Matthew W. State - US grants

This application presents a career development award proposal spanning the fields of child psychiatry, molecular cytogenetics and molecular genetics. The near-term objective of this submission is to develop an independent program in patient-oriented research that focuses on identifying genes that contribute to serious psychiatric disorders. The ultimate aim of the applicant is to contribute to the translation of advances in genetics into improvements in diagnosis, treatment and prevention of childhood developmental and neuropsychiatric illnesses. After completing clinical training in adult and child psychiatry, the applicant participated in a three-year NIMH funded patient-oriented research fellowship at the Yale Child Study Center (YCSC). During this time, he simultaneously pursued an expertise in molecular genetics by enrolling in the Ph.D. program in the Department of Genetics at Yale. Dr. State was appointed Assistant Professor in the Child Study Center (Department of Child Psychiatry) in July of 2000. He currently divides his time between attending in the Tourette syndrome (TS) and Obsessive Compulsive Disorder (OCD) clinics and conducting research in the laboratory. This career award will provide vital support for his efforts to bridge clinical and basic science research. It will facilitate his continued patient-oriented research training, allow him to develop further expertise in relevant areas of molecular genetics and molecular cytogenetics, and provide the opportunity to achieve full scientific independence. The research plan presented below centers on the identification and characterization of genes that reside within a small region around a chromosomal inversion breakpoint found in a patient with a Tourette syndrome/Obsessive Compulsive Disorder (TS/OCD) phenotype. The developmental expression pattern of these genes will be assessed and the transcripts will be prioritized for further study with respect to their role in the TS/OCD spectrum of disorders. The proposal also plans for the development of a repository of cytogenetic abnormalities in well- characterized patients with TS/OCD phenotypes. The overarching objective of the award proposal, comprising both the career development and research plans, is to identify candidate genes in childhood neuropsychiatric disorders as a prelude to further investigations within the Child Study Center and the Children's Clinical Research Center (CCRC) that will focus on the relevance of these genes for the diagnosis, treatment, and natural history of TS/OCD. To help reach his long-term career objectives, the applicant has arranged for an outstanding group of mentors and advisors to provide guidance with respect to the design and conduct of his research, assistance in mastering the organizational challenges of running a successful research program, and training in the ethical issues attending research. He has formulated a plan for additional didactics and intensive workshops that will deepen his understanding of clinical statistical methodology, population genetics, gene expression analysis, genomics, and bioinformatics. Finally, his overall career development plan is made possible by the existence at Yale of a multidisciplinary team conducting translational research into the pathogenesis and treatment of childhood neuropsychiatnc disorders including TS/OCD, as well as the availability of the Children's Clinical Research Center (CCRC) which serves as a key resource in the conduct of this ongoing research.

The goal of this proposal is to use molecular cytogenetic and molecular genetic tools to identify genes involved in Tourette syndrome (TS) and related phenotypes. TS is a neuropsychiatric disorder defined by the combination of persistent vocal and motor tics. Despite strong evidence for a genetic etiology, linkage studies undertaken over several decades have not yet identified a single gene clearly implicated in TS- spectrum disorders, which include chronic tics (CT) and tic- related Obsessive Compulsive Disorder (OCD). We have undertaken an alternative strategy for disease-gene identification based on the hypothesis that a small subset of patients presenting with this genetically heterogeneous disorder have their symptoms as the result of a structural or functional disruption of a gene of major effect due to a cytogenetic abnormality. We further propose that the identification of such a gene may illuminate biological pathways involved in more common forms of TS. Our lab has identified two patients with TS-related phenotypes: (1) a patient with CT and OCD and an inversion inv(18)(q21q22); and, (2) a patient with OCD and a balanced translocation t(18;2)(q22;p25). These abnormalities map approximately 500 kilobases (kb) and 4 megabases (Mb) respectively from a chromosome 18q22 breakpoint that segregates with TS, CT and OCD in a previously-described family (Bhogosian-Sell et al. 1996). We have obtained cell lines from this pedigree as well and have initiated an exhaustive molecular characterization of the 4.5 Mb interval defined by the three 18q22 breakpoints. Our preliminary data also demonstrates that the 18q22 inversion is altering the replication timing at this locus. This change in the epigenetic properties of the patient's inverted chromosome 18 suggests that the rearrangement is influencing the regulation of gene expression across this region. The data has prompted two associated avenues of investigation: (1) an assessment of the extent of epigenetic changes in all three 18q22 rearrangements; and, (2) an evaluation of the epigenetic properties of the 18q22 region in cytogenetically-normal subjects with TS-spectrum phenotypes. We now propose: (1) to complete the fine-mapping of the three chromosome 18q22 breakpoints at the nucleotide level; (2) to identify known and novel transcripts within the interval defined by these abnormalities; (3) to prioritize genes based on functional and structural data and to conduct mutation screening on selected candidates; (4) to investigate epigenetic phenomena in the region in cytogenetically-affected cases as well as in cytogenetically-normal TS, OCD and CT patients; and, (5) to perform screening karyotypes on well-characterized TS spectrum patients from the Yale Child Study Center and Genetics Clinic as the basis for future mapping experiments.

