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
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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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.

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Research Evaluating the Value of Augmenting Medication with Psychotherapy (REVAMP) #2153

General
Experiments (0)
Shared Data
Publications (9)
Associated Studies (3)

Collection Title	Collection Investigators	Collection Description
Collection Title:	Research Evaluating the Value of Augmenting Medication with Psychotherapy (REVAMP)
Collection Investigators:	James P. McCullough
Collection Description:	Chronic depression affects approximately 5% of adults in the United States and is associated with significant functional impairment and high health care utilization. The combination of drug treatment and psychotherapy may be most effective in treating depression. This study will determine the effects of adjunctive psychotherapy in depressed patients who have failed to respond or have responded only partially to an initial trial medication.Participants receive an initial trial of antidepressant medication for 8 to 12 weeks. Participants who continue to have depressive symptoms are randomly assigned to add Cognitive Behavioral Analysis System of Psychotherapy (CBASP) or supportive therapy to their medication regimens or to continue pharmacotherapy alone for an additional 12 weeks. Assessments are made at 6 and 12 months post-treatment. Note: The original medication file indicates start and stop dates or continuing codes. The new file specifies the medications for the visit time period
Data Repository:	NIMH Data Archive
Permission Group:
Collection Creation Date:	03/31/2015
Collection Phase:	Funding Completed
Collection Sub-Phase:	Close Out
Blinded Clinical Trial:	No
Total Funded Amount:	$1,669,762.00
Subjects Shared:	1,132

{"values":[]}

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Funding Sources:

Funding Source Name	Funding Source URL
NIH - Extramural	None

Supporting Documentation:

File Name	File Type	Description	Audience
REVAMP_Overview.pdf	Background	Overview	Qualified Researchers
REVAMP_RAND_coding.docx	Methods	Randomization coding	Qualified Researchers
Additional_Notes.docx	Other	Additional Notes	Qualified Researchers
REVAMP_Schedule_of_Assessments.pdf	Methods	Schedule of Assessments	Qualified Researchers
REVAMP_RAND.xlsx	Results	Randomization data	Qualified Researchers
REVAMP_Protocol.pdf	Analysis Protocol	Protocol	Qualified Researchers
REVAMP_Published_Reports.pdf	Publication	Published Reports	Qualified Researchers
REVAMP_Document_Tracking_Form.docx	Other	Document Tracking Form	Qualified Researchers
REVAMP_Scoring_Conventions.pdf	Other	Scoring Conventions	Qualified Researchers
REVAMP_Manual_of_Operations.pdf	Methods	Manual of Operations	Qualified Researchers
REVAMP_SCID.pdf	Methods	SCID Form	Qualified Researchers

Grant Information:

Project Number	Project Title	Start Date	End Date	Planned Enrollment	Actual Enrollment	Organization	Funds Obligated
U01MH062475-01	CBASP Augmentation for Treatment of Chronic Depression	09/24/2002	06/30/2009	226	62	WEILL MEDICAL COLL OF CORNELL UNIV	$1,669,762.00

Clinical Trials:

Brief Summary	Status	Clinical Trial ID	Study ID	Principal Investigator	Start Date	End Date
This 24-week study, with a 12-month follow up period, will compare the effectiveness of antidepressant medication alone to the combination of psychotherapy and antidepressant medication in patients with chronic depression.	Completed	NCT00057551	U01MH062475	James H Kocsis	April 2003	March 2007

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
No records found.

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
Antidepressant Treatment History Questionnaire	Clinical Assessments	803
Antidepressant Treatment Response Questionnaire	Clinical Assessments	366
Arizona Sexual Side Effects Form	Clinical Assessments	801
Brief Psychiatric Rating Scale	Clinical Assessments	363
Clinic Visit	Clinical Assessments	808
Couple Satisfaction Index	Clinical Assessments	802
Demographics Form	Clinical Assessments	808
Depressive Experiences Questionnaire	Clinical Assessments	798
Dysfunctional Attitudes Scale	Clinical Assessments	798
Early Termination Form	Clinical Assessments	407
End of Study Form	Clinical Assessments	332
Endicott Work Productivity Scale	Clinical Assessments	807
Family Assessment Measure	Clinical Assessments	800
Frequency Intensity Burden Side Effects	Clinical Assessments	768
Hamilton Rating Scale for Depression	Clinical Assessments	808
Insight and Treatment Attitudes Questionnaire	Clinical Assessments	798
Inventory of Depressive Symptomatology	Clinical Assessments	805
Life - RIFT (The Range of Impaired Functioning Tool)	Clinical Assessments	808
Measure of Parental Style	Clinical Assessments	797
Medical History	Clinical Assessments	795
Medications and Treatments Form	Clinical Assessments	288
Mood and Anxiety Symptom Questionnaire	Clinical Assessments	800
Patient-Rated Inventory of Side Effects	Clinical Assessments	804
Protocol Eligibility	Clinical Assessments	1062
Protocol Violators	Clinical Assessments	636
Psychosocial Intervention Session Tracking Form	Clinical Assessments	465
Quick Inventory of Depressive Symptomatology	Clinical Assessments	807
SF-36 Health Survey	Clinical Assessments	799
Serious Adverse Events	Clinical Assessments	26
Social Adjustment Scale	Clinical Assessments	809
Social Problem-Solving Inventory	Clinical Assessments	800
Structured Clinical Interview for DSM-IV	Clinical Assessments	808
Treatment Efficacy Expectation Questionnaire	Clinical Assessments	613
Working Alliance Scale	Clinical Assessments	362

