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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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Shared

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General

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Funding Source

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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
Induced pluripotent cells in ASD with macrocephaly
Flora Vaccarino 
R01MH89176 - This project will develop lines of pluripotent cells (iPSC) from a longitudinally acquired cohort of patients with autism spectrum disorders (ASD) and macrocephaly and their family members, as well as typically developing children, using cells obtained by a skin biopsy. We will produce several iPSC lines per individual and characterize them with respect to their biology and their structural genetic variation. The aim is create a resource and analytical tool, which will allow us to examine neuronal differentiation in ASD. R33MH87879 - Our project capitalizes on recent procedures that allow derivation of pluripotent stem cells from fibroblastsobtainable through a small skin biopsy from living individuals. These induced pluripotent stem cells (iPSC) candifferentiate into any cell types of the body, including neural stem cells (NSCs). We will use these methods toinvestigate neuronal differentiation in autism spectrum disorders (ASD). Our hypothesis states that increasedbrain size, a highly replicated biological phenotype in ASD, is attributable to altered dynamics of cellproliferation and/or differentiation intrinsic to NSCs, which, in turn, will correlate with specific changes in geneexpression and the underlying changes in genomic sequence and/or epigenomic imprinting. To test thishypothesis, we have assembled a group of investigators with the range of expertise necessary for a multi-leveland multi-dimensional approach to this problem. In Specific Aim 1, we will derive iPSC lines from patients withASD exhibiting an increase in head size and from typically developing children. These iPSC lines will bedifferentiated into NSCs. The NSC lines from ASD individuals will be compared to those derived from typicallydeveloping individuals with respect to their proliferation, cell death and differentiation into different neuronalsubtypes, as well as synaptic specification. In Specific Aim 2, we will use advanced genomics and epigenomicstechnologies to generate high-resolution and comprehensive datasets of variation in the genomic sequence,epigenetic marks, and transcript abundance at progenitor and mature stages of neuronal cell differentiation.We will integrate multi-level genomics and gene expression datasets with findings from cell biology and clinicalphenotypes. In Specific Aim 3, we will transplant NSCs from control and patients into the ventricles of mouseembryos in order to determine their in vivo phenotype and their ability to contribute neurons to various brainregions. The potential impact of our research is to develop cell lines derived directly from patients that willrecapitulate in vitro the biological steps that enable an embryonic stem cell to differentiate into multiple CNScell types. This project will lay the foundations for beginning to correlate genomic sequence, regulation andintensity of gene expression, cellular (biological) consequences, and patient behavior, and thus understand thebiological mechanisms of disease. Candidate genes and regions found in iPSC lines can be subsequentlyvalidated with statistical significance in targeted large-scale screens. The direct analysis of specific differencesin gene expression and regulation that pertain to individual patients and their clinical phenotype may offerunique insights into disease pathogenesis.
NDAR
Closed
Shared
$3,272,916.00
29
50
20
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NIH - Extramural None

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

R21MH087879-01 Cellular and Genetic Correlates of Increased Head Size in Autism Spectrum Disorde 09/30/2009 08/31/2013 16 10 YALE UNIVERSITY $1,285,340.00
R01MH089176-01 Biological correlates of altered brain growth in autism 09/30/2009 08/31/2011 34 10 YALE UNIVERSITY $1,987,576.00

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
29Microarray family 03 (father, mother, sibling)03/24/2011ApprovedOmics
41Immunofluorescence05/11/2011ApprovedOmics
58iPS DNA Sequence03/09/2012ApprovedOmics
62Fibroblast DNA Sequence07/12/2012ApprovedOmics
55Illumina mRNA Seq02/13/2012ApprovedOmics
608Amplicon-seq01/31/2017ApprovedOmics
607Capture-seq01/31/2017ApprovedOmics

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.

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

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
28235832Create StudyOne thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin.Genome researchAbyzov A, Tomasini L, Zhou B, Vasmatzis N, Coppola G, Amenduni M, Pattni R, Wilson M, Gerstein M, Weissman S, Urban AE, Vaccarino FMApril 2017Not Relevant
26610635Create StudyCreating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders.Stem cell reportsBrennand KJ, Marchetto MC, Benvenisty N, Brüstle O, Ebert A, Izpisua Belmonte JC, Kaykas A, Lancaster MA, Livesey FJ, Mcconnell MJ, Mckay RD, Morrow EM, Muotri AR, Panchision DM, Rubin LL, Sawa A, Soldner F, Song H, Studer L, Temple S, Vaccarino FM, Wu J, Vanderhaeghen P, Gage FH, Jaenisch RDecember 8, 2015Not Relevant
26443267Create StudyImbalance of excitatory/inhibitory synaptic protein expression in iPSC-derived neurons from FOXG1(+/-) patients and in foxg1(+/-) mice.European journal of human genetics : EJHGPatriarchi T, Amabile S, Frullanti E, Landucci E, Lo Rizzo C, Ariani F, Costa M, Olimpico F, W Hell J, M Vaccarino F, Renieri A, Meloni IJune 2016Not Determined
26186191Create StudyFOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.CellMariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, Vaccarino FMJuly 16, 2015Not Relevant
23160490Study (289)Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells.NatureAbyzov A, Mariani J, Palejev D, Zhang Y, Haney MS, Tomasini L, Ferrandino AF, Rosenberg Belmaker LA, Szekely A, Wilson M, Kocabas A, Calixto NE, Grigorenko EL, Huttner A, Chawarska K, Weissman S, Urban AE, Gerstein M, Vaccarino FMDecember 20, 2012Relevant
23062309Create StudyNeurobiology meets genomic science: the promise of human-induced pluripotent stem cells.Development and psychopathologyStevens HE, Mariani J, Coppola G, Vaccarino FMNovember 2012Not Relevant
22761314Create StudyModeling human cortical development in vitro using induced pluripotent stem cells.Proceedings of the National Academy of Sciences of the United States of AmericaMariani J, Simonini MV, Palejev D, Tomasini L, Coppola G, Szekely AM, Horvath TL, Vaccarino FMJuly 31, 2012Not Determined
21371482Create StudyInduced pluripotent stem cells: a new tool to confront the challenge of neuropsychiatric disorders.NeuropharmacologyVaccarino FM, Stevens HE, Kocabas A, Palejev D, Szekely A, Grigorenko EL, Weissman SJune 2011Not Relevant
21204834Create StudyAnnual Research Review: The promise of stem cell research for neuropsychiatric disorders.Journal of child psychology and psychiatry, and allied disciplinesVaccarino FM, Urban AE, Stevens HE, Szekely A, Abyzov A, Grigorenko EL, Gerstein M, Weissman SApril 2011Not Relevant
20814258Create StudyBehavior, brain, and genome in genomic disorders: finding the correspondences.Journal of developmental and behavioral pediatrics : JDBPGrigorenko EL, Urban AE, Mencl ESeptember 2010Not Relevant
19643218Create StudyIncreased brain size in autism--what it will take to solve a mystery.Biological psychiatryVaccarino FM, Smith KMAugust 15, 2009Not Relevant
18850329Create StudyRegulation of cerebral cortical size and neuron number by fibroblast growth factors: implications for autism.Journal of autism and developmental disordersVaccarino FM, Grigorenko EL, Smith KM, Stevens HEMarch 2009Not Relevant
help.tab.dataexpected

