NDA Help Center

Collection - General Tab

Fields available for edit on the top portion of the page include:

  • Collection Title
  • Investigators
  • Collection Description
  • Collection Phase
  • Funding Source
  • Clinical Trials

Collection Status: The visibility status of an NDA Collection.  Collection Status can be Shared or Private.  Collections in Shared status are visible to all users and can be searched in the NDA Query Tool. Private Collections are not visible to NDA users.  The Status of an NDA Collection only affects the visibility of information about the Collection (metadata) and does not relate to the status of the record-level research data in the NDA Collection.

Collection Phase: The current status of a research project submitting data to an NDA Collection, based on the timing of the award and/or the data that have been submitted.
 

  • Pre-Enrollment: The default entry made when the NDA Collection is created.
     
  • Enrolling: Data have been submitted to the NDA Collection or the NDA Data Expected initial submission date has been reached for at least one data structure category in the NDA Collection.
     
  • Data Analysis: Subject level data collection for the research project is completed and has been submitted to the NDA Collection.  The NDA Collection owner or the NDA Help Desk may set this phase when they’ve confirmed data submission is complete and submitted subject counts match at least 90% of the target enrollment numbers in the NDA Data Expected. Data submission reminders will be turned off for the NDA Collection.
     
  • Funding Completed: The NIH grant award (or awards) associated with the NDA Collection has reached its end date. NDA Collections in Funding Completed phase are assigned a subphase to indicate the status of data submission.
     
    • The Data Expected Subphase indicates that NDA expects more data will be submitted
    • The Closeout Subphase indicates the data submission is complete.
    • The Sharing Not Met Subphase indicates that data submission was not completed as expected. 

Blinded Clinical Trial Status:

  • This status is set by a Collection Owner and indicates the research project is a double blinded clinical trial.  When selected, the public view of Data Expected will show the Data Expected items and the Submission Dates, but the targeted enrollment and subjects submitted counts will not be displayed.
     
  • Targeted enrollment and subjects submitted counts are visible only to NDA Administrators and to the NDA Collection or as the NDA Collection Owner.
     
  • When an NDA Collection that is flagged Blinded Clinical Trial reaches the maximum data sharing date for that Data Repository (see https://nda.nih.gov/about/sharing-regimen.html), the embargo on Data Expected information is released.
     

Funding Source

The organization(s) responsible for providing the funding is listed here. 

Supporting Documentation

Users with Submission privileges, as well as Collection Owners, Program  Officers, and those with Administrator privileges, may upload and attach supporting documentation. By default, supporting documentation is shared to the general public, however, the option is also available to limit this information to qualified researchers only. 

Grant Information 

Identifiable details are displayed about the Project of which the Collection was derived from. You may click in the Project Number to view a full report of the Project captured by the NIH. 

Clinical Trials

Any data that is collected to support or further the research of clinical studies will be available here. Collection Owners and those with Administrator privileges may add new clinical trials. 

Frequently Asked Questions

  • When a Collection is created by NDA staff and marked as Shared, an email notification will automatically be sent to the PI(s) of the grant(s) associated with the Collection to notify them.

  • During Collection creation, NDA staff determine the appropriate Permission Group based on the type of data to be submitted, the type of access that will be available to data access users, and the information provided by the Program Officer during grant award.

  • The NDA system does not allow for a single grant to be associated with more than one Collection; therefore, a single grant will not be listed in the Grant Information section of a Collection for more than one Collection.

  • In general, each Collection is associated with only one grant; however, multiple grants may be associated if the grant has multiple competing segments for the same grant number or if multiple different grants are all working on the same project and it makes sense to hold the data in one Collection (e.g., Cooperative Agreements).

Glossary

  • Number of human subjects enrolled in an NIH-funded clinical research study. The data is provided in annual progress reports.

  • A privilege provided to a user associated with an NDA Collection or NDA Study whereby that user can perform a full range of actions including providing privileges to other users. 

  • Generally, the Collection Owner is the contact PI listed on a grant. Only one NDA user is listed as the Collection owner. Most automated emails are primarily sent to the Collection Owner.

  • The Collection Phase provides information on data submission as opposed to grant/project completion so while the Collection phase and grant/project phase may be closely related they are often different.  Collection users with Administrative Privileges are encouraged to edit the Collection Phase.  The Program Officer as listed in eRA (for NIH funded grants) may also edit this field. Changes must be saved by clicking the Save button at the bottom of the page.  This field is sortable alphabetically in ascending or descending order. Collection Phase options include: 

    • Pre-Enrollment:  A grant/project has started, but has not yet enrolled subjects.
    • Enrolling:  A grant/project has begun enrolling subjects.  Data submission is likely ongoing at this point.
    • Data Analysis:  A grant/project has completed enrolling subjects and has completed all data submissions.
    • Funding Completed:  A grant/project has reached the project end date.
  • The Collection State indicates whether the Collection is viewable and searchable.  Collections can be either Private, Shared, or an Ongoing Study.  A Collection that is shared does not necessarily have shared data as the Collection State and state of data are independent of each other.  This field can be edited by Collection users with Administrative Privileges and the Program Officer as listed in eRA (for NIH funded grants). Changes must be saved by clicking the Save button at the bottom of the page.

  • An editable field with the title of the Collection, which is often the title of the grant associated with the Collection.

  • Data Use Limitations (DULs) describe the appropriate secondary use of a dataset and are based on the original informed consent of a research participant. NDA only accepts consent-based data use limitations defined by the NIH Office of Science Policy.

  • Provides the grant number(s) for the grant(s) associated with the Collection.  The field is a hyperlink so clicking on the Grant number will direct the user to the grant information in the NIH Research Portfolio Online Reporting Tools (RePORT) page.

  • A virtual container and organization structure for data and associated documentation from one grant or one large project/consortium. It contains tools for tracking data submission and allows investigators to define a wide array of other elements that provide context for the data, including all general information regarding the data and source project, experimental parameters used to collect any event-based data contained in the Collection, methods, and other supporting documentation. They also allow investigators to link underlying data to an NDA Study, defining populations and subpopulations specific to research aims. 

  • NDA Collections may be organized by scientific similarity into NIH Research Initiatives, to facilitate query tool user experience. NIH Research Initiatives map to one or multiple Funding Opportunity Announcements. 

  • Access to shared record-level data in NDA is provisioned at the level of a Permission Group. NDA Permission Groups consist of one or multiple NDA Collections that contain data with the same subject consents.

  • Number of human subject participants to be enrolled in an NIH-funded clinical research study. The data is provided in competing applications and annual progress reports.

  • Various documents and materials to enable efficient use of the data by investigators unfamiliar with the project and may include the research protocol, questionnaires, and study manuals.  

  • The total number of unique subjects for whom data have been shared and are available for users with permission to access data.

NDA Help Center

Collection - Shared Data Tab

This tab provides a quick overview of the Data Structure title, Data Type, and Number of Subjects that are currently Shared for the Collection. The information presented in this tab is automatically generated by NDA and cannot be edited. If no information is visible on this tab, this would indicate the Collection does not have shared data or the data is private.

The shared data is available to other researchers who have permission to access data in the Collection's designated Permission Group(s). Use the Download button to get all shared data from the Collection to the Filter Cart.

 

Frequently Asked Questions

  • To see what data your project have submitted are being used by a study, simply go the Associated Studies tab of your collection.  Alternatively, you may review an NDA Study Attribution Report available on the General tab.  

  • Often it becomes more difficult to organize and format data electronically after the project has been completed and the information needed to create a GUID may not be available; however, you may still contact a program staff member at the appropriate funding institution for more information.

  • Unlike completed projects where researchers may not have the information needed to create a GUID and/or where the effort needed to organize and format data becomes prohibitive, ongoing projects have more of an opportunity to overcome these challenges.  Please contact a program staff member at the appropriate funding institution for more information.

