Consequences of a network view for genetic association studies

American Journal of Psychiatry, 2009

The authors conducted a review of the history and empirical basis of genomewide association studies (GWAS), the rationale for GWAS of psychiatric disorders, results to date, limitations, and plans for GWAS meta-analyses. Method: A literature review was carried out, power and other issues discussed, and planned studies assessed.

Biological Psychiatry, 1999

The genetic association strategy is currently being applied to a number of psychiatric phenotypes including disease vulnerability, personality variation and clinical response to psychotropic drugs. Association studies offer the prospect of identification of the specific alleles that confer significant effects on clinical phenotype. However, it should be noted that this strategy has additional advantages as well as unique drawbacks. In this paper, we review the basic methodology utilized in each step of a typical psychiatric genetic association study and discuss their potential benefits and pitfalls with particular emphasis on the selection of clinical phenotype, the identification of a candidate gene, the selection of a candidate variant, clinical data set design, and the statistical analysis of association data. With appropriate design and execution, it is hoped that the association strategy will prove to be as successful in psychiatry as it has proven to be in other branches of medicine.

Frontiers in Psychology, 2021

Borsboom and colleagues have recently proposed a "network theory" of psychiatric disorders that conceptualizes psychiatric disorders as relatively stable networks of causally interacting symptoms. They have also claimed that the network theory should include non-symptom variables such as environmental factors. How are environmental factors incorporated in the network theory, and what kind of explanations of psychiatric disorders can such an "extended" network theory provide? The aim of this article is to critically examine what explanatory strategies the network theory that includes both symptoms and environmental factors can accommodate. We first analyze how proponents of the network theory conceptualize the relations between symptoms and between symptoms and environmental factors. Their claims suggest that the network theory could provide insight into the causal mechanisms underlying psychiatric disorders. We assess these claims in light of network analysis, Woodward's interventionist theory, and mechanistic explanation, and show that they can only be satisfied with additional assumptions and requirements. Then, we examine their claim that network characteristics may explain the dynamics of psychiatric disorders by means of a topological explanatory strategy. We argue that the network theory could accommodate topological explanations of symptom networks, but we also point out that this poses some difficulties. Finally, we suggest that a multilayer network account of psychiatric disorders might allow for the integration of symptoms and non-symptom factors related to psychiatric disorders and could accommodate both causal/mechanistic and topological explanations.

Molecular Psychiatry, 2008

Genome-wide association studies (GWAS) have yielded a plethora of new findings in the past 3 years. By early 2009, GWAS on 47 samples of subjects with attention-deficit hyperactivity disorder, autism, bipolar disorder, major depressive disorder and schizophrenia will be completed. Taken together, these GWAS constitute the largest biological experiment ever conducted in psychiatry (59 000 independent cases and controls, 7700 family trios and > 40 billion genotypes). We know that GWAS can work, and the question now is whether it will work for psychiatric disorders. In this review, we describe these studies, the Psychiatric GWAS Consortium for meta-analyses of these data, and provide a logical framework for interpretation of some of the conceivable outcomes.

PLOS One, 2011

Background: Mental disorders are highly comorbid: people having one disorder are likely to have another as well. We explain empirical comorbidity patterns based on a network model of psychiatric symptoms, derived from an analysis of symptom overlap in the Diagnostic and Statistical Manual of Mental Disorders-IV (DSM-IV).

Psychotherapy and Psychosomatics

Background: Network analysis (NA) is an analytical tool that allows one to explore the map of connections and eventual dynamic influences among symptoms and other elements of mental disorders. In recent years, the use of NA in psychopathology has rapidly grown, which calls for a systematic and critical analysis of its clinical utility. Methods: Following PRISMA guidelines, a systematic review of published empirical studies applying NA in psychopathology, between 2010 and 2017, was conducted. We included the literature published in PubMed and PsycINFO using as keywords any combination of "network analysis" with the terms "anxiety," "affective disorders," "depression," "schizophrenia," "psychosis," "personality disorders," "substance abuse" and "psychopathology." Results: The review showed that NA has been applied in a plethora of mental disorders in adults (i.e., 13 studies on anxiety disorders; 19 on mood disorders; 7 on psychosis; 1 on substance abuse; 1 on borderline personality disorder; 18 on the association of symptoms between disorders), and 6 on childhood and adolescence. Conclusions: A critical examination of the results of each study suggests that NA helps to identify, in an innovative way, important aspects of psychopathology like the centrality of the symptoms in a given disorder as well as the mutual dynamics among symptoms. Yet, despite these promising results, the clinical utility of NA is still uncertain as there are important limitations on the analytic procedures (e.g., reliability of indices), the type of data included (e.g., typically restricted to secondary analysis of already published data), and ultimately, the psychometric and clinical validity of the results.

Journal of Psychiatric Research, 1987

Analysis of the distribution of diagnoses in families (segregation analysis) has not, so far, advanced us toward the goal of resolving the inheritance of the major psychiatric disorders. Recent advances in genetics, particularly the development of new molecular genetic linkage methods, have made it, at least theoretically, feasible to scan the entire human genome, so that in a properly designed and executed set of studies it will be possible to demonstrate whether there exists single locus transmission for a particular disorder, and to map the locus. We present here an analysis of feasibility of moderate-sized pedigrees (approximately 15 persons, two generations) and affected-sib-pair sets in such studies. Eight to ten moderate-sized pedigrees are sufficient to perform definitive mapping under the tested conditions, of recessive or additive inheritance, low penetrance of the heterozygote, and a genetically homogeneous disorder. The affected-sib-pair method required 25 pairs of sibs to detect linkage under such conditions in a recessive model, and 45 in a dominant model. When there is genetic heterogeneity, moderate-sized pedigrees are much less useful, but the affected-sib-pair method retains considerable power.

