Journal of Human Genetics

https://doi.org/10.1038/s10038-020-0791-1

ARTICLE

Study of genetic correlation between children’s sleep and obesity

Hao Mei1 Fan Jiang2 Lianna Li3 Michael Griswold4 Shijian Liu2 Thomas Mosley4,5
● ● ● ● ●

Received: 9 October 2019 / Revised: 3 June 2020 / Accepted: 3 June 2020

© The Author(s), under exclusive licence to The Japan Society of Human Genetics 2020

Abstract
Laboratory and epidemiological studies have shown that short sleep time is associated with obesity. In this study, we
conducted a post-GWAS analysis to test genetic correlation between children’s sleep and obesity due to linkage
disequilibrium (LD) SNPs, shared genes and pathways. Our analysis showed that genetic heritability was 0.14 (p-value =
0.0005) and 0.41 (p-value = 1.18E−24) for children’s sleep and obesity, respectively, but genetic correlation due to LD
SNPs was insignificant. Gene associations at children’s GWAS were measured based on SNP associations and ranked by
their uniform score (U-score). After adjusting for gene size, measured as the number of independent SNPs, children’s sleep
and obesity GWAS had significant gene correlation (r = 0.23). Pathway enrichment analysis showed that “Suz12 target
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genes” was the significant pathway for both children’s sleep and obesity; pathways were significantly shared among top
enriched pathways with an OR of 8.1–59.4; and significant correlation coefficient of pathway U-score was r = 0.36.
Analysis of sleep time and obesity GWAS variants for all ages in the NHGRI-EBI GWAS Catalog also presented significant
pathway correlation (r = 0.30). The “PAX3-FOXO1 target genes” was the significant pathway for all-age obesity phenotype
and ranked as the second top associated pathway for all-age sleep time. Our study suggested that genetic correlation of
children’s sleep time and obesity is attributed to genes with pleiotropy effects and common pathway regulations that may
contain only weak SNP associations.

Introduction prevalence of obesity has increased strikingly in recent

Obesity is a multifactorial condition, identified as a dele-
terious factor associated with a range of diseases, including
cardiovascular diseases, diabetes and cancers [1]. The
Supplementary information The online version of this article (https://
doi.org/10.1038/s10038-020-0791-1) contains supplementary
material, which is available to authorized users.
* Hao Mei
hmei@umc.edu
* Shijian Liu
liushijian@scmc.com.cn
1
Department of Data Science, School of Population Health,
University of Mississippi Medical Center, Jackson, MS, USA
2
Shanghai Children’s Medical Center, Shanghai Jiao Tong
University School of Medicine, Shanghai, China
3
Department of Biology, Tougaloo College, Jackson, MS, USA
4
Department of Medicine, The MIND Center, University of
Mississippi Medical Center, Jackson, MS, USA
5
Department of Neurology, University of Mississippi Medical
Center, Jackson, MS, USA
decades among children and adults and has become a major
global public health concern because it leads to an increased
likelihood of obesity-related complications and decreased
life expectancy [2]. Obesity in childhood has been shown to
be associated with increased overall mortality in later life
[3]. Thus, reducing the prevalence of overweight and obe-
sity in early childhood has major public health significance.
Obesity is influenced by lifestyle and environment. As a
modifiable lifestyle factor, sleep curtailment has been
shown in both laboratory and epidemiology studies to be
associated with increased obesity risk for both children and
adults [4, 5]. Sleep characteristics are also associated with a
variety of obesity risk factors, including leptin, ghrelin,
appetite, fatigue and physical activity [4, 6], suggesting that
associations between sleep and obesity may be mediated
through pathway regulation of these factors, leading to
increased risk of obesity. Studies have also shown that the
association of sleep characteristics with obesity is stronger
in children than in adults, and declines further with aging
[5]. Both sleep disruption and obesity in childhood have
long-term effects on health in later life [7, 8]. Genetic
investigation of associations between children’s sleep and
obesity may lead to discovery of underlying causes and

