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
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
76Whole Genome Sequencing in Autism FamiliesOmics01/03/2013
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
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Collection Summary Collection Charts
Collection Title Collection Investigators Collection Description
Autism Genetics, Phase II: Increasing Representation of Human Diversity
Daniel Geschwind 
Autism Spectrum Disorder (ASD) is a common, often devastating neuropsychiatric condition with largely unknown pathophysiology. Although ASD has a multifactorial etiology, it encompasses a large genetic component. The investigators in this proposal aim to continue and enhance our collaborative effort that has produced significant advances in our understanding of ASD over the last four years and generated highly successful, open data and biomaterials resources for the research community, the NIMH Genetics Initiative and the Autism Genetic Resource Exchange (AGRE). Our Network has met or exceeded our original aims. We have built patient resources for research, identified rare and common ASD susceptibility alleles, defined models of ASD genetic susceptibility, provided evidence for convergent pathophysiology, and led development of animal and cell culture models. Here we propose to take a major new direction, filling a significant gap in ASD research, by recruiting underserved subjects of self-reported African ancestry (African-American; AA), an important population that has not previously been well-represented in ASD genetics research. Our Network involves six research sites and the AGRE DCC, collaborating in a systematic, comprehensive investigation of ASD genetics in order to identify rare mutations, chromosomal abnormalities, and common variation contributing to ASD susceptibility in the AA population. Specifically, we will enrich existing resources by recruiting at least 600 AA probands and additional family members. Our recruitment plan includes an embedded health disparities project that will evaluate access to care for AAs with ASD and clarify factors influencing participation of AA individuals in genetic research. We will employ novel methods to define the ancestral origin of specific chromosomal segments and ascertain the background on which susceptibility alleles occur. We will perform follow up GWA on ASD-related endophenotypes or co-variates, such as language delay, sex and head circumference. In parallel, we will conduct whole exome sequencing (WES) and analysis of copy number variation (CNV) using 2.5M SNP arrays yielding high resolution molecular karyotypes and providing a resource on genome-wide CNV and coding sequence variation (SNV) in ASD. Gene expression profiling and network analysis will be used to prioritize variants. Genetic risk factors identified in the mostly European samples will be tested for association in the AA sample to determine whether these cohorts share the same genetic risk factors, using a sample size providing power to replicate previous associations and to identify rare, recurrent CNV and SNV. The observation of new forms or different population frequencies of ASD-related variation in this sample as well as the sharing of most CNV and SNV with other cohorts are both outcomes that will have great significance for future studies and clinical care. As has been our practice, our Network will make all phenotypic and genotype data accessible via the internet on a rolling basis, further enhancing the value of this resource to the community. In addition to the behavioral and genomic data in our NDA collection, whole-genome sequence generated for our cohort in collaboration with the Center for Common Disease Genomics (CCDG) can be found via dbGaP study accession number phs002042.v1.p1 and will be distributed through AnVIL (https://anvilproject.org/data).
NIMH Data Archive
05/31/2013
Autism Centers of Excellence (ACE)
Funding Completed
Close Out
Shared
No
$3,168,451.00
5,113
Loading Chart...
NIH - Extramural None


R01MH100027-06 Autism Genetics, Phase II: Increasing Representation of Human Diversity 03/25/2013 02/28/2018 3360 1870 UNIVERSITY OF CALIFORNIA LOS ANGELES $3,168,451.00

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
321Omni2.5-806/10/2015ApprovedOmics
3262013-489 targeted linkage peaks06/12/2015ApprovedOmics
474Single All AGRE, MBV33-10 (CHOP)06/07/2016ApprovedOmics
475MB1-10 (CHOP)06/07/2016ApprovedOmics
517Exomes 2014-407_UCLA; 2014-207_UCSF; 2016-912311/05/2016ApprovedOmics
1712Whole-genome sequence (CCDG)03/15/2021ApprovedOmics
1830Illumina Global Screening Array08/02/2021ApprovedOmics
1980Whole-exome sequence: Kapa HyperPrep, SeqCAP EZ Human Exome v303/24/2022ApprovedOmics
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.

ACE Family Medical History Clinical Assessments 452
ACE Subject Physical Exam Clinical Assessments 445
Diagnostic Odyssey Instrument Clinical Assessments 479
Genomics Genetic Test Genomics 185
Genomics Sample Genomics 4073
Genomics Subject Genomics 4073
Mullen Scales of Early Learning Clinical Assessments 20
Peabody Picture Vocabulary Test, Fourth Edition-Form A Clinical Assessments 89
Ravens Coloured Progressive Matrices (CPM) Clinical Assessments 275
Ravens Standard Progressive Matrices Clinical Assessments 499
Research Subject Clinical Assessments 1571
SRS-2. Adult, Preschool and School Age Clinical Assessments 974
