NIMH Data Archive - Data

Genomics

Neuroimaging

Phenotype¹

New Trial
Clinical Trial

¹ Numbers reported are subjects by age

New Project
Grant/Project Number

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

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.

Select	Experiment Id	Experiment Name	Experiment Type	Created On

24	HI-NGS_R1	Omics	02/16/2011
475	MB1-10 (CHOP)	Omics	06/07/2016
490	Illumina Infinium PsychArray BeadChip Assay	Omics	07/07/2016
501	PharmacoBOLD Resting State	fMRI	07/27/2016
506	PVPREF	Omics	08/05/2016
509	ABC-CT Resting v2	EEG	08/18/2016
13	Comparison of FI expression in Autistic and Neurotypical Homo Sapiens	Omics	12/28/2010
18	AGRE/Broad Affymetrix 5.0 Genotype Experiment	Omics	01/06/2011
22	Stitching PCR Sequencing	Omics	02/14/2011
26	ASD_Methylation	Omics	03/01/2011
37	Standard paired-end sequencing of BCRs	Omics	04/19/2011
38	Illumina Mate-Pair BCR sequencing	Omics	04/19/2011
39	Custom Jumping Libraries	Omics	04/19/2011
40	Custom CapBP	Omics	04/19/2011
43	Autism brain sample genotyping, Illumina	Omics	05/16/2011
47	ARRA Autism Sequencing Collaboration at Baylor. SOLiD 4 System	Omics	08/01/2011
53	AGRE Omni1-quad	Omics	10/11/2011
59	AGP genotyping	Omics	04/03/2012
60	Ultradeep 454 sequencing of synaptic genes from postmortem cerebella of individuals with ASD and neurotypical controls	Omics	06/23/2012
63	Microemulsion PCR and Targeted Resequencing for Variant Detection in ASD	Omics	07/20/2012
76	Whole Genome Sequencing in Autism Families	Omics	01/03/2013
519	Resting	fMRI	11/08/2016
90	Genotyped IAN Samples	Omics	07/09/2013
91	NJLAGS Axiom Genotyping Array	Omics	07/16/2013
93	AGP genotyping (CNV)	Omics	09/06/2013
106	Longitudinal Sleep Study. H20 200. Channel set 2	EEG	11/07/2013
107	Longitudinal Sleep Study. H20 200. Channel set 3	EEG	11/07/2013
108	Longitudinal Sleep Study. AURA 200	EEG	11/07/2013
105	Longitudinal Sleep Study. H20 200. Channel set 1	EEG	11/07/2013
109	Longitudinal Sleep Study. AURA 400	EEG	11/07/2013
116	Gene Expression Analysis WG-6	Omics	01/07/2014
131	Jeste Lab UCLA ACEii: Charlie Brown and Sesame Street - Project 1	Eye Tracking	02/27/2014
132	Jeste Lab UCLA ACEii: Animacy - Project 1	Eye Tracking	02/27/2014
133	Jeste Lab UCLA ACEii: Mom Stranger - Project 2	Eye Tracking	02/27/2014
134	Jeste Lab UCLA ACEii: Face Emotion - Project 3	Eye Tracking	02/27/2014
145	AGRE/FMR1_Illumina.JHU	Omics	04/14/2014
146	AGRE/MECP2_Sanger.JHU	Omics	04/14/2014
147	AGRE/MECP2_Junior.JHU	Omics	04/14/2014
151	Candidate Gene Identification in familial Autism	Omics	06/09/2014
152	NJLAGS Whole Genome Sequencing	Omics	07/01/2014
154	Math Autism Study - Vinod Menon	fMRI	07/15/2014
155	Resting	fMRI	07/25/2014
156	Speech	fMRI	07/25/2014
159	Emotion	fMRI	07/25/2014
160	syllable contrast	EEG	07/29/2014
167	School-age naturalistic stimuli	Eye Tracking	09/19/2014
44	AGRE/Broad Affymetrix 5.0 Genotype Experiment	Omics	06/27/2011
45	Exome Sequencing of 20 Sporadic Cases of Autism Spectrum Disorder	Omics	07/15/2011
78	MET Genotypes	Omics	03/18/2013
61	Ultradeep Illumina sequencing of A-to-I edited sites in synaptic genes from postmortem cerebella of individuals with ASD and neurotypical controls	Omics	06/23/2012

