National Database for Autism Research - Data

Link

Investigators:	Richman DM; Barnard-Brak L, Bosch A, Thompson S, Grubb L, Abby L
Abstract:	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:...
Results:	Results published in J Intellect Disabil Res, May 2013 Study Notes
Documents:
DOI:	10.15154/1226464
Data Use:	Secondary Analysis

Cohorts:	Test - SIB Cohort (611)
Measures:	Primary Measures (1) Secondary Measures (62)
Data Analysis:	Statistical

Link

Investigators:	Levitt P; Gorrindo P, Williams KC, Lee EB, Walker LS, McGrew SG
Abstract:	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...
Results:	Results published in Autism Res, Apr 2012
Documents:
DOI:	10.15154/1163508
Data Use:	Primary Analysis

Cohorts:

Control - ASD-only (39)

Control - GID-only (22)

Test - ASD-GID (30)

Measures:

Primary Measures (16)

Secondary Measures (23)

Data Analysis:

Statistical

Link

Investigators:	Menon, Vinod; Superkar, K; Uddin, LQ; Khouzam, A; Phillips, J; Gaillard, WD; Kenworthy, LE; Yerys, BE; Vaidya, CJ
Abstract:	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...
Results:	Paper in Cell Reports Study Notes
Documents:
DOI:	10.15154/1223791
Data Use:	Secondary Analysis

Cohorts:

Baseline - ASD Subjects (15)

Control - Non-ASD Subjects (28)

Measures:

Primary Measures (1)

Secondary Measures (0)

Data Analysis:

Neuro Signal Recordings

Link

Investigators:	Warren S
Abstract:	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...
Results:	p values for CpG probes
Documents:
DOI:	10.15154/1165651
Data Use:	Primary Analysis

Cohorts:

Control - ASD-Siblings (159)

Test - ASD-Probands (415)

Measures:

Primary Measures (5)

Secondary Measures (1)

Data Analysis:

Statistical

Link

Investigators:	Scherer S, Devlin B
Abstract:	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...
Results:	Genotype Calls Genotype Calls, part 2
Documents:
DOI:	10.15154/1165652
Data Use:	Primary Analysis

Cohorts:

Control - Parents (2,933)

Test - Non-verbal (483)

Test - Verbal subjects (1,000)

Measures:

Primary Measures (2)

Secondary Measures (4)

Data Analysis:

Genotyping/NGS

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Investigators:	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
Abstract:	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...
Results:	Results published in Nature, Dec 2012
Documents:	SFARI GRANT 137055 R09345 R01MH89176 R33MH087879
DOI:	10.15154/1163509
Data Use:	Primary Analysis

Cohorts:

Control - Control (7)

Test - Test (2)

Measures:

Primary Measures (20)

Secondary Measures (10)

Data Analysis:

Genotyping/NGS

Microarray/Protein Analysis

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Investigators:	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
Abstract:	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...
Results:	Results published in PLoS Genet, Apr 2012 Readme file for study results
Documents:
DOI:	10.15154/1163510
Data Use:	Primary Analysis

Cohorts:	Test - Selected (18)
Measures:	Primary Measures (1) Secondary Measures (4)
Data Analysis:	Genotyping/NGS

Link

Investigators:	Warren S
Abstract:	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...
Results:	P values for differentially methylated loci between ASD probands and Siblings
Documents:
DOI:	10.15154/1163512
Data Use:	Primary Analysis

Cohorts:

Control - Sibling (360)

Test - Proband (345)

Measures:

Primary Measures (3)

Secondary Measures (2)

Data Analysis:

Statistical

Link

Investigators:	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
Abstract:	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)...
Results:	Results published in Am J Hum Genet, Feb 2013
Documents:
DOI:	10.15154/1163513
Data Use:	Primary Analysis

Cohorts:

Control - NIMH Controls (197)

Control - Parental (848)

Test - Probands (2,240)

Measures:

Primary Measures (3)

Secondary Measures (5)

Data Analysis:

Genotyping/NGS

Statistical

Microarray/Protein Analysis

Link

Investigators:	Storch EA; Wood JJ, Ehrenreich-May J, Jones AM, Park JM, Lewin AB, Murphy TK
Abstract:	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...
Results:	Results published in J Autism Dev Disord, Nov 2012
Documents:
DOI:	10.15154/1226467
Data Use:	Primary Analysis

Cohorts:

Test - ASD with Anxiety. UCLA cohort (27)

Test - ASD with Anxiety. USF cohort (27)

Measures:

Primary Measures (11)

Secondary Measures (8)

Data Analysis:

Statistical

Link

Investigators:	Anjali J; Burke JP, Yang W, Kelly JP, Kaiser M, Becker L, Lawer L, Newschaffer CJ
Abstract:	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...
Results:	Study Data File Results published in Autism, Jun 2013 NIMH - Task A Chart Study Report Final Task B Health Conditions Final Report Task B Health Conditions Executive Summary Task C Health Utilization Executive Summary Task D Risk Factor Final Report Task C Health Utilization Final Report Task D Final Report
Documents:
DOI:	10.15154/1163514
Data Use:	Primary Analysis

Cohorts:	Test - Study sample (cohorts not on individual subject level)
Measures:	Primary Measures (1) Secondary Measures (0)
Data Analysis:	Statistical