Social Communication Questionnaire (SCQ) - Current Form Clinical Assessments 51
Social Communication Questionnaire (SCQ) - Lifetime Clinical Assessments 478
Vineland-II - Survey Form (2005) Clinical Assessments 445
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
35982160Create StudyRare coding variation provides insight into the genetic architecture and phenotypic context of autism.Nature geneticsFu, Jack M; Satterstrom, F Kyle; Peng, Minshi; Brand, Harrison; Collins, Ryan L; Dong, Shan; Wamsley, Brie; Klei, Lambertus; Wang, Lily; Hao, Stephanie P; Stevens, Christine R; Cusick, Caroline; Babadi, Mehrtash; Banks, Eric; Collins, Brett; Dodge, Sheila; Gabriel, Stacey B; Gauthier, Laura; Lee, Samuel K; Liang, Lindsay; Ljungdahl, Alicia; Mahjani, Behrang; Sloofman, Laura; Smirnov, Andrey N; Barbosa, Mafalda; Betancur, Catalina; Brusco, Alfredo; Chung, Brian H Y; Cook, Edwin H; Cuccaro, Michael L; Domenici, Enrico; Ferrero, Giovanni Battista; Gargus, J Jay; Herman, Gail E; Hertz-Picciotto, Irva; Maciel, Patricia; Manoach, Dara S; Passos-Bueno, Maria Rita; Persico, Antonio M; Renieri, Alessandra; Sutcliffe, James S; Tassone, Flora; Trabetti, Elisabetta; Campos, Gabriele; Cardaropoli, Simona; Carli, Diana; Chan, Marcus C Y; Fallerini, Chiara; Giorgio, Elisa; Girardi, Ana Cristina; Hansen-Kiss, Emily; Lee, So Lun; Lintas, Carla; Ludena, Yunin; Nguyen, Rachel; Pavinato, Lisa; Pericak-Vance, Margaret; Pessah, Isaac N; Schmidt, Rebecca J; Smith, Moyra; Costa, Claudia I S; Trajkova, Slavica; Wang, Jaqueline Y T; Yu, Mullin H C; Autism Sequencing Consortium (ASC); Broad Institute Center for Common Disease Genomics (Broad-CCDG); iPSYCH-BROAD Consortium; Cutler, David J; De Rubeis, Silvia; Buxbaum, Joseph D; Daly, Mark J; Devlin, Bernie; Roeder, Kathryn; Sanders, Stephan J; Talkowski, Michael ESeptember 1, 2022Not Determined
34932941Create StudyOxytocin normalizes altered circuit connectivity for social rescue of the Cntnap2 knockout mouse.NeuronChoe, Katrina Y; Bethlehem, Richard A I; Safrin, Martin; Dong, Hongmei; Salman, Elena; Li, Ying; Grinevich, Valery; Golshani, Peyman; DeNardo, Laura A; Peñagarikano, Olga; Harris, Neil G; Geschwind, Daniel HMarch 2, 2022Not Determined
34553489Create StudyRethinking autism spectrum disorder assessment for children during COVID-19 and beyond.Autism research : official journal of the International Society for Autism ResearchZwaigenbaum, Lonnie; Bishop, Somer; Stone, Wendy L; Ibanez, Lisa; Halladay, Alycia; Goldman, Sylvie; Kelly, Amy; Klaiman, Cheryl; Lai, Meng-Chuan; Miller, Meghan; Saulnier, Celine; Siper, Paige; Sohl, Kristin; Warren, Zachary; Wetherby, AmyNovember 1, 2021Not Determined
34313757Create StudyThree decades of ASD genetics: building a foundation for neurobiological understanding and treatment.Human molecular geneticsEyring, Katherine W; Geschwind, Daniel HOctober 1, 2021Not Determined
34172755Create StudyNeuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders.Nature communicationsHu, Benxia; Won, Hyejung; Mah, Won; Park, Royce B; Kassim, Bibi; Spiess, Keeley; Kozlenkov, Alexey; Crowley, Cheynna A; Pochareddy, Sirisha; PsychENCODE Consortium; Li, Yun; Dracheva, Stella; Sestan, Nenad; Akbarian, Schahram; Geschwind, Daniel HJune 25, 2021Not Determined
33272361Create StudyPolygenicity in Psychiatry-Like It or Not, We Have to Understand It.Biological psychiatryGandal, Michael J; Geschwind, Daniel HJanuary 1, 2021Not Determined
33009972Create StudyVisual Traces of Language Acquisition in Toddlers with Autism Spectrum Disorder During the Second Year of Life.Journal of autism and developmental disordersHabayeb, Serene; Tsang, Tawny; Saulnier, Celine; Klaiman, Cheryl; Jones, Warren; Klin, Ami; Edwards, Laura AJuly 1, 2021Not Determined
32839243Create StudyTiming of the Diagnosis of Autism in African American Children.PediatricsConstantino, John N; Abbacchi, Anna M; Saulnier, Celine; Klaiman, Cheryl; Mandell, David S; Zhang, Yi; Hawks, Zoe; Bates, Julianna; Klin, Ami; Shattuck, Paul; Molholm, Sophie; Fitzgerald, Robert; Roux, Anne; Lowe, Jennifer K; Geschwind, Daniel HSeptember 2020Not Determined
32634676Create StudyFunctional genomics links genetic origins to pathophysiology in neurodegenerative and neuropsychiatric disease.Current opinion in genetics & developmentWamsley, Brie; Geschwind, Daniel HDecember 1, 2020Not Determined
32027831Create StudyHigh-Risk, High-Reward Genetics in ASD.NeuronCastellani, Christina A; Arking, Dan EFebruary 5, 2020Not Determined
31835028Create StudyGenomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders.CellCross-Disorder Group of the Psychiatric Genomics Consortium. Electronic address: plee0@mgh.harvard.edu; Cross-Disorder Group of the Psychiatric Genomics ConsortiumDecember 12, 2019Not Determined
31626773Create StudyGenetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms.CellWalker, Rebecca L; Ramaswami, Gokul; Hartl, Christopher; Mancuso, Nicholas; Gandal, Michael J; de la Torre-Ubieta, Luis; Pasaniuc, Bogdan; Stein, Jason L; Geschwind, Daniel HOctober 17, 2019Not Determined
31548702Create StudyA framework for the investigation of rare genetic disorders in neuropsychiatry.Nature medicineSanders, Stephan J; Sahin, Mustafa; Hostyk, Joseph; Thurm, Audrey; Jacquemont, Sebastien; Avillach, Paul; Douard, Elise; Martin, Christa L; Modi, Meera E; Moreno-De-Luca, Andres; Raznahan, Armin; Anticevic, Alan; Dolmetsch, Ricardo; Feng, Guoping; Geschwind, Daniel H; Glahn, David C; Goldstein, David B; Ledbetter, David H; Mulle, Jennifer G; Pasca, Sergiu P; Samaco, Rodney; Sebat, Jonathan; Pariser, Anne; Lehner, Thomas; Gur, Raquel E; Bearden, Carrie EOctober 1, 2019Not Determined
