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Predictors of self-injurious behaviour exhibited by individuals with autism spectrum disorder #258
Richman DM; Barnard-Brak L, Bosch A, Thompson S, Grubb L, Abby L
Presence of an autism spectrum disorder is a risk factor for development of self-injurious behaviour (SIB) exhibited by individuals with developmental disorders. The most salient SIB risk factors historically studied within developmental disorders are level of intellectual disability, communication deficits and presence of specific genetic disorders. Recent SIB research has expanded the search for risk factors to include less commonly studied variables for people with developmental disorders:...

Test - SIB Cohort (611)

Gastrointestinal Dysfunction in Autism: Parental Report, Clinical Evaluation, and Associated Factors #268
Levitt P; Gorrindo P, Williams KC, Lee EB, Walker LS, McGrew SG
The objectives of this study were to characterize gastrointestinal dysfunction (GID) in autism spectrum disorder (ASD), to examine parental reports of GID relative to evaluations by pediatric gastroenterologists, and to explore factors associated with GID in ASD. One hundred twenty-one children were recruited into three groups: co-occurring ASD and GID, ASD without GID, and GID without ASD. A pediatric gastroenterologist evaluated both GID groups. Parents in all three groups completed...

Control - ASD-only (39)

Control - GID-only (22)

Test - ASD-GID (30)

Brain Hyperconnectivity in Children with Autism and its Links to Social Deficits #269
Menon, Vinod; Superkar, K; Uddin, LQ; Khouzam, A; Phillips, J; Gaillard, WD; Kenworthy, LE; Yerys, BE; Vaidya, CJ
Autism spectrum disorder (ASD), a neurodevelopmental disorder affecting nearly 1 in 88 children, is thought to result from aberrant brain connectivity. Remarkably, there have been no systematic attempts to characterize whole-brain connectivity in children with ASD. Here, we use neuroimaging to show that there are more instances of greater functional connectivity in the brains of children with ASD in comparison to those of typically developing children. Hyperconnectivity in ASD was observed at...

Baseline - ASD Subjects (15)

Control - Non-ASD Subjects (28)

Neuro Signal Recordings
Epigenetics Marks as Peripheral Biomarkers of Autism #287
Warren S
We are studying a potential epigenetic component to the autism spectrum disorders (ASD) by interrogating DNA methylation (DNAm) using an established high-throughput assay that interrogates DNA methylation (DNAm) at 27578 highly informative CpG dinucleotides. To date, we have determined the DNA methylation (DNAm) profiles from whole blood-extracted DNA of over four hundred male sib-pairs discordant for ASD. A close statistical examination may ultimately identify ASD peripheral biomarkers and...

Control - ASD-Siblings (159)

Test - ASD-Probands (415)

Autism Genome Project #288
Scherer S, Devlin B
The Autism Genome Project (AGP) Consortium represents more than 50 centers in North America and Europe. In an ongoing effort, the international AGP Consortium is collecting ASD families for ongoing genetic studies. The first phase of this initiative involved examining genetic linkage and chromosomal rearrangements in 1,168 families having at least two ASD individuals (PMID: 17322880). In this second phase of the project, we collected more families and genotyped them to examine for Copy Number...

Control - Parents (2,933)

Test - Non-verbal (483)

Test - Verbal subjects (1,000)

Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cell #289
Vaccarino FM; Abyzov 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
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...

Control - Control (7)

Test - Test (2)

Microarray/Protein Analysis
Whole-Exome Sequencing and Homozygosity Analysis Implicate Depolarization-Regulated Neuronal Genes in Autism #293
Walsh CA; Chahrour MH, Yu TW, Lim ET, Ataman B, Coulter ME, Hill RS, Stevens CR, Schubert CR; ARRA Autism Sequencing Collaboration, Greenberg ME, Gabriel SB
Although autism has a clear genetic component, the high genetic heterogeneity of the disorder has been a challenge for the identification of causative genes. We used homozygosity analysis to identify probands from nonconsanguineous families that showed evidence of distant shared ancestry, suggesting potentially recessive mutations. Whole-exome sequencing of 16 probands revealed validated homozygous, potentially pathogenic recessive mutations that segregated perfectly with disease in 4/16...

Test - Selected (18)

Study of potential epigenetic component to the autism spectrum disorders (ASD) by interrogating DNA methylation (DNAm) using an established high-throughput assay that interrogates DNA methylation (DNAm) at over 450,000 CpG dinucleotid #300
Warren S
We are studying a potential epigenetic component to the autism spectrum disorders (ASD) by interrogating DNA methylation (DNAm) using an established high-throughput assay that interrogates DNA methylation (DNAm) at over 450,000 highly informative CpG dinucleotides. To date, we have determined the DNA methylation (DNAm) profiles from whole blood-extracted DNA of over four hundred male sib-pairs discordant for ASD. A close statistical examination may ultimately identify ASD peripheral biomarkers...

Control - Sibling (360)

Test - Proband (345)

Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder. #301
Eichler EE; Girirajan S, Dennis MY, Baker C, Malig M, Coe BP, Campbell CD, Mark K, Vu TH, Alkan C, Cheng Z, Biesecker LG, Bernier R
Rare copy-number variants (CNVs) have been implicated in autism and intellectual disability. These variants are large and affect many genes but lack clear specificity toward autism as opposed to developmental-delay phenotypes. We exploited the repeat architecture of the genome to target segmental duplication-mediated rearrangement hotspots (n = 120, median size 1.78 Mbp, range 240 kbp to 13 Mbp) and smaller hotspots flanked by repetitive sequence (n = 1,247, median size 79 kbp, range 3-96 kbp)...

Control - NIMH Controls (197)

Control - Parental (848)

Test - Probands (2,240)

Microarray/Protein Analysis
Convergent and Discriminant Validity and Reliability of the Pediatric Anxiety Rating Scale in Youth with Autism Spectrum Disorders #304
Storch EA; Wood JJ, Ehrenreich-May J, Jones AM, Park JM, Lewin AB, Murphy TK
The psychometric properties of the Pediatric Anxiety Rating Scale (PARS), a clinician-administered measure for assessing severity of anxiety symptoms, were examined in 72 children and adolescents diagnosed with an autism spectrum disorder (ASD). The internal consistency of the PARS was 0.59, suggesting that the items were related but not repetitive.The PARS was strongly correlated with clinician-ratings of overall anxiety severity and parent- report anxiety measures, supporting convergent...

Test - ASD with Anxiety. UCLA cohort (27)

Test - ASD with Anxiety. USF cohort (27)

The Study of Health Outcomes in Children with Autism and their Families #306
Anjali J; Burke JP, Yang W, Kelly JP, Kaiser M, Becker L, Lawer L, Newschaffer CJ
The purpose of this study was to validate autism spectrum disorder cases identified through claims-based case identification algorithms against a clinical review of medical charts. Charts were reviewed for 432 children who fell into one of the three following groups: (a) more than or equal to two claims with an autism spectrum disorder diagnosis code (n = 182), (b) one claim with an autism spectrum disorder diagnosis code (n = 190), and (c) those who had no claims for autism spectrum disorder...

Test - Study sample (cohorts not on individual subject level)

Elucidating the Genetic Architecture of Autism by Deep Genomic Sequencing #307
Daly MJ; Sutcliffe J, Gibbs R, Buxbaum J, Schellenberg G
ARRA Autism Sequencing Collaboration The VCF files provided as Study Results for this study are what was provided at the time the study was created and consist of the Autism Only consent group. There is an additional General Research Use cohort, but those data are not provided here in this study. To obtain data from the General Research Use cohort please visit the dbGaP Study phs000298. It should be noted that the dbGaP study has been updated since the time this study was created, and the...

Control - Control (1,059)

Test - Autism (1,036)

Transmission disequilibrium of small CNVs in simplex autism. #312
Eichler EE; Krumm N, O'Roak BJ, Karakoc E, Mohajeri K, Nelson B, Vives L, Jacquemont S, Munson J, Bernier R
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...

Control - Parental Controls (822)

Control - Probands (411)

Control - Sibling Controls (411)

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. #316
Eichler EE; O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J
In addition to cohorts of Parents (N=418), Siblings (N=50), and Probands (N=209), the publication publication describes a subset of male (N=47) and female (N=26) autistic subjects, with significant impairment and intellectual disability, and with cognitive impairment, respectively. These subsets have been defined based on hi/low IQ value in Supplementary Table 1 from the publication. Publication Abstract: It is well established that autism spectrum disorders (ASD) have a strong genetic...

Control - Parental (418)

Control - Siblings (50)

Test - Female Probands (Low IQ) (26)

Test - Male Probands (Low IQ) (47)

Test - Probands (High IQ) (136)

Microarray/Protein Analysis
Patterns and rates of exonic de novo mutations in autism spectrum disorders. #317
Daly MJ; Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, et al.
Notes: Data submitted to NDAR did not include interview age. Publication Abstract: Autism spectrum disorders (ASD) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified. To identify further genetic risk factors, here we assess the role of de novo mutations in ASD by sequencing the exomes of ASD cases and their parents (n = 175 trios). Fewer than half of the cases (46.3%) carry a missense or nonsense de...