Glossary

  • A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points. Data structures that have been defined in the NDA Data Dictionary are available at https://nda.nih.gov/general-query.html?q=query=data-structure

  • A grouping of data by similar characteristics such as Clinical Assessments, Omics, or Neurosignal data.

  • The term 'Shared' generally means available to others; however, there are some slightly different meanings based on what is Shared.  A Shared NDA Collection or NDA Study is viewable and searchable publicly regardless of the user's role or whether the user has an NDA account.  A Shared Collection or NDA Study does not necessarily mean that data submitted to the Collection or used in the NDA Study have been shared as this is independently determined.  Data are shared according the schedule defined in a Collection's Data Expected Tab and/or in accordance with data sharing expectations in the NDA Data Sharing Terms and Conditions.  Additionally, Supporting Documentation uploaded to a Collection may be shared independent of whether data are shared, but will only be viewable and accessible if the Collection is Shared.

NDA Help Center

fMRi

fMRI stands for functional magnetic resonance imaging. fMRI tests measure blood flow, providing detailed functional images of the brain or body. 

Acquisition
The Acquisition parameters needed for an experiment include the following:

The name of the experiment is required. Please be concise and specific as possible.
Following experiment name, selection boxes are provided for the Equipment, Software, or other items specific to the experiment type. At least one selection is required for each. If NDAR does not have the appropriate listing, select Add New to add the information provided. Following the selection boxes, provide additional information may be required depending on the experiment type. Any required items are denoted by an asterisk (*).

Block/Event Design
At least one block/event is required. Note that any fields denoted with an asterisk (*) are required. All data must be devoid of personally identifiable data, including the contents of any files attached to the experiment.

Note: To simplify the definition of multiple events, we provide an Import from XML function. This function supports importing data from all three experiment sections (Acquisition, Block/Event Design, and Post Processing), at this time files cannot be uploaded from XML A test format is provided here and our XML Schema Definition (xsd) can be found here.

Post Processing
If you have completed any post-processing on your data, please choose 'Yes' for Has Postprocessing? If not, select 'No'. Depending on this selection the remaining post-processing fields will be enabled (some of which will be required). If you are initially providing data you can select 'No', then return to the experiment to add post-processing steps at a later date when the data are being provided.

Please provide information about post-processing manipulations, i.e. artifact detection algorithms, segmentation used for post data collection, items denoted with an asterisk (*) are required.

Frequently Asked Questions

Glossary

  • This button will add all selections to the Filter Cart. 

  • This button will allow you to copy all of the Experiment details as a template for a new experiment. 

  • Adds all data from the current selections in a Collection or NDA Study to the Filter Cart.

  • This button will allow you to return to the Experiments tab. 

NDA Help Center

Collection - Submissions Tab

Users with permission to access Shared data in the Collection’s assigned Permission Group may use this tab. 

Here, you can:

  • Review your uploads to your Collection, monitor their status, and download them individually to verify their contents.
  • Download individual datasets as a secondary user of the data approved for access.
  • Identify and download datasets containing errors identified by NDA's QA/QC process for review and resolution.
  • Report suspected or discovered Personally Identifiable Information in a submission via the Actions column.

Frequently Asked Questions

Glossary

  • The default view of Datasets within a Collection's Submission tab.

  • A Submission Loading Status on a Collection's Submission Tab that indicates that an issue has prevented the successful loading of the submission.  Users should contact the NDA Help Desk for assistance at NDAHelp@mail.nih.gov.

  • The NDA has two Submission Cycles per year - January 15 and July 15.

  • An interface to notify NDA that data may not be submitted during the upcoming/current submission cycle.  

  • The unique and sequentially assigned ID for a submission (e.g. a discrete upload via the Validation and Upload Tool), which may contain any number of datafiles, Data Structures and/or Data Types, regardless of the Submission Loading Status. A single submission may be divided into multiple Datasets, which are based on Data Type.

  • The total number of unique subjects for whom data have been shared and are available for users with permission to access data.

  • The total number of unique subjects for whom data have been submitted, which includes data in both a Private State and a Shared State.

NDA Help Center

Collection - Publications Tab

The number of Publications is displayed in parentheses next to the tab name. Clicking on any of the Publication Titles will open the Publication in a new internet browsing tab. 

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may mark a publication as either Relevant or Not Relevant in the Status column. 

 

Frequently Asked Questions

  • Publications are considered relevant to a collection when the data shared is directly related to the project or collection.

  • PubMed, an online library containing journals, articles, and medical research. Sponsored by NiH and National Library of Medicine (NLM). 

Glossary

  • A link to the Create an NDA Study page that can be clicked to start creating an NDA Study with information such as the title, journal and authors automatically populated.

  • Indicates that the publication has not yet been reviewed and/or marked as Relevant or Not Relevant so it has not been determined whether an NDA Study is expected.

  • A publication that is not based on data related to the aims of the grant/project associated with the Collection or not based on any data such as a review article and, therefore, an NDA Study is not expected to be created.

  • PubMed provides citation information for biomedical and life sciences publications and is managed by the U.S. National Institutes of Health's National Library of Medicine.

  • The PUBMed ID is the unique ID number for the publication as recorded in the PubMed database.  

  • A publication that is based on data related to the aims of the grant/project associated with the Collection and, therefore, an NDA Study is expected to be created.

NDA Help Center

EEG

EEG stands for electroencencephalogram and is a test used to measure electrical activity in the brain.

Acquisition
The Acquisition parameters needed for an experiment include the following:

Name of the experiment is required. Please be concise and specific as possible.
Following experiment name, selection boxes are provided for the Equipment, Software, or other items specific to experiment type. At least one selection is required for each. If NDAR does not have the appropriate listing, select Add New to add the information provided. Following the selection boxes, provide additional information may be required depending on experiment type. Any required items are denoted by an asterisk (*).

Block/Event Design
At least one block/event is required. Note that any fields denoted with an asterisk (*) are required. All data must be devoid of personally identifiable data, including the contents of any files attached to the experiment.

Note: To simplify definition of multiple events, we provide an Import from XML function. This function supports importing data from all three experiment sections (Acquisition, Block/Event Design, and Post Processing), at this time files cannot be uploaded from XML A test format is provided here and our XML Schema Definition (xsd) can be found here.

Post Processing
If you have completed any post processing on your data, please choose 'Yes' for Has Postprocessing? If not, select 'No'. Depending on this selection the remaining post processing fields will be enabled (some of which will be required). If you are initially providing data you can select 'No', then return to the experiment to add post processing steps at a later date when the data are being provided.

Please provide information about post-processing manipulations, i.e. artifact detection algorithms, segmentation used for post data collection, items denoted with an asterisk (*) are required.

Frequently Asked Questions

Glossary

  • This button will add all selections to the Filter Cart. 

  • This button will allow you to copy all of the Experiment details as a template for a new experiment. 

  • Adds all data from the current selections in a Collection or NDA Study to the Filter Cart.

  • This button will allow you to return to the Experiments tab. 

NDA Help Center

Collection - Data Expected

The Data Expected tab displays the list of all data that NDA expects to receive in association with the Collection as defined by the contributing researcher, as well as the dates for the expected initial upload of the data, and when it is first expected to be shared, or with the research community. Above the primary table of Data Expected, any publications determined to be relevant to the data within the Collection are also displayed - members of the contributing research group can use these to define NDA Studies, connecting those papers to underlying data in NDA.

The tab is used both as a reference for those accessing shared data, providing information on what is expected and when it will be shared, and as the primary tracking mechanism for contributing projects. It is used by both contributing primary researchers, secondary researchers, and NIH Program and Grants Management staff.