31303374Create StudyA Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.NeuronPolioudakis, Damon; de la Torre-Ubieta, Luis; Langerman, Justin; Elkins, Andrew G; Shi, Xu; Stein, Jason L; Vuong, Celine K; Nichterwitz, Susanne; Gevorgian, Melinda; Opland, Carli K; Lu, Daning; Connell, William; Ruzzo, Elizabeth K; Lowe, Jennifer K; Hadzic, Tarik; Hinz, Flora I; Sabri, Shan; Lowry, William E; Gerstein, Mark B; Plath, Kathrin; Geschwind, Daniel HSeptember 2019Not Determined
31202490Create StudyDomain-Specific Cognitive Impairments in Humans and Flies With Reduced CYFIP1 Dosage.Biological psychiatryWoo YJ, Kanellopoulos AK, Hemati P, Kirschen J, Nebel RA, Wang T, Bagni C, Abrahams BSAugust 2019Not Determined
31150625Create StudyHuman Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice.CellSharon, Gil; Cruz, Nikki Jamie; Kang, Dae-Wook; Gandal, Michael J; Wang, Bo; Kim, Young-Mo; Zink, Erika M; Casey, Cameron P; Taylor, Bryn C; Lane, Christianne J; Bramer, Lisa M; Isern, Nancy G; Hoyt, David W; Noecker, Cecilia; Sweredoski, Michael J; Moradian, Annie; Borenstein, Elhanan; Jansson, Janet K; Knight, Rob; Metz, Thomas O; Lois, Carlos; Geschwind, Daniel H; Krajmalnik-Brown, Rosa; Mazmanian, Sarkis KMay 2019Not Determined
31056284Create StudySelenium Drives a Transcriptional Adaptive Program to Block Ferroptosis and Treat Stroke.CellAlim I, Caulfield JT, Chen Y, Swarup V, Geschwind DH, Ivanova E, Seravalli J, Ai Y, Sansing LH, Ste Marie EJ, Hondal RJ, Mukherjee S, Cave JW, Sagdullaev BT, Karuppagounder SS, Ratan RRMay 2019Not Determined
30901538Create StudyDefining the Genetic, Genomic, Cellular, and Diagnostic Architectures of Psychiatric Disorders.CellSullivan PF, Geschwind DHMarch 2019Not Determined
30545856Create StudyTranscriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder.Science (New York, N.Y.)Gandal, Michael J; Zhang, Pan; Hadjimichael, Evi; Walker, Rebecca L; Chen, Chao; Liu, Shuang; Won, Hyejung; van Bakel, Harm; Varghese, Merina; Wang, Yongjun; Shieh, Annie W; Haney, Jillian; Parhami, Sepideh; Belmont, Judson; Kim, Minsoo; Moran Losada, Patricia; Khan, Zenab; Mleczko, Justyna; Xia, Yan; Dai, Rujia; Wang, Daifeng; Yang, Yucheng T; Xu, Min; Fish, Kenneth; Hof, Patrick R; Warrell, Jonathan; Fitzgerald, Dominic; White, Kevin; Jaffe, Andrew E; PsychENCODE Consortium; Peters, Mette A; Gerstein, Mark; Liu, Chunyu; Iakoucheva, Lilia M; Pinto, Dalila; Geschwind, Daniel HDecember 2018Not Relevant
30111840Create StudyAutism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing.NatureParras A, Anta H, Santos-Galindo M, Swarup V, Elorza A, Nieto-González JL, Picó S, Hernández IH, Díaz-Hernández JI, Belloc E, Rodolosse A, Parikshak NN, Peñagarikano O, Fernández-Chacón R, Irimia M, Navarro P, Geschwind DH, Méndez R, Lucas JJAugust 2018Not Relevant
30008175Create StudyExome sequencing of 85 Williams-Beuren syndrome cases rules out coding variation as a major contributor to remaining variance in social behavior.Molecular genetics & genomic medicineKopp ND, Parrish PCR, Lugo M, Dougherty JD, Kozel BASeptember 2018Not Relevant
29930110Create StudyAnalysis of shared heritability in common disorders of the brain.Science (New York, N.Y.)Brainstorm Consortium; Anttila, Verneri; Bulik-Sullivan, Brendan; Finucane, Hilary K; Walters, Raymond K; Bras, Jose; Duncan, Laramie; Escott-Price, Valentina; Falcone, Guido J; Gormley, Padhraig; Malik, Rainer; Patsopoulos, Nikolaos A; Ripke, Stephan; Wei, Zhi; Yu, Dongmei; Lee, Phil H; Turley, Patrick; Grenier-Boley, Benjamin; Chouraki, Vincent; Kamatani, Yoichiro; Berr, Claudine; Letenneur, Luc; Hannequin, Didier; Amouyel, Philippe; Boland, Anne; Deleuze, Jean-François; Duron, Emmanuelle; Vardarajan, Badri N; Reitz, Christiane; Goate, Alison M; Huentelman, Matthew J; Kamboh, M Ilyas; Larson, Eric B; Rogaeva, Ekaterina; St George-Hyslop, Peter; Hakonarson, Hakon; Kukull, Walter A; Farrer, Lindsay A; Barnes, Lisa L; Beach, Thomas G; Demirci, F Yesim; Head, Elizabeth; Hulette, Christine M; Jicha, Gregory A; Kauwe, John S K; Kaye, Jeffrey A; Leverenz, James B; Levey, Allan I; Lieberman, Andrew P; Pankratz, Vernon S; Poon, Wayne W; Quinn, Joseph F; Saykin, Andrew J; Schneider, Lon S; Smith, Amanda G; Sonnen, Joshua A; Stern, Robert A; Van Deerlin, Vivianna M; Van Eldik, Linda J; Harold, Denise; Russo, Giancarlo; Rubinsztein, David C; Bayer, Anthony; Tsolaki, Magda; Proitsi, Petra; Fox, Nick C; Hampel, Harald; Owen, Michael J; Mead, Simon; Passmore, Peter; Morgan, Kevin; Nöthen, Markus M; Rossor, Martin; Lupton, Michelle K; Hoffmann, Per; Kornhuber, Johannes; Lawlor, Brian; McQuillin, Andrew; Al-Chalabi, Ammar; Bis, Joshua C; Ruiz, Agustin; Boada, Mercè; Seshadri, Sudha; Beiser, Alexa; Rice, Kenneth; van der Lee, Sven J; De Jager, Philip L; Geschwind, Daniel H; Riemenschneider, Matthias; Riedel-Heller, Steffi; Rotter, Jerome I; Ransmayr, Gerhard; Hyman, Bradley T; Cruchaga, Carlos; Alegret, Montserrat; Winsvold, Bendik; Palta, Priit; Farh, Kai-How; Cuenca-Leon, Ester; Furlotte, Nicholas; Kurth, Tobias; Ligthart, Lannie; Terwindt, Gisela M; Freilinger, Tobias; Ran, Caroline; Gordon, Scott D; Borck, Guntram; Adams, Hieab H H; Lehtimäki, Terho; Wedenoja, Juho; Buring, Julie E; Schürks, Markus; Hrafnsdottir, Maria; Hottenga, Jouke-Jan; Penninx, Brenda; Artto, Ville; Kaunisto, Mari; Vepsäläinen, Salli; Martin, Nicholas