Link

Investigators:	Daly MJ; Sutcliffe J, Gibbs R, Buxbaum J, Schellenberg G
Abstract:	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...
Results:	Genotype calls BCM hg19 indel Genotype calls BCM hg18 indel Genotype calls BCM hg18 Genotype calls BCM hg19 Genotype calls BROAD hg19
Documents:
DOI:	10.15154/1163515
Data Use:	Primary Analysis

Cohorts:

Control - Control (1,059)

Test - Autism (1,036)

Measures:

Primary Measures (3)

Secondary Measures (38)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Eichler EE; Krumm N, O'Roak BJ, Karakoc E, Mohajeri K, Nelson B, Vives L, Jacquemont S, Munson J, Bernier R
Abstract:	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...
Results:	Results published in Am J Hum Genet, Oct 2013
Documents:
DOI:	10.15154/1163542
Data Use:	Secondary Analysis

Cohorts:

Control - Parental Controls (822)

Control - Probands (411)

Control - Sibling Controls (411)

Measures:

Primary Measures (3)

Secondary Measures (3)

Data Analysis:

Genotyping/NGS

Statistical

Link

Investigators:	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
Abstract:	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...
Results:	Results published in Nature, Apr 2012
Documents:
DOI:	10.15154/1163543
Data Use:	Primary Analysis

Cohorts:

Control - Parental (418)

Control - Siblings (50)

Test - Female Probands (Low IQ) (26)

Test - Male Probands (Low IQ) (47)

Test - Probands (High IQ) (136)

Measures:

Primary Measures (5)

Secondary Measures (5)

Data Analysis:

Genotyping/NGS

Microarray/Protein Analysis

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Investigators:	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.
Abstract:	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...
Results:	Results published in Nature, Apr 2012
Documents:
DOI:	10.15154/1163544
Data Use:	Primary Analysis

Cohorts:

Control - Parents (cohorts not on individual subject level)

Test - Probands (104)

Measures:

Primary Measures (5)

Secondary Measures (6)

Data Analysis:

Genotyping/NGS

Microarray/Protein Analysis

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Investigators:	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
Abstract:	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...
Results:	Results published in Neuron, Apr 2012
Documents:
DOI:	10.15154/1163545
Data Use:	Primary Analysis

Cohorts:

Control - Parental (686)

Control - Siblings (343)

Test - Probands (343)

Measures:

Primary Measures (9)

Secondary Measures (7)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Kunkel LM; Eran A, Li JB, Vatalaro K, McCarthy J, Rahimov F, Collins C, Markianos K, Margulies DM, Brown EN, Calvo SE, Kohane IS
Abstract:	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...
Results:	Results published in Mol Psychiatry, Sep 2013
Documents:
DOI:	10.15154/1163546
Data Use:	Primary Analysis

Cohorts:

Control - Typical Control (14)

Test - Autism (8)

Test - Autism Suspected (3)

Measures:

Primary Measures (3)

Secondary Measures (4)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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:	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...
Results:	Results published in Science, Dec 2012
Documents:
DOI:	10.15154/1163547
Data Use:	Primary Analysis

Cohorts:

Control - Typical Control (768)

Test - Probands (2,494)

Measures:

Primary Measures (5)

Secondary Measures (4)

Data Analysis:

Genotyping/NGS

Microarray/Protein Analysis

Link

Investigators:	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
Abstract:	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...
Results:	Results published in Cell, Dec 2012 combined-74-0352-vqsr-recalibrated-snps-only.vcf combined-74-0355-vqsr-recalibrated-snps-only.vcf combined-74-0265-vqsr-recalibrated-snps-only.vcf combined-74-0117-vqsr-recalibrated-snps-only.vcf combined-74-0115-vqsr-recalibrated-snps-only.vcf combined-74-0075-vqsr-recalibrated-snps-only.vcf combined-63-449-vqsr-recalibrated-snps-only.vcf combined-63-343-vqsr-recalibrated-snps-only.vcf combined-60-2027-vqsr-recalibrated-snps-only.vcf 74-0688-vqsr-recalibrated-snps-only.vcf
Documents:
DOI:	10.15154/1163548
Data Use:	Primary Analysis

Cohorts:

Control - Parental (20)

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

Test - Autism (MZ Twins) (20)

Measures:

Primary Measures (6)

Secondary Measures (3)

Data Analysis:

Genotyping/NGS

Statistical

Link

Investigators:	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
Abstract:	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...
Results:	Results published in Nature Genetics, Jun 2011
Documents:
DOI:	10.15154/1163549
Data Use:	Primary Analysis

Cohorts:

Control - Parental (40)

Test - Autism (20)

Measures:

Primary Measures (7)

Secondary Measures (5)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Eichler EE; Karakoc E, Alkan C, O'Roak BJ, Dennis MY, Vives L, Mark K, Rieder MJ, Nickerson DA
Abstract:	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.
Results:	Results published in Nature Methods, Dec 2011
Documents:
DOI:	10.15154/1163550
Data Use:	Primary Analysis

Cohorts:

Control - Parental (40)

Test - Probands (20)

Measures:

Primary Measures (7)

