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NDAR provides a single access to de-identified autism research data. For permission to download data, you will need an NDAR account with approved access to NDAR or a connected repository (AGRE, IAN, or the ATP). For NDAR access, you need to be a research investigator sponsored by an NIH recognized institution with federal wide assurance. See Request Access for more information.

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

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

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Shared

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

General

Title, investigators, and Collection Description may be edited along with the Collection Phase. For Collection Phase, the options Pre-enrollment, Enrollment, and Completed can be chosen allowing the Collection Owner to indicate the stage of data collection.

Funding Source

The ability to associate the funding source for the project is provided. For NIH funded grants, linkage to Project Reporter information (e.g. R01MH123456) is supported. Projects funded by others, including the URL of the project, are listed. Non NIH funded projects will become available here to link that data with the appropriate funding agency.

Supporting Documentation

Any documents related to the project may be uploaded clarifying the data or acquisition methods used may be uploaded and made available here. The default is to share these documents to the general public. An option to share only to qualified Researchers is also an option.

Clinical Trials

For clinical trials, the option to link to the clinical trial in clinicaltrials.gov is optionally provided.

Collection Summary Collection Charts
Collection Title Collection Investigators Collection Description
Methylomic and genomic impacts of organic pollutants in Dup15q syndrome
Janine LaSalle 
This study is designed to test a novel paradigm that the human genome dynamically interacts with the environment and that epigenetic mechanisms are at the interface of genome environment interactions. This study is designed to experimentally determine if PCB-95 and/or BDE-47 play a causal or compounding role in structural rearrangements of 15q using combined genomic and epigenomic approaches. In addition, this study will directly investigate the effect of combined genomic and environmental insults on the integrity of the methylome and transcriptome in human brain samples. The first aim seeks to experimentally model chromosome 15 duplication in a novel human cell line system to examine effects of PCB-95 or BDE-47 exposures on genomic stability (DNA-seq) and DNA methylation (MethylC-seq) using next generation sequencing technology. In the second aim, the effect of genetic and epigenetic changes on long-range chromatin loop structure within 15q11-q13 will be examined by chromatin conformation capture sequencing (4C-seq) and correlated to specific transcriptional alterations. The third aim seeks to directly investigate specific 15q gene targets for epigenetic and transcriptional changes in human brain samples with and without chromosome 15 duplication and high PCB-95 levels. The results of these studies are expected to formally test the hypothesis that DNA methylation levels reduced by specific environmental pollutants may result in genomic rearrangements and alterations in long-range chromatin,leading to transcriptional changes. In addition, epigenetic alterations of autism candidate genes involved in synaptogenesis in human brain samples are expected to be uncovered by this approach. Finally, the results of these studies are expected to be broadly relevant to understanding the relationship between the genome, environmental exposures, and the epigenome in human health and disease.
NDAR
Enrolling
Shared
$1,840,993.00
0
0
0

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NIH - Extramural None


R01ES021707-01 Methylomic and genomic impacts of organic pollutants in Dup15q syndrome 06/12/2012 02/28/2018 Not Reported Not Reported UNIVERSITY OF CALIFORNIA AT DAVIS $1,840,993.00

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

Experiments

To create a new Omics, eye tracking, fMRI, or EEG experiment, press the "+ New Experiment" button. Once an experiment is created, then raw files for these types of experiments should be provided, associating the experiment – through Experiment_ID – with the metadata defined in the experiments interface.

IDNameCreated DateStatusType
362MARBLES placenta MethylC-seq07/28/2015ApprovedOmics