Collection - Add Experiment

Add Supporting Documentation

Funding Source:
URL:

To add an existing Data Structure, enter its title in the search bar. If you need to request changes, select the indicator "No, it requires changes to meet research needs" after selecting the Structure, and upload the file with the request changes specific to the selected Data Structure. Your file should follow the Request Changes Procedure. If the Data Structure does not exist, select "Request New Data Structure" and upload the appropriate zip file.

Use/Modify Existing Data Structure

Request New Data Structure

Targeted Enrollment:

Initial Submission Date:

Initial Share Date:

Data Structure Search:

Data Structures:

Submit

Request Submission Exemption

Not Eligible

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

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

Collection Updated

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

[CMS] Error

[CMS]

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

You have requested to move the sharing dates for the following assessments:

Data Expected Item	Original Sharing Date	New Sharing Date

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

Explanation must be between 20 and 200 characters in length.

Please press Save or Cancel

Induced pluripotent cells in ASD with macrocephaly #1201

General
Experiments (7)
Shared Data
Publications (12)
Data Expected (7)
Associated Studies (7)

Collection Title	Collection Investigators	Collection Description
Collection Title:	Induced pluripotent cells in ASD with macrocephaly
Collection Investigators:	Flora Vaccarino
Collection Description:	R01MH89176 - This project will develop lines of pluripotent cells (iPSC) from a longitudinally acquired cohort of patients with autism spectrum disorders (ASD) and macrocephaly and their family members, as well as typically developing children, using cells obtained by a skin biopsy. We will produce several iPSC lines per individual and characterize them with respect to their biology and their structural genetic variation. The aim is create a resource and analytical tool, which will allow us to examine neuronal differentiation in ASD. R33MH87879 - Our project capitalizes on recent procedures that allow derivation of pluripotent stem cells from fibroblasts obtainable through a small skin biopsy from living individuals. These induced pluripotent stem cells (iPSC) can differentiate into any cell types of the body, including neural stem cells (NSCs). We will use these methods to investigate neuronal differentiation in autism spectrum disorders (ASD). Our hypothesis states that increased brain size, a highly replicated biological phenotype in ASD, is attributable to altered dynamics of cell proliferation and/or differentiation intrinsic to NSCs, which, in turn, will correlate with specific changes in gene expression and the underlying changes in genomic sequence and/or epigenomic imprinting. To test this hypothesis, we have assembled a group of investigators with the range of expertise necessary for a multi-leveland multi-dimensional approach to this problem. In Specific Aim 1, we will derive iPSC lines from patients with ASD exhibiting an increase in head size and from typically developing children. These iPSC lines will be differentiated into NSCs. The NSC lines from ASD individuals will be compared to those derived from typically developing individuals with respect to their proliferation, cell death and differentiation into different neuronal subtypes, as well as synaptic specification. In Specific Aim 2, we will use advanced genomics and epigenomics technologies to generate high-resolution and comprehensive datasets of variation in the genomic sequence, epigenetic marks, and transcript abundance at progenitor and mature stages of neuronal cell differentiation.We will integrate multi-level genomics and gene expression datasets with findings from cell biology and clinical phenotypes. In Specific Aim 3, we will transplant NSCs from control and patients into the ventricles of mouse embryos in order to determine their in vivo phenotype and their ability to contribute neurons to various brain regions. The potential impact of our research is to develop cell lines derived directly from patients that will recapitulate in vitro the biological steps that enable an embryonic stem cell to differentiate into multiple CNS cell types. This project will lay the foundations for beginning to correlate genomic sequence, regulation and intensity of gene expression, cellular (biological) consequences, and patient behavior, and thus understand the biological mechanisms of disease. Candidate genes and regions found in iPSC lines can be subsequently validated with statistical significance in targeted large-scale screens. The direct analysis of specific differences in gene expression and regulation that pertain to individual patients and their clinical phenotype may offer unique insights into disease pathogenesis.
Data Repository:	NIMH Data Archive
Permission Group:
Collection Creation Date:	06/23/2010
NIH Research Initiative:	NIMH Repository & Genomics Resource (NRGR)
Collection Phase:	Funding Completed
Collection Sub-Phase:	Close Out
Blinded Clinical Trial:	No
Total Funded Amount:	$3,272,916.00
Subjects Shared:	29

