NIMH Data Archive - Data

Genomics

Neuroimaging

Phenotype¹

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Clinical Trial

¹ Numbers reported are subjects by age

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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
29	Microarray family 03 (father, mother, sibling)	Omics	03/24/2011
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
41	Immunofluorescence	Omics	05/11/2011
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

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.

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

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Data Expected Item	Original Sharing Date	New Sharing Date

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Dissecting recurrent microdeletion syndromes using dual-guide genome editing #2304

General
Experiments (3)
Shared Data
Publications (18)
Data Expected (2)
Associated Studies (5)

Collection Title	Collection Investigators	Collection Description
Collection Title:	Dissecting recurrent microdeletion syndromes using dual-guide genome editing
Collection Investigators:	James Gusella
Collection Description:	Recurrent microdeletion syndromes (rMDS), such as those associated with 16p11.2, 1q21 and 22q11.2, represent a major component (10-15%) of the genetic etiology of neurodevelopmental disorders, including autism spectrum disorder (ASD). In each rMDS, a distinct set of genes is reproducibly reduced to haploid dosage due to non-allelic homologous recombination (NHAR) mediated by flanking segmental duplications. The neurodevelopmental phenotypes in rMDS could theoretically derive primarily from a single gene driver, as we have shown is often the case for non-recurrent MDS, or from the combined effects of multiple genes that are dysregulated in concert. This project will test the hypothesis that the transcriptional effects of these three common rMDS converge on a small number of pathways/processes that are critical for abnormal neurodevelopment. It will further evaluate whether there are individual genetic drivers responsible for the dysregulated networks associated with these rMDS, and whether the transcriptional changes that occur can be rescued either by directly re-introducing the driver gene into a cellular system or through trans-rescue of secondary networks. The project will capitalize on our recent advances in CRISPR/Cas9 genome editing to efficiently generate large deletions in induced pluripotent stem cells (iPSC) using a novel dual-guide approach. These isogenic cells eliminate the confound of differing genetic backgrounds and thereby provide a powerful assay system. Specifically, we aim to compare the transcriptional consequences of full deletion in these three rMDS regions and identify overlapping genes/pathways that are altered due to haploinsufficiency for each full microdeletion (Aim 1). We will then seek to identify key genetic drivers within each rMDS by systematic single gene ablation within the rMDS region (Aim 2). Finally, we will test whether critical network alterations can be rescued by re-introducing a single driver gene or manipulating hub genes within dysregulated networks (Aim 3). At its conclusion, this study will have deconstructed three of the most common rMDS to yield critical neurodevelopment-associated networks that can be rescued by secondary manipulation, thereby offering a direct route to the discovery of neuronal biomarkers and targeted therapeutic intervention.
Data Repository:	NIMH Data Archive
Permission Group:
Collection Creation Date:	08/19/2015
Collection Phase:	Funding Completed
Collection Sub-Phase:	Close Out
Blinded Clinical Trial:	No
Total Funded Amount:	$1,216,536.00
Subjects Shared:	2

{"values":[]}

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Funding Sources:

Funding Source Name	Funding Source URL
NIH - Extramural	None

Supporting Documentation:

File Name	File Type	Description	Audience
QA-notification.txt	Other	Quality Assurance Notification	Qualified Researchers
SupportingDoc_ C2304.docx	Other	Indication that The data we have submitted is only from cultured cells. There is no enrolment target and we only have one anonymous cell line, so no pedigree.	Qualified Researchers

Grant Information:

Project Number	Project Title	Start Date	End Date	Planned Enrollment	Actual Enrollment	Organization	Funds Obligated
R01NS093200-01	Dissecting recurrent microdeletion syndromes using dual-guide genome editing	07/01/2015	06/30/2021	Not Reported	Not Reported	MASSACHUSETTS GENERAL HOSPITAL	$1,216,536.00

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
495	16p11.2 CRISPR edited human iPSCs and the NSC and iN derivatives RNA-Seq	07/12/2016	Approved	Omics
2402	15q13.3 CRISPR edited human NSC and iN derivatives RNA-Seq	10/26/2023	Approved	Omics
2404	Whole genome sequencing of iPSC backgrounds	11/08/2023	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
Genomics Sample	Genomics	2
Genomics Subject	Genomics	2