Control - Parents (cohorts not on individual subject level)

Test - Probands (104)

Microarray/Protein Analysis
De Novo Gene Disruptions in Children on the Autistic Spectrum #318
Wigler M; Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, Yamrom B, Lee YH, Narzisi G, Leotta A, Kendall J, Grabowska E, Ma B, Marks S, Rodgers L, Stepansky A, Troge J, Andrews P, Bekritsky M, Pradhan K, Ghiban E, Kramer M, Parla J, Demeter R, Fulton LL, Fulton RS, Magrini VJ, Ye K, Darnell JC, Darnell RB, Mardis ER, Wilson RK, Schatz MC, McCombie WR
Public Abstract: Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point substitutions, which come mostly from the paternal line in an age-dependent manner. We do not see significantly greater numbers of de novo missense mutations in affected versus unaffected children, but gene-disrupting mutations (nonsense, splice site, and frame shifts) are twice as frequent, 59 to 28. Based on this...

Control - Parental (686)

Control - Siblings (343)

Test - Probands (343)

Comparative RNA editing in autistic and neurotypical cerebella. #319
Kunkel LM; Eran A, Li JB, Vatalaro K, McCarthy J, Rahimov F, Collins C, Markianos K, Margulies DM, Brown EN, Calvo SE, Kohane IS
Adenosine-to-inosine (A-to-I) RNA editing is a neurodevelopmentally regulated epigenetic modification shown to modulate complex behavior in animals. Little is known about human A-to-I editing, but it is thought to constitute one of many molecular mechanisms connecting environmental stimuli and behavioral outputs. Thus, comprehensive exploration of A-to-I RNA editing in human brains may shed light on gene-environment interactions underlying complex behavior in health and disease. Synaptic...

Control - Typical Control (14)

Test - Autism (8)

Test - Autism Suspected (3)

Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders #320
Eichler EE; O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O'Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Shendure J
Abstract: Exome sequencing studies of autism spectrum disorders (ASDs) have identified many de novo mutations but few recurrently disrupted genes. We therefore developed a modified molecular inversion probe method enabling ultra-low-cost candidate gene resequencing in very large cohorts. To demonstrate the power of this approach, we captured and sequenced 44 candidate genes in 2446 ASD probands. We discovered 27 de novo events in 16 genes, 59% of which are predicted to truncate proteins or...

Control - Typical Control (768)

Test - Probands (2,494)

Microarray/Protein Analysis
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. #322
Sebat J; Michaelson JJ, Shi Y, Gujral M, Zheng H, Malhotra D, Jin X, Jian M, Liu G, Greer D, Bhandari A, Wu W, Corominas R, Peoples A, Koren A, Gore A, Kang S, Lin GN, Estabillo J, Gadomski T, Singh B, Zhang K, Akshoomoff N, Corsello C, McCarroll S, Iakoucheva LM, Li Y, Wang J
De novo mutation plays an important role in autism spectrum disorders (ASDs). Notably, pathogenic copy number variants (CNVs) are characterized by high mutation rates. We hypothesize that hypermutability is a property of ASD genes and may also include nucleotide-substitution hot spots. We investigated global patterns of germline mutation by whole-genome sequencing of monozygotic twins concordant for ASD and their parents. Mutation rates varied widely throughout the genome (by 100-fold) and...

Control - Parental (20)

Control - Sibling Control (cohorts not on individual subject level)

Test - Autism (MZ Twins) (20)

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations #323
Eichler EE; O'Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, Karakoc E, Mackenzie AP, Ng SB, Baker C, Rieder MJ, Nickerson DA, Bernier R, Fisher SE, Shendure J
Evidence for the etiology of autism spectrum disorders (ASDs) has consistently pointed to a strong genetic component complicated by substantial locus heterogeneity. We sequenced the exomes of 20 individuals with sporadic ASD (cases) and their parents, reasoning that these families would be enriched for de novo mutations of major effect. We identified 21 de novo mutations, 11 of which were protein altering. Protein-altering mutations were significantly enriched for changes at highly conserved...

Control - Parental (40)

Test - Autism (20)

Detection of structural variants and indels within exome data. #324
Eichler EE; Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L, Mark K, Rieder MJ, Nickerson DA
We report an algorithm to detect structural variation and indels from 1 base pair (bp) to 1 Mbp within exome sequence data sets. Splitread uses one end-anchored placements to cluster the mappings of subsequences of unanchored ends to identify the size, content and location of variants with high specificity and sensitivity. The algorithm discovers indels, structural variants, de novo events and copy number-polymorphic processed pseudogenes missed by other methods.

Control - Parental (40)

Test - Probands (20)

A genome-wide scan for common alleles affecting risk for autism. #325
Devlin B; Anney R, Klei L, Pinto D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Sykes N, Pagnamenta AT, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Carson AR, Casallo G, Casey J, et al.
Publication authors did not provide a list of Subject IDs used in this publication, cohorts in this study consist of all subjects with SNP genotyping data deposited with NDAR under data-set 8133. Publication Abstract: Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558...

Control - Non-ASD - European Ancestry (66)

Control - Non-ASD - Non-European Ancestry (19)

Control - Parental Control - European Ancestry (2,554)

Control - Parental Control - Non-European Ancestry (286)

Test - Probands - European Ancestry - Broad Spectrum Definition of Autism (excluding Strict) (464)

Test - Probands - European Ancestry - Strict Definition of Autism (762)

Test - Probands - Non-European Ancestry - Broad Spectrum Definition of Autism (excluding strict) (38)

Test - Probands - Non-European Ancestry - Strict Definition of Autism (87)

Functional impact of global rare copy number variation in autism spectrum disorders. #327
Devlin B; Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, et al.
Data submitter did not provide a listing of specific Subject IDs used in this publication. Cohorts consist of all subjects with CNV data deposited in NDAR from the Autism Genome Project. Data was not provided for non-parental controls. Publication Abstract: The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary...

Control - Parental - European Ancestry (2,267)

Control - Parental - Non-European Ancestry (284)

Test - Autism - European Ancestry (1,096)

Test - Autism - Non-European Ancestry (128)

Microarray/Protein Analysis
A protein interaction network of alternatively-spliced isoforms from brain links genetic risk factors for autism #330
Iakoucheva LM; Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M
Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by...

Control - Brain pool (cohorts not on individual subject level)

Microarray/Protein Analysis
Derivation of Quality Measures for Structural Images by Neuroimaging Pipelines #331
Kennedy D; Haselgrove C
Using the National Database for Autism Research cloud platform, MRI data were analyzed using neuroimaging pipelines that included packages available as part of the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) Computational Environment to derive standardized measures of MR image quality. Structural QA was performed according to Haselgrove, et al (http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00052/abstract) to provide values for Signal to Noise (SNR) and...

Test - FSPGR Scan Type (64)

Test - MPRAGE Scan Type (343)

Test - T1 Scan Type (18)

Neuro Signal Recordings
Derivation of Brain Structure Volumes from MRI Neuroimages hosted by NDAR using NITRC-CE #332
Kennedy D; Haselgrove C
A draft publication is in progress. GitHub repository with code for working with NDAR Data is available here: https://github.com/chaselgrove/ndar **Note this study is ongoing; additional may be added.**

Test - FIRST Processed (285)

Test - FreeSurfer Processed (340)

Neuro Signal Recordings
Derivation of Brain Structure Volumes from MRI Neuroimages hosted by NDAR using LONI Workflows #333
Van Horn JD; Liu, Zhizhong Petrosyan, Petros Torgerson, Carinna
LONI utilized de-identified data from NDAR's cloud and a LONI Pipeline (pipeline.loni.usc.edu) processing workflow to perform a secondary structural MRI examination. The workflow used in this study pulls data from and provided by NDAR to an instance on the LONI compute cluster, aligns data to a standard orientation using FSLreorient2stsd, and undergoes further image processing to eventually identify, extract, and analyze cortical and sub-cortical structures in different MRI brain volumes. Two...

Test - LONI Pipeline Processed Images (FIRST, FreeSurfer) (780)

Neuro Signal Recordings
Complete Realignment of Whole Exome Sequencing data from 2415 families in SSC Collection #334
Krumm, N; Eichler, E
Whole Exome Sequencing has been completed for ~ 2500 families from the Simons Simplex Collection. Sequencing was performed at three individual sequencing centers with original data submitted to NDAR Collections 1878, 1895, and 1936; subsets of these data have been analyzed by various methods and published. This study represents an effort to realign sequencing data from all three collection sin a uniform manner using the latest toolchains and algorithms available, which can be used as a resource...

Control - Parental Controls (4,819)

Control - Sibling Controls (1,822)

Test - Probands (2,406)

De novo mutations revealed by whole exome sequencing are strongly associated with autism #336
State MW; Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, et al.
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...

Control - Parents (476)

Control - Siblings (214)

Test - Probands (238)

Microarray/Protein Analysis
Autism spectrum disorder: interaction of air pollution with the MET receptor tyrosine kinase gene. #340
Volk HE; Kerin T, Lurmann F, Hertz-Picciotto I, McConnell R, Campbell DB
Background: Independent studies report association of autism spectrum disorder with air pollution exposure and a functional promoter variant (rs1858830) in the MET receptor tyrosine kinase (MET) gene. Toxicologic data find altered brain Met expression in mice after prenatal exposure to a model air pollutant. Our objective was to investigate whether air pollution exposure and MET rs1858830 genotype interact to alter ASD risk. Methods: We studied 252 cases of autism spectrum disorder and...

Test - Autism and ASD Diagnosis (155)

Test - Probands (54)

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. #341
Willsey 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, Xu X, et al.
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...

Control - Parental Controls (112)

Control - Sibling Controls (56)

Test - Probands (56)

Derivation of Brain Structure Volumes from MRI Neuroimages hosted by NDAR using C-PAC pipeline and ANTs #342
Craddock C; Clark D
An automated pipeline was developed to reference Neuroimages hosted by the National Database for Autism Research (NDAR) and derive volumes for distinct brain structures using Advanced Normalization Tools (ANTs) and the Configurable-Pipeline for the Analysis of Connectomes (C-PAC) platform. This pipeline utilized the ANTs cortical thickness methodology discuessed in "Large-Scale Evaluation of ANTs and Freesurfer Cortical Tchickness Measurements" [http://www.ncbi.nlm.nih.gov/pubmed/24879923] to...

