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Collection Summary Collection Charts
Collection Title Collection Investigators Collection Description
Genomic Profiling and Functional Mutation Analysis in Autism Spectrum Disorders
Matthew State 
This proposal is in response to a request for applications to address "Genomic Profiling of Mental Disorders", and proposes intensive genomic profiling and functional analysis of Contactin Associated Protein 2 (CNTNAP2) as well as the presynaptic cytomatrix protein Piccolo (PCLO), in an effort to clarify their roles in Autism Spectrum Disorders (ASD). In addition, the application proposes to deeply sequence genes in the Contactin and Contactin Associated pathways, as well as genes coding for proteins known to interact with PCLO.
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NIH - Extramural None

sequencing_files_readme_col_1895.pdf Background Readme for sequencing files Qualified Researchers

RC2MH089956-01 Genomic Profiling and Functional Mutation Analysis in Autism Spectrum Disorders 09/30/2009 08/31/2011 Not Reported Not Reported YALE UNIVERSITY $2,245,837.00

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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
63Microemulsion PCR and Targeted Resequencing for Variant Detection in ASD07/20/2012ApprovedOmics
135Whole Exome Sequencing of SSC Samples03/10/2014ApprovedOmics

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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
26833134Create StudyEstrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2.NeuronHoffman EJ, Turner KJ, Fernandez JM, Cifuentes D, Ghosh M, Ijaz S, Jain RA, Kubo F, Bill BR, Baier H, Granato M, Barresi MJ, Wilson SW, Rihel J, State MW, Giraldez AJFebruary 17, 2016Not Determined
25621974Study (370)No evidence for association of autism with rare heterozygous point mutations in Contactin-Associated Protein-Like 2 (CNTNAP2), or in Other Contactin-Associated Proteins or Contactins.PLoS geneticsMurdoch JD, Gupta AR, Sanders SJ, Walker MF, Keaney J, Fernandez TV, Murtha MT, Anyanwu S, Ober GT, Raubeson MJ, DiLullo NM, Villa N, Waqar Z, Sullivan C, Gonzalez L, Willsey AJ, Choe SY, Neale BM, Daly MJ, State MWJanuary 2015Relevant
25464374Create StudyAutism spectrum disorders: from genes to neurobiology.Current opinion in neurobiologyWillsey AJ, State MWFebruary 2015Not Relevant
25385366Create StudyModeling non-syndromic autism and the impact of TRPC6 disruption in human neurons.Molecular psychiatryGriesi-Oliveira K, Acab A, Gupta AR, Sunaga DY, Chailangkarn T, Nicol X, Nunez Y, Walker MF, Murdoch JD, Sanders SJ, Fernandez TV, Ji W, Lifton RP, Vadasz E, Dietrich A, Pradhan D, Song H, Ming GL, Gu X, Haddad G, Marchetto MC, Spitzer N, Passos-Bueno MR, State MW, Muotri ARNovember 2015Not Determined
24618187Create StudyRecent challenges to the psychiatric diagnostic nosology: a focus on the genetics and genomics of neurodevelopmental disorders.International journal of epidemiologyKim YS, State MWApril 2014Not Relevant
24565942Create StudyThe developmental transcriptome of the human brain: implications for neurodevelopmental disorders.Current opinion in neurologyTebbenkamp AT, Willsey AJ, State MW, Sestan NApril 2014Not Relevant
24267886Create StudyCoexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.CellWillsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, et al.November 21, 2013Not Relevant
23259942Create StudyThe autism sequencing consortium: large-scale, high-throughput sequencing in autism spectrum disorders.NeuronBuxbaum JD, Daly MJ, Devlin B, Lehner T, Roeder K, State MW, Barrett JBilder DBoerwinkle EBrudno MBurbach PBuxbaum JDCamp NChahrour MCook EHCoon HCoppola GCoulter MCutler DDaly MJdePristo MDevlin BEichler EEFromer MGeschwind DHGibbs RAGill MGoldberg APHaines JLHakonarson HHill SIonita-Laza IKoeleman BPKolevzon AKrumm NLehner TLese Martin CLowe JKMarkianos KMorris DNeale BO'Roak BJPalotie APericak-Vance MAPinto DPoultney CSPurcell SMRoeder KSabo ASanders SSchadt EESchafer CSchellenberg GDScherer SSchmitz-Abe KShendure JSklar PState MWSutcliffe JSSzatmari PTierney EVorstman JAWalker SWalsh CAWang LSWarren STWei LWigler MYu TMYuen RZwick MEDecember 20, 2012Not Relevant
22984058Create StudyNeuroscience. The emerging biology of autism spectrum disorders.Science (New York, N.Y.)State MW, Šestan NSeptember 14, 2012Not Relevant
22956686Create StudyMutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy.Science (New York, N.Y.)Novarino G, El-Fishawy P, Kayserili H, Meguid NA, Scott EM, Schroth J, Silhavy JL, Kara M, Khalil RO, Ben-Omran T, Ercan-Sencicek AG, Hashish AF, Sanders SJ, Gupta AR, Hashem HS, Matern D, Gabriel S, Sweetman L, Rahimi Y, Harris RA, State MW, Gleeson JGOctober 19, 2012Not Determined
22037497Create StudyThe conundrums of understanding genetic risks for autism spectrum disorders.Nature neuroscienceState MW, Levitt PDecember 2011Not Relevant
21151135Create StudySelection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA).Nature methodsSander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JKJanuary 2011Not Relevant
20955933Create StudyThe genetics of child psychiatric disorders: focus on autism and Tourette syndrome.NeuronState MWOctober 21, 2010Not Relevant
20159341Create StudyThe genetics of autism: key issues, recent findings, and clinical implications.The Psychiatric clinics of North AmericaEl-Fishawy P, State MWMarch 2010Not Relevant
20152922Create StudyMicroRNAs as genetic sculptors: fishing for clues.Seminars in cell & developmental biologyTakacs CM, Giraldez AJSeptember 2010Not Relevant