{"values":[["SNP and CNV: sequencing",13],["Gene expression: sequencing",12],["Gene expression: microarray",3],["Stem cell markers screening: Immunostaining",4]]}

{"values":[]}

{"values":[["Neurological Control",2],["Sibling Control",4],["Parental Control",20],["Autism Spectrum Mildly Affected",4],["Autism Spectrum Affected",2],["Typical Control",9],["Autism Spectrum Severely Affected",9]]}

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Funding Sources:

Funding Source Name	Funding Source URL
NIH - Extramural	None

Supporting Documentation:

File Name	File Type	Description	Audience
sequencing_files_readme_col_1201.pdf	Background	Readme for sequencing files	Qualified Researchers
Illumina_mRNA-Seq_protocol.doc	Methods	mRNA-seq protocol	Qualified Researchers
Sample_preparation_protocol-Illumina.pdf	Methods	Sample preparation protocol	Qualified Researchers

Grant Information:

Project Number	Project Title	Start Date	End Date	Planned Enrollment	Actual Enrollment	Organization	Funds Obligated
R21MH087879-01	Cellular and Genetic Correlates of Increased Head Size in Autism Spectrum Disorde	09/30/2009	12/31/2013	16	10	YALE UNIVERSITY	$1,285,340.00
R01MH089176-01	Biological correlates of altered brain growth in autism	09/30/2009	08/31/2012	34	10	YALE UNIVERSITY	$1,987,576.00

Clinical Trials:

helpcenter.collection.general-tab

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 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/nda/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

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.
How do I know when a NDA Collection has been created?

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

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.
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.
Collection Title

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

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

Contact NDA Help Desk

ID	Name	Created Date	Status	Type
29	Microarray family 03 (father, mother, sibling)	03/24/2011	Approved	Omics
41	Immunofluorescence	05/11/2011	Approved	Omics
55	Illumina mRNA Seq	02/13/2012	Approved	Omics
58	iPS DNA Sequence	03/09/2012	Approved	Omics
62	Fibroblast DNA Sequence	07/12/2012	Approved	Omics
607	Capture-seq	01/31/2017	Approved	Omics
608	Amplicon-seq	01/31/2017	Approved	Omics

helpcenter.collection.experiments-tab

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.

Contact NDA Help Desk

Shared Data:

Title	Type	Number of Subjects
Autism Diagnostic Interview, Revised (ADI-R)	Clinical Assessments	4
Autism Diagnostic Observation Schedule (ADOS)- Module 1	Clinical Assessments	1
Autism Diagnostic Observation Schedule (ADOS)- Module 2	Clinical Assessments	1
Autism Diagnostic Observation Schedule (ADOS)- Module 3	Clinical Assessments	2
Autism Diagnostic Observation Schedule (ADOS)- Module 3 (2007)	Clinical Assessments	1
DAS-II: Differential Ability Scales 2nd Ed. School Age	Clinical Assessments	2
DAS-II:Differential Ability Scales 2nd Ed. Early Years	Clinical Assessments	1
Genomics Sample	Genomics	16
Genomics Subject	Genomics	29
Mullen Scales of Early Learning	Clinical Assessments	1
Vineland-II - Survey Form (2005)	Clinical Assessments	3
Wechsler Intelligence Scale for Children - IV [part 1]	Clinical Assessments	1
Wechsler Intelligence Scale for Children - IV [part 2]	Clinical Assessments	1
Wechsler Intelligence Scale for Children - IV [part 3]	Clinical Assessments	1
Wechsler Intelligence Scale for Children -IV [part 4]	Clinical Assessments	1