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
26829714	Create Study	Convergence in patient-therapist therapeutic alliance ratings and its relation to outcome in chronic depression treatment.	Psychotherapy research : journal of the Society for Psychotherapy Research	Laws, Holly B; Constantino, Michael J; Sayer, Aline G; Klein, Daniel N; Kocsis, James H; Manber, Rachel; Markowitz, John C; Rothbaum, Barbara O; Steidtmann, Dana; Thase, Michael E; Arnow, Bruce A	July 1, 2017	Not Determined
23102821	Create Study	Dysfunctional attitudes as a moderator of pharmacotherapy and psychotherapy for chronic depression.	Journal of psychiatric research	Shankman SA, Campbell ML, Klein DN, Leon AC, Arnow BA, Manber R, Keller MB, Markowitz JC, Rothbaum BO, Thase ME, Kocsis JH	January 2013	Not Determined
22767424	Create Study	Patient treatment preference as a predictor of response and attrition in treatment for chronic depression.	Depression and anxiety	Steidtmann, Dana; Manber, Rachel; Arnow, Bruce A; Klein, Daniel N; Markowitz, John C; Rothbaum, Barbara O; Thase, Michael E; Kocsis, James H	October 2012	Not Determined
21500885	Create Study	Social problem solving and depressive symptoms over time: a randomized clinical trial of cognitive-behavioral analysis system of psychotherapy, brief supportive psychotherapy, and pharmacotherapy.	Journal of consulting and clinical psychology	Klein, Daniel N; Leon, Andrew C; Li, Chunshan; D'Zurilla, Thomas J; Black, Sarah R; Vivian, Dina; Dowling, Frank; Arnow, Bruce A; Manber, Rachel; Markowitz, John C; Kocsis, James H	June 2011	Not Determined
19884606	Create Study	Cognitive behavioral analysis system of psychotherapy and brief supportive psychotherapy for augmentation of antidepressant nonresponse in chronic depression: the REVAMP Trial.	Archives of general psychiatry	Kocsis, James H; Gelenberg, Alan J; Rothbaum, Barbara O; Klein, Daniel N; Trivedi, Madhukar H; Manber, Rachel; Keller, Martin B; Leon, Andrew C; Wisniewski, Steven R; Arnow, Bruce A; Markowitz, John C; Thase, Michael E; REVAMP Investigators	November 2009	Not Determined
19434623	Create Study	Early adversity in chronic depression: clinical correlates and response to pharmacotherapy.	Depression and anxiety	Klein, Daniel N; Arnow, Bruce A; Barkin, Jennifer L; Dowling, Frank; Kocsis, James H; Leon, Andrew C; Manber, Rachel; Rothbaum, Barbara O; Trivedi, Madhukar H; Wisniewski, Stephen R	2009	Not Determined
19015627	Create Study	REVAMP - Research Evaluating the Value of Augmenting Medication with Psychotherapy: rationale and design.	Psychopharmacology bulletin	Trivedi MH, Kocsis JH, Thase ME, Morris DW, Wisniewski SR, Leon AC, Gelenberg AJ, Klein DN, Niederehe G, Schatzberg AF, Ninan PT, Keller MB	2008	Not Determined
18461844	Create Study	Therapists' responses to training in brief supportive psychotherapy.	American journal of psychotherapy	Markowitz JC, Manber R, Rosen P	2008	Not Determined
18272232	Create Study	Chronic forms of major depression are still undertreated in the 21st century: systematic assessment of 801 patients presenting for treatment.	Journal of affective disorders	Kocsis, James H; Gelenberg, Alan J; Rothbaum, Barbara; Klein, Daniel N; Trivedi, Madhukar H; Manber, Rachel; Keller, Martin B; Howland, Robert; Thase, Michael E	September 2008	Not Determined

