Nature GeNetics VOLUME 45 | NUMBER 8 | AUGUST 2013 907
L E T T E R S
Allergic disease is very common and carries substantial
public-health burdens. We conducted a meta-analysis of
genome-wide associations with self-reported cat, dust-mite
and pollen allergies in 53,862 individuals. We used generalized
estimating equations to model shared and allergy-specific
genetic effects. We identified 16 shared susceptibility loci
with association P < 5 × 10
−8
, including 8 loci previously
associated with asthma, as well as 4p14 near TLR1, TLR6 and
TLR10 (rs2101521, P = 5.3 × 10
−21
); 6p21.33 near HLA-C
and MICA (rs9266772, P = 3.2 × 10
−12
); 5p13.1 near PTGER4
(rs7720838, P = 8.2 × 10
−11
); 2q33.1 in PLCL1 (rs10497813,
P = 6.1 × 10
−10
), 3q28 in LPP (rs9860547, P = 1.2 × 10
−9
);
20q13.2 in NFATC 2 (rs6021270, P = 6.9 × 10
−9
), 4q27 in
ADAD1 (rs17388568, P = 3.9 × 10
−8
); and 14q21.1 near
FOXA1 and TTC6 (rs1998359, P = 4.8 × 10
−8
). We identified
one locus with substantial evidence of differences in effects
across allergies at 6p21.32 in the class II human leukocyte
antigen (HLA) region (rs17533090, P = 1.7 × 10
−12
), which was
strongly associated with cat allergy. Our study sheds new light
on the shared etiology of immune and autoimmune disease.
Allergies and allergic asthma are among the most common diseases
in the industrialized world. In the United States, a nationwide survey
found that over half the population tested positive for sensitization to
at least one common allergen, showing a considerable increase in prev-
alence compared to results collected approximately 10 years earlier
1
.
The cause of this apparent increase in prevalence is unknown, but
the rapidity with which it has occurred implicates an environmental
component
2
. Still, estimates of the heritability of allergy are high
3,4
,
suggesting that understanding the genetic liability underlying these
conditions is key to understanding disease.
A number of genes implicated in allergy and asthma through asso-
ciation and functional studies belong to pathways involved in immune
and inflammatory processes, such as innate immunity, adaptive
immunity and allergic inflammation
5
. These genes belong to a range
of gene families that encode Toll-like receptors, interleukins, chemo-
kines and various other signaling molecules and transcription fac-
tors. Published genome-wide association studies (GWAS) on allergic
conditions have focused on asthma and atopic dermatitis, resulting
in the identification of a substantial number of loci associated with
asthma (HLA-DQB1, IL33, IL18R1, SMAD3, GSDMA, IL2RB, RORA,
GSDMB, IL13, SLC22A5, DENND1B, PDE4D, ORMDL3, IL6R, 5q22.1
and 11q13.5)
6–11
and a smaller number associated with atopic der-
matitis (FLG, OVOL1, ACTL9, 5q22.1, 11q13.5 and 20q13.33)
12–14
.
Studies using other measures of atopy have been less definitive, likely
owing to limited sample sizes
15–17
; the largest study, of allergic rhinitis
and immunoglobulin E (IgE) sensitization to grass pollen, identified
three regions with genome-wide significant association (the class II
HLA region, 5q22.1 and 11q13.5).
We selected three common self-reported allergy phenotypes
(pollen allergy, dust-mite allergy and cat allergy) for which compa-
rable data were available in the 23andMe participant cohort
18
and
in a cohort of mothers from the Avon Longitudinal Study of Parents
and Children (ALSPAC)
19
(Table 1). We used generalized estimat-
ing equations (GEEs) to jointly model genetic effects across all three
phenotypes. The GEE approach accounts for correlations between
phenotypes and enabled us to estimate both shared and allergy-specific
effects. We first performed a genome-wide meta-analysis of GEE tests
for shared effects. Then, for a set of 3,725 markers with nominal evi-
dence of association with at least one allergy, we performed GEE tests
for allergy-specific effects (Supplementary Table 1).
In the GEE meta-analysis for shared effects across allergies, we
identified 16 genome-wide significant loci with association P < 5 ×
10
−8
(Fig. 1, Table 2 and Supplementary Fig. 1). Of these, eight
had association P < 5 × 10
−8
in the 23andMe cohort and association
P < 0.05 in the ALSPAC cohort (Supplementary Tables 2 and 3).
We identified six loci with suggestive evidence of association (5 ×
10
−8
< P < 1 × 10
−6
) (Supplementary Note). Many of these loci have
A genome-wide association meta-analysis of
self-reported allergy identifies shared and
allergy-specific susceptibility loci
David A Hinds
1
, George McMahon
2
, Amy K Kiefer
1
, Chuong B Do
1
, Nicholas Eriksson
1
, David M Evans
2
,
Beate St Pourcain
3
, Susan M Ring
3
, Joanna L Mountain
1
, Uta Francke
1
, George Davey-Smith
2
,
Nicholas J Timpson
2,4
& Joyce Y Tung
1,4
1
23andMe, Inc., Mountain View, California, USA.
