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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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General

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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
Genes disrupted by balanced genomic rearrangements in autism spectrum disorders
James Gusella 
Sequencing rearrangements in ASD
NDAR
Closed
Shared
$617,446.00
65
0
0
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NIH - Extramural None

NDAR_Methods.pdf Methods methods documentation Qualified Researchers
sequencing_files_readme_col_1700.pdf Background Readme for sequencing files Qualified Researchers

R21HD065286-01 Genes disrupted by balanced genomic rearrangements in autism spectrum disorders 09/30/2009 08/31/2011 Not Reported Not Reported MASSACHUSETTS GENERAL HOSPITAL $617,446.00

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
37Standard paired-end sequencing of BCRs04/19/2011ApprovedOmics
38Illumina Mate-Pair BCR sequencing04/19/2011ApprovedOmics
39Custom Jumping Libraries04/19/2011ApprovedOmics
40Custom CapBP04/19/2011ApprovedOmics
14816p11.2 CNV mouse cortex RNA-Seq05/21/2014ApprovedOmics
14916p11.2 CNV human LCL RNA-Seq05/21/2014ApprovedOmics

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.

Genomics Sample Genomics 65
Genomics Subject Genomics 65

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
28120936Create StudyPotential molecular consequences of transgene integration: The R6/2 mouse example.Scientific reportsJacobsen JC, Erdin S, Chiang C, Hanscom C, Handley RR, Barker DD, Stortchevoi A, Blumenthal I, Reid SJ, Snell RG, Macdonald ME, Morton AJ, Ernst C, Gusella JF, Talkowski MEJanuary 2017Not Determined
25497101Create StudyGenomic and functional overlap between somatic and germline chromosomal rearrangements.Cell reportsvan Heesch S, Simonis M, van Roosmalen MJ, Pillalamarri V, Brand H, Kuijk EW, de Luca KL, Lansu N, Braat AK, Menelaou A, Hao W, Korving J, Snijder S, van der Veken LT, Hochstenbach R, Knegt AC, Duran K, Renkens I, Alekozai N, Jager M, Vergult S, Menten B, de Bruijn E, Boymans S, Ippel E, et al.December 24, 2014Not Relevant
24789519Create StudyDesign of large-insert jumping libraries for structural variant detection using Illumina sequencing.Current protocols in human geneticsHanscom C, Talkowski MJanuary 2014Not Determined
24746958Create StudyDescribing sequencing results of structural chromosome rearrangements with a suggested next-generation cytogenetic nomenclature.American journal of human geneticsOrdulu Z, Wong KE, Currall BB, Ivanov AR, Pereira S, Althari S, Gusella JF, Talkowski ME, Morton CCMay 1, 2014Not Relevant
23472757Create StudyMolecular analysis of a deletion hotspot in the NRXN1 region reveals the involvement of short inverted repeats in deletion CNVs.American journal of human geneticsChen X, Shen Y, Zhang F, Chiang C, Pillalamarri V, Blumenthal I, Talkowski M, Wu BL, Gusella JFMarch 7, 2013Not Relevant
23354975Create StudyHaploinsufficiency of KDM6A is associated with severe psychomotor retardation, global growth restriction, seizures and cleft palate.Human geneticsLindgren AM, Hoyos T, Talkowski ME, Hanscom C, Blumenthal I, Chiang C, Ernst C, Pereira S, Ordulu Z, Clericuzio C, Drautz JM, Rosenfeld JA, Shaffer LG, Velsher L, Pynn T, Vermeesch J, Harris DJ, Gusella JF, Liao EC, Morton CCMay 2013Not Relevant
23332918Create StudyExonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus.American journal of human geneticsBeunders G, Voorhoeve E, Golzio C, Pardo LM, Rosenfeld JA, Talkowski ME, Simonic I, Lionel AC, Vergult S, Pyatt RE, van de Kamp J, Nieuwint A, Weiss MM, Rizzu P, Verwer LE, van Spaendonk RM, Shen Y, Wu BL, Yu T, Yu Y, Chiang C, Gusella JF, Lindgren AM, Morton CC, van Binsbergen E, et al.February 7, 2013Not Relevant
23217328Create StudyDisruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities.American journal of human geneticsTalkowski ME, Maussion G, Crapper L, Rosenfeld JA, Blumenthal I, Hanscom C, Chiang C, Lindgren A, Pereira S, Ruderfer D, Diallo AB, Lopez JP, Turecki G, Chen ES, Gigek C, Harris DJ, Lip V, An Y, Biagioli M, Macdonald ME, Lin M, Haggarty SJ, Sklar P, Purcell S, Kellis M, et al.December 7, 2012Not Determined
23215558Create StudyClinical diagnosis by whole-genome sequencing of a prenatal sample.The New England journal of medicineTalkowski ME, Ordulu Z, Pillalamarri V, Benson CB, Blumenthal I, Connolly S, Hanscom C, Hussain N, Pereira S, Picker J, Rosenfeld JA, Shaffer LG, Wilkins-Haug LE, Gusella JF, Morton CCDecember 6, 2012Not Relevant
23044507Create StudyHighly penetrant alterations of a critical region including BDNF in human psychopathology and obesity.Archives of general psychiatryErnst C, Marshall CR, Shen Y, Metcalfe K, Rosenfeld J, Hodge JC, Torres A, Blumenthal I, Chiang C, Pillalamarri V, Crapper L, Diallo AB, Ruderfer D, Pereira S, Sklar P, Purcell S, Wildin RS, Spencer AC, Quade BF, Harris DJ, Lemyre E, Wu BL, Stavropoulos DJ, Geraghty MT, Shaffer LG, et al.December 2012Not Determined
22770980Create StudyTranslocations disrupting PHF21A in the Potocki-Shaffer-syndrome region are associated with intellectual disability and craniofacial anomalies.American journal of human geneticsKim HG, Kim HT, Leach NT, Lan F, Ullmann R, Silahtaroglu A, Kurth I, Nowka A, Seong IS, Shen Y, Talkowski ME, Ruderfer D, Lee JH, Glotzbach C, Ha K, Kjaergaard S, Levin AV, Romeike BF, Kleefstra T, Bartsch O, Elsea SH, Jabs EW, MacDonald ME, Harris DJ, Quade BJ, et al.July 13, 2012Not Determined
22521361Create StudySequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries.CellTalkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, Heilbut A, Ernst C, Hanscom C, Rossin E, Lindgren AM, Pereira S, Ruderfer D, Kirby A, Ripke S, Harris DJ, Lee JH, Ha K, Kim HG, Solomon BD, Gropman AL, Lucente D, Sims K, Ohsumi TK, Borowsky ML, Loranger S, et al.April 27, 2012Not Relevant
22388000Create StudyComplex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration.Nature geneticsChiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR, McLaughlan CJ, Bawden CS, Reid SJ, Faull RL, Snell RG, Hall IM, Shen Y, Ohsumi TK, Borowsky ML, Daly MJ, Lee C, Morton CC, MacDonald ME, Gusella JF, Talkowski MEApril 2012Not Relevant
22290657Create StudyHaploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features.Human mutationLamb AN, Rosenfeld JA, Neill NJ, Talkowski ME, Blumenthal I, Girirajan S, Keelean-Fuller D, Fan Z, Pouncey J, Stevens C, Mackay-Loder L, Terespolsky D, Bader PI, Rosenbaum K, Vallee SE, Moeschler JB, Ladda R, Sell S, Martin J, Ryan S, Jones MC, Moran R, Shealy A, Madan-Khetarpal S, McConnell J, et al.April 2012Not Determined
21981781Create StudyAssessment of 2q23.1 microdeletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder.American journal of human geneticsTalkowski ME, Mullegama SV, Rosenfeld JA, van Bon BW, Shen Y, Repnikova EA, Gastier-Foster J, Thrush DL, Kathiresan S, Ruderfer DM, Chiang C, Hanscom C, Ernst C, Lindgren AM, Morton CC, An Y, Astbury C, Brueton LA, Lichtenbelt KD, Ades LC, Fichera M, Romano C, Innis JW, Williams CA, Bartholomew D, et al.October 7, 2011Not Relevant
21473983Create StudyNext-generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research.American journal of human geneticsTalkowski ME, Ernst C, Heilbut A, Chiang C, Hanscom C, Lindgren A, Kirby A, Liu S, Muddukrishna B, Ohsumi TK, Shen Y, Borowsky M, Daly MJ, Morton CC, Gusella JFApril 8, 2011Not Relevant
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Relevant Publications
PubMed IDStudyTitleJournalAuthorsDate
No records found.
help.tab.dataexpected.addnew
Data Expected
Data ExpectedTargeted EnrollmentInitial SubmissionSubjects SharedStatus
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.