[unreadable] DESCRIPTION (provided by applicant): Tourette Disorder (TD) is a developmental neuropsychiatric syndrome defined by the presence of chronic vocal and motor tics that affects as many as 1 in 100 school aged children. Despite considerable evidence for a genetic contribution, no disease-related genes have been identified. SLIT and Trk-like family 1 (SLITRK1) has recently been found to be a strong candidate for involvement in TD, initially through the mapping of a de novo chromosomal abnormality in the only affected member of a three-generation pedigree. Mutation screening of 204 probands subsequently identified: 1) a truncating frameshift mutation that was present in two affected, and absent in three unaffected family members, and could not be found in 3600 control chromosomes; 2) A non-synonymous substitution at a highly conserved amino acid in the transmembrane domain in 2 affected siblings, not present in 4000 control chromosomes; and 3) in two unrelated individuals, the identical single base substitution at a highly conserved nucleotide in the binding domain for the brain expressed microRNA-189 (miR-189), not present in 4296 control chromosomes. Expression analysis demonstrates that SLITRK1 mRNA and miR-189 overlap in brain regions thought relevant to the pathogenesis of TD. Overexpression of wild-type Slitrkl, but not the frameshift mutant, in developing cortical neurons promotes dendritic elongation. We now propose to investigate further the role of SLITRK1 in TD through a continued cross-disciplinary collaboration involving pediatric psychiatry, genetics and neurobiology. Specifically we aim to: 1) search for additional mutations in SLITRK1 in an expanded group of patients with TD and related disorders; 2) further characterize the expression of SLITRK1 RNA and protein in developing mouse and human brain; 3) elaborate the function of wildtype and mutant SLITRK1 in developing cortical neurons; and 4) identify proteins that interact with SLITRK1 as a prelude to mutation screening of these genes. SLITRK1 is a gene implicated in some cases of Tourette Disorder (TD) by the finding of rare DNA sequence changes in a small number of patients that have not been found in unaffected persons. The purpose of this study is to better understand .what causes TD by identifying additional abnormalities in the SLITRK1 gene and by investigating the impact of these unusual genetic changes on the developing brain. [unreadable] [unreadable] [unreadable]

There is ample evidence that rare genetic variants may contribute to a small subset of individuals presenting with Autism Spectrum Disorders (ASDs). The characterization of these unusual cases may provide important insights into pathophysiological mechanisms underlying disease. Our laboratory has leveraged the comprehensive phenotyping capabilities of the Yale Autism Research Group to focus on the discovery of rare variants contributing to developmental and social disability. Recently we have studied three unrelated patients with ASD and/or Mental Retardation (MR) and chromosomal abnormalities, all of who were found to have disruptions of genes in the Contactin (CNTN) or Contactin Association Protein (CNTNAP) families, including CNTN4, CNTNAP2 and CNTNAP4. These neuronal adhesion and recognition molecules are known to play key roles in axon pathfinding, fasciculation and neuronal-glial interactions. We have undertaken extensive re-sequencing efforts and, in our initial analysis of Contactin Associated Protein, we have identified a statistically significant increase in the burden of potentially damaging missense mutations among 218 cases and 449 controls regardless of whether we consider all non-synonymous variants or only those predicted by bioinformatics approaches to be deleterious to protein function. This data is particularly compelling in light of two additional findings: a rare recessive mutation in this gene found in association with seizures, developmental delay and autistic features in Amish families;and, unpublished data from collaborators at UCLA showing a common haplotype of CNTNAP2 associated with language delay in individuals with Autism. Based on our recent findings we now propose to: 1) replicate the mutation burden analysis in CNTNAP2 and perform a similar preliminary study in patients with developmental delay but not social disability;2) perform initial and, if warranted, replication studies of the other molecules disrupted by chromosomal abnormalities, Contactin 4 and Contactin Associated Protein 4\ and 3) continue our gene discovery efforts using both conventional and array based cytogenetics on the well-characterized patients recruited under Projects 1-IV of this application focusing on the identification of rare, deleterious changes in chromosome structure.