Contributing researchers just getting started on their project will need to define this list by adding all of the items they are collecting under their grant and setting their schedule according to the NDA Data Sharing Regimen. If you fall into this category, you can begin by clicking "add new Data Expected" and selecting which data structures you will be using, saving the page after each change, or requesting new structures by adding and naming a new item, providing any materials NDA Data Dictionary Curators can use to help define your structure. For more information see the tutorial on creating Data Expected.

If you are a contributing researcher creating this list for the first time, or making changes to the list as your project progress, please note the following:

  • Although items you add to the list and changes you make are displayed, they are not committed to the system until you Save the entire page using the "Save" button at the bottom of your screen. Please Save after every change to ensure none of your work is lost.
  • If you attempt to add a new structure, the title you provide must be unique - if another structure exists with the same name your change will fail.
  • Adding a new structure to this list is the only way to request the creation of a new Data Dictionary definition.

 

Frequently Asked Questions

  • An NDA Data Structure is comprised of multiple Data Elements to make up an electronic definition of an assessment, measure, questionnaire, etc will have a corresponding Data Structure.

  • The NDA Data Dictionary is comprised of electronic definitions known as Data Structures.

Glossary

  • Data specific to the primary aims of the research being conducted (e.g. outcome measures, other dependent variables, observations, laboratory results, analyzed images, volumetric data, etc.) including processed images.

  • Items listed on the Data Expected list in the Collection which may be an individual and discrete Data Structure, Data Structure Category, or Data Structure Group.

  • A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points. Data structures that have been defined in the NDA Data Dictionary are available at https://nda.nih.gov/general-query.html?q=query=data-structure

  • An NDA term describing the affiliation of a Data Structure to a Category, which may be disease/disorder or diagnosis related (Depression, ADHD, Psychosis), specific to data type (MRI, eye tracking, omics), or type of data (physical exam, IQ).

  • A Data Item listed on the Data Expected tab of a Collection that indicates a group of Data Structures (e.g., ADOS or SCID) for which data may be submitted instead of a specific Data Structure identified by version, module, edition, etc. For example, the ADOS Data Structure Category includes every ADOS Data Structure such as ADOS Module 1, ADOS Module 2, ADOS Module 1 - 2nd Edition, etc. The SCID Data Structure Group includes every SCID Data Structure such as SCID Mania, SCID V Mania, SCID PTSD, SCID-V Diagnosis, and more. 

  • A new Data Structure category, Evaluated Data is analyzed data resulting from the use of computational pipelines in the Cloud and can be uploaded directly back to a miNDAR database.  Evaluated Data is expected to be listed as a Data Item in the Collection's Data Expected Tab.

  • Imaging+ is an NDA term which encompasses all imaging related data including, but not limited to, images (DTI, MRI, PET, Structural, Spectroscopy, etc.) as well as neurosignal data (EEG, fMRI, MEG, EGG, eye tracking, etc.) and Evaluated Data.

  • Initial Submission and Initial Share dates should be populated according to the NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data will be shared with authorized users upon publication (via an NDA Study) or 1-2 years after the grant end date specified on the first Notice of Award, as defined in the applicable Data Sharing Terms and Conditions.

  • Initial Submission and Initial Share dates should be populated according to these NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data for all subjects is not expected on the Initial Submission Date and modifications may be made as necessary based on the project's conduct.

  • An NDA created Data Structure used to convey basic information about the subject such as demographics, pedigree (links family GUIDs), diagnosis/phenotype, and sample location that are critical to allow for easier querying of shared data.

  • The NDA has two Submission Cycles per year - January 15 and July 15.

  • An interface to notify NDA that data may not be submitted during the upcoming/current submission cycle.  

NDA Help Center

Collection - Permissions

Collection Owners, Program Officers, and users with Administrator privileges may view this tab.

The available permission groups include:

  • Query: This read-only access is generally for NIH Program Officers
  • Submission: This will grant read access and allow the user to upload data and create experiment definitions. This is for the typical contributing personnel member.
  • Administrator: In addition to the access provided to Query and Submission users, Admins can also edit the Collection itself, create or edit the Data Expected list, and edit user permissions. This access is for the PI, data managers, and anyone they wish to delegate this to.

The PI has a special designation as the Collection Owner in addition to administrator access.

Frequently Asked Questions

  • Collection Owners and Admins may assign Collection Privileges to anyone.

  • Yes, you can assign various Privileges to other users with an NDA account.

  • If you are the Collection Owner or have Admin privileges, you can view and make changes to the list of individuals who have access to the Collection on the Collection's Permissions tab.  Information on users who have access to data Shared in your Collection because they were granted access to a Permission Group is not available.

  • Staff/collaborators who are working submitting data to the Collection, checking the quality of the data, and/or analyzing data should have access for the duration of the project until all data have been submitted, NDA Studies have been created for data used in publications, and/or a collaborative relationship with the user exists.  

  • The individual listed as an Investigator on the General tab of the NDA Collection will generally be able to provide a user access to the NDA Collection.  Additional users may also have this ability if granted Administrator access to an NDA Collection; however, these users are not viewable unless your account has access to the NDA Collection.  Given this, it is best to contact the Investigator to request access to the Collection.

  • Privileges that can be assigned to a user include:
    Submission allows a user to submit data to Collection
    Query allows the user to download data from Collection even when in a Private state
    Admin is both the Submission and Query Privilege + the ability to give privileges to other users.

  • You may have staff who are working on the submission of data or other activities associated with data sharing such as the definition of the Data Expected list or NDA Experiment creation.  Also, many projects have multiple performance sites and wish to share data among the site PIs.  Submitting to the NDA facilitates access by all investigators working on a project even before data have been shared with other users.  You can control who gets access to data while in a Private state.

Glossary

  • A privilege provided to a user associated with an NDA Collection or NDA Study whereby that user can perform a full range of actions including providing privileges to other users. 

  • Access to shared record-level data in NDA is provisioned at the level of a Permission Group. NDA Permission Groups consist of one or multiple NDA Collections that contain data with the same subject consents.

NDA Help Center

Eye Tracking

EyeTracking tests follow the movement of the eye. The visual trajectory or focus can help determine predictions and assist in diagnoses. 

Acquisition
The Acquisition parameters needed for an experiment include the following:

The name of the experiment is required. Please be concise and specific as possible.
Following experiment name, selection boxes are provided for the Equipment, Software, or other items specific to the experiment type. At least one selection is required for each. If NDAR does not have the appropriate listing, select Add New to add the information provided. Following the selection boxes, provide additional information may be required depending on the experiment type. Any required items are denoted by an asterisk (*).

Block/Event Design
At least one block/event is required. Note that any fields denoted with an asterisk (*) are required. All data must be devoid of personally identifiable data, including the contents of any files attached to the experiment.

Note: To simplify the definition of multiple events, we provide an Import from XML function. This function supports importing data from all three experiment sections (Acquisition, Block/Event Design, and Post Processing), at this time files cannot be uploaded from XML A test format is provided here and our XML Schema Definition (xsd) can be found here.

Post Processing
If you have completed any post-processing on your data, please choose 'Yes' for Has Postprocessing? If not, select 'No'. Depending on this selection the remaining post-processing fields will be enabled (some of which will be required). If you are initially providing data you can select 'No', then return to the experiment to add post-processing steps at a later date when the data are being provided.

Please provide information about post-processing manipulations, i.e. artifact detection algorithms, segmentation used for post data collection, items denoted with an asterisk (*) are required.

Frequently Asked Questions

Glossary

  • This button will add all selections to the Filter Cart. 

  • This button will allow you to copy all of the Experiment details as a template for a new experiment. 

  • Adds all data from the current selections in a Collection or NDA Study to the Filter Cart.

  • This button will allow you to return to the Experiments tab. 

NDA Help Center

Collection - Experiments Tab

The number of Experiments included is displayed in parentheses next to the tab name. You may download all experiments associated with the Collection via the Download button. You may view individual experiments by clicking the Experiment Name and add them to the Filter Cart via the Add to Cart button.