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
39210012	Create Study	An increased copy number of glycine decarboxylase (GLDC) associated with psychosis reduces extracellular glycine and impairs NMDA receptor function.	Molecular psychiatry	Kambali, Maltesh; Li, Yan; Unichenko, Petr; Feria Pliego, Jessica A; Yadav, Rachita; Liu, Jing; McGuinness, Patrick; Cobb, Johanna G; Wang, Muxiao; Nagarajan, Rajasekar; Lyu, Jinrui; Vongsouthi, Vanessa; Jackson, Colin J; Engin, Elif; Coyle, Joseph T; Shin, Jaeweon; Hodgson, Nathaniel W; Hensch, Takao K; Talkowski, Michael E; Homanics, Gregg E; Bolshakov, Vadim Y; Henneberger, Christian; Rudolph, Uwe	March 1, 2025	Not Determined
38496583	Create Study	Activation of the imprinted Prader-Willi Syndrome locus by CRISPR-based epigenome editing.	bioRxiv : the preprint server for biology	Rohm, Dahlia; Black, Joshua B; McCutcheon, Sean R; Barrera, Alejandro; Morone, Daniel J; Nuttle, Xander; de Esch, Celine E; Tai, Derek J C; Talkowski, Michael E; Iglesias, Nahid; Gersbach, Charles A	March 4, 2024	Not Determined
38091988	Create Study	Parallelized engineering of mutational models using piggyBac transposon delivery of CRISPR libraries.	Cell reports methods	Nuttle, Xander; Burt, Nicholas D; Currall, Benjamin; Moysés-Oliveira, Mariana; Mohajeri, Kiana; Bhavsar, Riya; Lucente, Diane; Yadav, Rachita; Tai, Derek J C; Gusella, James F; Talkowski, Michael E	January 22, 2024	Not Determined
36537238	Create Study	CHD8 suppression impacts on histone H3 lysine 36 trimethylation and alters RNA alternative splicing.	Nucleic acids research	Kerschbamer, Emanuela; Arnoldi, Michele; Tripathi, Takshashila; Pellegrini, Miguel; Maturi, Samuele; Erdin, Serkan; Salviato, Elisa; Di Leva, Francesca; Sebestyén, Endre; Dassi, Erik; Zarantonello, Giulia; Benelli, Matteo; Campos, Eric; Basson, M Albert; Gusella, James F; Gustincich, Stefano; Piazza, Silvano; Demichelis, Francesca; Talkowski, Michael E; Ferrari, Francesco; Biagioli, Marta	December 9, 2022	Not Determined
36283406	Create Study	Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models.	American journal of human genetics	Mohajeri, Kiana; Yadav, Rachita; D'haene, Eva; Boone, Philip M; Erdin, Serkan; Gao, Dadi; Moyses-Oliveira, Mariana; Bhavsar, Riya; Currall, Benjamin B; O'Keefe, Kathryn; Burt, Nicholas D; Lowther, Chelsea; Lucente, Diane; Salani, Monica; Larson, Mathew; Redin, Claire; Dudchenko, Olga; Aiden, Erez Lieberman; Menten, Björn; Tai, Derek J C; Gusella, James F; Vergult, Sarah; Talkowski, Michael E	November 3, 2022	Not Relevant
36280734	Study (2060)	Statistical and functional convergence of common and rare genetic influences on autism at chromosome 16p.	Nature genetics	Weiner, Daniel J; Ling, Emi; Erdin, Serkan; Tai, Derek J C; Yadav, Rachita; Grove, Jakob; Fu, Jack M; Nadig, Ajay; Carey, Caitlin E; Baya, Nikolas; Bybjerg-Grauholm, Jonas; iPSYCH Consortium; ASD Working Group of the Psychiatric Genomics Consortium; ADHD Working Group of the Psychiatric Genomics Consortium; Berretta, Sabina; Macosko, Evan Z; Sebat, Jonathan; O'Connor, Luke J; Hougaard, David M; Børglum, Anders D; Talkowski, Michael E; McCarroll, Steven A; Robinson, Elise B	November 1, 2022	Relevant
