – St. Louis. The expert curators review the submission to ensure that data submitted matches the expected data based on the study’s Notice of Grant Award and Data Sharing Plan. If any additional updates to the submission are required, the curator will reach out to the submitting study. If the data submitted is clean and in accordance with NIMH requirements, the data will be included in the next distribution released by NRGR.

The Auto-QC system can also be used for internal QC. Upon successful completion of Auto QC, the investigator can decide not to send the file on for manual curation. This way, the QC system can be used to ensure file formats are correct and data is clean well ahead of their required submission date.

Tools - Data Explorer

The NIMH-RGR Data Explorer is a tool that supports querying of the data available on the nimhgenetics.org website. Using an intuitive interface, a researcher can select various filtering criteria and immediately obtain the subset of the data of interest. Retrieved results can be saved for future analysis.

The tool provides summary counts of results for the general research community. For NIMH-approved researchers, the tool provides individual-level data (request access).

The Data Explorer supports

  • Exploring summary counts of individuals and biosamples, using intuitive graphics.
  • Querying by demographic, phenotypic, genotypic, and pedigree characteristics.
  • Selecting individuals based on biosample and genetic data availability.
  • Generating plots of the family structure (pedigree) of the individuals in query results.
  • Retrieving Rutgers ID information for pedigree/family of selected individuals.
  • Saving results as a .csv file or in PLINK format for further analysis.

Tools - Pedigree Service

The Pedigree Service is a tool that allows users to generate a Pedigree plots for multiple families by uploading a single file.

The Pedigree Service generates the plots as a single multi-page PDF file, with an index and legends.

The Pedigree Service also performs some data quality checks and reports about errors in the data. Some data quality checkes performed are; is an individual identified as someones father a Male, checking that parent is elder than their children, etc.

Tools - dbGaP Tools

dbGaP Tools is a downloadable software, which allows users to merge data from NRGR and dbGaP.

The tools merges records from NRGR and dbGaP files based on matching Cell IDs.

Optionally, the tools also allows to provide a Plink FAM file and update the assesments within them with alternative assesments from a assesments file provided separately.

A short 2 minute demo can be viewed here.

BioQ - Genomic Database Tools

The BioQ web application at https://bioq.saclab.net provides tools for querying large genomic databases including dbSNP, 1000 Genomes and Ensembl.

BioQ - Stem Cell Tools

This allows both public and private users to view the subjects and biotmaterials in the NIMH iPSC database. Users that log in with an NIMH account will access to more detailed information. The application is available at https://bioq.nimhgenetics.org/stemcells.