helpcenter.collection.shared-data-tab

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 Study is viewable and searchable publicly regardless of the user's role or whether the user has an NDA account. A Shared NDA Study does not necessarily mean that data 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.

Contact NDA Help Desk

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 ID	Study	Title	Journal	Authors	Date	Status
36447010	Create Study	Mispatterning and interneuron deficit in Tourette Syndrome basal ganglia organoids.	Molecular psychiatry	Brady, Melanie V; Mariani, Jessica; Koca, Yildiz; Szekely, Anna; King, Robert A; Bloch, Michael H; Landeros-Weisenberger, Angeli; Leckman, James F; Vaccarino, Flora M	December 1, 2022	Not Determined
28235832	Create Study	One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin.	Genome research	Abyzov, Alexej; Tomasini, Livia; Zhou, Bo; Vasmatzis, Nikolaos; Coppola, Gianfilippo; Amenduni, Mariangela; Pattni, Reenal; Wilson, Michael; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E; Vaccarino, Flora M	April 2017	Not Relevant
26610635	Create Study	Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders.	Stem cell reports	Brennand, Kristen J; Marchetto, M Carol; Benvenisty, Nissim; Brüstle, Oliver; Ebert, Allison; Izpisua Belmonte, Juan Carlos; Kaykas, Ajamete; Lancaster, Madeline A; Livesey, Frederick J; McConnell, Michael J; McKay, Ronald D; Morrow, Eric M; Muotri, Alysson R; Panchision, David M; Rubin, Lee L; Sawa, Akira; Soldner, Frank; Song, Hongjun; Studer, Lorenz; Temple, Sally; Vaccarino, Flora M; Wu, Jun; Vanderhaeghen, Pierre; Gage, Fred H; Jaenisch, Rudolf	December 8, 2015	Not Relevant
26443267	Create Study	Imbalance of excitatory/inhibitory synaptic protein expression in iPSC-derived neurons from FOXG1(+/-) patients and in foxg1(+/-) mice.	European journal of human genetics : EJHG	Patriarchi, Tommaso; Amabile, Sonia; Frullanti, Elisa; Landucci, Elisa; Lo Rizzo, Caterina; Ariani, Francesca; Costa, Mario; Olimpico, Francesco; W Hell, Johannes; M Vaccarino, Flora; Renieri, Alessandra; Meloni, Ilaria	June 2016	Not Determined
26186191	Create Study	FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.	Cell	Mariani, Jessica; Coppola, Gianfilippo; Zhang, Ping; Abyzov, Alexej; Provini, Lauren; Tomasini, Livia; Amenduni, Mariangela; Szekely, Anna; Palejev, Dean; Wilson, Michael; Gerstein, Mark; Grigorenko, Elena L; Chawarska, Katarzyna; Pelphrey, Kevin A; Howe, James R; Vaccarino, Flora M	July 16, 2015	Not Relevant
25966633	Create Study	Altered expression of neuropeptides in FoxG1-null heterozygous mutant mice.	European journal of human genetics : EJHG	Frullanti E, Amabile S, Lolli MG, Bartolini A, Livide G, Landucci E, Mari F, Vaccarino FM, Ariani F, Massimino L, Renieri A, Meloni I	February 2016	Not Determined
23160490	Study (289)	Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.	Nature	Abyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FM	December 20, 2012	Relevant
23062309	Create Study	Neurobiology meets genomic science: the promise of human-induced pluripotent stem cells.	Development and psychopathology	Stevens HE, Mariani J, Coppola G, Vaccarino FM	November 2012	Not Relevant
22761314	Create Study	Modeling human cortical development in vitro using induced pluripotent stem cells.	Proceedings of the National Academy of Sciences of the United States of America	Mariani J, Simonini MV, Palejev D, Tomasini L, Coppola G, Szekely AM, Horvath TL, Vaccarino FM	July 31, 2012	Not Determined
21371482	Create Study	Induced pluripotent stem cells: a new tool to confront the challenge of neuropsychiatric disorders.	Neuropharmacology	Vaccarino, Flora M; Stevens, Hanna E; Kocabas, Arif; Palejev, Dean; Szekely, Anna; Grigorenko, Elena L; Weissman, Sherman	June 2011	Not Relevant
21204834	Create Study	Annual Research Review: The promise of stem cell research for neuropsychiatric disorders.	Journal of child psychology and psychiatry, and allied disciplines	Vaccarino, Flora M; Urban, Alexander Eckehart; Stevens, Hanna E; Szekely, Anna; Abyzov, Alexej; Grigorenko, Elena L; Gerstein, Mark; Weissman, Sherman	April 2011	Not Relevant
20814258	Create Study	Behavior, brain, and genome in genomic disorders: finding the correspondences.	Journal of developmental and behavioral pediatrics : JDBP	Grigorenko EL, Urban AE, Mencl E	September 2010	Not Relevant