36152629	Study (2061)	Tissue- and cell-type-specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models.	American journal of human genetics	Tai, Derek J C; Razaz, Parisa; Erdin, Serkan; Gao, Dadi; Wang, Jennifer; Nuttle, Xander; de Esch, Celine E; Collins, Ryan L; Currall, Benjamin B; O'Keefe, Kathryn; Burt, Nicholas D; Yadav, Rachita; Wang, Lily; Mohajeri, Kiana; Aneichyk, Tatsiana; Ragavendran, Ashok; Stortchevoi, Alexei; Morini, Elisabetta; Ma, Weiyuan; Lucente, Diane; Hastie, Alex; Kelleher, Raymond J; Perlis, Roy H; Talkowski, Michael E; Gusella, James F	October 6, 2022	Relevant
35917817	Create Study	A cross-disorder dosage sensitivity map of the human genome.	Cell	Collins, Ryan L; Glessner, Joseph T; Porcu, Eleonora; Lepamets, Maarja; Brandon, Rhonda; Lauricella, Christopher; Han, Lide; Morley, Theodore; Niestroj, Lisa-Marie; Ulirsch, Jacob; Everett, Selin; Howrigan, Daniel P; Boone, Philip M; Fu, Jack; Karczewski, Konrad J; Kellaris, Georgios; Lowther, Chelsea; Lucente, Diane; Mohajeri, Kiana; Nõukas, Margit; Nuttle, Xander; Samocha, Kaitlin E; Trinh, Mi; Ullah, Farid; Võsa, Urmo; Epi25 Consortium; Estonian Biobank Research Team; Hurles, Matthew E; Aradhya, Swaroop; Davis, Erica E; Finucane, Hilary; Gusella, James F; Janze, Aura; Katsanis, Nicholas; Matyakhina, Ludmila; Neale, Benjamin M; Sanders, David; Warren, Stephanie; Hodge, Jennelle C; Lal, Dennis; Ruderfer, Douglas M; Meck, Jeanne; Mägi, Reedik; Esko, Tõnu; Reymond, Alexandre; Kutalik, Zoltán; Hakonarson, Hakon; Sunyaev, Shamil; Brand, Harrison; Talkowski, Michael E	August 4, 2022	Not Determined
35688811	Study (2065)	Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder.	Nature communications	Lim, Elaine T; Chan, Yingleong; Dawes, Pepper; Guo, Xiaoge; Erdin, Serkan; Tai, Derek J C; Liu, Songlei; Reichert, Julia M; Burns, Mannix J; Chan, Ying Kai; Chiang, Jessica J; Meyer, Katharina; Zhang, Xiaochang; Walsh, Christopher A; Yankner, Bruce A; Raychaudhuri, Soumya; Hirschhorn, Joel N; Gusella, James F; Talkowski, Michael E; Church, George M	June 10, 2022	Relevant
34006844	Study (2046)	16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro.	Nature communications	Sundberg, Maria; Pinson, Hannah; Smith, Richard S; Winden, Kellen D; Venugopal, Pooja; Tai, Derek J C; Gusella, James F; Talkowski, Michael E; Walsh, Christopher A; Tegmark, Max; Sahin, Mustafa	May 18, 2021	Relevant
32533064	Create Study	Functional annotation of rare structural variation in the human brain.	Nature communications	Han, Lide; Zhao, Xuefang; Benton, Mary Lauren; Perumal, Thaneer; Collins, Ryan L; Hoffman, Gabriel E; Johnson, Jessica S; Sloofman, Laura; Wang, Harold Z; Stone, Matthew R; CommonMind Consortium; Brennand, Kristen J; Brand, Harrison; Sieberts, Solveig K; Marenco, Stefano; Peters, Mette A; Lipska, Barbara K; Roussos, Panos; Capra, John A; Talkowski, Michael; Ruderfer, Douglas M	June 12, 2020	Not Relevant