DESCRIPTION (provided by applicant): This proposal is in response to a request for applications to address "Genomic Profiling of Mental Disorders," and proposes intensive genomic profiling and functional analysis of Contactin Associated Protein 2 (CNTNAP2) as well as the presynaptic cytomatrix protein Piccolo (PCLO), in an effort to clarify their roles in Autism Spectrum Disorders (ASD). In addition, the application proposes to deeply sequence genes in the Contactin and Contactin Associated pathways, as well as genes coding for proteins known to interact with PCLO. We propose to leverage ongoing collaborations among the State, De Camilli and Giraldez labs at Yale to allow for rapid functional assays (both in vitro and in vivo) of identified rare sequence mutations, which will be used to clarify genomic findings and to confirm the relevance of rare mutations for disease risk. The organizing principles supporting this application are as follows: 1) Rare genetic variation is likely to play a significant role in the etiology of ASD;2) Methods of detecting rare (MAF<5%) and very rare (MAF<1%) variation in large numbers of patients and controls are now economically and technically feasible;3) Rare and very rare variations, including those in highly conserved coding regions, are widespread throughout the genomes of both affected and unaffected individuals;4) Rare and very rare alleles of intermediate effect will likely require association as opposed to linkage strategies to evaluate disease risk;and 5) That among the most pressing issues at this stage in the success of genomic profiling of mental disorders are differentiating disease-related mutations from low frequency neutral mutations and addressing the methodolgical challenges of assessing disease association in the case of rare and very rare alleles. This application proposes to address these issues as follows: 1) Deep-resequencing using next generation technologies to identify rare and very rare mutations in a large, extremely well-characterized and carefully ethnically matched case-control sample;2) To use quantitative ASD phenotyping in addition to categorical diagnoses in an effort to enhance the power of case-control association of rare variants;3) To leverage well established association methodologies, including genomic control, mutation burden analyses for very rare mutations, correction for multiple comparisons and replication samples, to decrease type 1 error;4) To use both in vitro and in vivo methods to evaluate the functional consequences of rare mutations identified in cases and controls, specifically in the genes CNTNAP2 and PCLO;and importantly, 5) To test the hypothesis that functional assays stratifying rare functional from neutral variation in CNTNAP2 will clarify the results of association analyses, as has been successfully employed in other rare variant studies (1). PUBLIC HEALTH RELEVANCE: This study seeks to identify the role of specific genes in Autism Spectrum Disorders. The research plan utilizes high throughput sequencing technologies and combines these with molecular in vitro and in vivo biological studies in an effort to clarify the precise contribution of two brain expressed molecules Contactin Associated Protein 2 and Picollo as well as related genes to Autism and related conditions.

DESCRIPTION (provided by applicant): SUMMARY/ABSTRACT: Tourette Disorder (TD) is a developmental neuropsychiatric syndrome characterized by the combination of persistent vocal and motor tics. While initially considered rare, the world-wide prevalence is now estimated to be 0.3-1%. Both as a consequence of potentially disabling symptoms as well as very high rates of psychiatric co-morbidity, particularly with obsessive-compulsive disorder (OCD) and attention deficit hyperactivity disorder (ADHD), TD represents a significant public health concern. Despite decades of evidence supporting a significant genetic contribution, progress in identifying risk alleles has been slow. This difficulty is thought to be, in part, a consequence of complex inheritance and substantial genetic and phenotypic heterogeneity. This collaborative study unites an international group of highly expert clinicians specializing in TD with statistical and molecular geneticists and is motivated by three central hypotheses: 1) that a key rate- limiting factor for TD gene discovery has been the paucity of publically available, large-scale biomaterial resources of the kind that are now commonplace for many neuropsychiatric disorders; 2) based on recent data from a host of other genetically complex disorders, a comprehensive genomics study of TD will require large samples sizes and should focus on the potential contribution of rare as well as common alleles and both sequence and structural variants; and 3) an increased understanding of the genetic etiology of TD will translate into novel and more effective approaches to treating this often-debilitating disorder, and consequently will have marked public health benefits. The application elaborates three specific aims: Specific Aim 1: To recruit 5050 individuals with TD (and their family members), and make DNA, cell-lines, cDNA/RNA and phenotypic data publicly available within one year of collection. The sample will include a subset of 3195 European Caucasian (EC) probands; 1250 Korean probands, and 3295 parent-child trios allowing for the study of de novo variation. We will also recruit each year at least 10 TD pedigrees with 4 or more affected members as a resource for family-based gene discovery. Specific Aim 2: To employ state-of-the-art techniques to identify and confirm rare and common variants contributing to TD. We will genotype the sample on Illumina HumanOmni2.5 -Quad BeadChips to support copy number variation (CNV) analysis (Aim 2A) and genome wide association studies (GWAS) (Aim 2B); whole exome sequencing will be employed in select, multiply-affected TD pedigrees (Aim 2C); and we will follow up on the most promising loci identified in the aforementioned studies using a pooled next generation re-sequencing strategy (Aim 2D) at two time points, evaluating a minimum of 50 genes in a total of 3195 EC and 3195 matched controls; Specific Aim 3: To perform preliminary analyses of 300 transcriptomes of TD subjects to investigate the implications of selected structural and sequence variations for cis, trans and genome-wide expression. With no cost to this project, PAXgene tubes will be collected from all subjects and made available to the scientific community to enable future studies by our group and others.

