David C. Glahn - US grants

DESCRIPTION (provided by applicant): The goal of this project is to identify quantitative trait loci associated with variation in brain structure and function. The ultimate promise of this research is the discovery of genes that predispose to brain disorders and mental illnesses. We believe that the analysis of genetic influences on brain structure and function in randomly sampled extended pedigrees will provide significant clues regarding the genes that are involved in both normal and pathological brain function. The focus of the project is on the genetic dissection of quantitative endophenotypes that more directly index the underlying biological basis of brain function than do discrete disease states themselves. To this end, we will perform neuroimaging and conduct neuropsychological examinations on Mexican American individuals who have been part of our ongoing genetic research studies for the past 15 years. All participants were previously genotyped and our plan is to utilize existing genome scan and genome-wide quantitative transcriptomic data for correlation with neuroanatomic and neurocognitive variables. Our specific aims are to: 1) perform high quality brain magnetic resonance imaging and neuropsychological examinations on 1,000 Mexican Americans who are members of approximately 30 large extended families, 2) assess the quantitative genetic architecture of brain-related phenotypes by estimating their heritabilities and their genetic correlations, 3) classify specific brain morphological variables and quantitative leukocyte-derived gene expression measures as endophenotypes related to brain function, 4) localize QTLs influencing variation in the quantitative brain-related phenotypes by performing linkage-based genome scanning using the variance component method, 5) refine the position of localized QTLs and identify positional candidate loci using an objective prioritization strategy that jointly utilizes in silico bioinformatics, genetic, and transcriptional data, and 6) identify the most likely functional variations within the two best positional candidate genes. This project involves coordinated R01 applications from Dr. John Blangero, Southwest Foundation for Biomedical Research, and Drs. David Glahn and Peter Fox, University of Texas Health Science Center at San Antonio. If funded, our data and biomaterials will be incorporated into the NIMH Human Genetics Initiative making them available to qualified researchers in the wider scientific community. Relevance to agency mission: Brain-related mental diseases are a major public health burden whose biology is still largely unknown. By identifying genes involved in brain function and structure, we will provide novel biological candidates for the determinants of such diseases and thus improve potential for intervention.

DESCRIPTION (provided by applicant): The aims in this study will (1) develop candidate neurocognitive and neuroimaging endophenotypes for bipolar I disorder (BPI), (2) examine the association of history of psychosis and these brain-behavior markers in BPI patients, and (3) determine if markers are sensitive to liability for psychosis. Thus, the project has two overlapping goals: the development of candidate endophenotypes for BPI broadly and the identification of candidate endophenotypes for psychosis. The ultimate promise of this research is to develop markers that will characterize the biological mechanisms of BPI and facilitate the discovery of genes that predispose the illness. We believe that a comprehensive assessment of neuropsychological functioning and brain structure and function in sibling pairs discordant for bipolar disorder and stratified for psychosis history is a strategically strong first step towards reaching these goals. To this end, we will perform anatomic and functional neuroimaging and conduct neuropsychological examinations on 130 euthymic patients with BPI (65 with history of psychosis), 130 of their unaffected same-sex siblings and 65 unrelated comparison subjects. Markers found to be aberrant in both affected individuals (regardless of history of psychosis) and in their unaffected relatives will be considered candidate endophenotypes for BPI (Aim 1). Neuropsychological and neuroimaging measures that distinguish between BPI patients with and without history of psychosis (Aim 2) and their siblings (Aim 3) will be considered potential endophenotypes for psychosis. Bipolar I disorder represents a significant economic burden and is associated with substantial morbidity and mortality rates. Although it is well established that BPI is substantially heritable, the molecular genetic basis for this illness remains elusive, potentially because of illness complexity, heterogeneity of disease expression, and comorbidity with other disorders that may distort clinical presentation. In the face of evidence that genes predisposing to BPI may be transmitted without expression of the clinical phenotype, interest has arisen in developing endophenotypes for the illness, indicators of processes mediating between genotype and phenotype. Given the high rates of psychosis in BPI and that history of psychosis may alter brain structure and function, we believe that elucidating neurocognitive and neuroimaging endophenotypes for the disorder must account for the potential impact of hallucinations and delusions on these markers. This research will established biomarkers that could improve the identification and treatment of BPI patients and, potentially, patients with psychotic disorders, independent of their formal diagnosis. PUBLIC HEALTH RELEVANCE: Bipolar I disorder is a major public health burden whose biology is still largely unknown. Through the development of brain-behavior markers sensitive to genetic liability for bipolar disorder, the proposed research should significantly aid the discovery of genes that predispose the illness and facilitate the identification of the biological determinants of bipolar disorder. This, in turn, should lead to improved characterization and treatment of bipolar disorder.