contribute to the establishment of effective preventive
strategies in early life.
Both obesity and sleep duration are influenced by genetic
factors. Longitudinal studies in twins have shown genetic
effects on obesity over 43 years of adult life [9]. This study
indicated that genetic influences explain up to 90% of the
variance in body mass index (BMI) among twins [10].
There are also significant findings regarding the heritability
of sleep duration in both children and adults and heritability
may decrease with age, which was estimated to be up to
40% for adults and over 50% for children [11, 12]. Genetic
effects on obesity are influenced by sleep, and effects tend
to decrease as sleep duration increases. The heritability of
BMI was 70% among individuals sleeping fewer than 7 h
per night, and the heritability was 32% among individuals
with a nightly sleep duration over 9 h [12]. These studies
indicate that genetic components play an important role in
associations between sleep duration and the development of
obesity.
Genome-wide association studies (GWAS) in the past
decade have been conducted to discover genetic risk var-
iants associated with obesity and sleep time separately.
These findings are helpful in understanding the effects of
single genetic variants, but they are not sufficient to extra-
polate genetic regulation mechanisms underlying associa-
tions between sleep duration and obesity. Many of the risk
variants in GWAS are outside of gene boundaries, and due
to stringent significance criteria and weak effects of single
variants, gene variants that influence both sleep and obesity
are potentially overlooked for identification. Furthermore, a
gene effect may arise from different single nucleotide
polymorphisms (SNPs), and the same pathway may be
activated by different genes. All of these challenges make it
difficult to interpret underlying complex genetic compo-
nents from single GWAS variants. Compared to adults,
children’s obesity and sleep characteristics are potentially
influenced more by genetic components [11]. In this study,
we conducted a post-GWAS analysis of children’s sleep
and obesity and investigated their genetic correlation arising
from linkage disequilibrium (LD) SNPs, shared gene and
pathway components.
Materials and methods
GWAS of children’s obesity and sleep duration
The GWAS of children’s obesity was performed through a
collaborative meta-analysis of 14 studies in North America,
Australia and Europe, consisting of 5530 cases and 8318
controls with Caucasian ancestry [13]. BMI was mainly
measured in childhood at an age of 2–18 years except for
one study that collected data from children who were <2
H. Mei et al.
years old. Male and female BMI percentiles for age in
children were calculated based on national standard growth
curves, and obesity cases and controls were respectively
defined as ≥95th and <50th percentile of BMI for age.
Genotypes were collected from high-density SNP arrays
and imputed from HapMap CEU reference panels. Obesity
status was regressed against genotyped and imputed var-
iants that have minor allele frequencies ≥0.01 and imputed
R2 ≥ 0.3, assuming an additive model, to test associations
with every SNP via logistic regression analysis. Findings of
genetic risk variants were examined for replication in nine
independent and phenotypically comparable cohorts. Fixed-
effects meta-analysis of every SNP’s effect weighted by
inverse variance was conducted for every SNP association.
Complete GWAS results can be accessed from the genome-
wide repository of associations between SNPs and pheno-
types (GRASP) [14].
The GWAS of children’s sleep time was conducted
within the framework of the EArly Genetics and Lifecourse
Epidemiology (EAGLE) Consortium [11]. The study com-
prises 10,554 children of European ancestry from five
population-based cohorts for discovery analysis, and 1250
children from two independent cohorts for replication ana-
lysis. All children were between 2 and 14 years of age.
Sleep duration was ascertained from parents’ answers to the
question, “How many hours does your child sleep per day,
including naps?” or calculated from the usual bed and rise
times during school days. Genetic variants were genotyped
through high-density SNP arrays using the Illumina or
Affymetrix platform, and imputed to the 1000 GENOME
reference panel, yielding up to 8 million SNPs in each
cohort for analysis. Sleep duration in hours was regressed
against every variant’s genotype, assuming an additive
model, or imputed using allele dosage with adjustments for
age, sex and principal components. BMI was excluded from
the model; thus, common SNPs associated with BMI and
sleep were potentially included in identification. A fixed-
effect inverse variance weighted meta-analysis was per-
formed to report the association of every SNP with
sleep duration over all studies (results are accessible via
GRASP [14]).
The NHGRI-EBI GWAS Catalog is a manually curated
resource which is publicly available to provide results of
single-variant associations from eligible published GWAS
studies going back to 2005 [15]. In the catalog, all GWAS
traits are mapped to standard ontology terms, defined as
“mapped traits”, enabling structured queries of specific trait
associations. We accessed the catalog and searched mapped
traits of ontology terms that included “obesity” and “sleep
time” or “sleep duration”. SNP associations with obesity and
sleep characteristics for all ages that had p-values ≤ 10−5
were retrieved from the catalog to facilitate analysis of
common genetic components between sleep and obesity.
Study of genetic correlation between children’s sleep and obesity
Genetic heritability and correlation analysis
GWAS common SNPs that do not reach genome-wide
significance may contribute to genetic heritability for
common traits which is distributed over thousands of SNPs
with small effects [16]. Variants that are in LD tend to have
elevated test statistics in GWAS, and expected χ2-statistic of
variant j is linearly associated with the variant LD score
which measures total genetic variation tagged by variant j
[17]. The LD score of GWAS SNP was computed using
1000 Genomes Project data and EUR reference panel.
The linear regression model of variant j is: E(χ2 | ℓj) = Nh2ℓj/
M + α, where χ2 is the chi-square association statistic; α is
regression intercept; ℓj is the LD score of variant j; N is the
sample size; M is the number of SNPs; and h2/M is the
average heritability per SNP. LD score regression (LDSR)
analysis was applied to estimate genetic heritability of
children’s sleep and obesity separately using all GWAS
SNPs, rather than just genome-wide significant variants.
Lambda GC is estimated as median of χ2 statistics divided
by 0.455, measuring genomic inflation due to population
stratification and cryptic relatedness [18].
Genetic variants that have pleiotropy effects on diverse
phenotypes can lead to genetic correlation among them
[19]. In this study, LDSR was also applied to estimate
genetic correlation between children’s sleep time and obe-
sity using all GWAS SNPs, including variants that do not
reach genome-wide significance [16]. If a variant j has
pleiotropic effects on two phenotypes, the SNP’s LD score
has linear association with production of Z statistics. The