DESCRIPTION (provided by applicant): While there has been great progress in understanding the genomic architecture of autism, only a moderate number of the hundreds of genes and genomic regions thought to be involved in ASD have been identified. Next-generation sequencing (NGS) has proven its utility to rapidly identify variants underlying ASD, and this approach is being carried out in ca. 6,000 independent ASD samples through multiple studies. There is an urgent need to develop a framework to integrate and expand these current studies, and to jointly analyze emerging data to maximize the identification of valid ASD loci, because validated risk variants present opportunities for genetic counseling, understanding pathogenesis, and drug development. The Autism Sequencing Consortium (ASC) represents a coordinated effort by more than 20 independent groups to rapidly identify and validate ASD risk genes, which represent lead targets for neurobiological analyses and drug discovery. The long-term goal of the ASC is to make use of genetics to identify therapeutic targets in ASD, while contributing to translating such research findings to clinical practice. The overall objective of tis proposal is to rapidly identify ASD genes representing lead targets for high impact neurobiological studies and drug discovery. Our central hypothesis - formulated based on data with SNV, indels, and CNV, as well as review of medical genetic conditions in ASD and targeted sequencing in ASD - is that multiple independent rare variants account for a very significant proportion of risk to ASD. Our rationale for this proposal is that the identification of genetic variants conferring high-risk risk to ASD and associated neurodevelopmental disorders can form the bases of studies to understand pathogenesis as well as the bases for novel therapies. Moreover, such variants have direct implications for patients and their families in terms of etiological diagnosis, genetic counseling and patient care. These objectives will be accomplished with the following Specific Aims: 1) Maintain the infrastructure to support the ASC objectives; 2) Deploy pipelines for data cleaning and harmonization and variant calling; 3) Implement novel statistical methods for identifying ASD-associated genes; and, 4) Carry out whole-exome sequencing of 3,000 ASD subjects and parents. This contribution is significant because it represents the first step in research to understand pathogenesis of ASD and to the development of pharmacological strategies for treatment of core symptoms of ASD and etiologically related neurodevelopmental disorders. The research proposed in this application is innovative, in our opinion, because it involves an entirely new model of sharing data before publication, uses state-of-the-art methods for calling diverse types of variants in NGS data, incorporates novel methods for updating variant calling and sharing data, and includes highly innovative statistical methods to identify risk loci. This is a new and substantively different approach to gene discovery in ASD that departs significantly from the status quo and provides the means to achieve these important goals.

DESCRIPTION (provided by applicant): PROJECT SUMMARY/ ABSTRACT DESCRIPTION: See instructions. State the application's broad, long-term objectives and specific aims, making reference to the health relatedness of the project (i.e., relevance to the mission of the agency). Describe concisely the research design and methods for achieving these goals. Describe the rationale and techniques you will use to pursue these goals. In addition, in two or three sentences, describe in plain, lay language the relevance of this research to public health. If the application is funded, this description, as is, will become public information. Therefore, do not include proprietary/confidential information. DO NOT EXCEED THE SPACE PROVIDED. Autism Spectrum Disorder (ASD) is a common, often devastating neuropsychiatric condition with largely unknown pathophysiology. Although ASD has a multifactorial etiology, it encompasses a large genetic component. The investigators in this proposal aim to continue and enhance our collaborative effort that has produced significant advances in our understanding of ASD over the last four years and generated highly successful, open data and biomaterials resources for the research community, the NIMH Genetics Initiative and the Autism Genetic Resource Exchange (AGRE). Our Network has met or exceeded our original aims. We have built patient resources for research, identified rare and common ASD susceptibility alleles, defined models of ASD genetic susceptibility, provided evidence for convergent pathophysiology, and led development of animal and cell culture models. Here we propose to take a major new direction, filling a significant gap in ASD research, by recruiting underserved subjects of self-reported African ancestry (African-American; AA), an important population that has not previously been well-represented in ASD genetics research. Our Network involves six research sites and the AGRE DCC, collaborating in a systematic, comprehensive investigation of ASD genetics in order to identify rare mutations, chromosomal abnormalities, and common variation contributing to ASD susceptibility in the AA population. Specifically, we will enrich existing resources by recruiting at least 600 AA probands and additional family members. Our recruitment plan includes an embedded health disparities project that will evaluate access to care for AAs with ASD and clarify factors influencing participation of AA individuals in genetic research. We will employ novel methods to define the ancestral origin of specific chromosomal segments and ascertain the background on which susceptibility alleles occur. We will perform follow up GWA on ASD-related endophenotypes or co-variates, such as language delay, sex and head circumference. In parallel, we will conduct whole exome sequencing (WES) and analysis of copy number variation (CNV) using 2.5M SNP arrays yielding high resolution molecular karyotypes and providing a resource on genome-wide CNV and coding sequence variation (SNV) in ASD. Gene expression profiling and network analysis will be used to prioritize variants. Genetic risk factors identified in the mostly European samples will be tested for association in the AA sample to determine whether these cohorts share the same genetic risk factors, using a sample size providing power to replicate previous associations and to identify rare, recurrent CNV and SNV. The observation of new forms or different population frequencies of ASD-related variation in this sample as well as the sharing of most CNV and SNV with other cohorts are both outcomes that will have great significance for future studies and clinical care. As has been our practice, our Network will make all phenotypic and genotype data accessible via the internet on a rolling basis, further enhancing the value of this resource to the community.