G; Montgomery, Grant W; Kurki, Mitja I; Hämäläinen, Eija; Huang, Hailiang; Huang, Jie; Sandor, Cynthia; Webber, Caleb; Muller-Myhsok, Bertram; Schreiber, Stefan; Salomaa, Veikko; Loehrer, Elizabeth; Göbel, Hartmut; Macaya, Alfons; Pozo-Rosich, Patricia; Hansen, Thomas; Werge, Thomas; Kaprio, Jaakko; Metspalu, Andres; Kubisch, Christian; Ferrari, Michel D; Belin, Andrea C; van den Maagdenberg, Arn M J M; Zwart, John-Anker; Boomsma, Dorret; Eriksson, Nicholas; Olesen, Jes; Chasman, Daniel I; Nyholt, Dale R; Avbersek, Andreja; Baum, Larry; Berkovic, Samuel; Bradfield, Jonathan; Buono, Russell J; Catarino, Claudia B; Cossette, Patrick; De Jonghe, Peter; Depondt, Chantal; Dlugos, Dennis; Ferraro, Thomas N; French, Jacqueline; Hjalgrim, Helle; Jamnadas-Khoda, Jennifer; Kälviäinen, Reetta; Kunz, Wolfram S; Lerche, Holger; Leu, Costin; Lindhout, Dick; Lo, Warren; Lowenstein, Daniel; McCormack, Mark; Møller, Rikke S; Molloy, Anne; Ng, Ping-Wing; Oliver, Karen; Privitera, Michael; Radtke, Rodney; Ruppert, Ann-Kathrin; Sander, Thomas; Schachter, Steven; Schankin, Christoph; Scheffer, Ingrid; Schoch, Susanne; Sisodiya, Sanjay M; Smith, Philip; Sperling, Michael; Striano, Pasquale; Surges, Rainer; Thomas, G Neil; Visscher, Frank; Whelan, Christopher D; Zara, Federico; Heinzen, Erin L; Marson, Anthony; Becker, Felicitas; Stroink, Hans; Zimprich, Fritz; Gasser, Thomas; Gibbs, Raphael; Heutink, Peter; Martinez, Maria; Morris, Huw R; Sharma, Ma (see original citation for additional authors)June 22, 2018Not Determined
29439242Create StudyShared molecular neuropathology across major psychiatric disorders parallels polygenic overlap.Science (New York, N.Y.)Gandal, Michael J; Haney, Jillian R; Parikshak, Neelroop N; Leppa, Virpi; Ramaswami, Gokul; Hartl, Chris; Schork, Andrew J; Appadurai, Vivek; Buil, Alfonso; Werge, Thomas M; Liu, Chunyu; White, Kevin P; CommonMind Consortium; PsychENCODE Consortium; iPSYCH-BROAD Working Group; Horvath, Steve; Geschwind, Daniel HFebruary 2018Not Relevant
29307494Create StudyThe Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis.Cellde la Torre-Ubieta, Luis; Stein, Jason L; Won, Hyejung; Opland, Carli K; Liang, Dan; Lu, Daning; Geschwind, Daniel HJanuary 2018Not Relevant
29066808Create StudyCross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder.Nature communicationsAndrews, Shan V; Ellis, Shannon E; Bakulski, Kelly M; Sheppard, Brooke; Croen, Lisa A; Hertz-Picciotto, Irva; Newschaffer, Craig J; Feinberg, Andrew P; Arking, Dan E; Ladd-Acosta, Christine; Fallin, M DanieleOctober 24, 2017Not Determined
29057378Create StudySystems biology in the central nervous system: a brief perspective on essential recent advancements.Current opinion in systems biologyDougherty, Joseph D; Yang, Chengran; Lake, Allison MJune 2017Not Relevant
29020636Create StudySelf-Organized Cerebral Organoids with Human-Specific Features Predict Effective Drugs to Combat Zika Virus Infection.Cell reportsWatanabe M, Buth JE, Vishlaghi N, De La Torre-Ubieta L, Taxidis J, Khakh BS, Coppola G, Pearson CA, Yamauchi K, Gong D, Dai X, Damoiseaux R, Aliyari R, Liebscher S, Schenke-Layland K, Caneda C, Huang EJ, Zhang Y, Cheng G, Geschwind DH, Golshani P, Sun R, Novitch BGOctober 2017Not Relevant
28540026Create StudyMeta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia.Molecular autismAutism Spectrum Disorders Working Group of The Psychiatric Genomics ConsortiumJanuary 1, 2017Not Determined
28533516Create StudyASD restricted and repetitive behaviors associated at 17q21.33: genes prioritized by expression in fetal brains.Molecular psychiatryCantor, R M; Navarro, L; Won, H; Walker, R L; Lowe, J K; Geschwind, D HApril 2018Relevant
28504703Create StudyPolygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders.Nature geneticsWeiner, Daniel J; Wigdor, Emilie M; Ripke, Stephan; Walters, Raymond K; Kosmicki, Jack A; Grove, Jakob; Samocha, Kaitlin E; Goldstein, Jacqueline I; Okbay, Aysu; Bybjerg-Grauholm, Jonas; Werge, Thomas; Hougaard, David M; Taylor, Jacob; iPSYCH-Broad Autism Group; Psychiatric Genomics Consortium Autism Group; Skuse, David; Devlin, Bernie; Anney, Richard; Sanders, Stephan J; Bishop, Somer; Mortensen, Preben Bo; Børglum, Anders D; Smith, George Davey; Daly, Mark J; Robinson, Elise BJuly 1, 2017Not Determined
28316770Create StudyExaggerated CpH methylation in the autism-affected brain.Molecular autismEllis SE, Gupta S, Moes A, West AB, Arking DEJanuary 2017Not Relevant
27919067Create StudyGenome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism.NatureParikshak, Neelroop N; Swarup, Vivek; Belgard, T Grant; Irimia, Manuel; Ramaswami, Gokul; Gandal, Michael J; Hartl, Christopher; Leppa, Virpi; Ubieta, Luis de la Torre; Huang, Jerry; Lowe, Jennifer K; Blencowe, Benjamin J; Horvath, Steve; Geschwind, Daniel HDecember 2016Not Relevant
27814521Create StudyThe Central Nervous System and the Gut Microbiome.CellSharon, Gil; Sampson, Timothy R; Geschwind, Daniel H; Mazmanian, Sarkis KNovember 2016Not Relevant
27760116Create StudyChromosome conformation elucidates regulatory relationships in developing human brain.NatureWon H, De La Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, Gandal MJ, Sutton GJ, Hormozdiari F, Lu D, Lee C, Eskin E, Voineagu I, Ernst J, Geschwind DHOctober 2016Not Relevant
27677376Create StudyDexmedetomidine Protects Against Glucocorticoid Induced Progenitor Cell Apoptosis in Neonatal Mouse Cerebellum.The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal ObstetriciansO'Connor SD, Cabrera OH, Dougherty JD, Singh S, Swiney BS, Salinas-Contreras P, Farber NB, Noguchi KKSeptember 2016Not Relevant