Study Name Description Number of Subjects
Collection / Total
Data Use State
Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families Publication Abstract: Reciprocal copy number variation (CNV) of a 593 kb region of 16p11.2 is a common genetic cause of autism spectrum disorder (ASD), yet it is not completely penetrant and can manifest in a wide array of phenotypes. To explore its molecular consequences, we performed RNA-sequencing of cerebral cortex from mouse models with CNV of the syntenic 7qF3 region, and lymphoblast lines from 34 members of seven multiplex ASD families harboring the 16p11.2 CNV. Expression of all genes in the CNV region correlated well with their DNA copy number, with no evidence of dosage compensation. We observed effects on gene expression outside the CNV region, including apparent positional effects in cis and in trans at genomic segments with evidence of physical interaction in Hi-C chromosome conformation data. One of the most significant positional effects was telomeric to the 16p11.2 CNV and includes the previously described 'distal' 16p11.2 microdeletion. Overall, 16p11.2 CNV was associated with altered expression of genes and networks that converge on multiple hypotheses of ASD pathogenesis, including synaptic function (e.g., NRXN1, NRXN3), chromatin modification (e.g., CHD8, EHMT1, MECP2), transcriptional regulation (e.g.,TCF4, SATB2), and intellectual disability (e.g., FMR1, CEP290). However, there were differences between tissues and species, with the strongest effects being consistently within the CNV region itself. Our analyses suggest that through a combination of indirect regulatory effects and direct effects on nuclear architecture, alteration of 16p11.2 genes disrupts expression networks that involve other genes and pathways known to contribute to ASD, suggesting an overlap in mechanisms of pathogenesis. 50 / 50 Primary Analysis Shared
* Data not on individual level
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