 pffiffiffiffiffiffiffiffiffiffiffi
N1 N 2 ρ g
regression model is: E Z1j Z2j ¼ M ιj þ pρN ffiffiffiffiffiffiffi
N N
s ffi
, where
1 2
Z1j and Z2j are Z statistics and N1 and N2 are sample sizes for
children’s sleep and obesity GWAS, respectively; ρg is the
genetic correlation; ρ is the phenotypic correlation; Ns is the
overlapping sample size; and ιj is the LD score for variant j.
Both heritability and genetic correlation were estimated
using LDSC software package (github.com/bulik/ldsc).
Measure of gene association and correlation
We employed the R package snpGeneSets [20] to map
SNPs to genes with boundaries from 2 kilobase pairs (kbp)
upstream to 2 kbp downstream of transcripts. Positions of
the SNPs and genes were determined via the dbSNP [21]
and Gene [22] databases, respectively, referencing the Build
37 genome. Within each gene, pairwise SNP correlation
coefficients (r2), based on the European reference data from
the 1000 Genomes project, were calculated using VCFtools
[23]. Independent SNPs were selected through an iterative
process; at each step, we selected the SNP with the strongest
association and removed SNPs correlated to it (r2 > 0.2). For
K independent SNPs mapped to a gene with GWAS
p-values (p1, p2,…pk), the best p-value (minP), defined as
minP = p(1), was used to measure gene association in
GWAS [24].
Gene measures were transformed to uniform scores
(U-score) [24]. The uniform score of the ith gene is calcu-
P P
lated as, Ui ¼ ð j IðMj <Mi Þ þ 0:5  j IðMj ¼ Mi ÞÞ=L,
where L was the total number of mapped genes in the
GWAS and Mi was the minP. The Ui estimates the per-
centage of genes with stronger associations than the ith gene
in the genome. Two regression models were applied to
estimate gene correlation between children’s sleep and
obesity GWAS. The first model regressed gene U-score of
children’s obesity on gene U-score of children’s sleep
without adjustment for gene size, while the second model
added the adjustment for gene sizes in children’s obesity
GWAS, measured as the number of independent SNPs.
Regression analyses were conducted using the R function of
lm and plots were produced with the R package of ggplot2.
For identified genes from the GWAS catalog, the Fisher’s
exact test was conducted using the Bioconductor package
“GeneOverlap” [25] to examine whether children’s obesity
and sleep significantly shared associated genes.
Pathway enrichment analysis and correlation test
The Molecular Signatures Database (MSigDB) is a knowl-
edge base that contains curated gene sets from online path-
way databases, publications in PubMed, and knowledge of
domain experts [26]. Pathway enrichment analyses were
performed to test enrichment of curated gene set for SNP
associations at children’s sleep and obesity GWAS. For
pathway enrichment analysis of GWAS [20, 24], enrichment
effect was estimated as K=S  l=L with a standard error (SE)
pffiffiffi
of ðl=LÞ  ð1  l=LÞ= S, where L is the number of genes
mapped from GWAS SNPs with l top associated genes, and
S is the number of genes in a tested pathway with K top
associated genes. The pathway enrichment p-value was
    
PK S LS L
computed as pe ¼ 1  i¼0 = , based
i li l
on hypergeometric distribution. To adjust for multiple test-
ing, 1000 permutations, which used the number of inde-
pendent SNPs inside gene as adjusted gene length, were
conducted to generate null distribution of top associated
genes and pathway enrichment, and compute permutation p-
value [27]. For obesity and sleep genes that were identified
from the NHGRI-EBI GWAS Catalog, pathway enrichment
effect, SE, and p-value were computed as above, where L is
the number of MSigDB genes with l candidate genes, and S
is the number of genes in a tested pathway with K candidate
genes. Significance of the p-value was assessed by
 H. Mei et al.

Table 1 Summary of children’s obesity and sleep GWAS

Child Child Sleep GWAS Obesity GWAS
sleep GWAS obesity GWAS catalog catalog

Total SNPs 8,525,134 2,442,738 121 127

SNP MAF >0.01 >0.01 [0.01, 0.48] [0.02, 0.49]
% SNPs (MAF < 0.05) 23.35 NA 21.05 6.06
SNP p-value >2.27E−08 >1.16E−13 [2e–23, 9e−06] [5e−110, 9e−06]
Total SNPs (p-value < 5E−08) 2 229 7 78
Total SNPs (p-value < 1E−05) 190 442 121 127
5th percentile SNP p-value 0.04963 4.65E−02 NA NA
Total mapped genes 36,511 34,093 64 63
Total gene SNPs 4,125,229 1,209,264 67 71
Gene SNP p-value >2.27e−08 >1.16E−13 [2e–23, 9e−06] [5e−110, 6e−06]
Total genes (minimum SNP p-value < 5E−08) 1 9 5 34
Total gene SNPs (p-value < 5E−08) 2 114 6 43
Total genes (minimum SNP
p-value < 1E−05) 25 22 64 63
Total gene SNPs (p-value < 1E−05) 115 207 67 71