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may create or edit an Experiment.

Please note: The creation of an NDA Experiment does not necessarily mean that data collected, according to the defined Experiment, has been submitted or shared.

Frequently Asked Questions

  • Yes -see the “Copy” button in the bottom left when viewing an experiment. There are two actions that can be performed via this button:

    1. Copy the experiment with intent for modifications.  
    2. Associate the experiment to the collection. No modifications can be made to the experiment.

     

Glossary

  • An Experiment must be Approved before data using the associated Experiment_ID may be uploaded.

  • The ID number automatically generated by NDA which must be included in the appropriate file when uploading data to link the Experiment Definition to the subject record.

NDA Help Center

Omics

Omics is a collective group of technologies, related to a field of study in Biology such as Genomics or proteomics. 

Experiment Parameters

To define an Omics experiment, provide a meaningful name and select a single molecule. The standard molecules are listed. However, if you are doing proteomic or environmental experiments, simply “Add New” and the new selection will be created. Only one value for molecule is permitted.

Next the technology (box 2) associated with the molecule will be presented along with its application. Again, only one selection is possible. If you wish to see all of NDAR’s options for any one box, Select “Show All”.

Platform

Continue to select the Platform (box 3).

Extraction

Next, the Extraction Protocol (box 4) and Kits (box 5) are presented based upon the Molecule selected and the Processing Protocol (box 6) and Kits (box 7) are presented based upon the Molecule and Technology Application (Box 1 and 2)

Processing

Note that for each of these (boxes 4, 5, 6, and 7) multiple selections are possible.

Additional Information

Lastly, the Software (box 8) and Equipment (box 9) is expected.

 

Once saved, the experiment will be associated with the Collection and by using the returned Experiment_ID, the NDA makes it possible to associate the experiment meta data directly with the data from the experiment.

Frequently Asked Questions

Glossary

  • This button will add all selections to the Filter Cart. 

  • This button will allow you to copy all of the Experiment details as a template for a new experiment. 

  • Adds all data from the current selections in a Collection or NDA Study to the Filter Cart.

  • This button will allow you to return to the Experiments tab. 

NDA Help Center

Collection - Associated Studies

Clicking on the Study Title will open the study details in a new internet browser tab. The Abstract is available for viewing, providing the background explanation of the study, as provided by the Collection Owner. 

Primary v. Secondary Analysis: The Data Usage column will have one of these two choices. An associated study that is listed as being used for Primary Analysis indicates at least some and potentially all of the data used was originally collected by the creator of the NDA Study. Secondary Analysis indicates the Study owner was not involved in the collection of data, and may be used as supporting data. 

Private v. Shared State: Studies that remain private indicate the associated study is only available to users who are able to access the collection. A shared study is accessible to the general public. 

Frequently Asked Questions

  • Studies are associated to the Collection automatically when the data is defined in the Study. 

Glossary

  • A tab in a Collection that lists the NDA Studies that have been created using data from that Collection including both Primary and Secondary Analysis NDA Studies.

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Format should be in the following format: Activity Code, Institute Abbreviation, and Serial Number. Grant Type, Support Year, and Suffix should be excluded. For example, grant 1R01MH123456-01A1 should be entered R01MH123456

Please select an experiment type below

Collection - Use Existing Experiment

To associate an experiment to the current collection, just select an axperiment from the table below then click the associate experiment button to persist your changes (saving the collection is not required). Note that once an experiment has been associated to two or more collections, the experiment will not longer be editable.

The table search feature is case insensitive and targets the experiment id, experiment name and experiment type columns. The experiment id is searched only when the search term entered is a number, and filtered using a startsWith comparison. When the search term is not numeric the experiment name is used to filter the results.

SelectExperiment IdExperiment NameExperiment Type
Created On
24HI-NGS_R1Omics02/16/2011
475MB1-10 (CHOP)Omics06/07/2016
490Illumina Infinium PsychArray BeadChip AssayOmics07/07/2016
501PharmacoBOLD Resting StatefMRI07/27/2016
506PVPREFOmics08/05/2016
509ABC-CT Resting v2EEG08/18/2016
13Comparison of FI expression in Autistic and Neurotypical Homo SapiensOmics12/28/2010
18AGRE/Broad Affymetrix 5.0 Genotype ExperimentOmics01/06/2011
22Stitching PCR SequencingOmics02/14/2011
26ASD_MethylationOmics03/01/2011
29Microarray family 03 (father, mother, sibling)Omics03/24/2011
37Standard paired-end sequencing of BCRsOmics04/19/2011
38Illumina Mate-Pair BCR sequencingOmics04/19/2011
39Custom Jumping LibrariesOmics04/19/2011
40Custom CapBPOmics04/19/2011
41ImmunofluorescenceOmics05/11/2011
43Autism brain sample genotyping, IlluminaOmics05/16/2011
47ARRA Autism Sequencing Collaboration at Baylor. SOLiD 4 SystemOmics08/01/2011
53AGRE Omni1-quadOmics10/11/2011
59AGP genotypingOmics04/03/2012
60Ultradeep 454 sequencing of synaptic genes from postmortem cerebella of individuals with ASD and neurotypical controlsOmics06/23/2012
63Microemulsion PCR and Targeted Resequencing for Variant Detection in ASDOmics07/20/2012
519RestingfMRI11/08/2016
90Genotyped IAN SamplesOmics07/09/2013
91NJLAGS Axiom Genotyping ArrayOmics07/16/2013
93AGP genotyping (CNV)Omics09/06/2013
106Longitudinal Sleep Study. H20 200. Channel set 2EEG11/07/2013
107Longitudinal Sleep Study. H20 200. Channel set 3EEG11/07/2013
108Longitudinal Sleep Study. AURA 200EEG11/07/2013
105Longitudinal Sleep Study. H20 200. Channel set 1EEG11/07/2013
109Longitudinal Sleep Study. AURA 400EEG11/07/2013
116Gene Expression Analysis WG-6Omics01/07/2014
131Jeste Lab UCLA ACEii: Charlie Brown and Sesame Street - Project 1Eye Tracking02/27/2014
132Jeste Lab UCLA ACEii: Animacy - Project 1Eye Tracking02/27/2014
133Jeste Lab UCLA ACEii: Mom Stranger - Project 2Eye Tracking02/27/2014
134Jeste Lab UCLA ACEii: Face Emotion - Project 3Eye Tracking02/27/2014
145AGRE/FMR1_Illumina.JHUOmics04/14/2014
146AGRE/MECP2_Sanger.JHUOmics04/14/2014
147AGRE/MECP2_Junior.JHUOmics04/14/2014
151Candidate Gene Identification in familial AutismOmics06/09/2014
152NJLAGS Whole Genome SequencingOmics07/01/2014
154Math Autism Study - Vinod MenonfMRI07/15/2014
155RestingfMRI07/25/2014
156SpeechfMRI07/25/2014
159EmotionfMRI07/25/2014
160syllable contrastEEG07/29/2014
167School-age naturalistic stimuliEye Tracking09/19/2014
44AGRE/Broad Affymetrix 5.0 Genotype ExperimentOmics06/27/2011
45Exome Sequencing of 20 Sporadic Cases of Autism Spectrum DisorderOmics07/15/2011
78MET GenotypesOmics03/18/2013
Collection - Add Experiment
Add Supporting Documentation
Select File

Please enter the name of the data structure to search or if your definition does not exist, please upload that definition so that it can be appropriately defined for submission. Multiple data structures may be associated with a single Data Expected entry. Please add only one data structure per assessment.

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The Data Expected list for this Collection shows some raw data as missing. Contact the NDA Help Desk with any questions.

Please confirm that you will not be enrolling any more subjects and that all raw data has been collected and submitted.