Relevant Publications
PubMed IDStudyTitleJournalAuthorsDate
No records found.
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Data Expected
Data ExpectedTargeted EnrollmentInitial SubmissionSubjects SharedStatus
genomics/omics info iconApproved
Vineland (Parent and Caregiver) info iconApproved
Wechsler Intelligence Scale for Children info iconApproved
Mullen Scales of Early Learning info iconApproved
DAS-II: Differential Ability Scales info iconApproved
ADI-R info iconApproved
ADOS 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
Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cell Reprogramming human somatic cells into induced pluripotent stem cells (iPSC) has been suspected of causing de novo copy number variations (CNVs). To explore this issue, we performed a whole-genome and transcriptome analysis of 20 human iPSC lines derived from primary skin fibroblasts of 7 individuals using next-generation sequencing. We find that, on average, an iPSC line manifests two CNVs not apparent in the fibroblasts from which the iPSC was derived. Using qPCR, PCR, and digital droplet PCR (ddPCR) to amplify across the CNVs' breakpoints, we show that at least 50% of those CNVs are present as low frequency somatic genomic variants in parental fibroblasts and are manifested in iPSC colonies due to their clonal origin. Hence, reprogramming does not necessarily lead to de novo CNVs in iPSC, since most of line-manifested CNVs reflect somatic mosaicism in the human skin. Moreover, our findings demonstrate that clonal expansion, and iPSC lines in particular, can be used as a discovery tool to reliably detect low frequency CNVs in the tissue of origin. Overall, we estimate that approximately 30% of the fibroblast cells have somatic CNVs, suggesting widespread somatic mosaicism in the human body. Our study paves the way to understanding the fundamental question of the extent to which cells of the human body normally acquire structural alterations in their DNA post-zygotically. 9 / 9 Primary Analysis Shared
One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin Few studies have been conducted to understand post-zygotic accumulation of mutations in cells of the healthy human body. We reprogrammed 32 skin fibroblast cells from families of donors into human induced pluripotent stem cell (hiPSC) lines. The clonal nature of hiPSC lines allows a high-resolution analysis of the genomes of the founder fibroblast cells without being confounded by the artifacts of single cell whole genome amplification. We estimate that on average a fibroblast cell in children has 1,035 mostly benign mosaic SNVs. On average, 235 SNVs could be directly confirmed in the original fibroblast population by ultra-deep sequencing, down to an allele frequency (AF) of 0.1%. More sensitive droplet digital PCR experiments confirmed more SNVs as mosaic with AF as low as 0.01%, suggesting that 1,035 mosaic SNVs per fibroblast cell is the true average. Similar analyses in adults revealed no significant increase in the number of SNVs per cell, suggesting that a major fraction of mosaic SNVs in fibroblasts arises during development. Mosaic SNVs were distributed uniformly across the genome and were enriched in a mutational signature previously observed in cancers and in de novo variants and which, we hypothesize, is a hallmark of normal cell proliferation. Finally, AF distribution of mosaic SNVs had distinct narrow peaks, which could be a characteristic of clonal cell selection, clonal expansion, or both. These findings reveal a large degree of somatic mosaicism in healthy human tissues, link de novo and cancer mutations to somatic mosaicism and couple somatic mosaicism with cell proliferation. 12 / 12 Secondary Analysis Shared
The evolution and population diversity of human-specific segmental duplications Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families). We show that HSDs are non-randomly organized, associate preferentially with ancestral ape duplications termed “core duplicons”, and evolved primarily in an interspersed inverted orientation. In addition to Homo sapiens-specific gene expansions (e.g., TCAF1/2), we highlight ten gene families (e.g., ARHGAP11B and SRGAP2C) where copy number never returns to the ancestral state, there is evidence of mRNA splicing, and no common gene-disruptive mutations are observed in the general population. Such duplicates are candidates for the evolution of human-specific adaptive traits. 2 / 6360 Primary Analysis Shared
* Data not on individual level
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