permutation test. Pathway enrichment analyses were con-
ducted using the R package of “snpGeneSets” [20].
Pathway U-score was computed as above to estimate the
percentage of pathways with stronger enrichment effect
than the tested pathway. Pearson correlation analyses of
MSigDB pathway U-scores were conducted to test for
genetic correlation between obesity and sleep duration. An
overlapping analysis was performed to test whether chil-
dren’s obesity and sleep duration significantly shared
pathways, based on Fisher’s exact test using the Bio-
conductor package “GeneOverlap” [25] as above.
Results
GWAS SNP associations
SNPs and mapped genes for children’s sleep and obesity
GWAS are summarized in Table 1. In GWAS of children’s
sleep, all genotyped SNPs had minor allele frequency
(MAF) ≥ 0.01, and 23.35% of SNPs had MAF < 0.05. Two
SNPs had p-values ≤ 5 × 10−8 and 190 SNPs had p-values ≤
10−5. Mapping analysis revealed that 48.3% of SNPs were
mapped to 36,511 genes with the smallest p-value of 2.27 ×
10−8. There were 2 and 115 gene SNPs that had p-values ≤
5 × 10−8 and ≤10−5, respectively. In GWAS of children’s
obesity, 2,442,738 qualified SNPs with MAF ≥ 0.01 were
analyzed for associations. The GWAS analysis identified
229 SNPs with p-values ≤ 5 × 10−8 and 442 SNPs with p-
values ≤ 10−5. Gene mapping analysis revealed that 49.5%
of SNPs belonged to 34,093 genes, and 114 and 207 gene
SNPs had p-values ≤ 5 × 10−8 and ≤10−5, respectively.
There were many more gene SNPs reaching genome-wide
significance (p-values ≤ 5 × 10−8) in the children’s obesity
GWAS than in the children’s sleep GWAS. SNPs mapped
to multiple genes were summarized in the Supplementary
Table S1: 70,162 SNPs (1.70% of total gene SNPs) in the
children’s sleep GWAS were mapped to multiple genes,
with 91.2% of them (63,990 SNPs) mapped to 2 genes each,
and 24,643 SNPs (2.04% of total gene SNPs) in the chil-
dren’s obesity GWAS were mapped to multiple genes, with
91.3% of them (22,488 SNPs) mapped to 2 genes each.
We manually reviewed the search against the GWAS
Catalog and filtered results to exclude irrelevant SNP
associations with obesity and sleep time and duration.
Characteristics of associated SNPs and mapped genes are
summarized in Table 1. The search identified 121 sleep-
associated SNPs, and 21.05% of SNPs had MAF < 0.05.
There were 7 SNPs (5.79%) reaching genome-wide sig-
nificance (p-values ≤ 5 × 10−8). Mapping analysis showed
that 67 SNPs belonged to 64 genes, and 6 gene SNPs had p-
values ≤ 5 × 10−8. We also extended search to other sleep-
related traits. Detailed information regarding sleep-
associated SNPs—including PubMed ID, GWAS mapped
traits, and SNP-mapped genes—is shown in Supplementary
Table S2. A search of the GWAS Catalog identified 127
obesity-associated SNPs. Compared to the sleep GWAS,
only 6.06% of SNPs had MAF < 0.05. There were 61.42%
of SNPs reaching genome-wide significance. Mapping
analysis showed that 71 SNPs belonged to 63 genes and 43
gene SNPs had p-values ≤ 5 × 10−8 (Table 1). Obesity-
associated SNPs are summarized in Supplementary
Table S3. Although fewer obesity–SNP associations were
identified compared to sleep–SNPs, the majority of
Study of genetic correlation between children’s sleep and obesity
associated obesity SNPs were common variants (MAF ≥
0.05), and a much higher fraction of obesity SNPs had p-
values ≤ 5 × 10−8 (61.42% versus 8.18% for sleep). In the
GWAS catalog of sleep, seven SNPs were mapped to
multiple genes with five SNPs of them mapped to two genes
each, and in the GWAS catalog of obesity, 15 SNPs were
mapped to multiple genes with 11 of them mapped to two
genes each (Supplementary Table S1).
Genetic heritability and correlation of children’s
sleep and obesity
Single-trait LDSR of GWAS summary results for children’s
sleep and obesity were shown in Table 2. After merging
with 1000 Genomes Project EUR reference population,
1,172,571 and 1,059,340 SNPs were kept for LDSR ana-
lysis of children’s sleep and obesity GWAS, respectively.
Both GWAS results had lambda GC of 1.01, indicating
well-controlled population stratification in association test.
The intercept was estimated as 0.98 for children’s sleep and
0.92 for children’s obesity. The lower intercept than lambda
GC suggested that polygenicity mainly contributed to
increase in chi-square statistic and there were at most a
small contribution of bias to association test [17]. Genetic
heritability due to GWAS SNPs was 0.14 (SE = 0.04, p-
value = 0.0005) for children’s sleep time and 0.41 (SE =
0.04, p-value = 1.18E−24) for children’s obesity. There
were total 1,056,579 SNPs shared between children’s sleep
and obesity GWAS for correlation analysis (Supplementary
Table S4). Cross-trait LDSR had shown that the genetic
heritability of children’s sleep and obesity was almost the
same as the separate heritability analysis above. The genetic
correlation (ρg) between children’s sleep and obesity was
0.03 which had SE of 0.11 and insignificant p-value > 0.05.
Genetic correlation of associated genes between
sleep and obesity
The only gene with a minimum SNP p-value ≤ 5 × 10−8 was
ARAP1 in the children’s sleep GWAS (Supplementary
Table S5), and 9 genes were found to have SNPs reaching
Table 2 Heritability and genetic correlation of children’s sleep and
obesity
Children’s sleep Children’s obesity
SNPs for LDSC 1,172,571 1,059,340
Lambda GC 1.01 1.01
Intercept 0.98 0.92
h2 estimate 0.14 0.41
h2 SE 0.04 0.04
h2 p-value 0.0005 1.18E−24
Genetic correlation (ρg) = 0.03, SE = 0.11, p-value > 0.05
genome-wide significance in the children’s obesity
GWAS (Supplementary Table S6). GWAS SNPs with p-
values ≤ 10−5 were mapped to 25 genes for children’s sleep
and 22 genes for children’s obesity (Table 1). Genes were
classified into 20 groups based on gene U-scores in the
children’s sleep GWAS using an interval of 0.05, and for
each group, the mean of gene U-scores in the children’s
obesity GWAS (black points) with a range of ±1 SE was
shown in the connected scatterplot (Fig. 1), based on Sup-
plementary Data. The plot indicated that a gene with a
smaller U-score of children’s sleep tended to have smaller
U-score of children’s obesity. Two regression models were
then constructed to further evaluate linear association
between gene U-scores of children’s sleep and obesity
GWAS using the Supplementary Data. Model 1 regressed
gene U-score from children’s obesity GWAS against its
U-score from children’s sleep GWAS without adjustment
for gene size. Gene sizes in children’s sleep and obesity
GWAS, measured as the independent number of SNPs, had
strong correlation (r = 0.96). So, model 2 added adjustment
for gene size, using only estimates from the children’s
obesity GWAS, to model 1 for testing gene U-score asso-
ciation between two GWAS. Line plots of fitted values for
model 1 and mode 2 with a range of ±1 SE were presented
in Fig. 1. Table 3 summarized regression results of gene
correlation for both models. Without adjustment for gene
size, the Pearson correlation was estimated as 0.32 with
95% confidence interval (CI) of [0.31, 0.33] and t statistic of
62.49 (p-value < 2.2 × 10−16). After adjusting for gene size,
Pearson correlation was 0.23 with 95% CI of [0.22, 0.24]
and t statistic of 44.06 (p-value < 2.2 × 10−16).
All SNPs in the GWAS catalog were mapped to 12,182
genes, and sleep time and obesity associated SNPs were
mapped to 64 and 63 genes, respectively (Table 1). The
LINC01122 (long intergenic non-protein coding RNA
1122) was the only gene shared in common. After
expanding search to all sleep-related traits, associated SNPs
were mapped to 175 genes, and two additional genes of
FBN2 (fibrillin 2) and RGS6 (regulator of G protein sig-
naling 6) associated with sleep quality were found in
sharing (Supplementary Tables S2 and S3). Descriptions
of the common genes are shown in Supplementary
Table S7. Fisher’s exact test revealed that the OR was
3.10 (p-value = 0.28) for gene sharing between sleep
duration and obesity, and was 3.49 (p-value = 0.063) for
sleep-related traits and obesity (Table 3).
Genetic correlation of pathway enrichment between
sleep and obesity
Every curated gene set of MSigDB was analyzed for
enrichment of top 5% of associated genes in the children’s
sleep and obesity GWAS separately, and complete