27569545Study (393)Rare Inherited and De Novo CNVs Reveal Complex Contributions to ASD Risk in Multiplex Families.American journal of human geneticsLeppa, Virpi M; Kravitz, Stephanie N; Martin, Christa Lese; Andrieux, Joris; Le Caignec, Cedric; Martin-Coignard, Dominique; DyBuncio, Christina; Sanders, Stephan J; Lowe, Jennifer K; Cantor, Rita M; Geschwind, Daniel HSeptember 2016Relevant
27351196Create StudyA Common CYFIP1 Variant at the 15q11.2 Disease Locus Is Associated with Structural Variation at the Language-Related Left Supramarginal Gyrus.PloS oneWoo, Young Jae; Wang, Tao; Guadalupe, Tulio; Nebel, Rebecca A; Vino, Arianna; Del Bene, Victor A; Molholm, Sophie; Ross, Lars A; Zwiers, Marcel P; Fisher, Simon E; Foxe, John J; Abrahams, Brett SJanuary 1, 2016Not Determined
27219343Create StudyTranscriptome analysis of cortical tissue reveals shared sets of downregulated genes in autism and schizophrenia.Translational psychiatryEllis SE, Panitch R, West AB, Arking DEMay 2016Not Relevant
26998600Create StudySchizophrenia genetics complements its mechanistic understanding.Nature neuroscienceRuzzo EK, Geschwind DHApril 2016Not Relevant
26892004Create StudyGene expression in human brain implicates sexually dimorphic pathways in autism spectrum disorders.Nature communicationsWerling DM, Parikshak NN, Geschwind DH2016Not Relevant
26824476Create StudyReduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks.PloS oneNebel, Rebecca A; Zhao, Dejian; Pedrosa, Erika; Kirschen, Jill; Lachman, Herbert M; Zheng, Deyou; Abrahams, Brett S2016Not Relevant
26627310Create StudyJAKMIP1, a Novel Regulator of Neuronal Translation, Modulates Synaptic Function and Autistic-like Behaviors in Mouse.NeuronBerg, Jamee M; Lee, Changhoon; Chen, Leslie; Galvan, Laurie; Cepeda, Carlos; Chen, Jane Y; Peñagarikano, Olga; Stein, Jason L; Li, Alvin; Oguro-Ando, Asami; Miller, Jeremy A; Vashisht, Ajay A; Starks, Mary E; Kite, Elyse P; Tam, Eric; Gdalyahu, Amos; Al-Sharif, Noor B; Burkett, Zachary D; White, Stephanie A; Fears, Scott C; Levine, Michael S; Wohlschlegel, James A; Geschwind, Daniel HDecember 16, 2015Not Relevant
26590343Create StudyCorrespondence between Resting-State Activity and Brain Gene Expression.NeuronWang GZ, Belgard TG, Mao D, Chen L, Berto S, Preuss TM, Lu H, Geschwind DH, Konopka GNovember 18, 2015Not Relevant
26500678Create StudyMoving from capstones toward cornerstones: successes and challenges in applying systems biology to identify mechanisms of autism spectrum disorders.Frontiers in geneticsKopp, Nathan; Climer, Sharlee; Dougherty, Joseph D2015Not Relevant
26404826Create StudyGenetics and genomics of psychiatric disease.Science (New York, N.Y.)Geschwind DH, Flint JSeptember 25, 2015Not Relevant
26149713Create StudySystems biology and gene networks in neurodevelopmental and neurodegenerative disorders.Nature reviews. GeneticsParikshak NN, Gandal MJ, Geschwind DHAugust 2015Not Relevant
26076356Create StudyReciprocal Relationship between Head Size, an Autism Endophenotype, and Gene Dosage at 19p13.12 Points to AKAP8 and AKAP8L.PloS oneNebel, Rebecca A; Kirschen, Jill; Cai, Jinlu; Woo, Young Jae; Cherian, Koshi; Abrahams, Brett S2015Not Relevant
25973164Create StudyRecurrence rates provide evidence for sex-differential, familial genetic liability for autism spectrum disorders in multiplex families and twins.Molecular autismWerling DM, Geschwind DH2015Relevant
25891009Create StudyGene hunting in autism spectrum disorder: on the path to precision medicine.The Lancet. NeurologyGeschwind, Daniel H; State, Matthew WNovember 2015Not Relevant
25789151Create StudyFmrp targets or not: long, highly brain-expressed genes tend to be implicated in autism and brain disorders.Molecular autismOuwenga RL, Dougherty JJanuary 2015Not Relevant
25727539Create StudySocial responsiveness, an autism endophenotype: genomewide significant linkage to two regions on chromosome 8.The American journal of psychiatryLowe JK, Werling DM, Constantino JN, Cantor RM, Geschwind DHMarch 1, 2015Relevant
25682262Create StudyThe RNA-binding protein Celf6 is highly expressed in diencephalic nuclei and neuromodulatory cell populations of the mouse brain.Brain structure & functionMaloney, Susan E; Khangura, Eakta; Dougherty, Joseph DFebruary 15, 2015Not Relevant
25599223Create StudyPsychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways.Nature neuroscienceNetwork and Pathway Analysis Subgroup of Psychiatric Genomics ConsortiumFebruary 1, 2015Not Determined
25494366Create StudyTranscriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism.Nature communicationsGupta S, Ellis SE, Ashar FN, Moes A, Bader JS, Zhan J, West AB, Arking DE2014Not Relevant
25360157Create StudyAlteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome.Genome medicineTian Y, Voineagu I, Paşca SP, Won H, Chandran V, Horvath S, Dolmetsch RE, Geschwind DHJanuary 2014Not Relevant
24618187Create StudyRecent challenges to the psychiatric diagnostic nosology: a focus on the genetics and genomics of neurodevelopmental disorders.International journal of epidemiologyKim YS, State MWApril 2014Not Relevant
24574247Create StudyInvestigation of maternal genotype effects in autism by genome-wide association.Autism research : official journal of the International Society for Autism ResearchYuan, Han; Dougherty, Joseph DApril 2014Not Relevant