Baseline - ANTs-processed subjects (1,540)

Neuro Signal Recordings
Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families #343
Gusella JF; Blumenthal I, Ragavendran A, Erdin S, Klei L, Sugathan A, Guide JR, Manavalan P, Zhou JQ, Wheeler VC, Levin JZ, Ernst C, Roeder K, Devlin B, Talkowski ME
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...

Control - Human - 16p11.2 normal (20)

Control - Mouse - Wild Type (8)

Test - Human - 16p11.2 deletion (4)

Test - Human - 16p11.2 duplication (10)

Test - Mouse - 7qF3 deletion (4)

Test - Mouse - 7qF3 duplication (4)

Microarray/Protein Analysis
Genotypes of Swedish subjects used in "Most genetic risk for autism resides with common variation" study #346
Buxbaum JD; Gaugler T, Klei L , Sanders SJ, Bodea CA , Goldberg AP, Lee AB, Mahajan M, Manaa D, Pawitan Y, Reichert J, Ripke S, Sandin S, Sklar P, Svantesson O, Reichenberg A, Hultman CM, Devlin B, Roeder K
A key component of genetic architecture is the allelic spectrum influencing trait variability. For autism spectrum disorder (herein termed autism), the nature of the allelic spectrum is uncertain. Individual risk-associated genes have been identified from rare variation, especially de novo mutations. From this evidence, one might conclude that rare variation dominates the allelic spectrum in autism, yet recent studies show that common variation, individually of small effect, has substantial...

Control - Non-ASD Controls (91)

Test - Autistic Disorder (457)

Variant Recalling (GATK) from Whole Exome Sequencing data for 2415 families in SSC Collection #348
Krumm, N; Eichler, E
Whole Exome Sequencing has been completed for ~ 2500 families from the Simons Simplex Collection. Sequencing was performed at three individual sequencing centers with original data submitted to NDAR Collections 1878, 1895, and 1936; subsets of these data have been analyzed by various methods and published. This study represents an effort to call and annotate SNPs and Indels on data from all three collections in a uniform manner using the latest toolchains and algorithms available. Variant...

Control - Parental Controls (1,800)

Control - Sibling Controls (4,784)

Test - Probands (2,392)

Variant Recalling (FreeBayes) from Whole Exome Sequencing data for 2415 families in SSC Collection #349
Krumm, N; Eichler, E
Whole Exome Sequencing has been completed for ~ 2500 families from the Simons Simplex Collection. Sequencing was performed at three individual sequencing centers with original data submitted to NDAR Collections 1878, 1895, and 1936; subsets of these data have been analyzed by various methods and published. This study represents an effort to call and annotate SNPs and Indels on data from all three collections in a uniform manner using the latest toolchains and algorithms available. Variant...

Control - Parental Controls (4,784)

Control - Sibling Controls (1,800)

Test - Probands (2,392)

Derivation of Quality Measures for Time-Series Images by Neuroimaging Pipelines #350
Kennedy D; Haselgrove C
Using the National Database for Autism Research cloud platform, MRI data were analyzed using neuroimaging pipelines that included packages available as part of the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) Computational Environment to derive standardized measures of MR image quality. Time series QA was performed according to Friedman, et al. (http://www.ncbi.nlm.nih.gov/pubmed/16952468) providing values for Signal to Noise Ratio that can be compared to other subjects.

Test - Time Series QA (356)

Neuro Signal Recordings
The contribution of de novo coding mutations to autism spectrum disorder #352
Wigler, M; Iossifov, I., O'Roak, B.J., Sanders, S.J., Ronemus, M., Krumm, N., Levy, D., Stessman, H.A., Witherspoon, K.T., Vives, L., Patterson, K.E., Smith, J.D., Paeper, B., Nickerson, D.A., Dea, J., Dong, S., Gonzalez, L.E., Mandell, J.E., Mane, S.M., Murtha, M.T., Sullivan, C.A., Walker, M.F., Waqar, Z., Wei, L., Willsey, A.J., Yamrom, B., Lee, Y.H., Grabowska, E., Dalkic, E., Wang, Z., Marks, S., Andrews, P., Leotta, A., Kendall, J., Hakker, I., Rosenbaum, J., Ma, B., Rodgers, L., Troge, J., Narzisi, G., Yoon, S., Schatz, M.C., Ye, K., McCombie, W.R., Shendure, J., Eichler, E.E., State, M.W
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...

Control - Parental Control (5,036)

Control - Sibling Control (1,911)

Test - Autistic Probands (2,509)

Excess of rare inherited truncating mutations in autism #353
Eichler E; Krumm N, Turner TN, Baker C, Vives L, Mohajeri K, Witherspoon K, Raja A, Coe BP, Stessman HA, He Z, Leal SM, Bernier R
In order to quantify the effect of private, inherited mutations on autism risk, we generated a callset of both inherited and de novo single nucleotide variants (SNVs) and copy number variants (CNVs) across 2,377 Simons Simplex Collection families. The publically deposited dataset includes 1,786 parents-child-unaffected sibling "quads" allowing us to compare burden of inherited and de novo mutations between affected and unaffected siblings in simplex autism families. We find that private,...

Control - Parental Control (4,754)

Control - Unaffected Siblings (1,786)

Test - Probands (2,377)

Cryptic and complex chromosomal aberrations in early onset neuropsychiatric disorders #357
Doyle AE; Brand H, Pillalamarri V, Collins R, Eggert S, O'Dushlaine C, Braaten EB, Stone M, Chambert K, Doty ND, Hanscom C, Ditmars H, Blais J, Mills R, Lee C, Gusella JF, McCarroll S, Smoller JW, Talkowski ME
Structural variation (SV) is a significant component of the genetic etiology of both neurodevelopmental and psychiatric disorders; however, routine guidelines for clinical genetic screening have been established only in the former category. Genome-wide chromosomal microarray (CMA) can detect genomic imbalances such as copy-number variants (CNVs), but balanced chromosomal abnormalities (BCAs) still require karyotyping for clinical detection. Moreover, submicroscopic BCAs and subarray threshold...

Baseline - LOGIC baseline (32)

Psychometric Analysis of the Social Communication Questionnaire Using an Item-Response Theory Framework: Implications for the Use of the Lifetime and Current Forms #358
Richman DM; Wei T, Chestnut SR, Barnard-Brak L
The Social Communication Questionnaire (SCQ) was developed as a screener of Autism Spectrum Disorder (ASD). To date, the majority of the SCQ utility studies focused on its external validity (e.g., ROC curve analyses), but very few have addressed the internal validity issues. With samples consisting of 2,134 individuals available from the National Database for Autism Research (NDAR), the current study examined the factor structure, item-level characteristics, and measurement equivalence of the...

Test - SCQ Current (474)

Test - SCQ Current and Lifetime (295)

Test - SCQ Lifetime (1,365)

Predicting Health Utilities for Children With Autism Spectrum Disorders #360
Tilford, MJ; Payakachat, N; Kuhlthau, KA; van Exel, NJ; Kovacs, E; Bellando, J; Pyne, JM; Brouwer, WBF
Comparative effectiveness of interventions for children with autism spectrum disorders (ASDs) that incorporates costs is lacking due to the scarcity of information on health utility scores or preference-weighted outcomes typically used for calculating quality-adjusted life years (QALYs). This study created algorithms for mapping clinical and behavioral measures for children with ASDs to health utility scores. The algorithms could be useful for estimating the value of different interventions and...

Test - Autistic Children (216)

Copy Number Variants from SSC Collection ~ 2500 families by two Methods (XHMM and Conifer) #361
Krumm, N; Eichler, E
XHMM was run on a set of realigned BAM files from the SSC collection (see NDAR Study 334 for BAM files) using the attached scripts. These scripts calculate depth of coverage using GATK, pull the GATK output from an instance on NDAR's cloud, merge the output of GATK into a single matrix, process the read depth matrix (filter, center), normalize the matrix using principal component analysis (PCA), process the normalized read depth matrix (filter, z-score), run a hidden markov model (HMM) on...

Control - Parental Control (4,816)

Control - Sibling Control (1,820)

Test - Autistic Probands (2,405)

fMRI for affective psychological studies #365
Lee, Ray
Taking advantage a newly developed dyadic fMRI system, this project studied two brains interactions via eye contact. This is the first direct observation of the dyadic affective states mediated by reciprocal visual stimulation. The dual system activation due to in vivo reciprocity, empathy system and metallization system, are clear evidences, while such systems often are not fully activated by pictorial stimuli. This method offers a direct and quantitative approach to estimate deficiency of...

Test - Task A and B (19)

Neuro Signal Recordings
Recurrent de novo mutations implicate novel genes underlying simplex autism risk. #366
Eichler EE; O'Roak BJ, Stessman HA, Boyle EA, Witherspoon KT, Martin B, Lee C, Vives L, Baker C, Hiatt JB, Nickerson DA, Bernier R, Shendure J
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...