Fig. 1 Gene U-scores in the children’s sleep and obesity GWAS. The
connected scatterplot with error bar shows mean ± 1 standard error
(SE) of gene U-scores in the children’s obesity for every gene group.
The X-axis for the scatterplot shows the gene groups of U-scores with
an interval of 0.05 based on the children’s sleep GWAS, and the Y-axis
represents gene U-scores from the children’s obesity GWAS. The
regression line of “No size adjustment” with shaded region is the fitted
results are shown in Supplementary Table S8. The enrich-
ment analysis identified three significant pathways of chil-
dren’s sleep, and one significant pathways of children’s
obesity, after adjusting for multiple testing (Table 4). The
common significant pathway was ‘Suz12 target genes’
(PID: 4447; sleep enrichment effect = 4.89%, SE = 0.71%,
U-score = 0.01%; obesity enrichment effect = 4.39%,
SE = 0.72% and U-score = 0.01%). Additional two sig-
nificant pathways for children’s sleep were KEGG
arrhythmogenic right ventricular cardiomyopathy (ARVC)
(PID: 1447; enrichment effect = 20.00%, SE = 2.57%,
H. Mei et al.
gene U-score of children’s obesity (Y-axis) with a range of ±1 SE
against gene U-score of children’s sleep (X-axis), obtained from model
1 without adjustment for gene size, while the regression line of “Size
adjustment” with shaded region is the fitted gene U-score of children’s
obesity with a range of ±1 SE, obtained from regression model 2 with
adjustment for gene size, estimated as the number of independent
SNPs in children’s obesity GWAS
U-score = 0.03%) and PAX3-FOXO1 target genes
(PID: 17784; enrichment effect = 4.13%, SE = 0.71%, U-
score = 0.05%).
Pathway overlapping analysis was conducted separately at
the top 1, 2, 5, and 10 percentile of enriched pathways to
examine genetic sharing between children’s sleep and obe-
sity. The results revealed that the odds of a sleep top-enriched
pathway also being an obesity top-enriched pathways were
8.1–59.4 times of odds for a random pathway being an
obesity top-enriched pathway, which all had strongly sig-
nificant p-value, and pathway was more likely shared among
Study of genetic correlation between children’s sleep and obesity