32503625	Create Study	Transcriptional consequences of MBD5 disruption in mouse brain and CRISPR-derived neurons.	Molecular autism	Seabra, Catarina M; Aneichyk, Tatsiana; Erdin, Serkan; Tai, Derek J C; De Esch, Celine E F; Razaz, Parisa; An, Yu; Manavalan, Poornima; Ragavendran, Ashok; Stortchevoi, Alexei; Abad, Clemer; Young, Juan I; Maciel, Patricia; Talkowski, Michael E; Gusella, James F	June 5, 2020	Not Relevant
30590535	Create Study	Kctd13-deficient mice display short-term memory impairment and sex-dependent genetic interactions.	Human molecular genetics	Arbogast, Thomas; Razaz, Parisa; Ellegood, Jacob; McKinstry, Spencer U; Erdin, Serkan; Currall, Benjamin; Aneichyk, Tanya; Lerch, Jason P; Qiu, Lily R; Rodriguiz, Ramona M; Henkelman, R M; Talkowski, Michael E; Wetsel, William C; Golzio, Christelle; Katsanis, Nicholas	May 2019	Not Relevant
28965845	Create Study	The Immune Signaling Adaptor LAT Contributes to the Neuroanatomical Phenotype of 16p11.2 BP2-BP3 CNVs.	American journal of human genetics	Loviglio, Maria Nicla; Arbogast, Thomas; Jønch, Aia Elise; Collins, Stephan C; Popadin, Konstantin; Bonnet, Camille S; Giannuzzi, Giuliana; Maillard, Anne M; Jacquemont, Sébastien; 16p11.2 Consortium; Yalcin, Binnaz; Katsanis, Nicholas; Golzio, Christelle; Reymond, Alexandre	October 2017	Not Relevant
28691782	Create Study	A novel microduplication of ARID1B: Clinical, genetic, and proteomic findings.	American journal of medical genetics. Part A	Seabra, Catarina M; Szoko, Nicholas; Erdin, Serkan; Ragavendran, Ashok; Stortchevoi, Alexei; Maciel, Patrícia; Lundberg, Kathleen; Schlatzer, Daniela; Smith, Janice; Talkowski, Michael E; Gusella, James F; Natowicz, Marvin R	September 1, 2017	Not Relevant
28257685	Create Study	2016 William Allan Award: Human Disease Research: Genetic Cycling and Re-cycling.	American journal of human genetics	Gusella, James F	March 2017	Not Relevant
27240531	Create Study	Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes.	Molecular psychiatry	Loviglio MN, Leleu M, Männik K, Passeggeri M, Giannuzzi G, Van Der Werf I, Waszak SM, Zazhytska M, Roberts-Caldeira I, Gheldof N, Migliavacca E, Alfaiz AA, Hippolyte L, Maillard AM, Van Dijck A, Kooy RF, Sanlaville D, Rosenfeld JA, Shaffer LG, Andrieux J, Marshall C, Scherer SW, Shen Y, et al.	June 2017	Not Relevant
26829649	Study (414)	Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR.	Nature neuroscience	Tai, Derek J C; Ragavendran, Ashok; Manavalan, Poornima; Stortchevoi, Alexei; Seabra, Catarina M; Erdin, Serkan; Collins, Ryan L; Blumenthal, Ian; Chen, Xiaoli; Shen, Yiping; Sahin, Mustafa; Zhang, Chengsheng; Lee, Charles; Gusella, James F; Talkowski, Michael E	March 2016	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
Research Subject and Pedigree	1	07/15/2016	2	07/15/2016	2	Approved