Collection Updated

Your Collection is now in Data Analysis phase and exempt from biannual submissions. Analyzed data is still expected prior to publication or no later than the project end date.

[CMS] Attention
[CMS] Please confirm that you will not be enrolling any more subjects and that all raw data has been collected and submitted.
[CMS] Error

[CMS]

Unable to change collection phase where targeted enrollment is less than 90%

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You have requested to move the sharing dates for the following assessments:
Data Expected Item Original Sharing Date New Sharing Date

Please provide a reason for this change, which will be sent to the Program Officers listed within this collection:

Explanation must be between 20 and 200 characters in length.

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Shared
Collection Summary Collection Charts
Collection Title Collection Investigators Collection Description
The Role of Germline Mutation and Parental Age in Autism Spectrum Disorders
Jonathan Sebat 
In the new phase of our project, we will apply a whole genome sequencing-based approach to determine the role of ROHs in ASD. We will investigate the nature intrinsic hypermutability and the extrinsic forces, such as paternal age, that influence rates of germline mutation. We will accomplish these goals through the following specific aims: Specific Aim 1 will characterize germline de novo mutations (DNMs) by whole genome sequencing in families. These studies will identify and validate ~8,000 de novo point mutations and structural variants in a sample of 120 trios (60 ASD and 60 controls) and determine the parent of origin of DNMs. Specific Aim 2 will investigate the role of ROHs in ASD. We will identify ROHs based on the regional density of DNMs in the genome, and determine the effects of DNA sequence features on rates of mutation. We will determine the association of ROHs with ASD in the discovery sample and in exome and CNV datasets from an independent sample of 2700 cases and 2700 controls. Specific Aim 3 will characterize the effects of extrinsic factors, including parental age and environment, on genome-wide rates of mutation. We will quantify the effect of paternal age on pathogenic and neutral alleles in sperm and investigate whether some DNMs confer a germline selective advantage. The findings of this study will provide fundamental insights into the genetic basis of autism risk and the genetic mechanism of the observed parental age effects in ASD. We will identify genes that confer significant risk for autism, and we will determine how intrinsic properties of the genome interact with extrinsic forces to determining risk for disease in offspring.
NIMH Data Archive
11/20/2012
Funding Completed
Close Out
Shared
No
$2,589,475.00
1,140
Loading Chart...
NIH - Extramural None

sequencing_files_readme_col_2019.pdf Background Readme for sequencing files Qualified Researchers

R01MH076431-07 The Role of Germline Mutation and Parental Age in Autism Spectrum Disorders 09/01/2012 08/31/2016 330 287 UNIVERSITY OF CALIFORNIA, SAN DIEGO $2,589,475.00

helpcenter.collection.general-tab

NDA Help Center

Collection - General

Fields available for edit on the top portion of the page include:

  • Collection Title
  • Investigators
  • Collection Description
  • Collection Phase
  • Funding Source
  • Clinical Trials

Collection Status: The visibility status of an NDA Collection. Collection Status can be Shared or Private. Collections in Shared status are visible to all users and can be searched in the NDA Query Tool. Private Collections are not visible to NDA users. The Status of an NDA Collection only affects the visibility of information about the Collection (metadata) and does not relate to the status of the record-level research data in the NDA Collection.

Collection Phase: The current status of a research project submitting data to an NDA Collection, based on the timing of the award and/or the data that have been submitted.

  • Pre-Enrollment: The default entry made when the NDA Collection is created.
  • Enrolling: Data have been submitted to the NDA Collection or the NDA Data Expected initial submission date has been reached for at least one data structure category in the NDA Collection.
  • Data Analysis: Subject level data collection for the research project is completed and has been submitted to the NDA Collection. The NDA Collection owner or the NDA Help Desk may set this phase when they’ve confirmed data submission is complete and submitted subject counts match at least 90% of the target enrollment numbers in the NDA Data Expected. Data submission reminders will be turned off for the NDA Collection.
  • Funding Completed: The NIH grant award (or awards) associated with the NDA Collection has reached its end date. NDA Collections in Funding Completed phase are assigned a subphase to indicate the status of data submission.
    • The Data Expected Subphase indicates that NDA expects more data will be submitted
    • The Closeout Subphase indicates the data submission is complete.
    • The Sharing Not Met Subphase indicates that data submission was not completed as expected.

Blinded Clinical Trial Status:

  • This status is set by a Collection Owner and indicates the research project is a double blinded clinical trial. When selected, the public view of Data Expected will show the Data Expected items and the Submission Dates, but the targeted enrollment and subjects submitted counts will not be displayed.
  • Targeted enrollment and subjects submitted counts are visible only to NDA Administrators and to the NDA Collection or as the NDA Collection Owner.
  • When an NDA Collection that is flagged Blinded Clinical Trial reaches the maximum data sharing date for that Data Repository (see https://nda.nih.gov/about/sharing-regimen.html), the embargo on Data Expected information is released.

Funding Source

The organization(s) responsible for providing the funding is listed here.

Supporting Documentation

Users with Submission privileges, as well as Collection Owners, Program Officers, and those withAdministrator privileges, may upload and attach supporting documentation. By default, supporting documentation is shared to the general public, however, the optionis also available tolimit this information to qualified researchers only.

Grant Information

Identifiable details are displayed about the Project of which the Collection was derived from. You may click in the Project Number to view a full report of the Project capturedby the NIH.

Clinical Trials

Any data that is collected to support or further the research of clinical studies will be available here. Collection Owners and those with Administrator privileges may add new clinical trials.

Frequently Asked Questions

  • How do I know when a NDA Collection has been created?
    When a Collection is created by NDA staff and marked as Shared, an email notification will automatically be sent to the PI(s) of the grant(s) associated with the Collection to notify them.
  • How does the NIMH Data Archive (NDA) determine which Permission Group data are submitted into?
    During Collection creation, NDA staff determine the appropriate Permission Group based on the type of data to be submitted, the type of access that will be available to data access users, and the information provided by the Program Officer during grant award.
  • Is a single grant number ever associated with more than one Collection?
    The NDA system does not allow for a single grant to be associated with more than one Collection; therefore, a single grant will not be listed in the Grant Information section of a Collection for more than one Collection.
  • Why is there sometimes more than one grant included in a Collection?
    In general, each Collection is associated with only one grant; however, multiple grants may be associated if the grant has multiple competing segments for the same grant number or if multiple different grants are all working on the same project and it makes sense to hold the data in one Collection (e.g., Cooperative Agreements).