helpcenter.collection.publications-tab

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.

Contact NDA Help Desk

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.

For NIMH HIV-related research that involves human research participants: Select the dictionary or dictionaries most appropriate for your research. If your research does not require all three data dictionaries, just ignore the ones you do not need. There is no need to delete extra data dictionaries from your NDA Collection. You can adjust the Targeted Enrollment column in the Data Expected tab to “0” for those unnecessary data dictionaries. At least one of the three data dictionaries must have a non-zero value.

Data Expected	Targeted Enrollment	Initial Submission	Subjects Submitted	Initial Share	Subjects Shared	Status
No Mandatory Data Expected

To create your project's Data Expected list, use the "+New Data Expected" to add or request existing structures and to request new Data Structures that are not in the NDA Data Dictionary.

If the Structure you need already exists, locate it and specify your dates and enrollment when adding it to your Data Expected list. If you require changes to the Structure you need, select the indicator stating "No, it requires changes to meet research needs," and upload a file containing your requested changes.

If the structure you need is not yet defined in the Data Dictionary, you can select "Upload Definition" and attach the necessary materials to request its creation.

When selecting the expected dates for your data, make sure to follow the standard Data Sharing Regimen and choose dates within the date ranges that correspond to your project start and end dates.

Please visit the Completing Your Data Expected Tutorial for more information.

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 Expected	Targeted Enrollment	Initial Submission	Subjects Submitted	Initial Share	Subjects Shared	Status
Mullen Scales of Early Learning	10	12/31/2012	1	09/01/2013	1	Approved
Genomics/omics	10	01/15/2011	16	05/15/2011	16	Approved
ADOS	10	12/31/2012	5	09/01/2013	5	Approved
ADI-R	10	12/31/2012	4	09/01/2013	4	Approved
Wechsler Intelligence Scale for Children	10	12/31/2012	1	09/01/2013	1	Approved
DAS-II: Differential Ability Scales	10	12/31/2012	3	09/01/2013	3	Approved
Vineland (Parent and Caregiver)	10	12/31/2012	3	09/01/2013	3	Approved

Structure not yet defined

No Status history for this Data Expected has been recorded yet

helpcenter.collection.data-expected-tab

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.

Researchers who are starting their project need to update their Data Expected list to include all the Data Structures they are collecting under their grant and set their initial submission and sharing schedule according to the NDA Data Sharing Regimen.