Control - Unaffected Siblings (2,552)

Test - Proband (3,848)

Loss of delta-catenin function in severe autism #367
Chakravarti, Aravinda; Turner, TN; Sharma, K; Oh, EC; Liu, YP; Collins, RL; Sosa, MX; Auer, DR; Brand, H; Sanders, SJ; Moreno-De-Luca, D; Pihur, V; Plona, T; Pike, K; Soppet, DR; Smith, MW; Cheung, SW; Martin, CL; State, MW, Talkowski, ME; Cook, E; Huganir, R; Katsanis, N
Autism is a multifactorial neurodevelopmental disorder affecting more males than females; consequently, under a multifactorial genetic hypothesis, females are affected only when they cross a higher biological threshold. We hypothesize that deleterious variants at conserved residues are enriched in severely affected patients arising from female-enriched multiplex families with severe disease, enhancing the detection of key autism genes in modest numbers of cases. Here we show the use of this...

Control - Control (3)

Test - Proband (13)

Microarray/Protein Analysis
Decreased tryptophan metabolism in patients with Autism Spectrum Disorders #369
Charles Schwartz ; Boccuto, L; Chen, C; Pittman,A; Skinner, C; McCartney, H; Jones, K; Bochner, B; Stevenson, R.
Background: Autism spectrum disorders (ASDs) are relatively common neurodevelopmental conditions whose biological basis has been incompletely determined. Several biochemical markers have been associated with ASDs, but there is still no laboratory test for these conditions. Methods: We analyzed the metabolic profile of lymphoblastoid cell lines from 137 patients with neurodevelopmental disorders with or without ASDs and 78 normal individuals, using Biolog Phenotype MicroArrays. Results:...

Control - 50 Control (50)

Test - 50 Autism (50)

Microarray/Protein Analysis
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 #370
State, Matthew; Murdoch, J; Gupta, A; Sanders, S; Walker, M; Keaney, J; Fernandez, T; Murtha, M; Anyanwu, S; Ober, G; Raubeson, M; DiLullo, N; Villa, N; Waqar, Z; Sullivan, C; Gonzalez, L; Willsey, J; Choe, S; Neale, B; Daly, M
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...

Control - Discovery Cohort Psychiatrically Unscreened Controls (942)

Control - Exome Cohort Controls (1,060)

Test - Discovery Cohort Individuals Affected with ASD (1,082)

Test - Exome Cohort ASD Cases (1,034)

Rare-Variant Extensions of the Transmission Disequilibrium Test: Application to Autism Exome Sequence Data #371
Leal, Suzanne; He, Z; O'Roak, B; Smith, J; Wang, G; Hooker, S; Santos-Cortez, R; Li, B; Kan, M; Krumm, N; Nickerson, D; Shendure, J; Eichler, E
Many population-based rare-variant (RV) association tests, which aggregate variants across a region, have been developed to analyze sequence data. A drawback of analyzing population-based data is that it is difficult to adequately control for population substructure and admixture, and spurious associations can occur. For RVs, this problem can be substantial, because the spectrum of rare variation can differ greatly between populations. A solution is to analyze parent-child trio data, by using...

Control - Parental Control (378)

Test - Autistic Proband (189)

RNA-Seq studies of gene expression in micro-dissected samples from the brains of individuals with autism and controls #372
Allman, John; Wold, Barbara
We seek to understand the cellular bases of autism by using a new technology, RNA-Seq, to determine differences in gene expression in autopsy brains of subjects with well described autism versus age and sex matched neurotypical individuals. We have investigated two specific cortical areas involved in self-awareness and social reciprocity which are abnormal in autism and have found increased expression in a network of genes related to inflammation in autism group A, whereas the remaining cases,...

Control - Control (25)

Test - Autistic (10)

Development and validation of a brain maturation index using longitudinal neuroanatomical scans #374
Benson Mwangi PhD; Cao Bo, Hasan Khader, Selvaraj Sudhakar, Zeni Cristian, Zunta-Soares Giovan, Soares Jair.
Background Major psychiatric disorders are increasingly being conceptualized as ‘neurodevelopmental’, because they are associated with aberrant brain maturation. Several studies have hypothesized that a brain maturation index integrating patterns of neuroanatomical measurements may reliably identify individual subjects deviating from a normative neurodevelopmental trajectory. However, while recent studies have shown great promise in developing accurate brain maturation indices using...

Baseline - first visit (303)

Control - second-visit (115)

Neuro Signal Recordings
The Sensitivity and Specificity of the Social Communication Questionnaire for Autism Spectrum Disorder with Respect to Age #375
Barnard-Brak, Lucy; Brewer A; Chesnut S; Richman D; Shaeffer AM
Scientific Abstract The Social Communication Questionnaire (SCQ) assesses communication skills and social functioning in screening for symptoms of autism-spectrum disorder (ASD). The SCQ is recommended for individuals between 4 to 40 years with a cutoff score of 15 for referral. Mixed findings have been reported regarding the recommended cutoff score’s ability to accurately classify an individual as at-risk for ASD (sensitivity) versus an individual as not at-risk for ASD (specificity). Based...

Control - Control Cohort (90)

Test - ASD Cohort (249)

Revising the Social Communication Questionnaire scoring procedures for Autism Spectrum Disorder and potential Social Communication Disorder #376
Barnard-Brak, Lucy; Richman D; Chesnut S; Little TD
In analyzing data from the National Database for Autism Research, we examine revising the Social Communication Questionnaire (SCQ), a commonly used screening instrument for Autism Spectrum Disorder. A combination of Item Response Theory and Mokken scaling techniques were utilized to achieve this and abbreviated scoring of the SCQ is suggested. The psychometric sensitivity of this abbreviated SCQ was examined via bootstrapped Receiver Operator Characteristic (ROC) curve analyses. Additionally,...

Sample (mixed, ASD and non-ASD) (1,021)

Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort #377
Feinberg, Andrew P.; Fallin, M. Daniele (Co-PIs); Feinberg, J; Bakulski, K; Jaffe, A; Tryggvadottir, R; Brown, S; Goldman, L; Croen, L; Hertz-Picciotto, I; Newschaffer, C
Epigenetic mechanisms such as altered DNA methylation have been suggested to play a role in autism, beginning with the classical association of Prader-Willi syndrome, an imprinting disorder, with autistic features. Here we tested for the relationship of paternal sperm DNA methylation with autism risk in offspring, examining an enriched-risk cohort of fathers of autistic children. We examined genome-wide DNA methylation (DNAm) in paternal semen biosamples obtained from an autism spectrum...

Test - Fathers (44)

Microarray/Protein Analysis
Cortical underconnectivity coupled with preserved visuospatial cognition in autism: Evidence from an fMRI study of an embedded figures task. #378
Damarla SR; Keller T, Kana R, Cherkassky V, Williams D, Minshew N, Just M
Individuals with high-functioning autism sometimes exhibit intact or superior performance on visuospatial tasks, in contrast to impaired functioning in other domains such as language comprehension, executive tasks, and social functions. The goal of the current study was to investigate the neural bases of preserved visuospatial processing in high-functioning autism from the perspective of the cortical underconnectivity theory. We used a combination of behavioral, functional magnetic resonance...

Control - Control Participants (13)

Test - High Functioning Autistic (13)

Neuro Signal Recordings
Autonomy of lower-level perception from global processing in autism: evidence from brain activation and functional connectivity. #379
Liu Y; Cherkassky V, Minshew N, Just M
Previous behavioral studies have shown that individuals with autism are less hindered by interference from global processing during the performance of lower-level perceptual tasks, such as finding embedded figures. The primary goal of this study was to examine the brain manifestation of such atypicality in high-functioning autism using fMRI. Fifteen participants with high-functioning autism and fifteen age- and IQ-matched typical controls were asked to perform a lower-level perceptual...

Control - Typical Control (15)

Test - High Functioning Autism (15)

Neuro Signal Recordings
The neural basis of deictic shifting in linguistic perspective-taking in high-functioning autism #380
Mizuno A; Liu Y, Williams D, Keller T, Minshew N, Just M
Personal pronouns, such as 'I' and 'you', require a speaker/listener to continuously re-map their reciprocal relation to their referent, depending on who is saying the pronoun. This process, called 'deictic shifting', may underlie the incorrect production of these pronouns, or 'pronoun reversals', such as referring to oneself with the pronoun 'you', which has been reported in children with autism. The underlying neural basis of deictic shifting, however, is not understood, nor has the...

Control - Control Participants (15)

Test - High Functioning Autism (15)

Neuro Signal Recordings
Distinctive Neural Processes during Learning in Autism #381
Schipul SE; Williams D, Keller T, Minshew N, Just M
This functional magnetic resonance imaging study compared the neural activation patterns of 18 high-functioning individuals with autism and 18 IQ-matched neurotypical control participants as they learned to perform a social judgment task. Participants learned to identify liars among pairs of computer-animated avatars uttering the same sentence but with different facial and vocal expressions, namely those that have previously been associated with lying versus truth-telling. Despite showing a...

Control - Neurotypical Controls (18)

Test - Autism (17)

Neuro Signal Recordings
Association between pupillary light reflex and sensory behaviors in children with autism spectrum disorders. #382
Yao, Gang; Daluwatte C; Miles JH; Sun J
Atypical pupillary light reflexes (PLR) has been observed in children with autism spectrum disorders (ASD), which suggests potential autonomic nervous system (ANS) dysfunction in ASD. ANS is also involved in modulating sensory processing and sensory dysfunction has been widely reported in children with ASD. However, the potential association between physiological measurements of PLR and behavioral observations (e.g. sensory behaviors) has not been examined extensively in literature. In this...

Control - TD Group (106)

Test - ASD Group (150)

Atypical pupillary light reflex and heart rate variability in children with autism spectrum disorder #383
Yao, Gang; Daluwatte C, Miles JH, Christ SE, Beversdorf DQ, Takahashi N,
We investigated pupillary light reflex (PLR) in 152 children with ASD, 116 typically developing (TD) children, and 36 children with non-ASD neurodevelopmental disorders (NDDs). Heart rate variability (HRV) was measured simultaneously to study potential impairments in the autonomic nervous system (ANS) associated with ASD. The results showed that the ASD group had significantly longer PLR latency, reduced relative constriction amplitude, and shorter constriction/redilation time than those of the...