Psychotherapy and psychosomatics, 2017

The British Journal of Psychiatry, 2009

Summary Over the past 2 years genome-wide association studies have made major contributions to understanding the genetic architecture of many common human diseases. This editorial outlines the development of such studies in psychiatry and highlights the opportunities for advancing understanding of the biological underpinnings and nosological structure of psychiatric disorders.

Psychometrics - New Insights [Working Title]

In this chapter, we present the main methodological principles of psychological networks as a way of conceptualizing mental disorders. In the network approach, mental disorders are conceptualized as the consequence of direct interactions between symptoms, which may involve biological, psychological, and social mechanisms. If these cause-and-effect relationships are strong enough, symptoms can generate a degree of feedback to sustain them. It is discussed how such an approach contrasts with the traditional psychometric approach, known as the Latent Variable Theory, which assumes that disorders are constructs that exist but are not directly observable. Furthermore, it is also discussed how new neuropsychological hypotheses have been derived in the network approach and how such hypotheses generate direct implications for the understanding of diagnosis and treatment of psychological disorders. Finally, the recentness of the network approach in psychology and how future studies can estab...

PloS one, 2014

The vast number of psychopathological syndromes that can be observed in clinical practice can be described in terms of a limited number of elementary syndromes that are differentially expressed. Previous attempts to identify elementary syndromes have shown limitations that have slowed progress in the taxonomy of psychiatric disorders. To examine the ability of network community detection (NCD) to identify elementary syndromes of psychopathology and move beyond the limitations of current classification methods in psychiatry. 192 patients with unselected mental disorders were tested on the Comprehensive Psychopathological Rating Scale (CPRS). Principal component analysis (PCA) was performed on the bootstrapped correlation matrix of symptom scores to extract the principal component structure (PCS). An undirected and weighted network graph was constructed from the same matrix. Network community structure (NCS) was optimized using a previously published technique. In the optimal network ...

Behavioral and Brain Sciences, 2019

In the past decades, reductionism has dominated both research directions and funding policies in clinical psychology and psychiatry. The intense search for the biological basis of mental disorders, however, has not resulted in conclusive reductionist explanations of psychopathology. Recently, network models have been proposed as an alternative framework for the analysis of mental disorders, in which mental disorders arise from the causal interplay between symptoms. In this target article, we show that this conceptualization can help explain why reductionist approaches in psychiatry and clinical psychology are on the wrong track. First, symptom networks preclude the identification of a common cause of symptomatology with a neurobiological condition; in symptom networks, there is no such common cause. Second, symptom network relations depend on the content of mental states and, as such, feature intentionality. Third, the strength of network relations is highly likely to depend partially on cultural and historical contexts as well as external mechanisms in the environment. Taken together, these properties suggest that, if mental disorders are indeed networks of causally related symptoms, reductionist accounts cannot achieve the level of success associated with reductionist disease models in modern medicine. As an alternative strategy, we propose to interpret network structures in terms of D. C. Dennett’s (1987) notion of real patterns, and suggest that, instead of being reducible to a biological basis, mental disorders feature biological and psychological factors that are deeply intertwined in feedback loops. This suggests that neither psychological nor biological levels can claim causal or explanatory priority, and that a holistic research strategy is necessary for progress in the study of mental disorders.

Behavioral and Brain Sciences, 2010

The network perspective will help, but is comorbidity the question?

PLoS Computational Biology, 2012

With the recent success of genome-wide association studies (GWAS), a wealth of association data has been accomplished for more than 200 complex diseases/traits, proposing a strong demand for data integration and interpretation. A combinatory analysis of multiple GWAS datasets, or an integrative analysis of GWAS data and other high-throughput data, has been particularly promising. In this study, we proposed an integrative analysis framework of multiple GWAS datasets by overlaying association signals onto the protein-protein interaction network, and demonstrated it using schizophrenia datasets. Building on a dense module search algorithm, we first searched for significantly enriched subnetworks for schizophrenia in each single GWAS dataset and then implemented a discovery-evaluation strategy to identify module genes with consistent association signals. We validated the module genes in an independent dataset, and also examined them through meta-analysis of the related SNPs using multiple GWAS datasets. As a result, we identified 205 module genes with a joint effect significantly associated with schizophrenia; these module genes included a number of well-studied candidate genes such as DISC1, GNA12, GNA13, GNAI1, GPR17, and GRIN2B. Further functional analysis suggested these genes are involved in neuronal related processes. Additionally, meta-analysis found that 18 SNPs in 9 module genes had P meta ,1610 24 , including the gene HLA-DQA1 located in the MHC region on chromosome 6, which was reported in previous studies using the largest cohort of schizophrenia patients to date. These results demonstrated our bi-directional networkbased strategy is efficient for identifying disease-associated genes with modest signals in GWAS datasets. This approach can be applied to any other complex diseases/traits where multiple GWAS datasets are available.

2010

Many psychiatric conditions and traits are associated with significant heritability. Genetic risk for psychiatric conditions encompass rare variants, identified due to major effect, as well as common variants, the latter analyzed by association analyses. We review guidelines for common variant association analyses, undertaking after assessing evidence of heritability. We highlight the importance of: suitably large sample sizes; an experimental design that controls for ancestry; careful data cleaning; correction for multiple testing; small P values for positive findings; assessment of effect size for positive findings; and, inclusion of an independent replication sample. We also note the importance of a critical discussion of any prior findings, biological follow-up where possible, and a means of accessing the raw data.