To add existing Data Structures from the Data Dictionary, to request new Data Structure that are not in the Dictionary, or to request changes to existing Data Structures, click "+New Data Expected".

For step-by-step instructions on how to add existing Data Structures, request changes to an existing Structure, or request a new Data Structure, please visit the Completing Your Data Expected Tutorial.

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.

Contact NDA Help Desk

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 NameFilter by Study Name	AbstractFilter by Abstract	Collection/Study SubjectsFilter by Collection/Study Subjects	Data UsageFilter by Data Usage	StateFilter by State
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.	5/17423	Secondary Analysis	Shared
The evolution and population diversity of human-specific segmental duplications	Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families). We show that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed “core duplicons”, and evolved primarily in an interspersed inverted orientation. In addition to Homo sapiens-specific gene expansions (e.g., TCAF1/2), we highlight ten gene families (e.g., ARHGAP11B and SRGAP2C) where copy number never returns to the ancestral state, there is evidence of mRNA splicing, and no common gene-disruptive mutations are observed in the general population. Such duplicates are candidates for the evolution of human-specific adaptive traits.	2/6360	Primary Analysis	Shared
The importance of low IQ to early diagnosis of autism	Some individuals can flexibly adapt to life’s changing demands while others, in particular those with Autism Spectrum Disorder (ASD), find it challenging. The origin of early individual differences in cognitive abilities, the putative tools with which to navigate novel information in life, including in infants later diagnosed with ASD remains unexplored. Moreover, the role of intelligence quotient (IQ) vis-à-vis core features of autism remains debated. We systematically investigate the contribution of early IQ in future autism outcomes in an extremely large, population-based study of 8,000 newborns, infants, and toddlers from the US between 2 and 68 months with over 15,000 cross-sectional and longitudinal assessments, and for whom autism outcomes are ascertained or ruled out by about 2-4 years. This population is representative of subjects involved in the National Institutes of Health (NIH)-funded research, mainly on atypical development, in the US. Analyses using predetermined age bins showed that IQ scores are consistently lower in ASD relative to TD at all ages (p<0.001), and IQ significantly correlates with calibrated severity scores (total CSS, as well as non-verbal and verbal CSS) on the ADOS. Note, VIQ is no better than the full-scale IQ to predict ASD cases. These findings raise new, compelling questions about potential atypical brain circuitry affecting performance in both verbal and nonverbal abilities and that precede an ASD diagnosis. This study is the first to establish prospectively that low early IQ is a major feature of ASD in early childhood.	1/6323	Secondary Analysis	Shared
Unravelling the Collective Diagnostic Power Behind the Features in the Autism Diagnostic Observation Schedule	Background: Autism is a group of heterogeneous disorders defined by deficits in social interaction and communication. Typically, diagnosis depends on the results of a behavioural examination called the Autism Diagnostic Observation Schedule (ADOS). Unfortunately, administration of the ADOS exam is time-consuming and requires a significant amount of expert intervention, leading to delays in diagnosis and access to early intervention programs. The diagnostic power of each feature in the ADOS exam is currently unknown. Our hypothesis is that certain features could be removed from the exam without a significant reduction in diagnostic accuracy, sensitivity or specificity. Objective: Determine the smallest subset of predictive features in ADOS module-1 (an exam variant for patients with minimal verbal skills). Methodology: ADOS module-1 datasets were acquired from the Autism Genetic Resource Exchange and the National Database for Autism Research. The datasets contained 2572 samples with the following labels: autism (1763), autism spectrum (513), and non-autism (296). The datasets were used as input to 4 different cost-sensitive classifiers in Weka (functional trees, LADTree, logistic model trees, and PART). For each classifier, a 10-fold cross validation was preformed and the number of predictive features, accuracy, sensitivity, and specificity was recorded. Results & Conclusion: Each classifier resulted in a reduction of the number of ADOS features required for autism diagnosis. The LADtree classifier was able to obtain the largest reduction, utilizing only 10 of 29 ADOS module-1 features (96.8% accuracy, 96.9% sensitivity, and 95.9% specificity). Overall, these results are a step towards a more efficient behavioural exam for autism diagnosis.	1/1832	Secondary Analysis	Shared