Secondary Measures (4)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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.
Abstract:	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...
Results:	Samples used in study (Table 1 from publication) Results from Primary Analysis (Table 2 from publication) Association results, presented as the -log(base 10) of the P-values, for an intronic region of MACROD2 (Figure 1 from publication) Results published in Hum Mol Genet, Oct 2010
Documents:
DOI:	10.15154/1163551
Data Use:	Primary Analysis

Cohorts:

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)

Measures:

Primary Measures (5)

Secondary Measures (5)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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.
Abstract:	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...
Results:	Figure 3 from publication (A functional map of ASD) Results published in Nature, Jul 2010 Table 1 from publication (Global burden of genic rare CNVs in cases vs. controls) Figure 2 from publication (CNV burden in known ASD and/or ID genes)
Documents:
DOI:	10.15154/1163552
Data Use:	Primary Analysis

Cohorts:

Control - Parental - European Ancestry (2,267)

Control - Parental - Non-European Ancestry (284)

Test - Autism - European Ancestry (1,096)

Test - Autism - Non-European Ancestry (128)

Measures:

Primary Measures (9)

Secondary Measures (5)

Data Analysis:

Genotyping/NGS

Microarray/Protein Analysis

Link

Investigators:	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
Abstract:	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...
Results:	Summary table of cloned and Y2H screened splicing isoforms of the autism risk factors List of 629 ASIN isoform-level PPIs List of 506 ASIN gene level PPIs Results published in Nature Communications, Apr 2014
Documents:
DOI:	10.15154/1163516
Data Use:	Primary Analysis

Cohorts:	Control - Brain pool (cohorts not on individual subject level)
Measures:	Primary Measures (3) Secondary Measures (0)
Data Analysis:	Genotyping/NGS Microarray/Protein Analysis

Link

Investigators:	Kennedy D; Haselgrove C
Abstract:	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...
Results:	Code Repository for NDAR-specific NITRC-CE pipeline
Documents:
DOI:	10.15154/1149599
Data Use:	Secondary Analysis

Cohorts:

Test - FSPGR Scan Type (64)

Test - MPRAGE Scan Type (343)

Test - T1 Scan Type (18)

Measures:

Primary Measures (0)

Secondary Measures (100)

Data Analysis:

Neuro Signal Recordings

Link

Investigators:	Kennedy D; Haselgrove C
Abstract:	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.
Results:	NDAR Specific Code Repository for NITRC-CE
Documents:
DOI:	10.15154/1149600
Data Use:	Secondary Analysis

Cohorts:

Test - FIRST Processed (285)

Test - FreeSurfer Processed (340)

Measures:

Primary Measures (2)

Secondary Measures (67)

Data Analysis:

Neuro Signal Recordings

Link

Investigators:	Van Horn JD; Liu, Zhizhong Petrosyan, Petros Torgerson, Carinna
Abstract:	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...
Results:	NDAR-specific LONI Workflow LONI Pipeline Definition for NDAR Workflow
Documents:
DOI:	10.15154/1169189
Data Use:	Secondary Analysis

Cohorts:	Test - LONI Pipeline Processed Images (FIRST, FreeSurfer) (780)
Measures:	Primary Measures (2) Secondary Measures (67)
Data Analysis:	Neuro Signal Recordings

Link

Investigators:	Krumm, N; Eichler, E
Abstract:	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...
Results:	Results published in Nat Genet, June 2015
Documents:
DOI:	10.15154/1169193
Data Use:	Secondary Analysis

Cohorts:

Control - Parental Controls (4,819)

Control - Sibling Controls (1,822)

Test - Probands (2,406)

Measures:

Primary Measures (3)

Secondary Measures (10)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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.
Abstract:	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...
Results:	Results published in Nature, May 2012 VCF file from Analysis of Whole Exome Sequencing Data
Documents:
DOI:	10.15154/1163553
Data Use:	Primary Analysis

Cohorts:

Control - Parents (476)

Control - Siblings (214)

Test - Probands (238)

Measures:

Primary Measures (14)

Secondary Measures (0)

Data Analysis:

Genotyping/NGS

Microarray/Protein Analysis

Link

Investigators:	Volk HE; Kerin T, Lurmann F, Hertz-Picciotto I, McConnell R, Campbell DB
Abstract:	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...
Results:	Results published in Epidemiology, Jan 2014 MET Genotyping Results
Documents:
DOI:	10.15154/1163517
Data Use:	Primary Analysis

Cohorts:

Test - Autism and ASD Diagnosis (155)

Test - Probands (54)

Measures:

Primary Measures (59)

Secondary Measures (6)

Data Analysis:

Genotyping/NGS

Statistical

Link

Investigators:	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.
Abstract:	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...
Results:	Results published in Cell, Nov 2013
Documents:
DOI:	10.15154/1226480
Data Use:	Primary Analysis

Cohorts:

Control - Parental Controls (112)

Control - Sibling Controls (56)

Test - Probands (56)

Measures:

Primary Measures (8)

Secondary Measures (0)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Craddock C; Clark D
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1165646
Data Use:	Secondary Analysis

Cohorts:	Baseline - ANTs-processed subjects (1,540)
Measures:	Primary Measures (2) Secondary Measures (0)
Data Analysis:	Neuro Signal Recordings