? DESCRIPTION (provided by applicant): The overarching goal of this study is the development of a framework to identify causal regulatory mutations in patients with serious neuropsychiatric presentations through the paired analyses of whole genome sequence and high resolution RNA sequence data from both accessible primary cells (PBMC and buccal cells) and reprogrammed neuronal cells from the same patients. The latter constitutes a particularly exciting opportunity as it will allow us to assay gene expression during different developmental stages of previously inaccessible cell types of much greater relevance to patient phenotype than the circulating cells DNA studies are customarily performed on. Specifically, we will interpret the effects of the regulatory variants in different developmental stages of the reprogrammed neuronal and other cells of interest with a comparison to the PBMC and buccal cells helping to interpret the specificity or generality of the relevant effects in different tissues. These analyses will focus nt only on mapping cis- and trans-acting eQTLs, but will also deploy new variant prioritization schemes that integrate knowledge of regulatory regions of the genome through ENCODE and related efforts as well as population genetic data. While an explicit aim of the work is to identif regulatory variants influencing risk of schizophrenia and autism, we emphasize that this work has primarily the broader goal of the development of appropriate frameworks for the eventual identification of such mutations, which inevitably will require substantially larger sample sizes that currently feasible to facilitate systematic discovery.

DESCRIPTION (provided by applicant): The development of human brain is an immensely complex process, which is likely reflected in the complexity of the underlying transcriptional processes. Gene expression and its precise spatio-temporal regulation, particularly by histone modifications and non-coding RNAs, are crucial for normal human brain development and are thought to be altered in major developmental psychiatric disorders, such as autism spectrum disorders (ASD). Moreover, changes in the developmental brain transcriptome are likely the major contributors to the evolution of the most distinctly human aspects of cognition, some of which are also affected in ASD and other psychiatric disorders However, our understanding of transcriptional and epigenetic processes involved in the development, evolution and dysfunction of the human brain is still elusive. Furthermore, most of our knowledge of transcriptional processes in the human brain is limited to the expression of protein coding genes. Given that the genomes of humans and other mammals have approximately the same protein-coding complexity, there is likely an additional reservoir of transcriptional complexity, especially in organs such as the brain, which has many structurally and functionally distinct regions in humans. This view is corroborated by recent findings of the ENCODE consortium, which found many cis-acting regulatory regions and that 60% of the human genome is transcribed, with a majority of the transcripts belonging to non-coding RNAs. Moreover, these and other studies have also uncovered pervasive involvement of regulatory DNA variations in common human diseases and evolution. However, how these findings on non-coding elements in cell lines relate to the complexity of human brain development and dysfunction is still largely unknown. The objective of this proposal is to employ unbiased and genome-wide approaches to (1) discover and characterize developmentally regulated and human-specific non-coding functional genomic elements in multiple regions of the developing human and non-human primate brains, (2) and elucidate their role(s) in the molecular pathophysiology of ASD, by using genomic analyses of post-mortem ASD brains, by screening for de novo mutations in ASD quartets, and by modeling functional consequences of ASD-associated elements in the developing mouse brain.

DESCRIPTION (provided by applicant): While there has been great progress in understanding the genomic architecture of autism, only a moderate number of the hundreds of genes and genomic regions thought to be involved in ASD have been identified. Next-generation sequencing (NGS) has proven its utility to rapidly identify variants underlying ASD, and this approach is being carried out in ca. 6,000 independent ASD samples through multiple studies. There is an urgent need to develop a framework to integrate and expand these current studies, and to jointly analyze emerging data to maximize the identification of valid ASD loci, because validated risk variants present opportunities for genetic counseling, understanding pathogenesis, and drug development. The Autism Sequencing Consortium (ASC) represents a coordinated effort by more than 20 independent groups to rapidly identify and validate ASD risk genes, which represent lead targets for neurobiological analyses and drug discovery. The long-term goal of the ASC is to make use of genetics to identify therapeutic targets in ASD, while contributing to translating such research findings to clinical practice. The overall objective of tis proposal is to rapidly identify ASD genes representing lead targets for high impact neurobiological studies and drug discovery. Our central hypothesis - formulated based on data with SNV, indels, and CNV, as well as review of medical genetic conditions in ASD and targeted sequencing in ASD - is that multiple independent rare variants account for a very significant proportion of risk to ASD. Our rationale for this proposal is that the identification of genetic variants conferring high-risk risk to ASD and associated neurodevelopmental disorders can form the bases of studies to understand pathogenesis as well as the bases for novel therapies. Moreover, such variants have direct implications for patients and their families in terms of etiological diagnosis, genetic counseling and patient care. These objectives will be accomplished with the following Specific Aims: 1) Maintain the infrastructure to support the ASC objectives; 2) Deploy pipelines for data cleaning and harmonization and variant calling; 3) Implement novel statistical methods for identifying ASD-associated genes; and, 4) Carry out whole-exome sequencing of 3,000 ASD subjects and parents. This contribution is significant because it represents the first step in research to understand pathogenesis of ASD and to the development of pharmacological strategies for treatment of core symptoms of ASD and etiologically related neurodevelopmental disorders. The research proposed in this application is innovative, in our opinion, because it involves an entirely new model of sharing data before publication, uses state-of-the-art methods for calling diverse types of variants in NGS data, incorporates novel methods for updating variant calling and sharing data, and includes highly innovative statistical methods to identify risk loci. This is a new and substantively different approach to gene discovery in ASD that departs significantly from the status quo and provides the means to achieve these important goals.