24533643Create StudyReplication of linkage at chromosome 20p13 and identification of suggestive sex-differential risk loci for autism spectrum disorder.Molecular autismWerling DM, Lowe JK, Luo R, Cantor RM, Geschwind DH2014Relevant
24453331Create StudyCell type-specific expression analysis to identify putative cellular mechanisms for neurogenetic disorders.The Journal of neuroscience : the official journal of the Society for NeuroscienceXu X, Wells AB, O'Brien DR, Nehorai A, Dougherty JDJanuary 22, 2014Not Relevant
24341889Create StudyRNA-Seq optimization with eQTL gold standards.BMC genomicsEllis, Shannon E; Gupta, Simone; Ashar, Foram N; Bader, Joel S; West, Andrew B; Arking, Dan EDecember 2013Not Relevant
24267887Create StudyIntegrative functional genomic analyses implicate specific molecular pathways and circuits in autism.CellParikshak NN, Luo R, Zhang A, Won H, Lowe JK, Chandran V, Horvath S, Geschwind DHNovember 21, 2013Not Relevant
24183016Create StudyCortical evolution: judge the brain by its cover.NeuronGeschwind, Daniel H; Rakic, PaskoOctober 30, 2013Not Relevant
24090431Create StudySFARI Gene 2.0: a community-driven knowledgebase for the autism spectrum disorders (ASDs).Molecular autismAbrahams BS, Arking DE, Campbell DB, Mefford HC, Morrow EM, Weiss LA, Menashe I, Wadkins T, Banerjee-Basu S, Packer AOctober 2013Not Relevant
23975140Create StudyDeNovoGear: de novo indel and point mutation discovery and phasing.Nature methodsRamu A, Noordam MJ, Schwartz RS, Wuster A, Hurles ME, Cartwright RA, Conrad DFOctober 2013Not Relevant
23933821Create StudyGenetic relationship between five psychiatric disorders estimated from genome-wide SNPs.Nature geneticsCross-Disorder Group of the Psychiatric Genomics Consortium; Lee, S Hong; Ripke, Stephan; Neale, Benjamin M; Faraone, Stephen V; Purcell, Shaun M; Perlis, Roy H; Mowry, Bryan J; Thapar, Anita; Goddard, Michael E; Witte, John S; Absher, Devin; Agartz, Ingrid; Akil, Huda; Amin, Farooq; Andreassen, Ole A; Anjorin, Adebayo; Anney, Richard; Anttila, Verneri; Arking, Dan E; Asherson, Philip; Azevedo, Maria H; Backlund, Lena; Badner, Judith A; Bailey, Anthony J; Banaschewski, Tobias; Barchas, Jack D; Barnes, Michael R; Barrett, Thomas B; Bass, Nicholas; Battaglia, Agatino; Bauer, Michael; Bayés, Mònica; Bellivier, Frank; Bergen, Sarah E; Berrettini, Wade; Betancur, Catalina; Bettecken, Thomas; Biederman, Joseph; Binder, Elisabeth B; Black, Donald W; Blackwood, Douglas H R; Bloss, Cinnamon S; Boehnke, Michael; Boomsma, Dorret I; Breen, Gerome; Breuer, René; Bruggeman, Richard; Cormican, Paul; Buccola, Nancy G; Buitelaar, Jan K; Bunney, William E; Buxbaum, Joseph D; Byerley, William F; Byrne, Enda M; Caesar, Sian; Cahn, Wiepke; Cantor, Rita M; Casas, Miguel; Chakravarti, Aravinda; Chambert, Kimberly; Choudhury, Khalid; Cichon, Sven; Cloninger, C Robert; Collier, David A; Cook, Edwin H; Coon, Hilary; Cormand, Bru; Corvin, Aiden; Coryell, William H; Craig, David W; Craig, Ian W; Crosbie, Jennifer; Cuccaro, Michael L; Curtis, David; Czamara, Darina; Datta, Susmita; Dawson, Geraldine; Day, Richard; De Geus, Eco J; Degenhardt, Franziska; Djurovic, Srdjan; Donohoe, Gary J; Doyle, Alysa E; Duan, Jubao; Dudbridge, Frank; Duketis, Eftichia; Ebstein, Richard P; Edenberg, Howard J; Elia, Josephine; Ennis, Sean; Etain, Bruno; Fanous, Ayman; Farmer, Anne E; Ferrier, I Nicol; Flickinger, Matthew; Fombonne, Eric; Foroud, Tatiana; Frank, Josef; Franke, Barbara; Fraser, Christine; Freedman, Robert; Freimer, Nelson B; Freitag, Christine M; Friedl, Marion; Frisén, Louise; Gallagher, Louise; Gejman, Pablo V; Georgieva, Lyudmila; Gershon, Elliot S; Geschwind, Daniel H; Giegling, Ina; Gill, Michael; Gordon, Scott D; Gordon-Smith, Katherine; Green, Elaine K; Greenwood, Tiffany A; Grice, Dorothy E; Gross, Magdalena; Grozeva, Detelina; Guan, Weihua; Gurling, Hugh; De Haan, Lieuwe; Haines, Jonathan L; Hakonarson, Hakon; Hallmayer, Joachim; Hamilton, Steven P; Hamshere, Marian L; Hansen, Thomas F; Hartmann, Annette M; Hautzinger, Martin; Heath, Andrew C; Henders, Anjali K; Herms, Stefan; Hickie, Ian B; Hipolito, Maria; Hoefels, Susanne; Holmans, Peter A; Holsboer, Florian; Hoogendijk, Witte J; Hottenga, Jouke-Jan; Hultman, Christina M; Hus, Vanessa; Ingason, Andrés; Ising, Marcus; Jamain, Stéphane; Jones, Edward G; Jones, Ian; Jones, Lisa; Tzeng, Jung-Ying; Kähler, Anna K; Kahn, René S; Kandaswamy, Radhika; Keller, Matthew C; Kennedy, James L; Kenny, Elaine; Kent, Lindsey; Kim, Yunjung; Kirov, George K; Klauck, Sabine M; Klei, Lambertus; Knowles, James A; Kohli, Martin A; Koller, Daniel L; Konte, Bettina; Korszun, Ania; Krabbendam, Lydia; Krasucki, Robert; Kuntsi, Jonna; Kwan, Phoenix; Landén, Mikael; Långström, Niklas; Lathrop, Mark; Lawrence, Jacob; Lawson, William B; Leboyer, Marion; Ledbetter, David H; Lee, Phil H; Lencz, Todd; Lesch, Klaus-Peter; Levinson, Douglas F; Lewis, Cathryn M; Li, Jun; Lichtenstein, Paul; Lieberman, Jeffrey A; Lin, Dan-Yu; Linszen, Don H; Liu, Chunyu; Lohoff, Falk W; Loo, Sandra K; Lord, Catherine; Lowe, Jennifer K; Lucae, Susanne; MacIntyre, Donald J; Madden, Pamela A F; Maestrini, Elena; Magnusson, Patrik K E; Mahon, Pamela B; Maier, Wolfgang; Malhotra, Anil K; Mane, Shrikant M; Martin, Christa L; Martin, Nicholas G; Mattheisen, Manuel; M (see original citation for additional authors)September 2013Not Relevant