Table 3 Gene correlation

Children’s GWAS: regression analysis of obesity gene U-score
analysis between sleep and
obesity Beta SE t p-value

Model 1 a
Sleep gene U-score 0.32 0.005 62.49 <2E−16
Model 2a Sleep gene U-score 0.23 0.005 44.06 <2E−16
Obesity gene size −0.007 0.0001 −50.86 <2E−16

GWAS Catalog: shared gene testb

Sleep-associated Obesity-associated Common genes OR p-value
genes genes

Sleep time and 64 63 1 3.10 0.28

duration
All sleep traits 175 63 3 3.49 0.06
a
Model 1 is the regression of obesity gene U-score against sleep gene U-score without adjustment for gene
sizes. Model 2 is the model 1 with adjustment for obesity gene sizes
b
The GWAS Catalog has total 12,122 genes for sharing test between sleep and obesity

Table 4 Significant pathways of sleep and obesity

MSigDB pathways PID Genes Phenotype Effect (%) SE (%) p-value U-score (%)

Suz12 target genes 4447 1038 Children’s sleep time 4.89 0.71 1.53E−10 0.01
Children’s obesity 4.39 0.72 8.99E−09 0.01
KEGG arrhythmogenic right ventricular cardiomyopathy 1447 76 Children’s sleep time 20 2.57 1.06E−08 0.03
PAX3-FOXO1 target genes 17,784 975 Children’s sleep time 4.13 0.71 3.40E−08 0.05
All-age sleep timea 0.68 0.16 4.97E−04 0.03
All-age obesity 0.96 0.17 1.11E−05 0.01
a
Down-regulated PAX3-FOXO1 target genes 17,786 428 All-age sleep time 0.93 0.24 3.67E−03 0.39
Down-regulated FGFR1 target genes 6695 308 All-age sleep timea 1.38 0.28 8.72E−04 0.09
a
These pathways did not reach significance after permutation adjustment, but they were significant for all sleep-related traits in the GWAS catalog

higher enriched pathways (Table 5). Among the top 1% of

Table 5 Analysis of shared pathways between sleep and obesity
enriched pathways, there were 14 common pathways
between children’s sleep and obesity GWAS (Supplementary Children’s GWAS
Table S8). Common genes were shared among top pathways. Top Top Common Total OR p-value
Three pathways of ‘Suz12 target genes’ (PID: 4447), ‘Tri- percentile pathways top pathways
methylated H3K27' (PID: 4449) and “EED target genes“ pathways
(PID: 4448) include “PRC2 target genes“ (PID: 4450). 1 47 14 4734 59.4 2.9E−18
However, only the pathway of ‘Suz12 target genes’ (PID: 2 95 27 4734 26.6 3.9E−25
4450) reached significance for both GWAS. A Box plot of 5 237 75 4734 12.4 3.1E−43
pathway U-scores depicted linear correlation between chil- 10 473 178 4734 8.1 4.5E−68
dren’s sleep and obesity shown in Fig. 2. The pathway group
with U-scores < 0.05 in the children’s sleep GWAS also had
the smallest average pathway U-score in the children’s obe- significant pathway associated with obesity after permuta-
sity GWAS, and there is a linear association trend between tion adjustment. This pathway was ranked as the second top
children’s sleep and obesity pathway U-scores. Linear cor- association with sleep time, but no pathway reached sig-
relation analysis identified a correlation coefficient of r = nificance after adjustment (Supplementary Table S9). Cor-
0.36 with a 95% CI of [0.33, 0.38], and the t statistic was relation analysis of pathway U-score showed that sleep time
26.45 with a significant p-value < 2.2 × 10−16. and duration had a strongly significant correlation with
Pathway enrichment results of sleep time and obesity in obesity (r = 0.30 and p-value < 2.2 × 10−16). After we
the GWAS catalog are summarized in Table 4. The “PAX3- extended our enrichment analysis to all sleep-related traits
FOXO1 target genes” (pid: 17784) was identified as the in the catalog, besides the “PAX3-FOXO1 target genes”,