Link

Investigators:	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
Abstract:	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...
Results:	Results published in Am J Hum Genet, Jun 2014
Documents:
DOI:	10.15154/1163554
Data Use:	Primary Analysis

Cohorts:

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)

Measures:

Primary Measures (3)

Secondary Measures (1)

Data Analysis:

Genotyping/NGS

Statistical

Microarray/Protein Analysis

Link

Investigators:	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
Abstract:	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...
Results:	Study results published in Nature Genetics, Jul 2014
Documents:
DOI:	10.15154/1165648
Data Use:	Primary Analysis

Cohorts:

Control - Non-ASD Controls (91)

Test - Autistic Disorder (457)

Measures:

Primary Measures (7)

Secondary Measures (0)

Data Analysis:

Genotyping/NGS

Statistical

Link

Investigators:	Krumm, N; Eichler, E
Abstract:	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...
Results:	Results published in Nat Genet, June 2015
Documents:
DOI:	10.15154/1169195
Data Use:	Secondary Analysis

Cohorts:

Control - Parental Controls (1,800)

Control - Sibling Controls (4,784)

Test - Probands (2,392)

Measures:

Primary Measures (4)

Secondary Measures (6)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Krumm, N; Eichler, E
Abstract:	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...
Results:	Results published in Nat Genet, June 2015
Documents:
DOI:	10.15154/1169197
Data Use:	Secondary Analysis

Cohorts:

Control - Parental Controls (4,784)

Control - Sibling Controls (1,800)

Test - Probands (2,392)

Measures:

Primary Measures (4)

Secondary Measures (6)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Kennedy D; Haselgrove C
Abstract:	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.
Results:	NDAR Specific Code Repository for NITRC-CE
Documents:
DOI:	10.15154/1149598
Data Use:	Secondary Analysis

Cohorts:	Test - Time Series QA (356)
Measures:	Primary Measures (2) Secondary Measures (82)
Data Analysis:	Neuro Signal Recordings

Link

Investigators:	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
Abstract:	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...
Results:	Results published in Nature, Nov 2014
Documents:
DOI:	10.15154/1149697
Data Use:	Secondary Analysis

Cohorts:

Control - Parental Control (5,036)

Control - Sibling Control (1,911)

Test - Autistic Probands (2,509)

Measures:

Primary Measures (0)

Secondary Measures (10)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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
Abstract:	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,...
Results:	NDAR Study 334 - Realigned BAM Files NDAR Study 348 - Variant Calls (GATK) NDAR Study 349 - Variant Calls (FreeBayes) NDAR Study 361 - Copy Number Variants (CNVs) Results published in Nat Genet, June 2015
Documents:
DOI:	10.15154/1151812
Data Use:	Secondary Analysis

Cohorts:

Control - Parental Control (4,754)

Control - Unaffected Siblings (1,786)

Test - Probands (2,377)

Measures:

Primary Measures (4)

Secondary Measures (0)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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
Abstract:	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...
Results:	Results published in AJHG
Documents:
DOI:	10.15154/1157584
Data Use:	Primary Analysis

Cohorts:	Baseline - LOGIC baseline (32)
Measures:	Primary Measures (3) Secondary Measures (0)
Data Analysis:	Genotyping/NGS Statistical

Link

Investigators:	Richman DM; Wei T, Chestnut SR, Barnard-Brak L
Abstract:	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...
Results:	Article Published in J Psychopathol Behav Assess, September 2014
Documents:
DOI:	10.15154/1158938
Data Use:	Secondary Analysis

Cohorts:

Test - SCQ Current (474)

Test - SCQ Current and Lifetime (295)

Test - SCQ Lifetime (1,365)

Measures:

Primary Measures (2)

Secondary Measures (0)

Data Analysis:

Statistical

Link

Investigators:	Tilford, MJ; Payakachat, N; Kuhlthau, KA; van Exel, NJ; Kovacs, E; Bellando, J; Pyne, JM; Brouwer, WBF
Abstract:	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...
Results:	Publication in Autism Research
Documents:
DOI:	10.15154/1170418
Data Use:	Primary Analysis

Cohorts:	Test - Autistic Children (216)
Measures:	Primary Measures (0) Secondary Measures (84)
Data Analysis:	Statistical

Link

Investigators:	Krumm, N; Eichler, E
Abstract:	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...
Results:	Readme file for CNV Callset Final CNV Callset Results published in Nat Genet, June 2015
Documents:
DOI:	10.15154/1169318
Data Use:	Secondary Analysis

Cohorts:

Control - Parental Control (4,816)

Control - Sibling Control (1,820)

Test - Autistic Probands (2,405)

Measures:

Primary Measures (2)

Secondary Measures (0)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Lee, Ray
Abstract:	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...
Results:	Results published in PLOS ONE, Apr 2015
Documents:
DOI:	10.15154/1170165
Data Use:	Primary Analysis

Cohorts:	Test - Task A and B (19)
Measures:	Primary Measures (1) Secondary Measures (0)
Data Analysis:	Neuro Signal Recordings

Link

Investigators:	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
Abstract:	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...
Results:	Article published in Nat Commun, Nov 2014
Documents:
DOI:	10.15154/1170505
Data Use:	Primary Analysis

Cohorts:

