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Drug and Alcohol Dependence 220 (2021) 108535

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Drug and Alcohol Dependence


journal homepage: www.elsevier.com/locate/drugalcdep

Short communication

Genomic relationships across psychiatric disorders including substance


use disorders
Abdel Abdellaoui 1, Dirk J.A. Smit 1, Wim van den Brink, Damiaan Denys, Karin J.H. Verweij *
Department of Psychiatry, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, the Netherlands

A R T I C L E I N F O A B S T R A C T

Keywords: Background: A recent study investigated the genetic associations and latent genetic structure among eight psy­
Substance use disorders chiatric disorders using findings from genome-wide association studies (GWASs). No data from substance use
Genetic correlations disorders were included, while these represent an important category of mental disorders and could influence the
Psychiatric disorders
latent genetic structure. We extended the original paper by recreating the genetic relationship matrix, graph, and
Genetic structure
latent genetic factor structure, including additional data from substance use disorders.
Dual disorder
Methods: We used GWAS summary statistics of 11 psychiatric disorders, including alcohol dependence, nicotine
dependence, and cannabis use disorder. We estimated genetic correlations between all traits in Linkage
Disequilibrium-Score Regression. A graph was created to illustrate the network of genetic correlations. We then
used the genetic relationships to model a latent genetic factor structure.
Results: Alcohol and nicotine dependence showed significant genetic correlations with several other psychiatric
disorders, including ADHD, schizophrenia, and major depression. Cannabis use disorder was only significantly
associated with ADHD. The addition of substance use disorders resulted in some changes in the latent structure of
the factor model when compared to the original model including eight disorders. All substance use disorders
contributed mostly to Factor 3, a heterogeneous factor with also loadings from ADHD, major depression, Autism
Spectrum Disorders, and Tourette Syndrome.
Conclusions: Alcohol and nicotine dependence show widespread genetic correlations with other psychiatric
disorders. Including substance use disorders in the factor analysis results in some changes in the underlying
genetic factor structure. Given the instability of such models, identified structures should be interpreted with
caution.

1. Introduction TS), the second by mood and psychotic disorders (MD, BIP, SCZ), and
the third by early-onset neurodevelopmental disorders (ASD, ADHD, TS)
Recently, Lee et al. (2019) published a paper in Cell in which they as well as MD. The authors conclude that their findings have important
combined genome-wide association study (GWAS) data from eight implications for psychiatric nosology, i.e., the classification of psychi­
psychiatric disorders - anorexia nervosa (AN), atric disorders.
attention-deficit/hyperactivity disorder (ADHD), autism spectrum dis­ Unfortunately, the authors did not include any data from substance
order (ASD), bipolar disorder (BIP), major depression (MD), abuse or dependence GWASs in their analyses, while substance use
obsessive-compulsive disorder (OCD), schizophrenia (SCZ), and Tour­ disorders form an important category of mental disorders. Substance use
ette syndrome (TS) – to identify novel pleiotropic genes and a latent disorders are highly impairing, causing great harm to the individual,
genetic structure underlying these eight disorders. Using exploratory their family and friends, and to the society as a whole (Whiteford et al.,
factor-analyses, and confirmed by hierarchical clustering analyses, they 2013). There is evidence for substantial phenotypic and genetic corre­
identified three (correlated) factors explaining approximately half of the lations between substance use disorders and other psychiatric disorders
genetic variation in these eight disorders. The first factor consisted (Vink and Schellekens, 2018). Not including substance use disorders in
primarily of disorders characterized by compulsive behaviors (AN, OCD, the analyses is a potential caveat, in particular because the investigated

* Corresponding author.
E-mail address: karin.verweij@amsterdamumc.nl (K.J.H. Verweij).
1
Shared first author.