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

Shared Data

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

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

PubMed IDStudyTitleJournalAuthorsDateStatus
28032673Create StudyDental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns.Stem cells (Dayton, Ohio)Dunaway K, Goorha S, Matelski L, Urraca N, Lein PJ, Korf I, Reiter LT, Lasalle JMDecember 2016Not Determined
27974215Create StudyCumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes.Cell reportsDunaway KW, Islam MS, Coulson RL, Lopez SJ, Vogel Ciernia A, Chu RG, Yasui DH, Pessah IN, Lott P, Mordaunt C, Meguro-Horike M, Horike SI, Korf I, Lasalle JMDecember 2016Not Determined
27611852Create StudyWilson Disease: Epigenetic effects of choline supplementation on phenotype and clinical course in a mouse model.EpigeneticsMedici V, Kieffer DA, Shibata NM, Chima H, Kim K, Canovas A, Medrano JF, Islas-Trejo AD, Kharbanda KK, Olson K, Su RJ, Islam MS, Syed R, Keen CL, Miller AY, Rutledge JC, Halsted CH, Lasalle JMNovember 2016Not Determined
27150399Create StudyThe landscape of DNA methylation amid a perfect storm of autism aetiologies.Nature reviews. NeuroscienceCiernia AV, Lasalle JJuly 2016Not Relevant
26830258Create StudyAutism and Cancer Share Risk Genes, Pathways, and Drug Targets.Trends in genetics : TIGCrawley JN, Heyer WD, LaSalle JMMarch 2016Not Relevant
26585570Create StudyEpigenetic regulation of UBE3A and roles in human neurodevelopmental disorders.EpigenomicsLaSalle JM, Reiter LT, Chamberlain SJOctober 2015Not Determined
26241857Create StudyEarly Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas.PLoS geneticsSchroeder DI, Jayashankar K, Douglas KC, Thirkill TL, York D, Dickinson PJ, Williams LE, Samollow PB, Ross PJ, Bannasch DL, Douglas GC, LaSalle JMAugust 2015Not Determined
26105183Create StudyEpigenetic mechanisms in diurnal cycles of metabolism and neurodevelopment.Human molecular geneticsPowell WT, Lasalle JMOctober 15, 2015Not Relevant
24810691Create StudyCharacterization of timed changes in hepatic copper concentrations, methionine metabolism, gene expression, and global DNA methylation in the Jackson toxic milk mouse model of Wilson disease.International journal of molecular sciencesLe A, Shibata NM, French SW, Kim K, Kharbanda KK, Islam MS, Lasalle JM, Halsted CH, Keen CL, Medici V2014Not Relevant
24734033Create StudyGenome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis.Frontiers in immunologySelmi C, Cavaciocchi F, Lleo A, Cheroni C, De Francesco R, Lombardi SA, De Santis M, Meda F, Raimondo MG, Crotti C, Folci M, Zammataro L, Mayo MJ, Bach N, Shimoda S, Gordon SC, Miozzo M, Invernizzi P, Podda M, Scavelli R, Martin MR, Seldin MF, Lasalle JM, Gershwin ME2014Not Relevant
24730561Create StudyMethylation and gene expression responses to ethanol feeding and betaine supplementation in the cystathionine beta synthase-deficient mouse.Alcoholism, clinical and experimental researchMedici V, Schroeder DI, Woods R, LaSalle JM, Geng Y, Shibata NM, Peerson J, Hodzic E, Dayal S, Tsukamoto H, Kharbanda KK, Tillman B, French SW, Halsted CHJune 2014Not Relevant
24502430Create StudyA survey of seizures and current treatments in 15q duplication syndrome.EpilepsiaConant KD, Finucane B, Cleary N, Martin A, Muss C, Delany M, Murphy EK, Rabe O, Luchsinger K, Spence SJ, Schanen C, Devinsky O, Cook EH, Lasalle J, Reiter LT, Thibert RLMarch 2014Not Determined
24404383Create StudyAutism genes keep turning up chromatin.OA autismLasalle JMJune 19, 2013Not Determined
24283879Create StudyHow has the study of the human placenta aided our understanding of partially methylated genes?EpigenomicsSchroeder DI, LaSalle JMDecember 2013Not Determined
24220304Create StudyMaternal choline modifies fetal liver copper, gene expression, DNA methylation, and neonatal growth in the tx-j mouse model of Wilson disease.EpigeneticsMedici V, Shibata NM, Kharbanda KK, Islam MS, Keen CL, Kim K, Tillman B, French SW, Halsted CH, LaSalle JMFebruary 2014Not Determined
23731492Create StudyEpigenetic layers and players underlying neurodevelopment.Trends in neurosciencesLaSalle JM, Powell WT, Yasui DHAugust 2013Not Determined
23677056Create StudyEpigenomic strategies at the interface of genetic and environmental risk factors for autism.Journal of human geneticsLaSalle JMJuly 2013Not Determined
23530188Create StudyThe human placenta methylome.Proceedings of the National Academy of Sciences of the United States of AmericaSchroeder DI, Blair JD, Lott P, Yu HO, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, LaSalle JMApril 9, 2013Not Determined
22945834Create StudyWilson's disease: changes in methionine metabolism and inflammation affect global DNA methylation in early liver disease.Hepatology (Baltimore, Md.)Medici V, Shibata NM, Kharbanda KK, LaSalle JM, Woods R, Liu S, Engelberg JA, Devaraj S, Török NJ, Jiang JX, Havel PJ, Lönnerdal B, Kim K, Halsted CHFebruary 2013Not Determined
22930557Create StudyLevels of select PCB and PBDE congeners in human postmortem brain reveal possible environmental involvement in 15q11-q13 duplication autism spectrum disorder.Environmental and molecular mutagenesisMitchell MM, Woods R, Chi LH, Schmidt RJ, Pessah IN, Kostyniak PJ, LaSalle JMOctober 2012Not Determined
22861365Create StudyX chromosome gene methylation in peripheral lymphocytes from monozygotic twins discordant for scleroderma.Clinical and experimental immunologySelmi C, Feghali-Bostwick CA, Lleo A, Lombardi SA, De Santis M, Cavaciocchi F, Zammataro L, Mitchell MM, Lasalle JM, Medsger T, Gershwin MESeptember 2012Not Determined
22343140Create StudyLong-lived epigenetic interactions between perinatal PBDE exposure and Mecp2308 mutation.Human molecular geneticsWoods R, Vallero RO, Golub MS, Suarez JK, Ta TA, Yasui DH, Chi LH, Kostyniak PJ, Pessah IN, Berman RF, LaSalle JMJune 1, 2012Not Determined
22207353Create StudyRole of DNMT3B in the regulation of early neural and neural crest specifiers.EpigeneticsMartins-Taylor K, Schroeder DI, LaSalle JM, Lalande M, Xu RHJanuary 1, 2012Not Determined
22152151Create StudyIncreased copy number for methylated maternal 15q duplications leads to changes in gene and protein expression in human cortical samples.Molecular autismScoles HA, Urraca N, Chadwick SW, Reiter LT, Lasalle JM2011Not Determined
21725066Create StudyNeuron-specific impairment of inter-chromosomal pairing and transcription in a novel model of human 15q-duplication syndrome.Human molecular geneticsMeguro-Horike M, Yasui DH, Powell W, Schroeder DI, Oshimura M, Lasalle JM, Horike SOctober 1, 2011Not Determined
21617367Create StudyA genomic point-of-view on environmental factors influencing the human brain methylome.EpigeneticsLaSalle JMJuly 2011Not Determined