? DESCRIPTION (provided by applicant): Autism Spectrum Disorders (ASDs) are a group of related neurodevelopmental syndromes defined by social communication deficits and by restricted and repetitive behaviors. The public health burden is enormous, with an estimated cost of $35 billion in the U.S alone. Behavioral approaches are currently the mainstay of treatment; options for somatic therapies remain extremely limited. A new generation of more effective treatments will require a far deeper understanding of the pathobiology of ASD. In addition, while there has been significant recent progress in clarifying the genomic architecture of autism, only a small number of the hundreds of genes and genomic regions thought to be involved in ASD have so far been identified. The current proposal focuses on discovering additional rare recessive mutations leading to autism via the study of consanguineous families from Egypt and Turkey. The project leverages a long-standing collaboration between the Gunel and State labs, which have independently and collectively demonstrated the productivity of homozygosity mapping and whole exome sequencing for a range of developmental disorders including autism. Our long-term goal is to make use of genetics to identify therapeutic targets in ASD while contributing to translating such findings to clinical practice. Our hypothesis is that th discovery of additional rare recessive, highly penetrant ASD mutations in consanguineous families will advance the understanding of molecular mechanisms; that these will show overlap with the emerging picture of the genetic architecture and biology of idiopathic ASD in outbred populations, and that, combined, these advances will lay the foundation for the development of novel, rational, and more efficacious treatments. Therefore, we focused on 3 specific aims: 1) To expand our current cohort of consanguineous ASD families with an additional 250 carefully diagnosed ASD kindreds from Egypt and Turkey, 2) To identify novel, rare, highly penetrant genetic variants that contribute to ASD by employing homozygosity mapping and whole-exome sequencing in 384 ASD subjects and parents; and 3) To search for clustering of these variants among unrelated families as well as to evaluate the overlap in risk loci for inbred versus outbred ASD populations, cross- referencing findings from these Middle Eastern families with data from the Simons Simplex Collection (SSC), which we have been studying for the past 5 years and to evaluate the identified homozygous variants with reference to ASD-associated developmental co-expression networks using high confidence ASD genes discovered in outbred families. Overall this proposal is aimed at advancing the understanding of the genetics and biology of ASD in the interests of identifying novel approaches to diagnosis, and therapeutic development.

? DESCRIPTION (provided by applicant): Autism Spectrum Disorder (ASD) is characterized by impairments in social communication and restricted or repetitive behavior or interests. The application of genomic technologies has led to the identification of many of the genes underlying ASD, presenting the opportunity to assess the insight these risk genes can give into the etiology of ASD. In this proposal we aim to: 1) Generate a list of ASD-associated genes; 2) Identify points of convergence between these genes in biological data (e.g. gene regulation and expression); and 3) Validate these points of convergence in model systems. Since ASD is a human neurodevelopmental disorder we will prioritize biological data that is collected longitudinally across development from human brain tissue. In our prior work we have demonstrated that de novo mutations, specifically copy number variants (CNVs) and loss of function (LoF) point mutations, are strongly associated with ASD. Furthermore, these mutations cluster at ASD risk genes and loci in cases but not in controls. By comparing the distribution of these mutations between cases and controls we can identify the points of mutational clustering that represent ASD risk loci (e.g. CNVs at the 500kbp 16p11.2 locus and LoFs at the gene CHD8). We have developed a statistical framework to assess this clustering as well as incorporating evidence from inherited variants and case-control data. This framework is called the Transmitted and De novo Associated Test (TADA). In Aim 1 we will develop this test further to incorporate all the available CNV, exome, genome, and targeted sequencing data into a single ASD gene list, ranked by the degree of ASD association. Previously we used the top nine ASD risk genes as seeds for gene co-expression networks and assessed the validity of these networks by their ability to incorporate 120 independent ASD risk genes. By limiting the co- expression input data to narrow windows of development and specific brain regions we could identify the spatiotemporal networks with the greatest enrichment, for example pre-frontal cortex in mid-fetal development. In Aim 2, we propose a similar approach, but using the DAWN (Detecting Association With Networks) method developed by our group. DAWN uses the narrow windows of co-expression data as before, but is able to incorporate evidence from other datasets such as gene regulation, and protein-protein interaction (PPI). By seeding the DAWN networks with the highest confidence genes we will assess the spatiotemporal networks that best predict other ASD genes. ASD shows a significant sex bias implicating an interaction between ASD etiology and sexually dimorphic factors. Building on our work of identifying sexually dimorphic transcripts in the developing human brain we will test their enrichment within specific networks identified by DAWN. To validate the ASD-associated networks, in Aim 3 we will identify the gene that best represents each network and assess if disrupting it also disrupts the other genes within the network. We will disrupt each gene using CRISPR/Cas9 in both mice and human-derived iPSCs and assess the genes disrupted using RNA-Seq.