https://doi.org/10.1016/j.drugalcdep.2021.108535
Received 7 August 2020; Received in revised form 8 December 2020; Accepted 23 December 2020
Available online 19 January 2021
0376-8716/© 2021 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
A. Abdellaoui et al. Drug and Alcohol Dependence 220 (2021) 108535

traits now lack most of the externalizing disorders. The limited inclusion 2015).
of traits may, therefore, have biased the identified latent structure of
disorders. 2.2.1. Genetic relationship graph
We investigated whether the genetic latent structure changes when A graph was plotted with the absolute genetic correlations as
using a broader set of psychiatric traits, including additional data from strength parameter for the edges (connections) using R version 3.5.1 (R
three GWASs on substance use disorders: alcohol, nicotine, and cannabis Core Team, 2018) and R package igraph (Csardi and Nepusz, 2006).
dependence. We investigated the genetic relationships between the 11 Layout followed the Fruchterman-Reingold algorithm. Non-significant
traits by recreating the genetic relationship matrix and graph, and by weights (p > 0.05 after Bonferroni correction) were removed. Central­
producing a new latent genetic factor structure. ity of each trait was assessed with eigenvector centrality (Bonacich,
1987), and reflects whether the trait has strong genetic overlap with
2. Material and methods traits that themselves have strong overlap with other traits.

2.1. GWAS data 2.3. Factor analysis

To enable direct comparison with the Lee et al. paper, we used data We used the genetic correlations to model the joint genetic archi­
from the same eight GWAS studies of psychiatric disorders conducted by tecture of the 11 psychiatric disorders, following the methods by Lee
the Psychiatric Genomics Consortium: ADHD, AN, ASD, BIP, MD, OCD, et al. (2019) to enable direct comparison. First, an exploratory factor
SCZ, TS (Table 1). For MD we only had access to data excluding analysis (EFA) was performed with a predefined three-factor extraction
23andMe. In addition, we included GWAS data from three GWASs for and promax rotation. This determined the factor structure for the sub­
substance use disorders: alcohol dependence (AD; DSM-IV-diagnosis; sequent confirmatory factor analysis (CFA), which we performed in
Walters et al., 2018), cannabis use disorder (CUD, ICD diagnosis; Genomic Structural Equation Modelling (Genomic SEM, Grotzinger
Demontis et al., 2019a), and nicotine dependence (ND, Fagerström Test et al., 2019). Three correlated factors were created, including only paths
collected among smokers; dividing the sample in: mild (scores 0–3; N = to traits with path loadings ≥.20 in the EFA. The diagonally weighted
14,184), moderate (scores 4–6; N = 9206), and severe (scores 7–10; N = least squares (DWLS) estimator was used. The full genetic relationship
5287); Hancock et al., 2018). In line with the paper from Lee et al. we matrix was used as input. Comparative fit index (CFI) and standardized
only included data based on individuals of European ancestry for the root-mean-square residual (SRMR) were used as model fit parameters.
substance use disorders. Table 1 presents sample sizes and SNP-based Secondly, we repeated the procedure adding a fourth factor, to establish
heritabilities for each disorder, and the reference to the original whether substance use disorders would form a separate factor from the
publications. other disorders.
As sensitivity analysis we also performed analyses in which we
included data from three GWASs for non-clinical substance use traits: 3. Results
alcoholic drinks per week (Liu et al., 2019), cigarettes smoked per day
(Liu et al., 2019), and lifetime cannabis use (Pasman et al., 2018). 3.1. Genetic correlations
Sample sizes and SNP-based heritabilities for these traits can be found in
Supplementary Table 1. The bivariate genetic correlations between all traits are presented in
Fig. 1A and the exact estimates, standard errors, and p-values in Sup­
2.2. Genetic correlations plementary Table 2. Of the initial eight disorders, ADHD and MD
showed the highest genetic correlations with the substance use disor­
We estimated bivariate genetic correlations between all traits using ders, with ADHD showing significant genetic correlations with all three
LD-score (LDSC) regression (Bulik-Sullivan et al., 2015a). The genetic substance use disorders (ADHD-AD: rg = .46, p = 3.8×10− 7, ADHD-ND:
correlations are based on the estimated slopes from the regressions of rg = .54, p = 3.3×10-13, ADHD-CUD: rg = .35, p = 7.1×10-4) and major
the product of z-scores from two sets of GWAS summary statistics on the depression only with alcohol and nicotine dependence (MD-AD: rg = .52,
linkage disequilibrium (LD) score and represent the genetic covariation p = 1.3×10-10, MD-ND: rg = .45, p = 9.4×10-12). Both alcohol and
between two traits based on all polygenic effects captured by the SNPs. nicotine dependence showed significant genetic correlations with four
The LD patterns we used were estimated in the European populations psychiatric disorders, whereas cannabis use disorder showed significant
included in the HapMap 3 reference panel (Bulik-Sullivan et al., 2015b; genetic correlations only with ADHD.
Finucane et al., 2015). The LDSC regression analyses were performed
using the 1,290,028 genome-wide HapMap SNPs used in the original 3.1.1. Genetic relationship graph
LD-score regression studies (Bulik-Sullivan et al., 2015b; Finucane et al., Fig. 1B shows the genetic relationship graph, displaying the