Control - TD Group (106)

Test - ASD Group (150)

Test - NDD Group (31)

Identification of Infants at High-Risk for Autism Spectrum Disorder Using Multiparameter Multiscale White Matter Connectivity Networks #385
Shen, Dinggang; Jin, Yan; Wee, Chong-Yaw; Shi, Feng; Thung, Kim-Han; Ni, Dong; Yap, Pew-Thian
Autism spectrum disorder (ASD) is a wide range of disabilities that cause life-long cognitive impairment and social, communication, and behavioral challenges. Early diagnosis and medical intervention are important for improving the life quality of autistic patients. However, in the current practice, diagnosis often has to be delayed until the behavioral symptoms become evident during childhood. In this study, we demonstrate the feasibility of using machine learning techniques for...

Control - Low Risk Cohort (128)

Test - High Risk Cohort (363)

Neuro Signal Recordings
Germline Mutations in Predisposition Genes in Pediatric Cancer #387
Jinghui Zhang; Michael F. Walsh, M.D.; Gang Wu, Ph.D.; Michael N. Edmonson, B.A.; Tanja A. Gruber, M.D.; Ph.D., John Easton; Ph.D., Dale Hedges; Ph.D., Xiaotu Ma; Ph.D., Xin Zhou; Ph.D., Donald A. Yergeau; Ph.D., Mark R. Wilkinson; B.S., Bhavin Vadodaria; B.A., Xiang Chen; Ph.D., Rose B. McGee; M.S., Stacy Hines-Dowell; D.N.P., Regina Nuccio; M.S., Emily Quinn; M.S., Sheila A. Shurtleff; Ph.D. Michael Rusch; B.A., Aman Patel; M.S., Jared B. Becksfort; M.S., Shuoguo Wang; Ph.D. Meaghann S. Weaver; M.D., Li Ding; Ph.D., Elaine R. Mardis; Ph.D., Richard K. Wilson; Ph.D., Amar Gajjar; M.D., David W. Ellison; M.D.; Ph.D., Alberto S. Pappo; M.D., Ching-Hon Pui; M.D., Kim E. Nichols, M.D.; and James R. Downing, M.D.
Background The prevalence and spectrum of predisposing mutations among children and adolescents with cancer are largely unknown. Knowledge of such mutations may improve the understanding of tumorigenesis, direct patient care, and enable genetic counseling of patients and families. Methods In 1120 patients younger than 20 years of age, we sequenced the whole genomes (in 595 patients), whole exomes (in 456), or both (in 69). We analyzed the DNA sequences of 565 genes, including 60 that have been...

Control - Control (208)

Test - ASD (515)

Genome sequencing of autism families reveals disruption of putative noncoding regulatory DNA #388
Eichler, Evan; Turner, Tychele N.; Hormozdiari, Fereydoun; Duyzend, Michael H.; McClymont, Sarah A.; Hook, Paul W.; Iossifov, Ivan; Raja, Archana; Baker, Carl; Hoekzema, Kendra; Stessman, Holly A.; Zody, Michael C.; Nelson, Bradley J.; Huddleston, John; Sandstrom, Richard; Smith, Joshua D.; Hanna, David; Swanson, James M.; Faustman, Elaine M.; Bamshad, Michael J.; Stamatoyannopoulos, John; Nickerson, Deborah A.; McCallion, Andrew S.; Darnell, Robert
We performed whole-genome sequencing (WGS) of 160 genomes from 40 simplex autism families, the majority of which had no copy number variant (CNV) or candidate de novo gene-disruptive single nucleotide variant (SNV) by microarray or whole-exome sequencing (WES). SNV and CNV calling was achieved by a number of variant calling algorithms. This accession contains SNV (FreeBayes) and CNV (digital comparative genomic hybridization [dCGH], GenomeSTRiP, VariationHunter) calls from this study.

Baseline - Simons Genome Project Pilot (160)

Maternal modifiers and parent-of-origin bias of the autism 16p11.2 CNV #389
Eichler EE; Duyzend MH, Nuttle X, Coe BP, Baker C, Nickerson DA, Bernier R
Recurrent deletions and duplications at chromosome 16p11.2 are a major genetic contributor to autism but also associate with a wider range of pediatric diagnoses. In order to investigate the potential genetic basis for phenotype variability, we assessed the parent-of-origin of the 16p11.2 copy number variant (CNV) and the presence of additional CNVs using commercial SNP microarrays in over 100 families where detailed phenotype data were available. Additional phenotypic and genotypic data is...

Control - 16p11.2 Family Members NOT carrying a 16p11.2 Deletion or Duplication (191)

Test - 16p11.2 Deletion Carrying Family Members (13)

Test - 16p11.2 Deletion Probands (72)

Test - 16p11.2 Duplication Carrying Family Members (31)

Test - 16p11.2 Duplication Probands (29)

Test - 16p11.2 Triplication Family (8)

Microarray/Protein Analysis
Targeted DNA Sequencing from Autism Spectrum Disorder Brains Implicates Multiple Genetic Mechanisms #391
Walsh, CA; D’Gama, I; Pochareddy, S; Li, M; Jamuar, S; Reiff, RE; Lam, A; Sestan, N
Single nucleotide variants (SNVs), particularly loss-of-function mutations, are significant contributors to autism spectrum disorder (ASD) risk. Here we report the first systematic deep sequencing study of 55 postmortem ASD brains for SNVs in 78 known ASD candidate genes. Remarkably, even without parental samples, we find more ASD brains with mutations that are protein-altering (26/55 cases versus 12/50 controls, p = 0.015), deleterious (16/55 versus 5/50, p = 0.016), or loss-of-function (6/55...

Control - Control (50)

Test - ASD (52)

Test - Other (17)

The topography of alpha-band activity tracks the content of spatial working memory #394
Awh, Edward & Vogel, Edward K.; Foster, J.J., Sutterer, D.S., Serences, J.T.
Working memory (WM) is a system for the online storage of information. An emerging view is that neuronal oscillations coordinate the cellular assemblies that code the content of WM. In line with this view, previous work has demonstrated that oscillatory activity in the alpha-band (8-12 Hz) plays a role in WM maintenance but the exact contributions of this activity have remained unclear. Here, we used an inverted spatial encoding model in combination with electroencephalography (EEG) to test...

Test - Foster et al. (2016) JNeurophysiol (56)

Neuro Signal Recordings
Trajectories of cortical thickness maturation in normal brain development #395
Ducharme, Simon; Albaugh M, Nguyen T, Hudziak J, Mateos-Pérez J, Labbe A, Evans A, Karama S
Several reports have described cortical thickness (CTh) developmental trajectories, with conflicting results. Some studies have reported inverted-U shape curves with peaks of CTh in late childhood to adolescence, while others suggested predominant monotonic decline after age 6. In this study, we reviewed CTh developmental trajectories in the NIH MRI Study of Normal Brain Development, and in a second step, evaluated the impact of post-processing quality control (QC) procedures on identified...

Control - Study Cohort (384)

Neuro Signal Recordings
Analysis of the contribution of experimental bias, experimental noise, and inter-subject biological variability on the assessment of developmental trajectories in diffusion MRI studies of the brain #396
Sadeghi, Neda; Nayak, Amritha; Walker, Lindsay; Irfanoglu, M; Albert, Paul; Pierpaoli, Carlo; Brain Development Cooperative Group
Metrics derived from the diffusion tensor, such as fractional anisotropy (FA) and mean diffusivity (MD) have been used in many studies of postnatal brain development. A common finding of previous studies is that these tensor-derived measures vary widely even in healthy populations. This variability can be due to inherent interindividual biological differences as well as experimental noise. Moreover, when comparing different studies, additional variability can be introduced by different...

Control - Study Cohort (128)

Neuro Signal Recordings
A new template to study callosal growth shows specific growth in anterior and posterior regions of the corpus callosum in early childhood #397
Ansado, Jennyfer; Collins, Louis; Fonov, Vladimir; Garon, Mathieu; Alexandrov, Lubomir; Karama, Sherif; Evans, Alan; Beauchamp, Miriam; and Brain Development Cooperative Group
Most of the studies conducted on the development of the corpus callosum (CC) have been limited to a relatively simple assessment of callosal area, providing an estimation of the size of the CC in two dimensions rather than its actual measurement. The goal of this study was to revisit callosal development in childhood and adolescence by using a three-dimensional (3D) magnetic resonance imaging template of the CC that considers the horizontal width of the CC and compares this with the...

Control - Study Cohort (433)

Neuro Signal Recordings
Prediction of brain maturity based on cortical thickness at different spatial resolutions #398
Khundrakpam, Budhachandra; Tohka, Jussi; Evans, Alan; and the Brain Development Cooperative Group
Several studies using magnetic resonance imaging (MRI) scans have shown developmental trajectories of cortical thickness. Cognitive milestones happen concurrently with these structural changes, and a delay in such changes has been implicated in developmental disorders such as attention-deficit/hyperactivity disorder (ADHD). Accurate estimation of individuals' brain maturity, therefore, is critical in establishing a baseline for normal brain development against which neurodevelopmental disorders...