Glossary

  • Actual Enrollment
    Number of human subjects enrolled in an NIH-funded clinical research study. The data is provided in annual progress reports.
  • Administrator Privilege
    A privilege provided to a user associated with an NDA Collection or NDA Study whereby that user can perform a full range of actions including providing privileges to other users.
  • Collection Owner
    Generally, the Collection Owner is the contact PI listed on a grant. Only one NDA user is listed as the Collection owner. Most automated emails are primarily sent to the Collection Owner.
  • Data Use Limitations
    Data Use Limitations (DULs) describe the appropriate secondary use of a dataset and are based on the original informed consent of a research participant. NDA only accepts consent-based data use limitations defined by the NIH Office of Science Policy.
  • Grant
    Provides the grant number(s) for the grant(s) associated with the Collection. The field is a hyperlink so clicking on the Grant number will direct the user to the grant information in the NIH Research Portfolio Online Reporting Tools (RePORT) page.
  • NDA Collection
    A virtual container and organization structure for data and associated documentation from one grant or one large project/consortium. It contains tools for tracking data submission and allows investigators to define a wide array of other elements that provide context for the data, including all general information regarding the data and source project, experimental parameters used to collect any event-based data contained in the Collection, methods, and other supporting documentation. They also allow investigators to link underlying data to an NDA Study, defining populations and subpopulations specific to research aims.
  • Permission Group
    Access to shared record-level data in NDA is provisioned at the level of a Permission Group. NDA Permission Groups consist of one or multiple NDA Collections that contain data with the same subject consents.
  • Collection Phase
    The Collection Phase provides information on data submission as opposed to grant/project completion so while the Collection phase and grant/project phase may be closely related they are often different. Collection users with Administrative Privileges are encouraged to edit the Collection Phase. The Program Officer as listed in eRA (for NIH funded grants) may also edit this field. Changes must be saved by clicking the Save button at the bottom of the page. This field is sortable alphabetically in ascending or descending order. Collection Phase options include:
    • Pre-Enrollment: A grant/project has started, but has not yet enrolled subjects.
    • Enrolling: A grant/project has begun enrolling subjects. Data submission is likely ongoing at this point.
    • Data Analysis: A grant/project has completed enrolling subjects and has completed all data submissions.
    • Funding Completed: A grant/project has reached the project end date.
  • Planned Enrollment
    Number of human subject participants to be enrolled in an NIH-funded clinical research study. The data is provided in competing applications and annual progress reports.
  • NIH Research Initiative
    NDA Collections may be organized by scientific similarity into NIH Research Initiatives, to facilitate query tool user experience. NIH Research Initiatives map to one or multiple Funding Opportunity Announcements.
  • Collection State
    The Collection State indicates whether the Collection is viewable and searchable. Collections can be either Private, Shared, or an Ongoing Study. A Collection that is shared does not necessarily have shared data as the Collection State and state of data are independent of each other. This field can be edited by Collection users with Administrative Privileges and the Program Officer as listed in eRA (for NIH funded grants). Changes must be saved by clicking the Save button at the bottom of the page.
  • Supporting Documentation
    Various documents and materials to enable efficient use of the data by investigators unfamiliar with the project and may include the research protocol, questionnaires, and study manuals.
  • Collection Title
    An editable field with the title of the Collection, which is often the title of the grant associated with the Collection.
  • Total Subjects Shared
    The total number of unique subjects for whom data have been shared and are available for users with permission to access data.
IDNameCreated DateStatusType
76Whole Genome Sequencing in Autism Families01/03/2013ApprovedOmics
466Whole Genome Sequencing05/18/2016ApprovedOmics
563Whole Genome Sequencing at HLI12/29/2016ApprovedOmics
helpcenter.collection.experiments-tab

NDA Help Center

Collection - Experiments

The number of Experiments included is displayed in parentheses next to the tab name. You may download all experiments associated with the Collection via the Download button. You may view individual experiments by clicking the Experiment Name and add them to the Filter Cart via the Add to Cart button.

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may create or edit an Experiment.

Please note: The creation of an NDA Experiment does not necessarily mean that data collected, according to the defined Experiment, has been submitted or shared.

Frequently Asked Questions

  • Can an Experiment be associated with more than one Collection?

    Yes -see the “Copy” button in the bottom left when viewing an experiment. There are two actions that can be performed via this button:

    1. Copy the experiment with intent for modifications.
    2. Associate the experiment to the collection. No modifications can be made to the experiment.

Glossary

  • Experiment Status
    An Experiment must be Approved before data using the associated Experiment_ID may be uploaded.
  • Experiment ID
    The ID number automatically generated by NDA which must be included in the appropriate file when uploading data to link the Experiment Definition to the subject record.

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Shared Data

Data structures with the number of subjects submitted and shared are provided.

Genomics Sample Genomics 1140
Genomics Subject Genomics 1140
helpcenter.collection.shared-data-tab

NDA Help Center

Collection - Shared Data

This tab provides a quick overview of the Data Structure title, Data Type, and Number of Subjects that are currently Shared for the Collection. The information presented in this tab is automatically generated by NDA and cannot be edited. If no information is visible on this tab, this would indicate the Collection does not have shared data or the data is private.

The shared data is available to other researchers who have permission to access data in the Collection's designated Permission Group(s). Use the Download button to get all shared data from the Collection to the Filter Cart.

Frequently Asked Questions

  • How will I know if another researcher uses data that I shared through the NIMH Data Archive (NDA)?
    To see what data your project have submitted are being used by a study, simply go the Associated Studies tab of your collection. Alternatively, you may review an NDA Study Attribution Report available on the General tab.
  • Can I get a supplement to share data from a completed research project?
    Often it becomes more difficult to organize and format data electronically after the project has been completed and the information needed to create a GUID may not be available; however, you may still contact a program staff member at the appropriate funding institution for more information.
  • Can I get a supplement to share data from a research project that is still ongoing?
    Unlike completed projects where researchers may not have the information needed to create a GUID and/or where the effort needed to organize and format data becomes prohibitive, ongoing projects have more of an opportunity to overcome these challenges. Please contact a program staff member at the appropriate funding institution for more information.

Glossary

  • Data Structure
    A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points. Data structures that have been defined in the NDA Data Dictionary are available at https://nda.nih.gov/general-query.html?q=query=data-structure
  • Data Type
    A grouping of data by similar characteristics such as Clinical Assessments, Omics, or Neurosignal data.
  • Shared
    The term 'Shared' generally means available to others; however, there are some slightly different meanings based on what is Shared. A Shared NDA Collection or NDA Study is viewable and searchable publicly regardless of the user's role or whether the user has an NDA account. A Shared Collection or NDA Study does not necessarily mean that data submitted to the Collection or used in the NDA Study have been shared as this is independently determined. Data are shared according the schedule defined in a Collection's Data Expected Tab and/or in accordance with data sharing expectations in the NDA Data Sharing Terms and Conditions. Additionally, Supporting Documentation uploaded to a Collection may be shared independent of whether data are shared, but will only be viewable and accessible if the Collection is Shared.

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Publications

Publications relevant to NDA data are listed below. Most displayed publications have been associated with the grant within Pubmed. Use the "+ New Publication" button to add new publications. Publications relevant/not relevant to data expected are categorized. Relevant publications are then linked to the underlying data by selecting the Create Study link. Study provides the ability to define cohorts, assign subjects, define outcome measures and lists the study type, data analysis and results. Analyzed data and results are expected in this way.