Control - Unaffected Siblings (2,552)

Test - Proband (3,848)

Measures:

Primary Measures (2)

Secondary Measures (5)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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
Abstract:	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...
Results:	Results published in Nature, Mar 2015
Documents:
DOI:	10.15154/1171641
Data Use:	Primary Analysis

Cohorts:

Control - Control (3)

Test - Proband (13)

Measures:

Primary Measures (4)

Secondary Measures (2)

Data Analysis:

Genotyping/NGS

Statistical

Microarray/Protein Analysis

Link

Investigators:	Charles Schwartz ; Boccuto, L; Chen, C; Pittman,A; Skinner, C; McCartney, H; Jones, K; Bochner, B; Stevenson, R.
Abstract:	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:...
Results:	Results published in Molecular Autism Journal
Documents:
DOI:	10.15154/1178660
Data Use:	Primary Analysis

Cohorts:

Control - 50 Control (50)

Test - 50 Autism (50)

Measures:

Primary Measures (1)

Secondary Measures (2)

Data Analysis:

Microarray/Protein Analysis

Link

Investigators:	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
Abstract:	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...
Results:	Results published in PLoS Genetics, Jan 2015 Listing of Variants
Documents:
DOI:	10.15154/1176904
Data Use:	Primary Analysis

Cohorts:

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)

Measures:

Primary Measures (2)

Secondary Measures (4)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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
Abstract:	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...
Results:	Results published in Am J Hum Genet, Jan 2014
Documents:
DOI:	10.15154/1177023
Data Use:	Primary Analysis

Cohorts:

Control - Parental Control (378)

Test - Autistic Proband (189)

Measures:

Primary Measures (2)

Secondary Measures (4)

Data Analysis:

Genotyping/NGS

Statistical

Link

Investigators:	Allman, John; Wold, Barbara
Abstract:	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,...
Results:	INSAR Conference Paper, May 2010
Documents:
DOI:	10.15154/1195995
Data Use:	Primary Analysis

Cohorts:

Control - Control (25)

Test - Autistic (10)

Measures:

Primary Measures (4)

Secondary Measures (2)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Benson Mwangi PhD; Cao Bo, Hasan Khader, Selvaraj Sudhakar, Zeni Cristian, Zunta-Soares Giovan, Soares Jair.
Abstract:	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...
Results:	Results published in Neuroimage, June 2015.
Documents:
DOI:	10.15154/1195991
Data Use:	Secondary Analysis

Cohorts:

Baseline - first visit (303)

Control - second-visit (115)

Measures:

Primary Measures (1)

Secondary Measures (2)

Data Analysis:

Statistical

Neuro Signal Recordings

Link

Investigators:	Barnard-Brak, Lucy; Brewer A; Chesnut S; Richman D; Shaeffer AM
Abstract:	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...
Results:	Results published in Autism Research, Dec 2015
Documents:
DOI:	10.15154/1195992
Data Use:	Secondary Analysis

Cohorts:

Control - Control Cohort (90)

Test - ASD Cohort (249)

Measures:

Primary Measures (5)

Secondary Measures (8)

Data Analysis:

Statistical

Link

Investigators:	Barnard-Brak, Lucy; Richman D; Chesnut S; Little TD
Abstract:	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,...
Results:	Results
Documents:
DOI:	10.15154/1195993
Data Use:	Secondary Analysis

Cohorts:	Sample (mixed, ASD and non-ASD) (1,021)
Measures:	Primary Measures (2) Secondary Measures (8)
Data Analysis:	Statistical

Link

Investigators:	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
Abstract:	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...
Results:	Data Annotation File Int. J. Epidemiol. April, 2015 XYS Files NimbleGen Human 4.3M (CHARM) Array Platform Processed Data
Documents:
DOI:	10.15154/1195994
Data Use:	Primary Analysis

Cohorts:	Test - Fathers (44)
Measures:	Primary Measures (12) Secondary Measures (1)
Data Analysis:	Statistical Microarray/Protein Analysis

Link

Investigators:	Damarla SR; Keller T, Kana R, Cherkassky V, Williams D, Minshew N, Just M
Abstract:	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...
Results:	Results published in Autism Res, Oct 2010
Documents:
DOI:	10.15154/1223858
Data Use:	Primary Analysis

Cohorts:

Control - Control Participants (13)

Test - High Functioning Autistic (13)

Measures:

Primary Measures (1)

Secondary Measures (3)

Data Analysis:

Neuro Signal Recordings

Link

Investigators:	Liu Y; Cherkassky V, Minshew N, Just M
Abstract:	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...
Results:	Results published in Neuropsychologia, Jun 2011
Documents:
DOI:	10.15154/1223859
Data Use:	Primary Analysis

Cohorts:

Control - Typical Control (15)

Test - High Functioning Autism (15)

Measures:

Primary Measures (1)

Secondary Measures (3)

Data Analysis:

Neuro Signal Recordings

Link

Investigators:	Mizuno A; Liu Y, Williams D, Keller T, Minshew N, Just M
Abstract:	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...
Results:	Results published in Brain, Aug 2011
Documents:
DOI:	10.15154/1223860
Data Use:	Primary Analysis

Cohorts:

Control - Control Participants (15)