ABSTRACT Genetic and genomic investigations have yielded important findings as to the genetic contributions to major psychiatric illnesses, illustrating significant etiological heterogeneity, as well as cross-disorder overlap. It has also become clear that understanding how this genetic variation leads to alterations in brain development and function that underlies psychiatric disease pathophysiology will be greatly advanced by a roadmap of the transcriptomic and epigenetic landscape of the human cerebral cortex across key developmental windows. Here, we propose, via a highly collaborative group of investigators, each with distinct areas of expertise and research focus, to create a scaffold of genomic data for understanding ASD pathophysiology, and psychiatric disorders more broadly. The work proposed here represents an ambitious multi-PI project (Yale, UCLA, and UCSF) that brings together three principal investigators and collaborators with strong publication records and expertise in all approaches necessary to perform this work using state-of-the-art and novel methodologies. We will perform time-, region-, and cell type-specific molecular profiling of control and ASD brains (Aim 1), including RNA-seq based transcriptomics, identifying cis-regulatory elements via ChIP-seq, and use Hi-C to determine the 3D chromatin architecture and physical relationships that underlie transcriptional regulation in three major regions implicated in neuropsychiatric disease (frontal and temporal cortex and striatum) across five major epochs representing disease-relevant stages in human brain development. This will include complementary genomic analyses in controls and matched post mortem ASD brain to identify genetic mechanisms underlying processes altered in ASD brain. We will address cellular heterogeneity via fluorescence-activated nuclear sorting (FANS) so as to profile neurons and non-neural cells separately, which will complement the whole tissue analyses. We will analyze and integrate these datasets to identify regional, developmental, and ASD-related processes to gain insight into underlying mechanisms, harmonizing these multi-omic data with other psychENCODE studies, as well as other large scale data sets, such as BrainSpan, ENCODE, GTEx and Roadmap Epigenomics Project (Aim 2). We will perform integrated analysis of germ-line ASD variations identified in more than 1000 families from the Simons Simplex Collection to characterize causal enrichments in developmental periods, brain regions, and cell types to better characterize the mechanisms by which genetic variation in humans alters brain development and function in health and disease (Aim 3). Completion of these aims will lead to a well-integrated resource across major periods in human cortical and striatal development that will permit generation of concrete testable hypotheses of ASD mechanisms, and inform our pathophysiological understanding of other related neuropsychiatric disorders.

Project Summary/Abstract The past decade has seen outstanding advances in the genetics of autism spectrum disorder (ASD), however only a moderate number of the hundreds of genes and genomic regions thought to be involved in ASD have been identified. Advances have come largely from the study of rare genetic variants, especially de novo varia- tion, including single nucleotide variation (SNV), insertion/deletions (indels), copy number variation (CNV), and larger chromosomal imbalances. A portion of the progress for ASD has come through the efforts of the Autism Sequencing Consortium (ASC), which represents a coordinated effort by more than 40 independent groups to rapidly identify ASD risk genes. Here we propose to continue the work of the ASC, largely by continued pro- duction and analysis of sequence data from ASD subjects and their families. The ASC benefits from substan- tial leveraging of resources, including the Exome Aggregation Consortium (ExAC) centered at the Broad Insti- tute (BI) and whole-exome sequencing (WES) of ASC samples, supported by an NHGRI Center Grant to BI, to make this renewal as low cost as possible. We also plan new avenues of research, such as integrating whole genome sequence (WGS) data and building on ideas that have emerged from the study of common variants to understand the interplay of common and rare variants to impact risk. Through this new research we will accel- erate our overall objective, which is the identification of ASD genes, thereby facilitating our long-term goal of building the foundation from which therapeutic targets for ASD emerge. Our rationale is that the identification of genes conferring significant risk to ASD and associated neurodevelopmental disorders can form the basis of studies to understand pathogenesis, as well as the basis for novel therapies. Moreover, such variants have direct implications for patients and their families in terms of etiological diagnosis, genetic counseling and pa- tient care. Our central hypothesis ? formulated based on results over the past decade ? is that rare and com- mon variation contributes additively to risk for ASD, but only certain rare variants confer substantial risk. The objectives will be accomplished with the following Specific Aims: 1) Produce and/or analyze WES of 30,000 new ASD subjects, parents and other controls, for a total of more than 50,000 samples; 2) Develop and apply approaches to find ?hidden? risk variants, and, 3) Use results from common and rare variant studies to describe the interplay of such variation in ASD risk. This contribution is significant because it represents the first step in research to understand pathogenesis of ASD and to the development of pharmacological strategies for treat- ment of core symptoms of ASD and etiologically related neurodevelopmental disorders. The research pro- posed is innovative, in our opinion, because it uses groundbreaking and novel statistical methods for identify- ing risk variants and for integrating rare and common variation. This is a new and substantively different ap- proach to gene discovery in ASD that departs significantly from the status quo and provides the means to achieve these important goals.