Relevant Publications
PubMed IDStudyTitleJournalAuthorsDate
No records found.
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
The contribution of de novo coding mutations to autism spectrum disorder Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females. PLEASE NOTE: Additional data on these subjects, unrelated to this publication exist in other NDAR Studies. These data include realigned BAM files, unfiltered SNV/InDel variant calls (made by GATK and FreeBayes), and CNVs. Please see this news item for more details: https://ndar.nih.gov/ndarpublicweb/aboutNDAR.html#news_item_201 3072 / 9456 Secondary Analysis Shared
De novo mutations revealed by whole exome sequencing are strongly associated with autism Multiple studies have confirmed the contribution of rare de novo copy number variations (CNVs) to the risk for Autism Spectrum Disorders (ASD). While de novo single nucleotide variants (SNVs) have been identified in affected individuals, their contribution to risk has yet to be clarified. Specifically, the frequency and distribution of these mutations has not been well characterized in matched unaffected controls, data that are vital to the interpretation of de novo coding mutations observed in probands. Here we show, via whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with ASD and carry large effects (OR=5.65; CI: 1.44-22.2; p=0.01 asymptotic test). Based on mutation rates in unaffected individuals, we demonstrate that multiple independent de novo SNVs in the same gene among unrelated probands reliably identifies risk alleles, providing a clear path forward for gene discovery. Among a total of 279 identified de novo coding mutations, there is a single instance in probands, and none in siblings, in which two independent nonsense variants disrupt the same gene, SCN2A (Sodium Channel, Voltage-Gated, Type II, Alpha Subunit), a result that is highly unlikely by chance (p=0.005). 928 / 928 Primary Analysis Shared
No Evidence for Association of Autism with Rare Heterozygous Point Mutations in Contactin-Associated Protein-Like 2 (CNTNAP2), or in Other Contactin-Associated Proteins or Contactins Contactins and Contactin-Associated Proteins, and Contactin-Associated Protein-Like 2 (CNTNAP2) in particular, have been widely cited as autism risk genes based on findings from homozygosity mapping, molecular cytogenetics, copy number variation analyses, and both common and rare single nucleotide association studies. However, data specifically with regard to the contribution of heterozygous single nucleotide variants (SNVs) have been inconsistent. In an effort to clarify the role of rare point mutations in CNTNAP2 and related gene families, we have conducted targeted next-generation sequencing and evaluated existing sequence data in cohorts totaling 2704 cases and 2747 controls. We find no evidence for statistically significant association of rare heterozygous mutations in any of the CNTN or CNTNAP genes, including CNTNAP2, placing marked limits on the scale of their plausible contribution to risk. 2024 / 4118 Primary 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. 954 / 6360 Primary Analysis Shared