23722009Create StudyMapping connectivity in the developing brain.International journal of developmental neuroscience : the official journal of the International Society for Developmental NeuroscienceDennis, Emily L; Thompson, Paul MNovember 2013Not Relevant
23453885Create StudyIdentification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.Lancet (London, England)Cross-Disorder Group of the Psychiatric Genomics ConsortiumApril 20, 2013Not 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
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
Research Subject and Pedigree info icon
1,52001/15/2014
5,092
Approved

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
Mullen Scales of Early Learning info icon
2001/15/2014
20
Approved
Ravens Coloured Progressive Matrices (CPM) info icon
20001/15/2014
275
Approved
Genomics/omics info icon
1,20002/28/2017
4,073
Approved
ADOS info icon
60001/15/2014
0
Approved
ADI-R info icon
60001/15/2014
0
Approved
Medical History info icon
60001/15/2014
452
Approved
Social Responsiveness Scale (SRS) info icon
60001/15/2014
974
Approved
Genetic Test info icon
18501/15/2014
185
Approved
Social Communication Questionnaire (SCQ) info icon
60001/15/2014
526
Approved
Demographics info icon
1,52001/15/2014
0
Approved
DAS-II: Differential Ability Scales info icon
50001/15/2014
0
Approved
Peabody Picture Vocabulary Test, Fourth Edition info icon
20001/15/2014
89
Approved
Physical Exam info icon
60001/15/2014
445
Approved
EHCI Diagnostic Odyssey Instrument info icon
60001/15/2014
479
Approved
Vineland (Parent and Caregiver) info icon
60001/15/2014
445
Approved
Ravens Standard Progressive Matrices (SPM) info icon
20001/15/2014
499
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
Examining the validity of the use of ratio IQs in psychological assessments IQ tests are amongst the most used psychological assessments, both in research and clinical settings. For participants who cannot complete IQ tests normed for their age, ratio IQ scores (RIQ) are routinely computed and used as a proxy of IQ, especially in large research databases to avoid missing data points. However, because it has never been scientifically validated, this practice is questionable. In the era of big data, it is important to examine the validity of this widely used practice. In this paper, we use the case of autism to examine the differences between standard full-scale IQ (FSIQ) and RIQ. Data was extracted from four databases in which ages, FSIQ scores and subtests raw scores were available for autistic participants between 2 and 17 years old. The IQ tests included were the MSEL (N=12033), DAS-II early years (N=1270), DAS-II school age (N=2848), WISC-IV (N=471) and WISC-V (N=129). RIQs were computed for each participant as well as the discrepancy (DSC) between RIQ and FSIQ. We performed two linear regressions to respectively assess the effect of FSIQ and of age on the DSC for each IQ test, followed by additional analyses comparing age subgroups as well as FSIQ subgroups on DSC. Participants at the extremes of the FSIQ distribution tended to have a greater DSC than participants with average FSIQ. Furthermore, age significantly predicted the DSC, with RIQ superior to FSIQ for younger participants while the opposite was found for older participants. These results question the validity of this widely used alternative scoring method, especially for individuals at the extremes of the normal distribution, with whom RIQs are most often employed.20/17423Secondary AnalysisShared
Controls for SCCRIPTo establish a well characterized cohort for pediatric patients living with sickle cell disease25/11185Secondary AnalysisPrivate
Investigating autism etiology and heterogeneity by decision tree algorithmAutism spectrum disorder (ASD) is a neurodevelopmental disorder that causes deficits in cognition, communication and social skills. ASD, however, is a highly heterogeneous disorder. This heterogeneity has made identifying the etiology of ASD a particularly difficult challenge, as patients exhibit a wide spectrum of symptoms without any unifying genetic or environmental factors to account for the disorder. For better understanding of ASD, it is paramount to identify potential genetic and environmental risk factors that are comorbid with it. Identifying such factors is of great importance to determine potential causes for the disorder, and understand its heterogeneity. Existing large-scale datasets offer an opportunity for computer scientists to undertake this task by utilizing machine learning to reliably and efficiently obtain insight about potential ASD risk factors, which would in turn assist in guiding research in the field. In this study, decision tree algorithms were utilized to analyze related factors in datasets obtained from the National Database for Autism Research (NDAR) consisting of nearly 3000 individuals. We were able to identify 15 medical conditions that were highly associated with ASD diagnoses in patients; furthermore, we extended our analysis to the family medical history of patients and we report six potentially hereditary medical conditions associated with ASD. Associations reported had a 90% accuracy. Meanwhile, gender comparisons highlighted conditions that were unique to each gender and others that overlapped. Those findings were validated by the academic literature, thus opening the way for new directions for the use of decision tree algorithms to further understand the etiology of autism. 5/3382Secondary AnalysisShared