DESCRIPTION (provided by applicant): The goal of this project is to identify genes that influence variation in brain structure and function using high- density genome-wide association (GWA) analysis. The ultimate promise of this research is the discovery of genes that predispose to brain disorders and mental illnesses. Our focus is on the genetic analysis of variation in brain structure and function in randomly sampled extended pedigrees to provide significant clues regarding the specific genes that are involved in both normal and pathological brain function. In 2006, we began collecting brain-related endophenotypes on related Mexican American individuals for linkage-based analyses (MH078111 &MH078143). However, given the number of recent successes using GWA, we believe that shifting our design to exploit the availability of high density SNPs will dramatically speed gene discovery by substantially reducing the genomic region of interest nominated in our linkage-based study. Using alternative funding, we have begun this process of high-density genotyping. Because of power issues due to multiple testing inherent in GWA, it is necessary to expand our original sample to obtain sufficient power for gene identification. By adding 500 new individuals from the same large pedigrees and completing the high-density genotyping in the original sample (n=1,000), we will have 80 percent power to detect relatively small genetic effects on brain-related endophenotypes. Our specific aims for this independent R01 are to: 1) extend our existing study by performing high quality brain magnetic resonance imaging and neuropsychological examinations on an additional 500 Mexican Americans who are members of 30 previously studied extended families, 2) perform GWA analysis to prioritize potential genes involved in brain structure/function, using 1 million SNPs genotyped on all 1,500 individuals, 3) increase our genome-wide transcriptional profile data by performing identical assays on the additional 500 samples to identify genes whose lymphocyte-derived expression levels correlate with measures of brain structure/function in the total sample, 4) identify the most likely functional variations within the five best empirically nominated candidate genes by resequencing 192 founder individuals, and 5) confirm the strongest association in an independent data set. Combining these new samples with those currently being collected represents the most cost effective and rapid approach for the discovery of genes associated with brain-related traits. The co-principal investigators on this single application include Dr. David Glahn, University of Texas HSC at San Antonio, and Dr. John Blangero, Southwest Foundation for Biomedical Research. If funded, our data and biomaterials will be incorporated into the NIMH Human Genetics Initiative, making them available to qualified researchers in the wider scientific community. PUBLIC HEALTH RELEVANCE: Brain-related mental diseases are a major public health burden whose biology is still largely unknown. By identifying genes involved in brain function and structure, we will provide novel biological candidates for the determinants of such diseases and thus improve potential for intervention. The use of genome-wide association methods should significantly speed gene discovery.

DESCRIPTION (provided by applicant): Cardiovascular disease (CVD) remains the leading cause of death in the United States. Although CVD risk is heritable, identification of causal genes in risk pathways has been slow. This project focuses on the identification of causal genes that influence variation in susceptibility to CVD by concentrating on genetic dissection of quantitative endophenotypes including carotid wall thickness, lipids, obesity-related phenotypes, blood pressure-related phenotypes, the insulin/glucose axis, inflammatory markers, oxidative stress markers, hemostasis/coagulation factors, and measures of brain white matter hyperintensities that are genetically correlated with CVD risk. We will utilize existing samples/data from a valuable genetic resource, the San Antonio Family Study (SAFS), involving large extended pedigrees of Mexican American individuals. This long- running highly successful project has produced a large number of quantitative trait locus (QTL) localizations of relevance for CVD risk. In this project, we move from QTL localization to causal gene identification. Our approach to CVD-risk gene discovery is comprehensive; we will utilize whole genome sequencing to capture all possible functional variants in 1,957 individuals from 45 large pedigrees. The large pedigrees to be used represent an optimal study design for the detection of rare functional variants. Advanced statistical genetic methods will be employed to identify the likely causal genes/variants in quantitative trait locus (QTL) regions influencing CVD risk. To achieve our objectives, we will (1) localize additional CVD-related QTLs due to rare functional variants using novel pedigree-specific localization methods, (2) obtain whole genome sequence information for 1,957 Mexican American individuals, (3) identify causal genes underlying existing QTLs influencing CVD risk using WGS information, (4) perform agnostic genome-wide direct association scans using non-synonymous coding variants to identify novel rare functional protein-altering variants influencing CVD risk and, (5) use a novel whole genome assay measuring variant-specific functional regulatory potential to permit genome-wide direct association scans using the predicted functional variants to identify novel rare regulatory variants influencing CVD risk. Given the enormous impact of CVD to mortality rates and the economic burden this disease imposes, it is clear that new methods of genomic analysis are necessary to enable the identification of novel genes and pathways involved in disease risk. The results of this project should identify causal genes underlying CVD risk. Identification of the causal genes will obligately generate on the pathways of these genes and will directly identify novel drug targets.