2
Medical Research Council (MRC) Centre for Causal Analyses in Translational Epidemiology, School of Social and
Community Medicine, University of Bristol, Bristol, UK.
3
School of Social and Community Medicine, University of Bristol, Bristol, UK.
4
These authors contributed
equally to this work. Correspondence should be addressed to D.A.H. (dhinds@23andMe.com).
Received 29 October 2012; accepted 5 June 2013; published online 30 June 2013; doi:10.1038/ng.2686
npg
© 2013 Nature America, Inc. All rights reserved.
908 VOLUME 45 | NUMBER 8 | AUGUST 2013 Nature GeNetics
L E T T E R S
previously been associated with other immunity-related pheno-
types, and eight have been associated with asthma in previous GWAS
(Supplementary Note). Although we describe loci in terms of their
proximal genes, in most cases, we have no functional evidence for a
specific target, and these variants may affect the regulation of more
distant genes.
To ensure that the results were not confounded by age or differ-
ences between genotyping platforms, we tested the index SNPs for
platform-specific effects and for interactions with age within the
23andMe cohort, but no tests yielded strong evidence of interaction
after adjusting for multiple comparisons (Supplementary Table 4).
We also tested for pairwise interactions between the 22 loci, but none
of these interactions were significant after adjustment for multiple
comparisons (Supplementary Table 5).
We assessed whether the identified associations were supported by
data from a companion study of allergic sensitization
20
(Table 3 and
Supplementary Table 6). All 22 loci had effects in the same direc-
tion in the 2 studies, and 10 of our 16 genome-wide significant loci
were supported with association P < 0.05 in the sensitization study.
We also annotated our findings on the basis of linkage disequilibrium
(LD) with results from published GWAS, coding variation, monocyte
expression quantitative trait loci (eQTLs)
21
and putative regulatory
regions identified by the Encyclopedia of DNA Elements (ENCODE)
Project (Table 3 and Supplementary Tables 7–10).
We examined evidence of association in our meta-analysis at other
loci previously associated with either asthma or atopic dermatitis
(Supplementary Tables 11 and 12). We found nominal support
(P < 0.05, consistent risk allele) for seven additional asthma-relevant
loci (IL6R, GAB1, RAD50, IL13, IKZF4, RORA and IL2RB), with a
false discovery rate (FDR) of 0.04 across these variants. For atopic
dermatitis, we found nominal support for associations at five addi-
tional loci (IL13, KIF3A, CARD11, MIR1208 and NCF4), with an
FDR of 0.07 for this group. These results indicate substantial overlap
between these phenotypes, beyond that observed for the loci meeting
our criteria for significant and suggestive associations.
To test for allergy-specific genetic effects, we included interaction
terms for specific allergies in our GEE models (Supplementary
Table 1). We found one locus with strong evidence of allergy-specific
effects on chromosome 6 in the major histocompatibility complex
(MHC) region, with the strongest signal 14 kb upstream of HLA-DQA1
(Fig. 2 and Supplementary Fig. 2). Index SNP rs17533090 had com-
bined P = 1.7 × 10
−12
for interaction with allergy type. Effects for
the three allergies were consistent across cohorts and indicated that
this locus was specifically associated with cat allergy (Fig. 3). Of the
SNPs listed in Table 2, only rs2101521 showed evidence of a specific
effect favoring cat allergy (unadjusted P = 0.0011), which was weak
compared to the evidence for shared effect (P = 5.3 × 10
−21
).
We performed an exploratory analysis to assess the associations
of allergy-associated loci with symptoms of allergic rhinitis, aller-
gic contact dermatitis and allergic asthma in the 23andMe cohort.
We reclassified cases on the basis of reported symptoms and used
the GEE approach to jointly model genetic effects across symptoms
(Supplementary Tables 13 and 14). All effects were in the same
direction at all index SNPs. At most loci, we did not see evidence of
differential effects across symptoms (P > 0.05 for interaction). One
exception was found in GSDMB, where the rs9303280 SNP was most
strongly associated with asthma (P = 0.000035 for interaction). Effect
sizes for contact dermatitis symptoms tended to be smaller than those
for asthma (20/23 loci; P = 0.0004) and rhinitis (18/23 loci; P = 0.007).
Effect sizes for asthma tended to be larger than those for rhinitis,
but not significantly so (14/23 loci; P = 0.30). However, in associa-
tion tests, most loci showed more significant association with rhinitis
than with asthma (18/23 loci; P = 0.007), with association P values
often differing by several orders of magnitude. Thus, although asthma
may be a slightly more specific atopy phenotype, rhinitis seems to
be more powerful in the discovery of atopy-related loci in cohort
studies because it is reported by a much higher proportion of indi-
viduals who report allergies.