Control - Study Cohort (343)

Neuro Signal Recordings
The diffusion tensor imaging (DTI) component of the NIH MRI study of normal brain development (PedsDTI) #399
Walker, Lindsay; Chang, Lin-Ching; Nayak, Amritha; Irfanoglu, Okan; Botteron, Kelly; McCracken, James; McKinstry, Robert; Rivkin, Michael; Wang, Dah-Jyuu; Rumsey, Judith; Pierpaoli, Carlo; the Brain Development Cooperative Group
The NIH MRI Study of normal brain development sought to characterize typical brain development in a population of infants, toddlers, children and adolescents/young adults, covering the socio-economic and ethnic diversity of the population of the United States. The study began in 1999 with data collection commencing in 2001 and concluding in 2007. The study was designed with the final goal of providing a controlled-access database; open to qualified researchers and clinicians,which could serve...

Control - High Resolution DTI Cohort (152)

Control - Low Resolution DTI Cohort (274)

Neuro Signal Recordings
Variants in adjacent oxytocin/vasopressin gene region and associations with ASD diagnosis and autism related endophenotypes #404
Cook, Edwin H.; Francis, Sunday M.; Kistner-Griffin, Emily; Yan, Zhongyu; Guter, Stephen; Jacob, Suma
Background: There has been increasing interest in oxytocin (peptide: OT, gene: OXT) as a treatment pathway for neurodevelopmental disorders such as Autism Spectrum Disorder (ASD). Neurodevelopmental disorders affect functional, social, and intellectual abilities. With advances in molecular biology, research has connected multiple gene regions to the clinical presentation of ASD. Studies have also shown that the neuropeptide hormones OT and arginine vasopressin (AVP) influence mammalian social...

Control - Parents (368)

Test - Probands (207)

The contribution of mosaic variants to autism spectrum disorder #405
Pevsner, Jonathan; Freed, Donald
De novo mutation is highly implicated in autism spectrum disorder (ASD). However, the contribution of post-zygotic mutation to ASD is poorly characterized. We performed both exome sequencing of paired samples and analysis of de novo variants from whole-exome sequencing of 2,388 families. While we find little evidence for tissue-specific mosaic mutation, multi-tissue post-zygotic mutation (i.e. mosaicism) is frequent, with detectable mosaic variation comprising 5.4% of all de novo mutations. We...

Control - Parental Controls (4,819)

Control - Sibling Controls (1,822)

Test - Probands (2,406)

De novo genic mutations among a Chinese autism spectrum disorder cohort #406
Eichler Evan; Tianyun W, Hui G, Bo X, Holly A.F. S, Huidan W, Bradley P. C, Tychele N. T, Yanling L, Wenjing Z, Kendra H, Laura V, Lu X, Meina T, Jianjun O, Biyuan C, Yidong S, Guanglei X, Min L, Janice L, Zev N. K, Yu P, Ting B, Honghui L, Xiaoyan K, Zhengmao H, Jingping Z, Xiaobing Z
Recurrent de novo (DN) and likely gene-disruptive (LGD) mutations are important risk factors for autism spectrum disorders (ASD) but have been primarily investigated in cohorts of European ancestry. We sequenced 189 risk genes in 1,543 ASD probands (1,045 from trios) with Chinese ancestry. We report an 11-fold increase in the odds of DN LGD mutations compared to expectation under an exome-wide mutational rate model based on chimpanzee–human divergence. This enrichment for DN LGD mutations...

Test - the Autism Clinical and Genetic Resources in China (ACGC) (1,647)

Acetaminophen Use for Fever in Children Associated with Autism Spectrum Disorder #407
Schultz, Stephen; Gould, G
Autism Spectrum Disorder (ASD) is characterized by persistent deficits in social communication and restrictive behavior, interests, and activities. Our previous case-control study showed that use of acetaminophen at age 12-18 months is associated with increased likelihood for ASD (OR 8.37, 95% CI 2.08-33.7). In this study, we again show that acetaminophen use is associated with ASD (p = 0.013). Because these children are older than in our first study, the association is reversed; fewer children...

Control - Control (79)

Test - ASD (118)

Cross-trial prediction of treatment outcome in depression: a machine learning approach #408
Chekroud, Adam; Corlett, P; Krystal, J; Cannon, T; Trivedi, M; Johnson, M; Gueorguieva, R; Shehzad, Z; Zotti, R
Background: Antidepressant treatment efficacy is low, but might be improved by matching patients to interventions. At present, clinicians have no empirically validated mechanisms to assess whether a patient with depression will respond to a specific antidepressant. We aimed to develop an algorithm to assess whether patients will achieve symptomatic remission from a 12-week course of citalopram. Methods: We used patient-reported data from patients with depression (n=4041, with 1949 completers)...

Test - Model Training Cohort (1,949)

Frequency and Complexity of De Novo Structural Mutation in Autism #410
Sebat, Jonathan; Corsello, Christina; Iakoucheva, Lilia; Courchesne, Eric
Genetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising...

Control - Parental Controls (136)

Control - Sibling Controls (25)

Control - Typical Control (3)

Test - Probands (71)

Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci #411
Sanders, Stephan; He X, Willsey AJ, Ercan-Sencicek AG, Samocha KE, Cicek AE, Murtha MT, Bal VH, Bishop SL, Dong S, Goldberg AP, Jinlu C, Keaney JF 3rd, Klei L, Mandell JD, Moreno-De-Luca D, Poultney CS, Robinson EB, Smith L, Solli-Nowlan T, Su MY, Teran NA, Walker MF, Werling DM, Beaudet AL, Cantor RM, Fombonne E, Geschwind DH, Grice DE, Lord C, Lowe JK, Mane SM, Martin DM, Morrow EM, Talkowski ME, Sutcliffe JS, Walsh CA, Yu TW: Autism Sequencing Consortium, Ledbetter DH, Martin CL, Cook EH, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MW
Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex Collection (SSC) (N = 2,591 families) replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci (1q21.1, 3q29, 7q11.23, 16p11.2, 15q11.2-13, and 22q11.2). The addition of published CNV data from the Autism Genome Project (AGP) and exome sequencing data from the SSC and the Autism Sequencing Consortium (ASC) shows that genes within small de novo deletions, but not within large...

Control - SSC Control Cohort (7,337)

Test - SSC ASD Cohort (2,638)

Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR. #414
James Gusella; Tai DJ, Ragavendran A, Manavalan P, Stortchevoi A, Seabra CM, Erdin S, Collins RL, Blumenthal I, Chen X, Shen Y, Sahin M, Zhang C, Lee C, Gusella JF, Talkowski ME
Recurrent, reciprocal genomic disorders resulting from non-allelic homologous recombination (NAHR) between near-identical segmental duplications (SDs) are a major cause of human disease, often producing phenotypically distinct syndromes. The genomic architecture of flanking SDs presents a challenge for modeling these syndromes; however, the capability to efficiently generate reciprocal copy number variants (CNVs) that mimic NAHR would represent a valuable modeling tool. We describe here a...

Control - Parental line and derivatives (cohorts not on individual subject level)

Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism. #416
Cook, Edwin H.; Chen, Rui; Davis, Lea K.; Guter, Stephen; Wie, Qiang; Jacob, Suma; Potter, Melissa H.; Cox, Nancy J.; Sutcliffe, James S.; Li, Bingshan
Background: Autism spectrum disorder (ASD) is one of the most highly heritable neuropsychiatric disorders, but underlying molecular mechanisms are still unresolved due to extreme locus heterogeneity. Leveraging meaningful endophenotypes or biomarkers is an effective strategy to reduce heterogeneity to identify novel ASD genes. Numerous lines of evidence suggest a link between hyperserotonemia, i.e., elevated serotonin (5-hydroxytryptamine or 5-HT) in whole blood, and ASD. However, the genetic...

Control - Parents (232)

Test - Probands - All (116)

The clinical relevance of self-reported premenstrual worsening of depressive symptoms in the management of depressed outpatients: a STAR*D report. #417
A. John Rush; Haley CL, Sung SC, Rush AJ, Trivedi MH, Wisniewski SR, Luther JF, Kornstein SG
OBJECTIVE: To determine the incidence, clinical and demographic correlates, and relationship to treatment outcome of self-reported premenstrual exacerbation of depressive symptoms in premenopausal women with major depressive disorder who are receiving antidepressant medication. METHOD: This post-hoc analysis used clinical trial data from treatment-seeking, premenopausal, adult female outpatients with major depression who were not using hormonal contraceptives. For this report, citalopram was...

Test - No premenstrual exacerbation of depressive symptoms (345)

Test - Premenstrual exacerbation of depressive symptoms (672)

Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. #418
Cai, James J; Guan, Jinting; Yang, Ence; Yang, Jizhou; Zeng, Yong; Ji, Guoli
Autism spectrum disorder (ASD) is characterized by substantial phenotypic and genetic heterogeneity, which greatly complicates the identification of genetic factors that contribute to the disease. Study designs have mainly focused on group differences between cases and controls. The problem is that, by their nature, group difference-based methods (e.g., differential expression analysis) blur or collapse the heterogeneity within groups. By ignoring genes with variable within-group expression, an...

Control - Control Subjects (40)

Test - Subjects with Autism Spectrum Disorders (32)

Preliminary findings suggest the number and volume of supragranular and infragranular pyramidal neurons are similar in the anterior superior temporal area of control subjects and subjects with autism. #420
Veronica Martinez Cerdeno; Kim E, Camacho J, Combs Z, Ariza J, Lechpammer M, Noctor SC, Martínez-Cerdeño V
We investigated the cytoarchitecture of the anterior superior temporal area (TA2) of the postmortem cerebral cortex in 9 subjects with autism and 9 age-matched typically developing subjects between the ages of 13 and 56 years. The superior temporal gyrus is involved in auditory processing and social cognition and its pathology has been correlated with autism. We quantified the number and soma volume of pyramidal neurons in the supragranular layers and pyramidal neurons in the infragranular...