Table 1
Sample sizes and SNP-based heritabilities as computed using LDSC regression.
Psychiatric Disorder Reference Cases Controls Total Effective Sample Size SNP-based h2 (SE)

ADHD Demontis et al. (2019b) 19,099 34,194 53,293 49,017 .26 (.01)
AN Duncan et al. (2017) 3,495 10,982 14,477 10,605 .33 (.05)
ASD Grove et al. (2019) 18,382 27,969 46,351 44,368 .20 (.02)
BIP Stahl et al. (2019) 20,353 31,358 51,710 49,369 .36 (.02)
MD Wray et al. (2018) 59,851 113,154 173,005 156,582 .08 (.01)
OCD Arnold et al. (2018) 2,688 7,037 9,725 7,780 .40 (.06)
SCZ Ripke et al. (2014) 33,640 43,456 77,096 75,846 .26 (.02)
TS Yu et al. (2019) 4,819 9,488 14,307 12,783 .41 (.05)
AD Walters et al. (2018) 11,569 34,999 46,568 34,780 .10 (.02)
CUD Demontis et al. (2019a) 2,387 48,985 51,372 9,104 .16 (.06)
ND Hancock et al. (2018) NA* NA* 28,677 28,677 .12 (.02)

ADHD = attention-deficit/hyperactivity disorder; AN = anorexia nervosa; ASD = autism spectrum disorder; BIP = bipolar disorder; MD = major depression; OCD =
obsessive-compulsive disorder; SCZ = schizophrenia; TS = Tourette syndrome; AD = alcohol dependence; CUD = cannabis use disorder; ND = nicotine dependence.
NA: Not applicable because nicotine dependence was not analyzed with a dichotomous, but an ordinal, variable.

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A. Abdellaoui et al. Drug and Alcohol Dependence 220 (2021) 108535

Fig. 1. Genetic relationships between eleven psychiatric disorders.


A. SNP-based genetic correlations (rg) between 11 psychiatric disorders (including 3 substance use disorders) using LD-Score regression. The size of the circles
represents the significance of the p-values, whereas the color represents the magnitude of the genetic correlation (darker = stronger). Asterisks indicate statistical
significance after Bonferroni correction for multiple testing (.05/55 = .0009).
B. Graphical representation of the SNP-based genetic correlations between 11 psychiatric disorders. Each vertex (node) represents a disorder. Edge strength was set to
the value of the genetic correlation between the traits. Only edges representing significant genetic correlations after Bonferroni correction are shown. The width and
coloring of the edges represent the strength of the genetic correlation (absolute values of rg). Positive genetic correlations are presented in blue, negative correlations
in orange.
C. Results of the genetic factor analysis. Each latent genetic factor represents shared genetic variance across the psychiatric disorders that load on it. One-headed
arrows connecting the latent genetic factors to the individual disorders represent standardized loadings, which can be interpreted as coefficients from a regres­
sion of the true genetic liability for the disorder on the common factor. Two-headed arrows between the three latent factors represent their correlations. Two-headed
arrows below the individual psychiatric disorders represent residual genetic variance not explained by the latent factor(s). Standardized parameter estimates are
shown with their standard errors in parentheses. In red we show qualitative changes between the results of our genetic factor analyses with 11 psychiatric disorders
and those of the original analysis by Lee et al. (2019) including eight disorders.