Transmission disequilibrium of small CNVs in simplex autism. Cohorts: 411 ASD Quads from Simons Simplex Collection 177 Quads from Sanders et al. (PubMed ID: 22495306) 166 Quads from I. Iossifov et al. (PubMed ID: 22542183) 71 Quads from O'Roak et al. (PubMed ID: 22495309) Publication Abstract: We searched for disruptive, genic rare copy-number variants (CNVs) among 411 families affected by sporadic autism spectrum disorder (ASD) from the Simons Simplex Collection by using available exome sequence data and CoNIFER (Copy Number Inference from Exome Reads). Compared to high-density SNP microarrays, our approach yielded ¿2× more smaller genic rare CNVs. We found that affected probands inherited more CNVs than did their siblings (453 versus 394, p = 0.004; odds ratio [OR] = 1.19) and that the probands' CNVs affected more genes (921 versus 726, p = 0.02; OR = 1.30). These smaller CNVs (median size 18 kb) were transmitted preferentially from the mother (136 maternal versus 100 paternal, p = 0.02), although this bias occurred irrespective of affected status. The excess burden of inherited CNVs among probands was driven primarily by sibling pairs with discordant social-behavior phenotypes (p < 0.0002, measured by Social Responsiveness Scale [SRS] score), which contrasts with families where the phenotypes were more closely matched or less extreme (p > 0.5). Finally, we found enrichment of brain-expressed genes unique to probands, especially in the SRS-discordant group (p = 0.0035). In a combined model, our inherited CNVs, de novo CNVs, and de novo single-nucleotide variants all independently contributed to the risk of autism (p < 0.05). Taken together, these results suggest that small transmitted rare CNVs play a role in the etiology of simplex autism. Importantly, the small size of these variants aids in the identification of specific genes as additional risk factors associated with ASD. 53 / 1644 Secondary Analysis Shared
Recurrent de novo mutations implicate novel genes underlying simplex autism risk. Autism spectrum disorder (ASD) has a strong but complex genetic component. Here we report on the resequencing of 64 candidate neurodevelopmental disorder risk genes in 5,979 individuals: 3,486 probands and 2,493 unaffected siblings. We find a strong burden of de novo point mutations for these genes and specifically implicate nine genes. These include CHD2 and SYNGAP1, genes previously reported in related disorders, and novel genes TRIP12 and PAX5. We also show that mutation carriers generally have lower IQs and enrichment for seizures. These data begin to distinguish genetically distinct subtypes of autism important for aetiological classification and future therapeutics. 1413 / 6400 Primary Analysis Shared
Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. NDAR Data for this study consist of Whole Exome sequencing for the additional 56 families from SSC collection. Other Whole Exome sequencing data and results used in this study were originally published elsewhere. NDAR Studies 340, 320, and 317 describe the data published in Iossifov et al., 2012; Neale et al., 2012; O'Roak et al., 2012b, respectively, as cited in this publication. The RNA-Seq data from this publication are available from NCBI at the given BioProject accession. Autism spectrum disorder (ASD) is a complex developmental syndrome of unknown etiology. Recent studies employing exome- and genome-wide sequencing have identified nine high-confidence ASD (hcASD) genes. Working from the hypothesis that ASD-associated mutations in these biologically pleiotropic genes will disrupt intersecting developmental processes to contribute to a common phenotype, we have attempted to identify time periods, brain regions, and cell types in which these genes converge. We have constructed coexpression networks based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood. By assessing enrichment of an independent set of probable ASD (pASD) genes, derived from the same sequencing studies, we demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons. This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology. 224 / 224 Primary Analysis Shared
* Data not on individual level