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
Genomics/omics	1	07/15/2016	2	07/15/2016	2	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
16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro.	Reciprocal copy number variations (CNVs) of 16p11.2 are associated with a wide spectrum of neuropsychiatric and neurodevelopmental disorders. Here, we use human induced pluripotent stem cells (iPSCs)-derived dopaminergic (DA) neurons carrying CNVs of 16p11.2 duplication (16pdup) and 16p11.2 deletion (16pdel), engineered using CRISPR-Cas9. We show that 16pdel iPSC-derived DA neurons have increased soma size and synaptic marker expression compared to isogenic control lines, while 16pdup iPSC-derived DA neurons show deficits in neuronal differentiation and reduced synaptic marker expression. The 16pdel iPSC-derived DA neurons have impaired neurophysiological properties. The 16pdel iPSC-derived DA neuronal networks are hyperactive and have increased bursting in culture compared to controls. We also show that the expression of RHOA is increased in the 16pdel iPSC-derived DA neurons and that treatment with a specific RHOA-inhibitor, Rhosin, rescues the network activity of the 16pdel iPSC-derived DA neurons. Our data suggest that 16p11.2 deletion-associated iPSC-derived DA neuron hyperactivation can be rescued by RHOA inhibition.	1/1	Secondary Analysis	Shared
Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR.	Recurrent, reciprocal genomic disorders resulting from non-allelic homologous recombination (NAHR) between near-identical segmental duplications (SDs) are a major cause of human disease, often producing phenotypically distinct syndromes. The genomic architecture of flanking SDs presents a challenge for modeling these syndromes; however, the capability to efficiently generate reciprocal copy number variants (CNVs) that mimic NAHR would represent a valuable modeling tool. We describe here a CRISPR/Cas9 genome engineering method, single-guide CRISPR/Cas targeting of repetitive elements (SCORE), to model reciprocal genomic disorders and demonstrate its capabilities by generating reciprocal CNVs of 16p11.2 and 15q13.3, including alteration of one copy-equivalent of the SDs that mediate NAHR in vivo. The method is reproducible, and RNA sequencing reliably clusters transcriptional signatures from human subjects with in vivo CNVs and their corresponding in vitro models. This new approach will provide broad applicability for the study of genomic disorders and, with further development, may also permit efficient correction of these defects.	1/1	Primary Analysis	Shared
Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder.	Cerebral organoids can be used to gain insights into cell type specific processes perturbed by genetic variants associated with neuropsychiatric disorders. However, robust and scalable phenotyping of organoids remains challenging. Here, we perform RNA sequencing on 71 samples comprising 1,420 cerebral organoids from 25 donors, and describe a framework (Orgo-Seq) to integrate bulk RNA and single-cell RNA sequence data. We apply Orgo-Seq to 16p11.2 deletions and 15q11-13 duplications, two loci associated with autism spectrum disorder, to identify immature neurons and intermediate progenitor cells as critical cell types for 16p11.2 deletions. We further applied Orgo-Seq to identify cell type-specific driver genes. Our work presents a quantitative phenotyping framework to integrate multi-transcriptomic datasets for the identification of cell types and cell type-specific co-expressed driver genes associated with neuropsychiatric disorders.	1/1	Primary Analysis	Shared
Statistical and functional convergence of common and rare genetic influences on autism at chromosome 16p.	The canonical paradigm for converting genetic association to mechanism involves iteratively mapping individual associations to the proximal genes through which they act. In contrast, in the present study we demonstrate the feasibility of extracting biological insights from a very large region of the genome and leverage this strategy to study the genetic influences on autism. Using a new statistical approach, we identified the 33-Mb p-arm of chromosome 16 (16p) as harboring the greatest excess of autism's common polygenic influences. The region also includes the mechanistically cryptic and autism-associated 16p11.2 copy number variant. Analysis of RNA-sequencing data revealed that both the common polygenic influences within 16p and the 16p11.2 deletion were associated with decreased average gene expression across 16p. The transcriptional effects of the rare deletion and diffuse common variation were correlated at the level of individual genes and analysis of Hi-C data revealed patterns of chromatin contact that may explain this transcriptional convergence. These results reflect a new approach for extracting biological insight from genetic association data and suggest convergence of common and rare genetic influences on autism at 16p.	1/1	Secondary Analysis	Shared
Tissue- and cell-type-specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models.	Chromosome 16p11.2 reciprocal genomic disorder, resulting from recurrent copy-number variants (CNVs), involves intellectual disability, autism spectrum disorder (ASD), and schizophrenia, but the responsible mechanisms are not known. To systemically dissect molecular effects, we performed transcriptome profiling of 350 libraries from six tissues (cortex, cerebellum, striatum, liver, brown fat, and white fat) in mouse models harboring CNVs of the syntenic 7qF3 region, as well as cellular, transcriptional, and single-cell analyses in 54 isogenic neural stem cell, induced neuron, and cerebral organoid models of CRISPR-engineered 16p11.2 CNVs. Transcriptome-wide differentially expressed genes were largely tissue-, cell-type-, and dosage-specific, although more effects were shared between deletion and duplication and across tissue than expected by chance. The broadest effects were observed in the cerebellum (2,163 differentially expressed genes), and the greatest enrichments were associated with synaptic pathways in mouse cerebellum and human induced neurons. Pathway and co-expression analyses identified energy and RNA metabolism as shared processes and enrichment for ASD-associated, loss-of-function constraint, and fragile X messenger ribonucleoprotein target gene sets. Intriguingly, reciprocal 16p11.2 dosage changes resulted in consistent decrements in neurite and electrophysiological features, and single-cell profiling of organoids showed reciprocal alterations to the proportions of excitatory and inhibitory GABAergic neurons. Changes both in neuronal ratios and in gene expression in our organoid analyses point most directly to calretinin GABAergic inhibitory neurons and the excitatory/inhibitory balance as targets of disruption that might contribute to changes in neurodevelopmental and cognitive function in 16p11.2 carriers. Collectively, our data indicate the genomic disorder involves disruption of multiple contributing biological processes and that this disruption has relative impacts that are context specific.	1/1	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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