Fig. 2 Box plot of pathway U-scores in the children’s sleep and
obesity GWAS. The X-axis shows ranges of sleep pathway U-scores.
The Y-axis shows the minimum, first quartile, median, third quartile,
and maximum of obesity pathway U-scores for each group of pathway
another two pathways of “Down-regulated PAX3-FOXO1
target genes” (pid: 17786) and “Down-regulated FGFR1
target genes” (pid: 6695) were also significantly identified
(Supplementary Table S10). All three gene sets ranked as
top-associated pathways for sleep time in the catalog with
U-score < 0.01.
Discussion
Obesity development and sleep characteristics are both
influenced by genetic factors. Epidemiology studies have
found that short sleep duration is a risk factor of obesity.
However, genetic mechanisms underlying the sleep and
obesity association remain unclear. In this study, we
H. Mei et al.
U-scores in the children’s sleep GWAS. The box plot suggests a linear
trend of correlation between children’s sleep and obesity pathway.
Genetic correlation of children’s sleep and obesity pathway U-scores:
r = 0.36, 95% CI = [0.33, 0.38], t = 26.45, and p-value < 2.2 × 10−16
analyzed children’s sleep and obesity GWAS to examine
their genetic correlation of genes and pathways, based on
GWAS SNP associations. We also analyzed risk SNPs of
sleep and obesity published in the NHGRI-EBI GWAS
Catalog and confirmed genetic correlations between sleep
and obesity for all ages.
We first examined genetic heritability of children’s sleep
(h2 = 0.14) and obesity (h2 = 0.41). The heritability esti-
mates were much smaller than published heritability by twin
study that was up to 0.90 for obesity [10] and over 0.50 for
sleep duration [12]. This big difference suggested that sin-
gle common SNPs contribute to only a small part of genetic
heritability of children’s sleep and obesity, and majority of
genetic heritability is likely attributed to non-common var-
iants and non-additive genetic effects. We tested genetic
Study of genetic correlation between children’s sleep and obesity
correlation due to pleiotropic effects from the same SNPs by
LDSR, but the correlation did not reach significance, indi-
cating genetic pleiotropy due to GWAS SNPs is not the
major contribution to genetic correlation. Our study next
examined genetic correlation due to pleiotropic effects from
the same genes and pathways that may involve different sets
of GWAS SNP associations with weak effects for children’s
sleep and obesity.
The only gene with significant SNP associations in the
children’s sleep GWAS (p-value ≤ 5 × 10−8) was ARAP1.
The gene is known to encode protein associated with the
Golgi apparatus and apoptosis. It remains unclear how
ARAP1 affects sleep. Although the gene was not among the
nine genes that contained significant SNP associations in
the children’s obesity GWAS, text mining of disease–gene
association showed that ARAP1 was involved in type 2
diabetes and metabolic traits [28, 29]. Because genetic
heritability of complex traits mainly lies in SNPs that do not
reach GWAS significance [30], we examined top genes,
instead of only genes with GWAS-significant SNPs, for
sharing between children’s sleep and obesity. Gene
regression analysis with adjustment for gene size evidenced
that children’s sleep and obesity GWAS had significant
linear association of their gene U-scores, suggesting that
genes with larger effects on children’s sleep also tend to
influence children’s obesity risk more than genes with
smaller or no effects on sleep.
Analysis of GWAS catalog for all-age sleep and obesity
phenotypes also suggested shared gene between them. Of
the three obesity genes in the GWAS catalog, LINC01122
is the gene associated with sleep duration, while RGS6 and
FBN2 are two genes associated with sleep quality, mea-
sured by sleep onset [31]. Gene pleiotropy for all-age sleep
and obesity observed in the GWAS Catalog was potentially
arisen from the same genes with different SNPs that were
rs36032616 and rs699363 of RGS6, rs115375165 and
rs374748 of FBN2, and rs17190618 and rs6731302 of
LINC01122 (Supplementary Tables S2 and S3). The gene
correlation study will enhance our understanding of GWAS
SNP associations and promote further research on gene
function with pleiotropic effects on sleep time and obesity
development. For example, RGS6 gene modulates functions
of G proteins by activating the intrinsic guanosine tripho-
sphatase (GTPase) activity [32], and G proteins are known
to regulate sleep [33] and obesity [34].
Our study also investigated genetic effects from the same
pathways on children’s sleep and obesity that were enriched
for GWAS SNP associations. “Suz12 target genes” was the
shared pathway between children’s sleep and obesity.
Suz12 gene encodes subunit of polycomb repressive com-
plex 2 (PRC2) protein, which is associated with the pro-
moters of target genes and regulation of their expression,
playing an important role in stem cell differentiation and
early embryonic development [35]. Identification of the
Suz12-related pathway suggested that genetic regulation
effects leading to genetic correlation between children’s
sleep and obesity originate from early embryonic develop-
ment. Among the top 1%, 2%, 5%, and 10% of pathway
enrichments, our study showed that children’s sleep and
obesity significantly shared common pathways with OR in
decreasing order, suggesting that a children’s sleep pathway
with stronger effect is more likely a children’s obesity
pathway, and vice versa. The results evidenced that genetic
correlation due to common pathways arises from weak SNP
associations that do not reach GWAS significance. Corre-
lation coefficient analysis further proved existence of
pathway correlation between children’s sleep and obesity
(r = 0.36), and proved that a pathway having no effect on
children’s sleep is also likely irrelevant to children’s obesity
development and vice versa.
Pathway analysis of all-age sleep time and obesity at the
GWAS Catalog did not show that “Suz12 target genes” was
significant. The results suggested that Suz12 regulation of
target genes may affect sleep and obesity at young age,
potentially originating during embryonic development [36].
The “PAX3–FOXO1 target genes” was significant pathway
for children’s sleep time, all-age sleep-related traits and
obesity, and it also ranked as top-associated pathway for
children’s obesity (U-score = 0.025) and all-age sleep time
(U-score = 0.0003). The fusion gene of PAX3–FOXO1
encodes a chimeric transcription factor with the transcrip-
tional activation domain of FOXO1 and the DNA-binding
domain of PAX3, where FOXO1 epigenetic effect was
related to sleep disturbance and involved in adipocyte
metabolism [37]. The findings indicated that epigenetic
function of PAX3–FOXO1 may play an important role in
genetic correlation of sleep and obesity, and regulation of
target genes may influence sleep duration more than obe-
sity, starting from the young age.
Our study has evidenced that there exists genetic corre-
lation between children’s sleep and obesity, arising from
gene pleiotropy and shared genetic pathways. The gene and
pathway analyses were based on measuring gene effect by
the minimum association p-value of SNPs inside gene.
However, a gene with a longer length tends to have a
smaller minimum p-value than a gene with shorter length,
but a gene with a longer length may also have stronger LD
among its SNPs. So, our study took the number of inde-
pendent SNPs as adjusted gene length for permutation to
select top-associated genes and generate null distribution for
getting permutation p-value [27]. After adjustment for gene
size, children’s sleep and obesity only had a moderate gene
(r = 0.23) and pathway correlation (r = 0.35), despite they
both had strong significance (p-value < 2E−16). In this
study, the GWAS of children’s obesity and sleep consisted
of 14 and 5 discovery cohort samples, respectively, and one