DESCRIPTION (provided by applicant): Recent advances in inexpensive whole exome and whole genome sequencing have opened up the prospect of identifying rare variants influencing common, complex diseases. Though only carried in a few individuals each, highly penetrant rare variants may collectively explain a large portion of disease risk. Such variants might be private to a single family, making them difficult to identify even in large case/control samples. However, the study of rare variants in extreme families has the potential to provide groundbreaking insights into the biology underlying common disease. For example, families with rare forms of hypercholesterolemia taught us much about the biology of heart disease. Schizophrenia (SCZ) is a heritable mental illness associated with substantial morbidity and mortality. Identifying genes that contribute to risk of psychosis, a defining feature of SCZ, shoul provide critical information regarding SCZ pathophysiology. We have identified a large extended family that has all the hallmarks of a potentially Mendelian, monogenic form of psychosis due to a highly penetrant founder mutation. There are at least 36 individuals with psychosis (verified by in person diagnostic interviews) in this family who are grandchildren or great grandchildren of a single couple. Additionally, the family comes from an isolated population in a remote location in Costa Rica and there is known consanguinity in the pedigree. Interestingly, there are also indications of immune system involvement in affected members of the family. The goal of this study is to utilize exome sequencing to identify the mutation responsible for psychosis in this family and characterize its effects, including penetrance, variable expressivity in the neurocognitive and neurological domains, and potential immune system involvement. We will also assess the prevalence of the mutation in individuals with SCZ in Costa Rica and test whether other mutations in this gene may influence SCZ risk in a sample of US Caucasian, Hispanic, and African American cases and controls.

DESCRIPTION (provided by applicant): The ultimate goal of our renewal application is the discovery of genes that predispose to mental illnesses. While a number of genome-wide significant quantitative trait loci (QTL) have been localized for mental illnesses, these findings have yet to result in true gene identifications. Yet, progress in elucidating the pathophysiology o major mental disorders, and subsequent treatment interventions, is predicated on causal gene identification. In our renewal application, we will utilize exhaustive genomic information obtained from whole genome sequencing (WGS) to identify causal variants/genes influencing endophenotypes for schizophrenia, bipolar disorder and/or major depression. An endophenotype is a heritable trait that is genetically correlated with disease liability, providing greater power to localize disease-related genes than affection status alone. Rare variants appear to be important in mental illness. Pedigree-based studies represent an implicit enrichment strategy for identifying rare variants and a pedigree-specific rare functional variant can be sufficient to verify that a given gene is involved in phenotypic variation. In the initial phase of our study, we acquired neuroanatomic, neurophysiologic and neurocognitive endophenotypes for mental illness in 1350 Mexican Americans from randomly selected extended pedigrees. Using existing high density SNP data, we successfully localized multiple genome-wide significant QTLs influencing endophenotypic variation. We will now move beyond QTL localization to the identification of genes that influence these endophenotypes. Achieving this goal is greatly enhanced by the availability of WGS data on ~2100 individuals, including all endophenotyped subjects. Our specific aims are to: (1) acquire structural and functional brain images and conduct neuropsychological examinations on 600 additional Mexican American family members with WGS data but without brain-related endophenotypes; (2) identify causal variants underlying existing QTLs influencing mental illness-relevant endophenotypes; (3) perform agnostic pedigree-based genome-wide association using only functional non-synonymous coding variants or putative regulatory variants to identify additional genes/variants influencing brain endophenotypes; and (4) Test for pleiotropic effects of the most likely variants identified in Aims 2 & 3 in a sample of 1000 schizophrenia cases, 1000 bipolar depression cases, 1000 major depressive disorder cases and 1000 controls from the NIMH's Center for Collaborative Genetic Studies of Mental Disorders. Our collaborative project includes applications from John Blangero, Texas Biomedical Research Institute, and David C Glahn, Yale University. Subcontracts for phenotyping (UTHSCSA; RE Olvera) and image analysis (University of Maryland, P Kochunov) are also included. This renewal application is designed to extend our initial study by identifying the specific genes that influence mental illness endophenotypes.