PubMed IDStudyTitleJournalAuthorsDateStatus
33219223Create StudyInferring the molecular and phenotypic impact of amino acid variants with MutPred2.Nature communicationsPejaver, Vikas; Urresti, Jorge; Lugo-Martinez, Jose; Pagel, Kymberleigh A; Lin, Guan Ning; Nam, Hyun-Jun; Mort, Matthew; Cooper, David N; Sebat, Jonathan; Iakoucheva, Lilia M; Mooney, Sean D; Radivojac, PredragNovember 20, 2020Not Determined
31873310Create StudyAutism risk in offspring can be assessed through quantification of male sperm mosaicism.Nature medicineBreuss, Martin W; Antaki, Danny; George, Renee D; Kleiber, Morgan; James, Kiely N; Ball, Laurel L; Hong, Oanh; Mitra, Ileena; Yang, Xiaoxu; Wirth, Sara A; Gu, Jing; Garcia, Camila A B; Gujral, Madhusudan; Brandler, William M; Musaev, Damir; Nguyen, An; McEvoy-Venneri, Jennifer; Knox, Renatta; Sticca, Evan; Botello, Martha Cristina Cancino; Uribe Fenner, Javiera; Pérez, Maria Cárcel; Arranz, Maria; Moffitt, Andrea B; Wang, Zihua; Hervás, Amaia; Devinsky, Orrin; Gymrek, Melissa; Sebat, Jonathan; Gleeson, Joseph GJanuary 2020Not Determined
29696747Create StudyMarker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes.Human mutationGrochowski CM, Gu S, Yuan B, Tcw J, Brennand KJ, Sebat J, Malhotra D, Mccarthy S, Rudolph U, Lindstrand A, Chong Z, Levy DL, Lupski JR, Carvalho CMBApril 2018Not Determined
29674594Create StudyPaternally inherited cis-regulatory structural variants are associated with autism.Science (New York, N.Y.)Brandler, William M; Antaki, Danny; Gujral, Madhusudan; Kleiber, Morgan L; Whitney, Joe; Maile, Michelle S; Hong, Oanh; Chapman, Timothy R; Tan, Shirley; Tandon, Prateek; Pang, Timothy; Tang, Shih C; Vaux, Keith K; Yang, Yan; Harrington, Eoghan; Juul, Sissel; Turner, Daniel J; Thiruvahindrapuram, Bhooma; Kaur, Gaganjot; Wang, Zhuozhi; Kingsmore, Stephen F; Gleeson, Joseph G; Bisson, Denis; Kakaradov, Boyko; Telenti, Amalio; Venter, J Craig; Corominas, Roser; Toma, Claudio; Cormand, Bru; Rueda, Isabel; Guijarro, Silvina; Messer, Karen S; Nievergelt, Caroline M; Arranz, Maria J; Courchesne, Eric; Pierce, Karen; Muotri, Alysson R; Iakoucheva, Lilia M; Hervas, Amaia; Scherer, Stephen W; Corsello, Christina; Sebat, JonathanApril 2018Not Determined
29300834Create StudySV2: accurate structural variation genotyping and de novo mutation detection from whole genomes.Bioinformatics (Oxford, England)Antaki D, Brandler WM, Sebat JMay 2018Not Determined
27018473Study (410)Frequency and Complexity of De Novo Structural Mutation in Autism.American journal of human geneticsBrandler, William M; Antaki, Danny; Gujral, Madhusudan; Noor, Amina; Rosanio, Gabriel; Chapman, Timothy R; Barrera, Daniel J; Lin, Guan Ning; Malhotra, Dheeraj; Watts, Amanda C; Wong, Lawrence C; Estabillo, Jasper A; Gadomski, Therese E; Hong, Oanh; Fajardo, Karin V Fuentes; Bhandari, Abhishek; Owen, Renius; Baughn, Michael; Yuan, Jeffrey; Solomon, Terry; Moyzis, Alexandra G; Maile, Michelle S; Sanders, Stephan J; Reiner, Gail E; Vaux, Keith K; Strom, Charles M; Zhang, Kang; Muotri, Alysson R; Akshoomoff, Natacha; Leal, Suzanne M; Pierce, Karen; Courchesne, Eric; Iakoucheva, Lilia M; Corsello, Christina; Sebat, JonathanApril 2016Relevant
26391891Create StudyThe Influence of Microdeletions and Microduplications of 16p11.2 on Global Transcription Profiles.Journal of child neurologyKusenda M, Vacic V, Malhotra D, Rodgers L, Pavon K, Meth J, Kumar RA, Christian SL, Peeters H, Cho SS, Addington A, Rapoport JL, Sebat JDecember 2015Not Determined
25587659Create StudyFrom de novo mutations to personalized therapeutic interventions in autism.Annual review of medicineBrandler, William M; Sebat, Jonathan2015Not Relevant
24722188Create StudyProtein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.Nature communicationsCorominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, et al.2014Not Relevant
23260136Study (322)Whole-genome sequencing in autism identifies hot spots for de novo germline mutation.CellMichaelson, Jacob J; Shi, Yujian; Gujral, Madhusudan; Zheng, Hancheng; Malhotra, Dheeraj; Jin, Xin; Jian, Minghan; Liu, Guangming; Greer, Douglas; Bhandari, Abhishek; Wu, Wenting; Corominas, Roser; Peoples, Aine; Koren, Amnon; Gore, Athurva; Kang, Shuli; Lin, Guan Ning; Estabillo, Jasper; Gadomski, Therese; Singh, Balvindar; Zhang, Kun; Akshoomoff, Natacha; Corsello, Christina; McCarroll, Steven; Iakoucheva, Lilia M; Li, Yingrui; Wang, Jun; Sebat, JonathanDecember 21, 2012Relevant
23176822Create StudyDifferential relationship of DNA replication timing to different forms of human mutation and variation.American journal of human geneticsKoren, Amnon; Polak, Paz; Nemesh, James; Michaelson, Jacob J; Sebat, Jonathan; Sunyaev, Shamil R; McCarroll, Steven ADecember 7, 2012Not Determined
helpcenter.collection.publications-tab

NDA Help Center

Collection - Publications

The number of Publications is displayed in parentheses next to the tab name. Clicking on any of the Publication Titles will open the Publication in a new internet browsing tab.

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may mark a publication as either Relevant or Not Relevant in the Status column.

Frequently Asked Questions

  • How can I determine if a publication is relevant?
    Publications are considered relevant to a collection when the data shared is directly related to the project or collection.
  • Where does the NDA get the publications?
    PubMed, an online library containing journals, articles, and medical research. Sponsored by NiH and National Library of Medicine (NLM).

Glossary

  • Create Study
    A link to the Create an NDA Study page that can be clicked to start creating an NDA Study with information such as the title, journal and authors automatically populated.
  • Not Determined Publication
    Indicates that the publication has not yet been reviewed and/or marked as Relevant or Not Relevant so it has not been determined whether an NDA Study is expected.
  • Not Relevant Publication
    A publication that is not based on data related to the aims of the grant/project associated with the Collection or not based on any data such as a review article and, therefore, an NDA Study is not expected to be created.
  • PubMed
    PubMed provides citation information for biomedical and life sciences publications and is managed by the U.S. National Institutes of Health's National Library of Medicine.
  • PubMed ID
    The PUBMed ID is the unique ID number for the publication as recorded in the PubMed database.
  • Relevant Publication
    A publication that is based on data related to the aims of the grant/project associated with the Collection and, therefore, an NDA Study is expected to be created.

Relevant Publications
PubMed IDStudyTitleJournalAuthorsDate
No records found.
Data Expected List: Mandatory Data Structures

These data structures are mandatory for your NDA Collection. Please update the Targeted Enrollment number to accurately represent the number of subjects you expect to submit for the entire study.

Data ExpectedTargeted EnrollmentInitial SubmissionSubjects SharedStatus
No Mandatory Data Expected

You can use "Add New Data Expected" to add exsiting structures and create your project's list. However, this is also the method you can use to request new structures be created for your project. When adding the Data Expected item, if the structure already exists you can locate it and specify your dates and enrollment. To add a new structure and request it be defined in the Data Dictionary, select Upload Definition and attach the definition or material needed to create it, including manual, codebooks, forms, etc. If you have multiple files, please upload a zipped archive containing them all.

Expected dates should be selected based on the standard Data Sharing Regimen and are restricted to within date ranges based on the project start and end dates.

Data Expected List: Data Structures per Research Aims

These data structures are specific to your research aims and should list all data structures in which data will be collected and submitted for this NDA Collection. Please update the Targeted Enrollment number to accurately represent the number of subjects you expect to submit for the entire study.

Data ExpectedTargeted EnrollmentInitial SubmissionSubjects SharedStatus
Genomics/omics info icon
37107/15/2013
1,140
Approved
Structure not yet defined
No Status history for this Data Expected has been recorded yet
helpcenter.collection.data-expected-tab

NDA Help Center

Collection - Data Expected

The Data Expected tab displays the list of all data that NDA expects to receive in association with the Collection as defined by the contributing researcher, as well as the dates for the expected initial upload of the data, and when it is first expected to be shared, or with the research community. Above the primary table of Data Expected, any publications determined to be relevant to the data within the Collection are also displayed - members of the contributing research group can use these to define NDA Studies, connecting those papers to underlying data in NDA.

The tab is used both as a reference for those accessing shared data, providing information on what is expected and when it will be shared, and as the primary tracking mechanism for contributing projects. It is used by both contributing primary researchers, secondary researchers, and NIH Program and Grants Management staff.