cohort was investigated in both GWAS [11, 13]. The
independent samples of obesity and sleep traits may have
reduced power of correlation analysis. In contrast, a col-
lection of samples with both obesity status and sleep traits
measured has the advantage to consistently control for
confounding factors and directly measure pleiotropy effects
from shared genetic components. Correlation between
children’s sleep and obesity is contributed by both shared
genetic components and environment factors, and moderate
genetic correlations indicate that shared environment factors
may contribute more to obesity and sleep correlation than
genetic factors.
However, our study also has several limitations. First,
although the analysis proved there were strongly sig-
nificant gene correlation, no gene was found to contain
GWAS-significant SNP associations with both children’s
sleep and obesity. Common pathway with significant
enrichment test was identified for sleep and obesity, but the
identified pathways are gene sets typically with a large
number of function-related genes: the size is 1038 and 975
for “ Suz12 target genes” and “PAX3–FOXO1 target
genes”, respectively. It remains challenging to unambigu-
ously find which genes and how they take effects on sleep
and obesity in the pathway. Besides, the identified path-
ways did not clarify causal mechanisms for sleep and
obesity association. For example, the “PAX3–FOXO1
target genes” was identified as significant pathway for
children’s sleep and all-age obesity, but a potential causal
mechanism may be that insufficient sleep influences
FOXO1 epigenetic regulation of target genes that cause
metabolic dysfunction later in the life [37]. A
protein–protein interaction (PPI) network presents a group
of proteins with functional contacts, which is essential to
almost all biological processes in a cell [38, 39]. Study of
PPI network can help to address these limitations, and
facilitate to identify a subset of genes in pathway that
encode proteins regulating children’s sleep and obesity,
which is an important direction for research in next step.
Last, the current study lacks replication data of children’s
sleep and obesity GWAS to improve analysis power and
confirm the findings. Follow-up analysis of independent
children’s GWAS and biological function study are crucial
to further investigate gene functions and pathway causal
mechanisms that underlie genetic correlation between
children’s sleep and obesity.
In spite of these limitations, our study extends research
on the existing GWAS of single-SNP associations, with an
emphasis on study of gene and pathway regulation even
when they do not contain GWAS-significant SNP associa-
tions. Our analyses present statistical evidence of gene and
pathway correlation between children’s sleep time and
obesity. The findings and identification of shared genetic
pathways will help to direct follow-up studies and
H. Mei et al.
illuminate genetic mechanisms influencing sleep and obe-
sity in early age.
Acknowledgements This study was supported in part by grants N01-
HC55021 and U01-HL096917 from the National Institutes of Health/
National Heart, Lung, and Blood Institute, Mississippi INBRE Grant
P20GM103476, and Chinese National Natural Science Foundation
(81728017).
Compliance with ethical standards
Conflict of interest The authors declare that they have no conflict of
interest.
Publisher’s note Springer Nature remains neutral with regard to
jurisdictional claims in published maps and institutional affiliations.
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