Test - High Functioning Autism (15)

Measures:

Primary Measures (1)

Secondary Measures (3)

Data Analysis:

Neuro Signal Recordings

Link

Investigators:	Schipul SE; Williams D, Keller T, Minshew N, Just M
Abstract:	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...
Results:	Results published in Cerebral Cortex, 2012
Documents:
DOI:	10.15154/1223861
Data Use:	Primary Analysis

Cohorts:

Control - Neurotypical Controls (18)

Test - Autism (17)

Measures:

Primary Measures (1)

Secondary Measures (3)

Data Analysis:

Neuro Signal Recordings

Link

Investigators:	Yao, Gang; Daluwatte C; Miles JH; Sun J
Abstract:	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...
Results:	Results published in Res Dev Disabil, Feb 2015
Documents:
DOI:	10.15154/1223865
Data Use:	Primary Analysis

Cohorts:

Control - TD Group (106)

Test - ASD Group (150)

Measures:

Primary Measures (2)

Secondary Measures (7)

Data Analysis:

Statistical

Link

Investigators:	Yao, Gang; Daluwatte C, Miles JH, Christ SE, Beversdorf DQ, Takahashi N,
Abstract:	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...
Results:	Results published in J Autism Dev Disord, Aug 2013
Documents:
DOI:	10.15154/1223868
Data Use:	Primary Analysis

Cohorts:

Control - TD Group (106)

Test - ASD Group (150)

Test - NDD Group (31)

Measures:

Primary Measures (2)

Secondary Measures (7)

Data Analysis:

Statistical

Link

Investigators:	Shen, Dinggang; Jin, Yan; Wee, Chong-Yaw; Shi, Feng; Thung, Kim-Han; Ni, Dong; Yap, Pew-Thian
Abstract:	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...
Results:	Results published in Hum Brain Mapp, Sep 2015
Documents:
DOI:	10.15154/1223873
Data Use:	Secondary Analysis

Cohorts:

Control - Low Risk Cohort (128)

Test - High Risk Cohort (363)

Measures:

Primary Measures (1)

Secondary Measures (1)

Data Analysis:

Statistical

Neuro Signal Recordings

Link

Investigators:	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.
Abstract:	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...
Results:	Results published in N Engl J Med. (Pubmed link)
Documents:
DOI:	10.15154/1334287
Data Use:	Secondary Analysis

Cohorts:

Control - Control (208)

Test - ASD (515)

Measures:

Primary Measures (1)

Secondary Measures (1)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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
Abstract:	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.
Results:	Study Note Results published in Am J Hum Genet, Jan 2016
Documents:
DOI:	10.15154/1226523
Data Use:	Secondary Analysis

Cohorts:	Baseline - Simons Genome Project Pilot (160)
Measures:	Primary Measures (2) Secondary Measures (0)
Data Analysis:	Genotyping/NGS

Link

Investigators:	Eichler EE; Duyzend MH, Nuttle X, Coe BP, Baker C, Nickerson DA, Bernier R
Abstract:	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...
Results:	Results Published in Am J Hum Genet, Dec 2015
Documents:
DOI:	10.15154/1226522
Data Use:	Primary Analysis

Cohorts:

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)

Measures:

Primary Measures (2)

Secondary Measures (0)

Data Analysis:

Genotyping/NGS

Microarray/Protein Analysis

Link

Investigators:	Walsh, CA; D’Gama, I; Pochareddy, S; Li, M; Jamuar, S; Reiff, RE; Lam, A; Sestan, N
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1227279
Data Use:	Primary Analysis

Cohorts:

Control - Control (50)

Test - ASD (52)

Test - Other (17)

Measures:

Primary Measures (2)

Secondary Measures (0)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Awh, Edward & Vogel, Edward K.; Foster, J.J., Sutterer, D.S., Serences, J.T.
Abstract:	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...
Results:	Link to resulting paper
Documents:
DOI:	10.15154/1334292
Data Use:	Primary Analysis

Cohorts:	Test - Foster et al. (2016) JNeurophysiol (56)
Measures:	Primary Measures (1) Secondary Measures (0)
Data Analysis:	Neuro Signal Recordings

Link

Investigators:	Ducharme, Simon; Albaugh M, Nguyen T, Hudziak J, Mateos-Pérez J, Labbe A, Evans A, Karama S
Abstract:	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...
Results:	Results published in NeuroImage Results in Neuroimage
Documents:
DOI:	10.15154/1240724
Data Use:	Secondary Analysis

Cohorts:	Control - Study Cohort (384)
Measures:	Primary Measures (1) Secondary Measures (1)
Data Analysis:	Statistical Neuro Signal Recordings

Link

Investigators:	Sadeghi, Neda; Nayak, Amritha; Walker, Lindsay; Irfanoglu, M; Albert, Paul; Pierpaoli, Carlo; Brain Development Cooperative Group
Abstract:	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...
Results:	Results published in NeuroImage
Documents:
DOI:	10.15154/1240725
Data Use:	Secondary Analysis

Cohorts:	Control - Study Cohort (128)
Measures:	Primary Measures (2) Secondary Measures (2)
Data Analysis:	Statistical Neuro Signal Recordings