significant SNP-based genetic correlations as determined in LD-score substantial differences, with the same good model fit (CFI = 0.97, SRMR
regression. Similar to the plot by Lee et al. (2019), major depression = 0.08) and roughly identical path loadings. Adding the substance use
takes a central place in the graph with many strong genetic correlations disorders also yielded a good CFI fit index (0.95), and reasonable SRMR
with other traits, now also including alcohol and nicotine dependence. (0.10). The three correlated latent factors together explained 51% of the
ADHD also takes in a central place, with additional significant and genetic variation in the 11 psychiatric disorders. Fig. 1C shows the re­
strong genetic correlations with all three substance use disorders. The sults of the CFA as obtained from Genomic SEM, including paths with
central positions of major depression and ADHD were reflected in the loadings ≥0.20 in the EFA. Qualitative changes when compared to the
fact that they showed the highest eigenvector centrality scores (0.47 and original model by Lee et al. are shown in red. The factor loadings largely
0.40, respectively). remained the same, however, some notable changes appeared compared
to the previous analysis. Similar to the results by Lee et al. (2019), Factor
3.2. Factor analysis 1 consists primarily of disorders characterized by compulsive/­
perfectionistic behaviors (AN, OCD, and TS), but - in contrast to their
To verify whether our approach matched that reported before, we results - we now also find a significant and substantial loading of MD.
replicated the EFA for eight disorders from Lee et al. (2019) without Our second factor is characterized by psychotic disorders (BIP and SCZ)

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A. Abdellaoui et al. Drug and Alcohol Dependence 220 (2021) 108535