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

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
Towards Outcome-Driven Patient Subgroups: A Machine Learning Analysis Across Six Depression Treatment Studies	Importance: Major depressive disorder (MDD) is a heterogeneous condition; multiple underlying neurobiological substrates could be associated with treatment response variability. Understanding the sources of this variability and predicting outcomes has been elusive. Machine learning (ML) has shown promise in predicting treatment response in MDD, but one limitation has been the lack of clinical interpretability of machine learning models, limiting clinician confidence in model results. Objective: To develop a machine learning model to derive treatment-relevant patient profiles using clinical and demographic information. Design: We analyzed data from six clinical trials of pharmacological treatment for depression (total n = 5438) using the Differential Prototypes Neural Network (DPNN), a neural network model that derives patient prototypes which can be used to derive treatment-relevant patient clusters while learning to generate probabilities for differential treatment response. A model classifying remission and outputting individual remission probabilities for five first-line monotherapies and three combination treatments was trained using clinical and demographic data. Setting: Previously-conducted clinical trials of antidepressant medications. Participants: Patients with MDD. Main outcomes and measures: Model validity and clinical utility were measured based on area under the curve (AUC) and expected improvement in sample remission rate with model-guided treatment, respectively. Post-hoc analyses yielded clusters (subgroups) based on patient prototypes learned during training. Prototypes were evaluated for interpretability by assessing differences in feature distributions (e.g. age, sex, symptom severity) and treatment-specific outcomes. Results: A 3-prototype model achieved an AUC of 0.66 and an expected absolute improvement in population remission rate of 6.5% (relative improvement of 15.6%). We identified three treatment-relevant patient clusters. Cluster A patients tended to be younger, to have increased levels of fatigue and more severe symptoms. Cluster B patients tended to be older, female with less severe symptoms, and the highest remission rates. Cluster C patients had more severe symptoms, lower remission rates, more psychomotor agitation, more intense suicidal ideation, more somatic genital symptoms, and showed improved remission with venlafaxine. Conclusion and Relevance: It is possible to produce novel treatment-relevant patient profiles using machine learning models; doing so may improve precision medicine for depression. Note: This model is not currently the subject of any active clinical trials and is not intended for clinical use.	875/6074	Secondary Analysis	Shared
Treatment selection using prototyping in latent-space with application to depression treatment	Machine-assisted treatment selection commonly follows one of two paradigms: a fully personalized paradigm which ignores any possible clustering of patients; or a sub-grouping paradigm which ignores personal differences within the identified groups. While both paradigms have shown promising results, each of them suffers from important limitations. In this article, we propose a novel deep learning-based treatment selection approach that is shown to strike a balance between the two paradigms using latent-space prototyping. Our approach is specifically tailored for domains in which effective prototypes and sub-groups of patients are assumed to exist, but groupings relevant to the training objective are not observable in the non-latent space. In an extensive evaluation, using both synthetic and Major Depressive Disorder (MDD) real-world clinical data describing 4754 MDD patients from clinical trials for depression treatment, we show that our approach favorably compares with state-of-the-art approaches. Specifically, the model produced an 8% absolute and 23% relative improvement over random treatment allocation. This is potentially clinically significant, given the large number of patients with MDD. Therefore, the model can bring about a much desired leap forward in the way depression is treated today.	876/5946	Secondary Analysis	Shared
Summary Measures for Quantifying the Extent of Visit Irregularity in Longitudinal Data: The STAR*D Study	This chapter applies the measures of irregularity from this thesis to the Sequenced Treatment Alternatives to Relieve Depression (STARD) study. The STARD study is the largest randomized clinical trial on patients suffering from major depression. This chapter focuses on the first phase of the study which pre-specified a common set of scheduled measurement occasions at weeks 2, 4, 6, 9, 12 post-baseline where individuals had their Quick Inventory of Depression Symptomatology (QIDS) questionnaire score recorded; however there were individuals who missed scheduled visits, and had unscheduled visits. Therefore, interest lies in determining whether visits can be treated as repeated measures. This is followed by a demonstration on how to select the appropriate modelling approach for the study outcome, and how to interpret the resulting parameter estimates. The target of inference of this chapter is to evaluate the mean QIDS score over the first 12 weeks of the trial.	67/4036	Secondary Analysis	Shared

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