Link

Investigators:	Ansado, Jennyfer; Collins, Louis; Fonov, Vladimir; Garon, Mathieu; Alexandrov, Lubomir; Karama, Sherif; Evans, Alan; Beauchamp, Miriam; and Brain Development Cooperative Group
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1240718
Data Use:	Secondary Analysis

Cohorts:	Control - Study Cohort (433)
Measures:	Primary Measures (1) Secondary Measures (1)
Data Analysis:	Statistical Neuro Signal Recordings

Link

Investigators:	Khundrakpam, Budhachandra; Tohka, Jussi; Evans, Alan; and the Brain Development Cooperative Group
Abstract:	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...
Results:	Results published in NeuroImage
Documents:
DOI:	10.15154/1240720
Data Use:	Secondary Analysis

Cohorts:	Control - Study Cohort (343)
Measures:	Primary Measures (1) Secondary Measures (1)
Data Analysis:	Statistical Neuro Signal Recordings

Link

Investigators:	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
Abstract:	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...
Results:	Results published in NeuroImage, January 2016
Documents:
DOI:	10.15154/1240722
Data Use:	Primary Analysis

Cohorts:

Control - High Resolution DTI Cohort (152)

Control - Low Resolution DTI Cohort (274)

Measures:

Primary Measures (2)

Secondary Measures (0)

Data Analysis:

Neuro Signal Recordings

Link

Investigators:	Cook, Edwin H.; Francis, Sunday M.; Kistner-Griffin, Emily; Yan, Zhongyu; Guter, Stephen; Jacob, Suma
Abstract:	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...
Results:	Frontiers in Neuroscience
Documents:
DOI:	10.15154/1303416
Data Use:	Primary Analysis

Cohorts:

Control - Parents (368)

Test - Probands (207)

Measures:

Primary Measures (1)

Secondary Measures (37)

Data Analysis:

Genotyping/NGS

Statistical

Link

Investigators:	Pevsner, Jonathan; Freed, Donald
Abstract:	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...
Results:	ssc_denovo_mosaic ssc_denovo_mosaic_index Results in PLOS Genetics
Documents:
DOI:	10.15154/1247692
Data Use:	Secondary Analysis

Cohorts:

Control - Parental Controls (4,819)

Control - Sibling Controls (1,822)

Test - Probands (2,406)

Measures:

Primary Measures (1)

Secondary Measures (2)

Data Analysis:

Genotyping/NGS

Statistical

Link

Investigators:	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
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1252218
Data Use:	Primary Analysis

Cohorts:	Test - the Autism Clinical and Genetic Resources in China (ACGC) (1,647)
Measures:	Primary Measures (41) Secondary Measures (87)
Data Analysis:	Genotyping/NGS

Link

Investigators:	Schultz, Stephen; Gould, G
Abstract:	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...
Results:	Article in Autism Open Acces Journal
Documents:
DOI:	10.15154/1334293
Data Use:	Secondary Analysis

Cohorts:

Control - Control (79)

Test - ASD (118)

Measures:

Primary Measures (1)

Secondary Measures (9)

Data Analysis:

Statistical

Link

Investigators:	Chekroud, Adam; Corlett, P; Krystal, J; Cannon, T; Trivedi, M; Johnson, M; Gueorguieva, R; Shehzad, Z; Zotti, R
Abstract:	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)...
Results:	Article in Lancet Psychiatry
Documents:
DOI:	10.15154/1334294
Data Use:	Secondary Analysis

Cohorts:	Test - Model Training Cohort (1,949)
Measures:	Primary Measures (1) Secondary Measures (8)
Data Analysis:	Statistical

Link

Investigators:	Sebat, Jonathan; Corsello, Christina; Iakoucheva, Lilia; Courchesne, Eric
Abstract:	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...
Results:	Publication Results Published in Am J Hum Genet, April 2016.
Documents:
DOI:	10.15154/1324432
Data Use:	Primary Analysis

Cohorts:

Control - Parental Controls (136)

Control - Sibling Controls (25)

Control - Typical Control (3)

Test - Probands (71)

Measures:

Primary Measures (6)

Secondary Measures (3)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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
Abstract:	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...
Results:	Results in Neuron
Documents:
DOI:	10.15154/1334312
Data Use:	Secondary Analysis

Cohorts:

Control - SSC Control Cohort (7,337)

Test - SSC ASD Cohort (2,638)

Measures:

Primary Measures (3)

Secondary Measures (0)

Data Analysis:

Statistical

Link

Investigators:	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
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1334313
Data Use:	Primary Analysis

Cohorts:	Control - Parental line and derivatives (cohorts not on individual subject level)
Measures:	Primary Measures (2) Secondary Measures (0)
Data Analysis:	Genotyping/NGS Statistical

Link

Investigators:	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
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1271285
Data Use:	Primary Analysis

Cohorts:

Control - Parents (232)

Test - Probands - All (116)

Measures:

Primary Measures (3)

Secondary Measures (1)

Data Analysis:

Genotyping/NGS

Link

Investigators:	A. John Rush; Haley CL, Sung SC, Rush AJ, Trivedi MH, Wisniewski SR, Luther JF, Kornstein SG
Abstract:	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...
Results:	Clinical Trials Registration
Documents:
DOI:	10.15154/1334299
Data Use:	Primary Analysis