DESCRIPTION (provided by applicant): Abnormal structural and functional connectivity (interaction between brain regions) is central to the pathophysiology of psychotic illnesses like schizophrenia and psychotic bipolar disorder. Modern neuroimaging techniques and analytic strategies provide an unprecedented capacity to more fully characterize the functional and structural psychotic disconnectivity. Individuals with psychotic illness and their unaffected relatives have abnormal connectivity, suggesting that at least a portion of psychotic disconnectivity is associated with genetic predisposition for the diseases. Imaging-based connectivity endophenotypes are ideally suited to aid the functional characterization of putative risk genes, allowing us to move beyond a genotype-phenotype association to delineating mechanisms that give rise to psychotic illnesses. Recently, large-scale exome sequencing in individuals of European ancestry provided the strongest evidence to date for specific genetic variants that increase risk for psychosis. These primarily rare mutations were spread across gene networks involved in neuronal processes, including calcium channels and postsynaptic signaling. Our goals are to replicate these promising genetic findings in a different ethnic group, African-Americans, and determine whether and how these gene sets impact psychotic disconnectivity. African-Americans, an underserved population, have ~32% more highly deleterious non-synonymous rare variants in these networks than individuals of European ancestry, improving our power to detect rare variants. Our aims are to: (1) use modern MRI acquisition and analysis techniques based on the Human Connectome Project to document psychotic disconnectivity in 750 African Americans (375 with a psychotic disorder and 375 demographically matched comparison subjects). We will test hypotheses that diagnostic and dimensional indices of psychosis are associated with reduced global functional connectivity but intact global structural connectivity, combined with aberrant connectivity between specific regions or tracts; (2) conduct whole exome sequencing (WES) to test the influence of rare non-synonymous variants from genes in previously identified gene sets on psychosis risk using a network-centered analysis strategy. We will test hypotheses that the voltage-gated calcium ion channel, and the ARC-associated scaffold protein and the NMDAR postsynaptic signaling complexes influence diagnostic and dimensional indices of psychosis; and (3) apply this same network-centric test to determine if gene sets implicated in illness risk also influence functional and structural psychotic disconnectivity. Linking these genetic pathways to psychotic disconnectivity will provide mechanistic insights into the genomic influences on psychotic illness. Our collaborative application includes sites at Yale/Hartford Hospital (DC Glahn PI), Stanford (RA Poldrack PI) and Texas Biomedical Research Institute (J Blangero PI). Our results should bolster our understanding of the genetic architecture of psychotic illness and provide important clues for traversing the chasm between identified genetic networks and the behaviorally defined disorder.