This tab provides a general status on the data expected to be shared. There are two types of data expected.

  1. By Relevant publications — Those publications that reported for the collection's grant and have a status of "relevant" for sharing are listed first. The grantee is expected to share the data specific to those publications using the NDA Study feature. If a publication is erroneously marked relevant, the PI should simply change the status. When sharing a study, only the outcome measures for the subjects/time-points are shared. Other data that have not met the share date, defined below, will remain embargoed. To initiate study creation, simply login, mark your publication as relevant and click on the link listed to begin.

  2. By Data Structure — The number of subjects expected, received and shared is provided. Investigators are expected to update the data that they are collecting, the initial submission date and initial share dates. The NIMH Data Archive shares data when those dates are met.

  3. Submission Exemption — Those with Administrative or Submission Access to the Collection may request an exemption for submission for a defined period by stating the reason and timeframe. Note that the program officer on the grant may review this request.


Relevant Publications
PubMed IDStudyTitleJournalAuthorsDate
No records found.

For those with privileges to edit the collection, it is possible to upload your data definitions using this interface. NDA support staff will then follow up with a harmonized data definition for you to use in providing additional data.

Data Expected
Data ExpectedTargeted EnrollmentInitial SubmissionSubjects SharedStatus
Research Subject and Pedigree info iconApproved
genomics/omics info iconApproved
Structure not yet defined

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.