Cohorts:

Test - No premenstrual exacerbation of depressive symptoms (345)

Test - Premenstrual exacerbation of depressive symptoms (672)

Measures:

Primary Measures (25)

Secondary Measures (0)

Data Analysis:

Statistical

Link

Investigators:	Cai, James J; Guan, Jinting; Yang, Ence; Yang, Jizhou; Zeng, Yong; Ji, Guoli
Abstract:	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...
Results:	Results Published in Hum Genet, July 2016.
Documents:
DOI:	10.15154/1334300
Data Use:	Secondary Analysis

Cohorts:

Control - Control Subjects (40)

Test - Subjects with Autism Spectrum Disorders (32)

Measures:

Primary Measures (10)

Secondary Measures (3)

Data Analysis:

Statistical

Link

Investigators:	Veronica Martinez Cerdeno; Kim E, Camacho J, Combs Z, Ariza J, Lechpammer M, Noctor SC, Martínez-Cerdeño V
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1334291
Data Use:	Primary Analysis

Cohorts:

Control - Control (9)

Test - Experimental (9)

Measures:

Primary Measures (1)

Secondary Measures (2)

Data Analysis:

Statistical

Link

Investigators:	Veronica Martinez Cerdeno; Hashemi E, Ariza J, Rogers H, Noctor SC, Martínez-Cerdeño V
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1336398
Data Use:	Primary Analysis

Cohorts:

Control - Control (10)

Test - Autism (10)

Measures:

Primary Measures (1)

Secondary Measures (2)

Data Analysis:

Statistical

Link

Investigators:	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
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1340671
Data Use:	Primary Analysis

Cohorts:

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)

Measures:

Primary Measures (1)

Secondary Measures (0)

Data Analysis:

Genotyping/NGS

Statistical

Link

Investigators:	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
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1338620
Data Use:	Primary Analysis

Cohorts:

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)

Measures:

Primary Measures (2)

Secondary Measures (1)

Data Analysis:

Genotyping/NGS

Link

Investigators:	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.
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1336394
Data Use:	Primary Analysis

Cohorts:	Test - Subset of Simons Simplex Collection (686)
Measures:	Primary Measures (1) Secondary Measures (0)
Data Analysis:	Genotyping/NGS Statistical

Link

Investigators:	Sebat, Jonathan; Brandler, W; Gujral, M; Antaki, D; Iakoucheva, L; Corsello, C; Hervas, A; Mutori, A
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1340302
Data Use:	Primary Analysis

Cohorts:

Control - Parental Controls (1,656)

Control - Sibling Controls (623)

Control - Typical Control (12)

Test - Probands (879)

Measures:

Primary Measures (2)

Secondary Measures (0)

Data Analysis:

Genotyping/NGS

Link

Investigators:	Corbett, Blythe; Key, A.P.; Qualls, L.; Fecteau, S.; Newsom, C.; & Yoder, P.
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1343428
Data Use:	Secondary Analysis

Cohorts:

Control - Summer 2014 (13)

Test - Winter 2014 (17)

Measures:

Primary Measures (6)

Secondary Measures (4)

Data Analysis:

Statistical

Link

Investigators:	Uchida, Hiroyuki; Yoshida, K; Roberts, R; Suzuki, T; Lebowitz, B; Reeves, S; Howard, R; Abe, T; Mimura, M
Abstract:	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)...
Results:
Documents:
DOI:	10.15154/1345184
Data Use:	Secondary Analysis

Cohorts:	Baseline - CATIE-AD (245)
Measures:	Primary Measures (2) Secondary Measures (1)
Data Analysis:	Statistical

Link

Investigators:	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
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1342749
Data Use:	Secondary Analysis

Cohorts:	Baseline - SNV (12)
Measures:	Primary Measures (1) Secondary Measures (1)
Data Analysis:	Genotyping/NGS

Link

Investigators:	Grossman, Ruth; Mertens, J.; Zane, E.R.; Neumeyer, K.; Grossman, R.B.
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1345819
Data Use:	Primary Analysis

Cohorts:

Control - Neurotypical peers (23)

Test - ASD (13)

Measures:

Primary Measures (1)

Secondary Measures (9)

Data Analysis:

Statistical

Link

Investigators:	Julie L. Taylor; Taylor JL, Hodapp RM, Burke MM, Waitz-Kudla SN, Rabideau C
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1346187
Data Use:	Primary Analysis

Cohorts:	VAP-T (41)
Measures:	Primary Measures (3) Secondary Measures (4)
Data Analysis:	Statistical

Link

Investigators:	Wedyan, Mohammad; Al-Jumaily,Adel
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1351615
Data Use:	Secondary Analysis

Cohorts:	Control - high risk for Autism (57)
Measures:	Primary Measures (1) Secondary Measures (25)
Data Analysis:	Statistical Neuro Signal Recordings

Link

Investigators:	Norman, Ken; Kim, Ghootae; Turk-Browne, Nick
Abstract:	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...
Results:
Documents:
DOI:	10.15154/1356633
Data Use:	Primary Analysis

Cohorts:	Test - Experimental Group (32)
Measures:	Primary Measures (1) Secondary Measures (0)
Data Analysis:	Statistical Neuro Signal Recordings