Contributing researchers just getting started on their project will need to define this list by adding all of the items they are collecting under their grant and setting their schedule according to the NDA Data Sharing Regimen. If you fall into this category, you can begin by clicking "Add New Data Expected" and selecting which data structures you will be using, saving the page after each change, or requesting new structures by adding and naming a new item, providing any materials NDA Data Dictionary Curators can use to help define your structure. For more information see the tutorial on creating Data Expected.

If you are a contributing researcher creating this list for the first time, or making changes to the list as your project progress, please note the following:

  • Although items you add to the list and changes you make are displayed, they are not committed to the system until you Save the entire page using the "Save"" button at the bottom of your screen. Please Save after every change to ensure none of your work is lost.
  • If you attempt to add a new structure, the title you provide must be unique - if another structure exists with the same name your change will fail.
  • Adding a new structure to this list is the only way to request the creation of a new Data Dictionary definition.

Frequently Asked Questions

  • What is an NDA Data Structure?
    An NDA Data Structure is comprised of multiple Data Elements to make up an electronic definition of an assessment, measure, questionnaire, etc will have a corresponding Data Structure.
  • What is the NDA Data Dictionary?
    The NDA Data Dictionary is comprised of electronic definitions known as Data Structures.

Glossary

  • Analyzed Data
    Data specific to the primary aims of the research being conducted (e.g. outcome measures, other dependent variables, observations, laboratory results, analyzed images, volumetric data, etc.) including processed images.
  • Data Item
    Items listed on the Data Expected list in the Collection which may be an individual and discrete Data Structure, Data Structure Category, or Data Structure Group.
  • Data Structure
    A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points. Data structures that have been defined in the NDA Data Dictionary are available at https://nda.nih.gov/general-query.html?q=query=data-structure
  • Data Structure Category
    An NDA term describing the affiliation of a Data Structure to a Category, which may be disease/disorder or diagnosis related (Depression, ADHD, Psychosis), specific to data type (MRI, eye tracking, omics), or type of data (physical exam, IQ).
  • Data Structure Group
    A Data Item listed on the Data Expected tab of a Collection that indicates a group of Data Structures (e.g., ADOS or SCID) for which data may be submitted instead of a specific Data Structure identified by version, module, edition, etc. For example, the ADOS Data Structure Category includes every ADOS Data Structure such as ADOS Module 1, ADOS Module 2, ADOS Module 1 - 2nd Edition, etc. The SCID Data Structure Group includes every SCID Data Structure such as SCID Mania, SCID V Mania, SCID PTSD, SCID-V Diagnosis, and more.
  • Evaluated Data
    A new Data Structure category, Evaluated Data is analyzed data resulting from the use of computational pipelines in the Cloud and can be uploaded directly back to a miNDAR database. Evaluated Data is expected to be listed as a Data Item in the Collection's Data Expected Tab.
  • Imaging Data
    Imaging+ is an NDA term which encompasses all imaging related data including, but not limited to, images (DTI, MRI, PET, Structural, Spectroscopy, etc.) as well as neurosignal data (EEG, fMRI, MEG, EGG, eye tracking, etc.) and Evaluated Data.
  • Initial Share Date
    Initial Submission and Initial Share dates should be populated according to the NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data will be shared with authorized users upon publication (via an NDA Study) or 1-2 years after the grant end date specified on the first Notice of Award, as defined in the applicable Data Sharing Terms and Conditions.
  • Initial Submission Date
    Initial Submission and Initial Share dates should be populated according to these NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data for all subjects is not expected on the Initial Submission Date and modifications may be made as necessary based on the project's conduct.
  • Research Subject and Pedigree
    An NDA created Data Structure used to convey basic information about the subject such as demographics, pedigree (links family GUIDs), diagnosis/phenotype, and sample location that are critical to allow for easier querying of shared data.
  • Submission Cycle
    The NDA has two Submission Cycles per year - January 15 and July 15.
  • Submission Exemption
    An interface to notify NDA that data may not be submitted during the upcoming/current submission cycle.

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Associated Studies

Studies that have been defined using data from a Collection are important criteria to determine the value of data shared. The number of subjects column displays the counts from this Collection that are included in a Study, out of the total number of subjects in that study. The Data Use column represents whether or not the study is a primary analysis of the data or a secondary analysis. State indicates whether the study is private or shared with the research community.

Study NameAbstractCollection/Study SubjectsData UsageState
Paternally inherited noncoding structural variants contribute to autismThe genetic architecture of autism spectrum disorder (ASD) is known to consist of contributions from gene-disrupting de novo mutations and common variants of modest effect. We hypothesize that the unexplained heritability of ASD also includes rare inherited variants with intermediate effects. We investigated the genome-wide distribution and functional impact of structural variants (SVs) through whole genome analysis (>30X coverage) of 3,169 subjects from 829 families affected by ASD. Genes that are intolerant to inactivating variants in the exome aggregation consortium (ExAC) were depleted for SVs in parents, specifically within fetal-brain promoters, UTRs and exons. Rare paternally-inherited SVs that disrupt promoters or UTRs were over-transmitted to cases (P = 0.0013) and not to their typically-developing siblings. Protein-coding SVs were also associated with ASD (P = 0.0025). Recurrent functional noncoding deletions implicate the gene LEO1 in ASD. Our results establish that rare inherited SVs predispose children to ASD, with differing contributions from each parent.1098/3170Primary AnalysisShared
Frequency and Complexity of De Novo Structural Mutation in AutismGenetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising 11 different classes. We found a high diversity of de novo mutations, the majority of which were undetectable by previous methods. In addition, we observed complex mutation clusters where combinations of de novo SVs, nucleotide substitutions, and indels occurred as a single event. We estimate a high rate of structural mutation in humans (20%) and propose that genetic risk for ASD is attributable to an elevated frequency of gene-disrupting de novo SVs, but not an elevated rate of genome rearrangement.235/235Primary AnalysisShared
Title of StudyAbstract41/45Primary AnalysisPrivate
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation.De novo mutation plays an important role in autism spectrum disorders (ASDs). Notably, pathogenic copy number variants (CNVs) are characterized by high mutation rates. We hypothesize that hypermutability is a property of ASD genes and may also include nucleotide-substitution hot spots. We investigated global patterns of germline mutation by whole-genome sequencing of monozygotic twins concordant for ASD and their parents. Mutation rates varied widely throughout the genome (by 100-fold) and could be explained by intrinsic characteristics of DNA sequence and chromatin structure. Dense clusters of mutations within individual genomes were attributable to compound mutation or gene conversion. Hypermutability was a characteristic of genes involved in ASD and other diseases. In addition, genes impacted by mutations in this study were associated with ASD in independent exome-sequencing data sets. Our findings suggest that regional hypermutation is a significant factor shaping patterns of genetic variation and disease risk in humans.41/41Primary AnalysisShared
* Data not on individual level
helpcenter.collection.associated-studies-tab

NDA Help Center

Collection - Associated Studies

Clicking on the Study Title will open the study details in a new internet browser tab. The Abstract is available for viewing, providing the background explanation of the study, as provided by the Collection Owner.

Primary v. Secondary Analysis: The Data Usage column will have one of these two choices. An associated study that is listed as being used for Primary Analysis indicates at least some and potentially all of the data used was originally collected by the creator of the NDA Study. Secondary Analysis indicates the Study owner was not involved in the collection of data, and may be used as supporting data.

Private v. Shared State: Studies that remain private indicate the associated study is only available to users who are able to access the collection. A shared study is accessible to the general public.

Frequently Asked Questions

  • How do I associate a study to my collection?
    Studies are associated to the Collection automatically when the data is defined in the Study.

Glossary

  • Associated Studies Tab
    A tab in a Collection that lists the NDA Studies that have been created using data from that Collection including both Primary and Secondary Analysis NDA Studies.
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