Autism Sensory Research Consortium Cross-lab Integrative Data Analysis Since 2013, when sensory features were officially added to the diagnostic criteria for autism, research into the sensory manifestations of the condition has increased dramatically. However, the majority of this research has primarily been conducted using small laboratory-based samples of children on the autism spectrum, substantially limiting the hypotheses that can be tested in any one dataset and the generalizability of results to the wider autistic population. The Autism Sensory Research Consortium (ASRC), funded by the Nancy Lurie Marks Family Foundation, represents the first major international collaboration of over a dozen research groups that study sensory functioning in autism. As a major thrust of this collaboration, the ASRC has begun a data sharing initiative, in which all participating labs can contribute existing data from their past and present research studies to a centralized database. These “Big Data” can then be systematically examined using powerful large-sample statistical techniques such as structural equation modeling and item response theory, which will allow researchers to test more complex hypotheses regarding the nature of sensory differences in autism and their relationships with sociodemographic and non-sensory clinical features. Once data from all sites has been pooled, it will be analyzed using a method called integrative data analysis, which is specially designed to derive insights from large and heterogeneous samples. One major advantage of this methodology is the ability to construct and test measurement models of sensory symptoms, determining the most appropriate set of questions for assessing each construct and making sure that the scales do not produce biased comparisons when they are examined across diagnostic groups or subsets of the autistic population. Furthermore, measurement models can be constructed to bridge multiple questionnaires, allowing for the calculation of robust composite scores that can be compared between studies that only administered items from one of the contributing questionnaires. These models can further facilitate pooling of data across studies, allowing us to amass even larger datasets to answer questions about sensory function in the autistic population. Furthermore, moving forward, the composite sensory measures from the integrative data analysis can be employed in other studies, providing investigators in sensory autism research with a suite of reliable and valid behavioral measures that can be used as outcomes in trials of interventions targeting these symptoms. In the long term, this project has the potential to help us better understand the nature of sensory function in persons on the spectrum, as well as how sensory alterations relate to broader features of the condition—specifically, for whom and/or at what point in development sensory features are most predictive of core autism behaviors or other meaningful clinical outcomes such as language acquisition and adaptive behavior. Incorporation of neuroscientific data collected within the ASRC can also possibly shed some light on the neural basis of sensory disruptions in the autistic population. All of this will help to lay a foundation for future work testing the efficacy of candidate interventions aimed at improving sensory function and more distal skills in autistic individuals.2/2110Secondary AnalysisPrivate
Personalized Autism Symptom Assessment with the Youth Top Problems Scale: Observational and Parent-Report Formats for Clinical Trials ApplicationsTo date, few measures of comorbid psychiatric symptoms in the context of autism spectrum disorder (ASD) have been established as both psychometrically robust and sensitive to the effects of treatment. Therefore, I propose to conduct an item response theory (IRT) analysis for this study using the Child and Adolescent Symptom Inventory (CASI) data from the National Database for Autism Research. Item parameters will be obtained through an IRT calibration of CASI items using flexMIRT.3 (Cai, 2016). In order to conduct IRT, the CASI calibration sample will include both these NDAR participants and a sample of 68 children with diagnoses of ASD and IQ>70 (ages 6-13 years) who participated in our recent NIMH-funded clinical trial of cognitive behavioral therapy, which will create a sample large enough for the IRT analysis. I plan to publish this data as part of a broader psychometric study of children with autism.5/746Secondary AnalysisPrivate
Relations between everyday executive functioning and language in youth with Down syndrome and youth with autism spectrum disorderLanguage and executive functioning are major impairments in many neurodevelopmental disorders, but little is known about the relations between these constructs, particularly using parent-report. Thus, the current research sought to examine relations between executive function and language in two groups -- Down syndrome (DS) and autism spectrum disorder (ASD). Forty-one youth with DS (Mage=11.2) and 91 youth with ASD (Mage= 7.7) were included. Results were as follows: in DS, executive function predicted pragmatic, but not structural language; in ASD, executive function predicted both. Findings highlight the interrelatedness of language and executive functioning and may have implications for intervention development. 1/91Secondary AnalysisPrivate
* 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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