Control - Control (9)

Test - Experimental (9)

The Number of Parvalbumin-Expressing Interneurons Is Decreased in the Medial Prefrontal Cortex in Autism. #421
Veronica Martinez Cerdeno; Hashemi E, Ariza J, Rogers H, Noctor SC, Martínez-Cerdeño V
UNASSIGNED: The cognitive phenotype of autism has been correlated with an altered balance of excitation to inhibition in the cerebral cortex, which could result from a change in the number, function, or morphology of GABA-expressing interneurons. The number of GABAergic interneuron subtypes has not been quantified in the autistic cerebral cortex. We classified interneurons into 3 subpopulations based on expression of the calcium-binding proteins parvalbumin, calbindin, or calretinin. We...

Control - Control (10)

Test - Autism (10)

Targeted sequencing identifies 91 neurodevelopmental disorder risk genes with autism and developmental disability biases #425
Eichler, Evan; Stessman, H; Xiong, B; Coe, B; Wang, T; Hoekzema, K; Fenckova, M; Kvarnung, M; Gerdts, J; Trinh, S; Cosemans, N; Vives, L; Lin, J; Turner, T; Santen, G; Gecz, J; Shaw, M; Anderlid, B; Nordgren, A; Lindstrand, A; Schwartz, C; Kooy, F; Vandeweyer, G; Helsmoortel, C; Romano, C; Alberti, A; Vinci, M; Avola, E; Giusto, S; Courchesne, E; Pramparo, T; Pierce, K; Nalabolu, S; Amaral, D; Scheffer, I; Delatycki, M; Lockhart, P; Hormozdiari, F; Harich, B; Castells-Hobau, A; Xia, K; Peeters, H; Nordenskjold, M; Schenck, A; Bernier, R
Gene-disruptive mutations contribute to the biology of neurodevelopmental disorders (NDDs), but most pathogenic genes are not known. We sequenced 208 candidate genes from >11,730 patients and >2,867 controls. We report 91 genes with an excess of de novo mutations or private disruptive mutations in 5.7% of patients, including 38 novel NDD genes. Drosophila functional assays of a subset bolster their involvement in NDDs. We identify 25 genes that show a bias for autism versus intellectual...

Control - Autism Genetic Resource Exchange (AGRE) Unaffected (593)

Control - Autism Phenome Project (APP) Unaffected (64)

Control - SAGE Unaffected (129)

Control - Simons Simplex Collection (SSC) Unaffected (1,384)

Control - The Autism Simplex Collection (TASC) Unaffected (174)

Test - Adelaide (2,226)

Test - Antwerp (1,087)

Test - Autism Clinical and Genetic Resources in China (ACGC) (1,647)

Test - Autism Genetic Resource Exchange (AGRE) (1,729)

Test - Autism Phenome Project (APP) (144)

Test - Greenwood (252)

Test - Leiden (210)

Test - Leuven (900)

Test - Melbourne (309)

Test - Murdoch (56)

Test - SAGE (429)

Test - San Deigo (488)

Test - Stockholm (1,500)

Test - The Autism Simplex Collection (TASC) (1,045)

Test - Troina (1,195)

The evolution and population diversity of human-specific segmental duplications #431
Eichler, EE; Dennis, MY; Dougherty, ML; Harshman, L; Nelson, BJ; Penn, O; Cantsilieris, S; Huddleston, J; Antonacci, F; Penewit, F; Denman, L; Raja, A; Baker, C; Mark, K; Malig, M; Janke, N; Espinoza, C; Stessman, HAF; Nuttle, X; Hoekzema, K; Lindsay-Graves, TA; Wilson, RK
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...

Control - AGRE Unaffected (560)

Control - SSC Unaffected (1,114)

Control - TASC Unaffected (174)

Test - AGRE Probands (1,725)

Test - SSC Probands (1,742)

Test - TASC Probands (1,045)

Defining the spectrum of large inversions, complex structural variation, and chromothripsis in the morbid genome #433
Talkowski, Michael; Collins, Ryan; Brand, Harrison; Redin, Claire; Hanscom, Carrie; Antolik, Caroline; Stone, Matthew; Glessner, Joseph; Mason, Tamara; Pregno, Giulia; Dorrani, Naghmeh; Mandrile, Giorgia; Giachino, Daniel; Perrin, Danielle; Walsh, Cole; Cipicchio, Michelle; Costello, Maura; Stortchevoi, Alexei; An, Joon-Yong; Currall, Benjamin; Seabra, Catarina; Ragavendran, Ashok; Margolin, Lauren; Martinez-Agosto, Julian; Lucente, Diane; Levy, Brynn; Sanders, Stephan; Wapner, Ronald; Quintero-Rivera, Fabiola; Kloosterman, Wigard; Talkowski, Michael.
Background: Structural variation (SV) influences genome organization and contributes to human disease. However, the complete mutational spectrum of SV has not been routinely captured in disease association studies. Results: We sequenced 689 subjects with autism spectrum disorder and other developmental abnormalities to construct a genome-wide map of large SV. Using long-insert jumping libraries at 105X mean physical coverage and linked-read whole-genome sequencing from 10X Genomics, we...

Test - Subset of Simons Simplex Collection (686)

Paternally inherited noncoding structural variants contribute to autism #434
Sebat, Jonathan; Brandler, W; Gujral, M; Antaki, D; Iakoucheva, L; Corsello, C; Hervas, A; Mutori, A
The genetic architecture of autism spectrum disorder (ASD) is known to consist of contributions from gene-disrupting de novo mutations and common variants of modest effect. We hypothesize that the unexplained heritability of ASD also includes rare inherited variants with intermediate effects. We investigated the genome-wide distribution and functional impact of structural variants (SVs) through whole genome analysis (>30X coverage) of 3,169 subjects from 829 families affected by ASD. Genes that...

Control - Parental Controls (1,656)

Control - Sibling Controls (623)

Control - Typical Control (12)

Test - Probands (879)

Improvement in Social Competence Using a Randomized Trial of a Theatre Intervention for Children with Autism Spectrum Disorder. #435
Corbett, Blythe; Key, A.P.; Qualls, L.; Fecteau, S.; Newsom, C.; & Yoder, P.
The efficacy of a peer-mediated, theatre-based intervention on social competence in participants with autism spectrum disorder (ASD) was tested. Thirty 8-to-14 year-olds with ASD were randomly assigned to the treatment (n = 17) or a wait-list control (n = 13) group. Immediately after treatment, group effects were seen on social ability, (d = .77), communication symptoms (d = -.86), group play with toys in the company of peers (d = .77), immediate memory of faces as measured by...

Control - Summer 2014 (13)

Test - Winter 2014 (17)

Lack of early improvement with antipsychotics is a marker for subsequent non-response in behavioral and psychological symptoms of dementia: Analysis of CATIE-AD data #439
Uchida, Hiroyuki; Yoshida, K; Roberts, R; Suzuki, T; Lebowitz, B; Reeves, S; Howard, R; Abe, T; Mimura, M
Objective: Prediction of response/non-response to antipsychotics is especially important in patients with behavioral and psychological symptoms of dementia (BPSD) in whom antipsychotic exposure increases risks of death. We aimed to examine whether presence/absence of early improvement of BPSD with antipsychotics is associated with subsequent response/non-response. Design: Post-hoc analysis of the Clinical Antipsychotic Trials in Intervention Effectiveness with Alzheimer’s Disease (CATIE-AD)...

Baseline - CATIE-AD (245)

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin #440
Flora M. Vaccarino; Alexej Abyzov, Livia Tomasini, Bo Zhou, Nikolaos Vasmatzis, Gianfilippo Coppola, Mariangela Amenduni, Reenal Pattni, Michael Wilson, Mark Gerstein, Sherman Weissman, Alexander E. Urban
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...

Baseline - SNV (12)

How anxious do you think I am? Relationship between state and trait anxiety in children with and without ASD during social tasks #445
Grossman, Ruth; Mertens, J.; Zane, E.R.; Neumeyer, K.; Grossman, R.B.
Individuals with autism spectrum disorder (ASD) often exhibit increased anxiety, even in non-stressful situations. We investigate general anxiousness (anxiety trait) and responses to stressful situations (anxiety state) in 22 adolescents with ASD and 32 typically developing controls. We measured trait anxiety with standardized self- and parent-reported questionnaires. We used a Biopac system to capture state anxiety via skin conductance responses, mean heart rate and heart rate variability...

Control - Neurotypical peers (23)

Test - ASD (13)

Training Parents of Youth with Autism Spectrum Disorder to Advocate for Adult Disability Services: Results from a Pilot Randomized Controlled Trial. #446
Julie L. Taylor; Taylor JL, Hodapp RM, Burke MM, Waitz-Kudla SN, Rabideau C
This study presents findings from a pilot randomized controlled trial, testing a 12-week intervention to train parents of youth with autism spectrum disorder (ASD) to advocate for adult disability services-the Volunteer Advocacy Program-Transition (VAP-T). Participants included 41 parents of youth with ASD within 2 years of high school exit, randomly assigned to a treatment (N = 20) or wait-list control (N = 21) group. Outcomes, collected before and after the intervention, included parental...

VAP-T (41)

Upper limb motor coordination based early diagnosis in high risk subjects for Autism #451
Wedyan, Mohammad; Al-Jumaily,Adel
Autism is a lifelong condition present from early childhood. Medical specialists' diagnosis autism based on observation is of great difficulty in communicating, difficulties for forming relationships with other people, and delayed speech. The scientists tried to discover other early signs to reach the early detection of Autism Spectrum Disorders (ASD). Early diagnosing is very important to initiate and improve treatment results. One of these signs is based on examination of upper limb motor...