Automated Autism Diagnosis using Phenotypic and Genotypic Attributes: Phase I	The ultimate goal of this project is to develop a predictive system that can automate the diagnosis process for autism using phenotypic and genotypic attributes for classification. At this time, only a first phase is being pursued: starting with scores from Autism Diagnostic Observation Schedule (ADOS) reports, use data-mining techniques to select the smallest set of the most informative evaluation points that can lead to similar behavioral diagnoses as using all report features. The effort began in March, 2016 after data access to NDAR was granted. This report describes the results from that date through the end of December 2016.	1/1045	Secondary Analysis	Shared
One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin	Few studies have been conducted to understand post-zygotic accumulation of mutations in cells of the healthy human body. We reprogrammed 32 skin fibroblast cells from families of donors into human induced pluripotent stem cell (hiPSC) lines. The clonal nature of hiPSC lines allows a high-resolution analysis of the genomes of the founder fibroblast cells without being confounded by the artifacts of single cell whole genome amplification. We estimate that on average a fibroblast cell in children has 1,035 mostly benign mosaic SNVs. On average, 235 SNVs could be directly confirmed in the original fibroblast population by ultra-deep sequencing, down to an allele frequency (AF) of 0.1%. More sensitive droplet digital PCR experiments confirmed more SNVs as mosaic with AF as low as 0.01%, suggesting that 1,035 mosaic SNVs per fibroblast cell is the true average. Similar analyses in adults revealed no significant increase in the number of SNVs per cell, suggesting that a major fraction of mosaic SNVs in fibroblasts arises during development. Mosaic SNVs were distributed uniformly across the genome and were enriched in a mutational signature previously observed in cancers and in de novo variants and which, we hypothesize, is a hallmark of normal cell proliferation. Finally, AF distribution of mosaic SNVs had distinct narrow peaks, which could be a characteristic of clonal cell selection, clonal expansion, or both. These findings reveal a large degree of somatic mosaicism in healthy human tissues, link de novo and cancer mutations to somatic mosaicism and couple somatic mosaicism with cell proliferation.	12/12	Secondary Analysis	Shared
Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cell	Reprogramming human somatic cells into induced pluripotent stem cells (iPSC) has been suspected of causing de novo copy number variations (CNVs). To explore this issue, we performed a whole-genome and transcriptome analysis of 20 human iPSC lines derived from primary skin fibroblasts of 7 individuals using next-generation sequencing. We find that, on average, an iPSC line manifests two CNVs not apparent in the fibroblasts from which the iPSC was derived. Using qPCR, PCR, and digital droplet PCR (ddPCR) to amplify across the CNVs' breakpoints, we show that at least 50% of those CNVs are present as low frequency somatic genomic variants in parental fibroblasts and are manifested in iPSC colonies due to their clonal origin. Hence, reprogramming does not necessarily lead to de novo CNVs in iPSC, since most of line-manifested CNVs reflect somatic mosaicism in the human skin. Moreover, our findings demonstrate that clonal expansion, and iPSC lines in particular, can be used as a discovery tool to reliably detect low frequency CNVs in the tissue of origin. Overall, we estimate that approximately 30% of the fibroblast cells have somatic CNVs, suggesting widespread somatic mosaicism in the human body. Our study paves the way to understanding the fundamental question of the extent to which cells of the human body normally acquire structural alterations in their DNA post-zygotically.	9/9	Primary Analysis	Shared

* Data not on individual level

helpcenter.collection.associated-studies-tab

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.

Contact NDA Help Desk

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