and alcohol dependence (with a weak loading), whereas the loading of significant negative correlation between Factor 1 and 3; in the original
major depression is no longer significant. Our third factor is character­ model by Lee et al. these factors were also negatively correlated, but the
ized by a large number of disorders, including MD, ADHD, ASD, and TS, correlation did not reach significance. This initial negative correlation
and all three substance use disorders. We now found a significant was strengthened by adding substance use traits, all of which showed
negative correlation between Factors 1 and 3. negative correlations with OCD, and to a lesser degree with AN.
Adding a fourth factor did not converge. To aid convergence, we Accordingly, the addition of the substance use disorders to the genetic
forced the removal of additional path loadings by increasing the factor analysis consolidated and strengthened the results and suggests
threshold from 0.20 to 0.35, which forced a single loading for each that liability to OCD and AN may be protective for the ADHD/substance
disorder. This model converged but yielded a poor fit (CFI < 0; RMSR > use factor. Certain characteristic features of OCD and AN (perfectionism,
1), suggesting that a four-factor model is not adequate. inhibition, high educational attainment) may underlie these protective
effects (Frost and Steketee, 1997; Pollack and Forbush, 2013; Yilmaz
3.3. Sensitivity analyses et al., 2020; Zucker et al. (2011).
While Lee et al. referred to their third factor as consisting mainly of
As a sensitivity analysis we also performed the genetic factor analysis early-onset neurodevelopmental disorders (ASD, ADHD, TS), the new
with each substance use disorder added separately to the model with the factor 3 is more heterogeneous. It includes four externalizing disorders
eight Lee et al. disorders. Model fit indices can be found in Supple­ (ADHD, AD, ND, CUD) as well as one internalizing disorder (MD) and
mentary Table 3 and Supplementary Fig. 1 shows the results of the CFA other less clearly positioned disorders (ASD and TS). Major depression is
as obtained from Genomic SEM. The addition of alcohol dependence led a very common mental health disorder and associated with the broad
to similar changes to what we found when adding all three-substance range of psychiatric problems, so its contribution to multiple factors,
use disorders, i.e., MD now loaded on Factor 1 and not on Factor 2, including this factor, is not particularly surprising. Note that sensitivity
alcohol dependence loaded on factors 2 and 3, and there was a signifi­ analyses pointed out that changes in the model were due to the addition
cant negative correlation between factors 1 and 3. Adding nicotine of alcohol dependence; adding nicotine dependence or cannabis use
dependence or cannabis use disorder did not lead to any notable changes disorder solely did not result in any changes.
to genetic factor structure compared to the Lee et al. model. The switch of major depression contributing significantly to Factor 2
We also repeated the main analyses using the Lee et al. data plus data in Lee et al.’s factor model and to Factor 1 in our model highlights the
from three GWASs for non-clinical substance use traits: alcoholic drinks sensitivity of such models to the input data. Aside from the additional
per week, cigarettes smoked per day, and lifetime cannabis use. Bivar­ input data for substance use traits, the input data for major depression in
iate correlations and the results of the CFA are presented in Supple­ our model was a subset of the data used by Lee et al. (i.e., their meta-
mentary Figure 2 and model fit indices can be found in Supplementary analytic sample without 23andMe data), which could also explain
Table 3. Significant positive genetic correlations are found between some of the differences in the model. This instability was further high­
substance use traits and schizophrenia, major depression, bipolar dis­ lighted when non-clinical substance use traits were added to the Lee
order, ADHD, and Autism Spectrum Disorder, but not Tourette Syn­ et al. model, resulting in different changes in underlying factor structure.
drome, anorexia nervosa, and OCD. Notable changes to the factor Accordingly, updating source data (when larger GWASs come out) and
structure compared to that of Lee et al. where: TS now no longer adding additional disorders will likely result in additional changes or
significantly loads on F1, cigarettes per day loads on F3, and lifetime refinements in the underlying genetic factor structure. Larger GWASs
cannabis use on F2. Markedly, alcohol drinks per week did not signifi­ will result in more power to detect significant genetic associations,
cantly load on any factor. changing the genetic correlation matrix and the genetic relationship
graph. For example, the cannabis use disorder GWAS has substantial
4. Discussion genetic correlations with some other traits (Supplementary Table 1), but
these were not significant likely due to the limited sample size of the
We extended analyses of a recent study investigating the genetic GWAS. Furthermore, it is likely that including GWAS data on other
associations and underlying genetic factor structure among eight psy­ diagnostic data, such as personality disorders, sleep-wake disorders,
chiatric disorders, by including three substance use disorders. We show panic disorders, sexual dysfunction, neurological disorders, as well as
that alcohol and nicotine dependence are significantly genetically non-clinical continuous/dimensional data for substance use traits and
correlated with several of the other mental health disorders, including mental health problems, would lead to further changes in the underlying
ADHD, schizophrenia, and major depression. Cannabis use disorder is structure. For some of these, and other, psychiatric disorders there are
only significantly associated with ADHD, but this may be due in part to currently no well-powered GWASs available focused on clinical diag­
the limited power of the cannabis use disorder GWAS. The considerable nostic information. Once these are available, a more comprehensive and
shared genetic influences of alcohol and nicotine dependence with accurate underlying structure could be identified that may indeed have
psychiatric disease may help explain why their co-occurrence in the important implications for psychiatric nosology. For example, the
form of dual disorders is significantly higher than would be expected by identified genetic associations and underlying structure may change the
chance (Szerman and Martinez-Raga, 2015). focus from the distinct clinical diagnoses currently presented in most
The addition of the substance use disorders to the genetic factor diagnostic manuals to more genetically and biologically-informed fluid
analysis provides additional information on the psychiatric three-factor disease presentations, with more attention for trans-diagnostic symp­
genetic structure identified by Lee et al. (2019). Factor 1 (AN, OCD, TS, tomatology and underlying pathways. By further increasing the sample
and MD) and 2 (BIP, SCZ, AD) remained quite similar, but MD now loads sizes of GWASs on psychiatric and substance use disorders, we could
on Factor 1, whereas in the original model MD loaded on Factor 2 potentially identify more stable underlying factors, which could aid in
(although MD still contributes to Factor 2 through the inter-factor cor­ the detection of novel pleiotropic loci, further elucidate biological
relations). In addition, alcohol dependence now also significantly con­ mechanisms that underlie comorbidity, improve traditional nosological
tributes to Factor 2. Factor 3 is characterized by its large number of delineations of psychiatric and substance use disorders, and potentially
disorders, including all the disorders identified in the original structure help explain the high incidence of dual disorders. Until then, given the
(TS, MD, ADHD, ASD) plus all three substance use disorders. A instability of the underlying genetic structure, the identified structure by
four-factor model did not fit the data well, suggesting that substance use Lee et al. and those identified in the current study, as well as the inferred
disorders do not form a latent factor separate from the previously implications for psychiatric nosology, should be interpreted with
identified factors or that substance use disorders together with ADHD caution.
form a simple externalizing genetic factor. Lastly, we now observe a In conclusion, our study illustrated that alcohol and nicotine

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A. Abdellaoui et al. Drug and Alcohol Dependence 220 (2021) 108535

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Declaration of Competing Interest overlap with psychiatric traits, and a causal influence of schizophrenia. Nat.
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