Control - high risk for Autism (57)

Neuro Signal Recordings
Violation Differentiation #454
Norman, Ken; Kim, Ghootae; Turk-Browne, Nick
When an item is predicted in a particular context but the prediction is violated, memory for that item is weakened (Kim et al., 2014). Here, we explore what happens when such previously mispredicted items are later reencountered. According to prior neural network simulations, this sequence of events-misprediction and subsequent restudy-should lead to differentiation of the item's neural representation from the previous context (on which the misprediction was based). Specifically, misprediction...

Test - Experimental Group (32)

Neuro Signal Recordings
Inflexible neurobiological signatures precede atypical development in infants at high risk for autism #455
Denisova, Kristina; Zhao, Guihu
Variability in neurobiological signatures is ubiquitous in early life but the link to adverse developmental milestones in humans is unknown. We examined how levels of signal and noise in movement signatures during the 1st year of life constrain early development in 71 healthy typically developing infants, either at High or Low familial Risk (HR or LR, respectively) for developing Autism Spectrum Disorders (ASD). Delays in early learning developmental trajectories in HR infants (validated in an...

HR infants (38)

LR infants (33)

Neuro Signal Recordings
Stimulation of the Posterior Cortical-Hippocampal Network Enhances Precision of Memory Recollection. #465
Joel Voss; Nilakantan AS, Bridge DJ, Gagnon EP, VanHaerents SA, Voss JL
Episodic memory is thought to critically depend on interaction of the hippocampus with distributed brain regions [1-3]. Specific contributions of distinct networks have been hypothesized, with the hippocampal posterior-medial (HPM) network implicated in the recollection of highly precise contextual and spatial information [3-6]. Current evidence for HPM specialization is mostly indirect, derived from correlative measures such as neural activity recordings. Here we tested the causal role of the...

Control - Subjects for Nilakantan et al. 2017 (26)

Neuro Signal Recordings
Early brain development in infants at high risk for autism spectrum disorder #468
Hazlett, Heather; Hazlett, Heather; Gu, Hongbin; Munsell, Brent C.; Kim, Sun Hyung; Styner, Martin; Wolff, Jason J.; Elison, Jed T.; Swanson, Meghan R.; Zhu, Hongtu; Botteron, Kelly N.; Collins, D. Louis; Constantino, John N.; Dager, Stephen R.; Estes, M.; Evans, Alan C.; Fonov, Vladimir S.; Gerig, Guido; Kostopoulos, Penelope; McKinstry, Robert C.; Pandey, Juhi; Paterson, Sarah; Pruett Jr., John R.; Schultz, Robert T.; Shaw, Dennis W.; Zwaigenbaum, Lonnie
Brain enlargement has been observed in children with autism spectrum disorder (ASD), but the timing of this phenomenon, and the relationship between ASD and the appearance of behavioural symptoms, are unknown. Retrospective head circumference and longitudinal brain volume studies of two-year olds followed up at four years of age have provided evidence that increased brain volume may emerge early in development1, 2. Studies of infants at high familial risk of autism can provide insight into the...

Control - HR- (88)

Control - LR- (35)

Test - HR+ (15)

Neuro Signal Recordings
Combining Gaze and Demographic Feature Descriptors for Autism Classification #472
Canavan, Shaun; Chen, Melanie; Chen, Song; Valdez, Robert; Yaeger, Miles; Lin, Huiyi; Yin, Lijun
People with autism suffer from social challenges and communication difficulties, which may prevent them from leading a fruitful and enjoyable life. It is imperative to diagnose and start treatments for autism as early as possible and, in order to do so, accurate methods of identifying the disorder are vital. We propose a novel method for classifying autism through the use of eye gaze and demographic feature descriptors that include a subject’s age and gender. We construct feature descriptors...

Test - ASD Test (836)

PING Genomics Derived Data #477
Jernigan, Terry; Dale, Anders; Jernigan, Terry; Dale, Anders
The PING Data Resource is the product of a multi-site project involving developmental researchers across the United States including UC San Diego the University of Hawaii UC Los Angeles Childrens Hospital of Los Angeles of the University of Southern California UC Davis Kennedy Krieger Institute of Johns Hopkins University Sackler Institute of Cornell University University of Massachusetts Massachusetts General Hospital at Harvard University and Yale University. The Data Resource includes...

Control - PING (1,493)

How We Transmit Memories to Other Brains: Constructing Shared Neural Representations Via Communication. #483
Hasson, Uri; Zadbood, Asieh; Chen, Janice; Leong, Yuan C.; Norman, Kenneth A.
Humans are able to mentally construct an episode when listening to another person's recollection, even though they themselves did not experience the events. However, it is unknown how strongly the neural patterns elicited by mental construction resemble those found in the brain of the individual who experienced the original events. Using fMRI and a verbal communication task, we traced how neural patterns associated with viewing specific scenes in a movie are encoded, recalled, and then...

Test - subjects (36)

Neuro Signal Recordings
Alpha-Band Oscillations Enable Spatially and Temporally Resolved Tracking of Covert Spatial Attention. #485
Edward Awh; Foster JJ, Sutterer DW, Serences JT, Vogel EK, Awh E
Covert spatial attention is essential for humans' ability to direct limited processing resources to the relevant aspects of visual scenes. A growing body of evidence suggests that rhythmic neural activity in the alpha frequency band (8-12 Hz) tracks the spatial locus of covert attention, which suggests that alpha activity is integral to spatial attention. However, extant work has not provided a compelling test of another key prediction: that alpha activity tracks the temporal dynamics of covert...

Test - Foster et al. (2017) Psychological Science (47)

Neuro Signal Recordings
Amplification of local changes along the timescale processing hierarchy. #487
Uri Hasson; Yeshurun Y, Nguyen M, Hasson U
Small changes in word choice can lead to dramatically different interpretations of narratives. How does the brain accumulate and integrate such local changes to construct unique neural representations for different stories? In this study, we created two distinct narratives by changing only a few words in each sentence (e.g., "he" to "she" or "sobbing" to "laughing") while preserving the grammatical structure across stories. We then measured changes in neural responses between the two stories....

Test - Subjects (54)

Neuro Signal Recordings
Mitochondrial DNA mutations in Autism Spectrum Disorder #495
Gu, Zhenglong; Wang, Yiqin
Mitochondrial dysfunction is frequently observed in Autism Spectrum Disorders (ASD). Thus, variations in the mitochondrial DNA (mtDNA) sequences may contribute to increased ASD risks. In the current study, we evaluated mtDNA variations, including homoplasmy and heteroplasmy, in 903 ASD individuals along with their mothers and non-ASD siblings by using off-target reads from whole-exome sequencing data sets of Simons Foundation Autism Research Initiative (SFARI) Simons Collection available on...

Control - Maternal Controls (903)

Control - Sibling Controls (903)

Test - ASD Probands (903)

Different mutational rates and mechanisms in human cells at pre-gastrulation and neurogenesis #496
Vaccarino Flora; Abyzov, Alexej; Bae, Taejeong; Tomasini, Livia; Mariani, Jessica; Zhou, Bo; Roychowdhury, Tanmoy; Franjic, Daniel; Pletikos, Mihovil; Pattni, Reenal; Chen, Bo-Juen; Venturini, Elisa; Riley-Gillis, Bridget; Sestan, Nenad; Urban, Alexander
Somatic mosaicism in the human brain may alter function of individual neurons. We analyzed genomes of single cells from the forebrains of three human fetuses (15 to 21 weeks post-conception) using clonal cell populations. We detected 200-400 single nucleotide variations (SNVs) per cell. SNV patterns resembled those found in cancer cell genomes, indicating a role of background mutagenesis in cancer. SNVs with a frequency of >2% in brain were shared with the spleen, revealing a pre-gastrulation...

Control - Control cell line (cohorts not on individual subject level)

Control - Fetal brains (4)

Adolescent Brain Cognitive Development Study (ABCD) - Annual Release 1.0 #500
Jernigan, Terry L; Casey, Bettybj; Clark, Duncan; Colrain, Ian; Dale, Anders; Ernst, Thomas; Gonzalez, Raul; Heitzeg, Mary; Lisdahl, Krista; Luciana, Monica; Nagel, Bonnie; Sowell, Elizabeth; Squeglia, Lindsay; Tapert, Susan; Yurgeluntodd, Deborah;
The ABCD Curated Annual Release 1.0 includes high quality baseline data from the first ~4,500 research participants, including minimally processed brain image volumes and tabulated structural MRI, diffusion MRI, resting-state fMRI and task fMRI results, as well as all non-imaging assessment data from the physical & mental health, neurocognition, substance use, biospecimens and culture & environment domains. All personally identifiable information is removed from the data to ensure participant...

Baseline - ABCD 1.0 Data Release (4,524)

Neuro Signal Recordings
Alpha-Band Activity Reveals Spontaneous Representations of Spatial Position in Visual Working Memory. #508
Edward Awh; Foster JJ, Bsales EM, Jaffe RJ, Awh E
An emerging view suggests that spatial position is an integral component of working memory (WM), such that non-spatial features are bound to locations regardless of whether space is relevant [1, 2]. For instance, past work has shown that stimulus position is spontaneously remembered when non-spatial features are stored. Item recognition is enhanced when memoranda appear at the same location where they were encoded [3-5], and accessing non-spatial information elicits shifts of spatial attention...

Test - Foster et al. (2017) Current Biology (82)

Neuro Signal Recordings
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