? DESCRIPTION (provided by applicant): The goal of this study is to localize and characterize genes that influence normal maturation-related changes in neurocognitive, neuroanatomic and neurophysiological indices. A substantial number of brain-related traits exhibit gene by age interactions, suggesting a heritable basis for neurocognitive, neuroanatomic and neurophysiological changes with age and highlighting the potential role of genes in differential brain maturation. We will utilize novel analytical approaches to investigate genetic and environmental influences on variation in brain, cognition, and behavior from a developmental perspective, modeling complex effects in both the genetic and environmental realms, and potential interactions between them, while allowing for changes in these effects across development, in the Philadelphia Neurodevelopmental Cohort (PNC). The PNC includes ~9500 individuals between the ages of 8 - 21 years who have been characterized for brain, behavior, and genetic variables. All participants were assessed neuropsychiatrically and completed a Computerized Neurocognitive Battery (CNB). Interviews included assessment of demographics, life events and stressors, school performance, medical history, and screening for psychopathology and presence and duration of associated symptoms. The CNB included an estimate of IQ as well as 14 tests designed to assess five neurobehavioral functions. A subset of ~1450 participants underwent neuroimaging, including structural and functional MRI and diffusion tensor imaging. Approximately 8700 PNC participants have been genotyped for 500K - 950K genome-wide SNPs, obtained on a diverse variety of genotyping platforms. The large size of this data set, combined with the rich and detailed assessments in a variety of phenotypic domains, provides an unparalleled opportunity to study gene-by-age and gene-by-environment interactions in neurodevelopment and their potential contribution to risk of mental illness. The specific aims of the proposed study are to: 1) Localize genes influencing variation in neurodevelopment in the PNC; 2) Assess whether these genetic effects change with age and identify additional loci exhibiting gene- by-age interactions; and 3) Assess complex environmental effects on neurodevelopment and test whether they interact with, and moderate or mediate, genetic effects. Laura Almasy, Texas Biomedical Research Institute, is contact PI of this application and co-PIs David Glahn, Yale University, and Raquel Gur, University of Pennsylvania, will lead subcontracts. Dr. Almasy provides expertise in genetic analysis of complex phenotypes, including gene-by-age and gene-by-environment interactions. Drs. Glahn and Gur provide expertise in cognitive neuropsychology, neuroimaging, and psychiatry.

? DESCRIPTION (provided by applicant): Our goal is to identify genes that increase risk for affective and psychotic disorders like schizophrenia, bipolar disorder and major depression. Although these highly heritable diseases are associated with substantial morbidity and mortality, their etiologies remain poorly understood. Identifying genes that contribute to their risk should provide critical information leading to the development of novel diagnostic and therapeutic strategies. We propose an eight site international consortium designed to identify rare causal variants for affective and psychotic illnesses using extended multiplex pedigrees. These multigenerational families were previously identified and include at least three individuals with confirmed diagnoses. We focus on the identification of rare variants (with population MAF d 0.01) that have a large absolute effect size, although it may be present in a small number of related affected individuals. While such rare functional variants may have a small effect on population attributable risk or variant-specific heritability, they can be sufficient to verify tha a given gene is involved in illness risk. Pedigree-based studies represent an implicit enrichment strategy for identifying the rarest (e.g., private or pedigree-specific) variants, as Mendelian transmissions from parents to offspring maximize the chance that multiple copies of rare variants exist in the pedigree. Whole genome sequencing (WGS) allows a comprehensive search for rare single nucleotide variants (SNVs) or more complex sequence variation such as CNVs or INDELS. To identify rare, potentially private, variants that increase risk for affective or psychotic illness, we will create a repository of 4043 individuals from previously collected multiplex pedigrees (n=331) that will be analyzed with WGS. 1915 of these individuals have available WGS and we will obtain sequence data for 2128 additional subjects. Phenotypes include classical dichotomous diagnoses, quantitative scales derived from standardized interviews reflecting dimensional symptom classes, and neurocognitive endophenotypes. Our specific aims are to: 1) synergize phenotypic assessments, create dimensional indices of psychopathology, and rank endophenotypes across sites; 2) obtain WGS on 2128 individuals from extended pedigrees by direct sequencing of 1000 samples at 30x coverage and perform highly accurate pseudo-sequencing using a high density SNP framework to obtained the remaining 1128; 3) localize and identify QTLs influencing illness phenotypes /endophenotypes; 4) perform pedigree-based genome-wide association using likely functional variants; 5) identify rare functional CNV/INDELs influencing illness risk or endophenotypes; 6) perform gene-centric association tests in an independent sample. Our collaborative project includes applications from Yale University (DC Glahn, PD/PI), Texas Biomedical Research Institute (J Blangero, PD/PI) and the University of Pennsylvania (RE Gur, PD/PI). In addition, the Universities of Pittsburgh (V Nimgaonkar), Costa Rica (H Ravents), Edinburgh (AM McIntosh), and Western Australia (A Jablensky) and the intramural NIMH (F McMahon) will participate.