ABSTRACT Recent advances in genetics and genomics have identified hundreds of coding variants that increase risk for major neuropsychiatric disorders, such autism spectrum disorder. Work to clarify the contribution of non- coding variants is also underway and is expected to accelerate rapidly in the next few years. While these advances have considerably improved our understanding of the genetic landscape neuropsychiatric disorders, a deeper understanding of molecular pathophysiology is still missing. This knowledge gap is due to, in part, the heterogeneity of risk loci involved, their potential roles in regulating expression of a large number of genes, the pleiotropic nature of risk genes, and the high likelihood that neuropsychiatric disorders result from dysfunctional circuitry involving multiple cell types and brain regions, altogether making the identification of molecular and cellular mechanisms underlying a disease problematic, especially in the context of the protractive and complex nature of brain development. Therefore, the discovery and characterization of the full spectrum of functional genomic elements active in the human brain, as well as their activity/expression patterns across the spatiotemporal dimensions, is essential for clarifying when, where, and what cell types are relevant to the etiology and treatment of neuropsychiatric disorders. This is particularly so in the context of non-coding variants, which are difficult to annotate, yet potentially hold the promise of providing highly specific spatial, temporal, and cell type specific information. To address this knowledge gap and to continue our contributions to the PsychENCODE Consortium, we propose four specific aims that identify gene regulatory and cell type-specific mechanisms of human neurodevelopment. In Aim 1, we identify functional genomic elements across single cells (nuclei), cell types, regions and developmental time points of neurotypical human and macaque postmortem brains. In Aim 2, we map the spatio-temporal proteome of neurotypical human and macaque postmortem brains. In Aim 3, we perform integrative identification of functional genomic elements and proteomics in diseased brains and iPSC-derived neural cells. In Aim 4, we integrate results from Aims 1-3, as well as with independent genetic datasets of neuropsychiatric populations, to identify non-coding elements, genes, or molecular pathways that will lead to a better understanding of the underlying pathophysiological mechanisms of neuropsychiatric disorders. Finally, these mechanisms will be functionally characterized in model systems. Data from this proposal will also serve as a critical new resource for members of the community, with which they can intersect their results and draw deeper and more meaningful conclusions, especially as the wealth of genomic data from neuropsychiatric disorders continues to accumulate.

PROJECT SUMMARY Despite strong evidence for a genetic contribution to Tourette disorder (TD), progress in the identification of specific risk genes has been, until quite recently, halting. However, building upon NIMH?s support for our initial efforts to ascertain TD trios as well as our highly successful experience with genomic investigations of autism spectrum disorders (ASD), we have now demonstrated a clear path forward for reliable, systematic gene discovery in TD. Our TD work, recently published in the journal Neuron, identified one high confidence and three probable novel TD risk genes collectively pointing to neurite outgrowth and axon pathfinding as potential pathological mechanisms1. More importantly, however, our findings demonstrate, for the first time, a clear excess of de novo damaging point mutations in individuals with TD, with effect sizes that rival our recent findings in ASD. This discovery strongly suggests that sequencing of larger cohorts will reliably and rapidly lead to the identification of many more highly penetrant risk genes. Moreover, our recent work suggests an increased yield of highly penetrant damaging de novo variants in probands who are affected both with TD and obsessive compulsive disorder or attention deficit hyperactivity disorder, suggesting that our efforts may well also offer avenues to study the overlap in genetic risks for these often-comorbid conditions. Our current application proposes to: (1) expand our well characterized TD trio cohort by an additional 1,000 simplex trios and make the phenotypic data and biological materials widely and rapidly available to the broad scientific community; (2) accelerate gene discovery, via genotyping (for large de novo CNV identification) and whole exome sequencing (for de novo single nucleotide variant, insertion/deletion variant, and small CNV identification) of these additional TD trios, making these data rapidly and widely available as well; (3) extend the process of in silico and in vitro genomics investigations to elaborate the biology of TD with the long term goal of developing novel and more effective treatment strategies; and (4) begin biological characterization of TD variants using iPSC-derived neuronal cells. Given the potentially debilitating nature of TD alone, and a population prevalence of approximately 1 in 100 individuals, such advances would confer a significant public health benefit. The study design again rests heavily on the collaborative R01 mechanism that will bring together deep experience with the TD phenotype at multiple sites across the globe with scientists with a strong track record of success in rare variant human genomics and gene discovery. Specifically, the proposal includes seven primary US sites, four direct subcontracts (two USA sites for clinical supervision and data analysis and two foreign coordinating sites), and fourteen secondary clinical sites within Europe and South Korea.