Genes implicated in our GWAS highlight key pathways in the eti-
ology of common allergy. In the 4p14 region near rs2101521, TLR1
(Toll-like receptor 1) and TLR6 (Toll-like receptor 6) encode pattern-
recognition receptors whose roles in recognizing external pathogens
and activating appropriate immune responses lie at the interface
between innate immunity and immunoregulation. Candidate gene
Chromosome
–log
10
(P value)
5
10
15
20
1 2 3 4 5 6 7 8 9 10 11 12 14 16 18 20 22
TLR1-TLR6-TLR10
TSLP
LRRC32
IL1RL2
HLA-DQB1
MICA
PTGER4
PLCL1
LPP
IL33
NFATC2
GSDMB
SMAD3
GATA3
ADAD1
FOXA1
ZBTB10
ID2
CLEC16A
IL4R
PEX14
ETS1
Figure 1 Manhattan plot of meta-analysis
results for shared effects. The plotted
values represent the most significant scores
from the meta-analyses of cat, pollen and
dust-mite allergy, with all results with
association P < 1 × 10
−4
recomputed using
GEEs to assess effects shared across allergens.
The gray line corresponds to P = 5 × 10
−8
, and
results above this threshold are shown in red.
Gene labels are provided for cross-referencing
with other results and are not intended to
suggest that we have established a causal basis
for the observed associations.
Table 1 Demographic characteristics of cohorts
23andMe ALSPAC
n Percent n Percent
Total 46,646 100.0 7,216 100.0
Sex
Male 26,344 56.5 0 0.0
Female 20,302 43.5 7,216 100.0
Age
≤30 4,300 14.6 4,829 67.0
>30 and ≤45 8,088 31.1 2,382 33.0
>45 and ≤60 6,282 25.6 0 0.0
>60 6,428 28.7 0 0.0
Allergy status
Cat allergy 10,509 22.5 704 9.8
Dust-mite allergy 9,815 21.0 964 13.4
Pollen allergy 16,133 34.6 1,201 16.6
Number of allergies
Three allergies 4,947 10.6 328 4.6
Any two allergies 6,228 13.3 536 7.4
Any one allergy 9,160 19.6 813 11.3
No allergy 26,311 56.4 5,539 76.8
npg
© 2013 Nature America, Inc. All rights reserved.
Nature GeNetics VOLUME 45 | NUMBER 8 | AUGUST 2013 909
L E T T E R S
studies have identified associations of TLR genes with asthma
22–24
, as
well as with sensitization to grass and rhinitis
17
. However, this region
has not been reported to show significant association in genome-
wide analyses.
We see substantial overlap between loci asso-
ciated with allergy and loci previously impli-
cated in autoimmune disease. In the 5p13.1
region, index SNP rs7720838 is upstream
of PTGER4, encoding prostaglandin E
receptor 4, previously implicated as a candi-
date asthma locus
25
. This SNP is in strong LD
(r
2
= 0.94) with rs10440635, which has been
associated with ankylosing spondylitis
26
.
Variants affecting PTGER4 expression have
also been associated with Crohn’s disease
27
,
and mouse studies point to a role for Ptger4 in
the initiation of skin immune responses
28,29
.
In the 2q33.1 region, our eQTL analysis sug-
gested that index SNP rs10497813 was associ-
ated with the expression of PLCL1, encoding
phospholipase C–like 1, involved in inositol
1,4,5-triphosphate intracellular signaling
30
.
Variation in PLCL1 (at rs6738825, r
2
= 0.97
with rs10497813) has also been associated
with Crohn’s disease
31
.
Several new allergy-associated loci are in
or near genes involved in helper T cell differ-
entiation. Index SNP rs9860547 in the 3q28
region falls in the LPP gene (lipoma-preferred
partner). A nearby variant in LPP (rs1464510,
r
2
= 0.70) has been associated with celiac dis-
ease
32,33
and vitiligo
34
. Our eQTL analysis sug-
gested that our association may be mediated
by an effect on the expression of BCL6
(B cell lymphoma 6), a transcription factor
that represses the STAT6-mediated response
to interleukin (IL)-4 and IL-13 and IgE class
switching
35
and inhibits type 2 helper T cell
(T
H
2) differentiation in a mouse model
36
.
In the 20q13.2 region, index SNP rs6021270
is in the NFATC2 gene, encoding a compo-
nent of the NFAT (nuclear factor of activated
T cells) transcription complex, which has
an important role in regulating helper T cell
differentiation
37
. Variation in NFATC2 has
not been associated with any allergic or auto-
immune phenotype; however, mice lacking
Nfatc2 show increased lung inflammation in
experimentally induced allergic asthma
38,39
.
In the 4q27 region, index SNP rs17388568
falls in the ADAD1 gene, but evidence for
association spans the nearby IL2 and IL21
genes. This same SNP has been associated
with the formation of autoantibodies in type 1
diabetes
40
and with ulcerative colitis
41
, and
a nearby SNP in strong LD associated with
the inhibition of IL-2 production (rs2069772,
r
2
= 0.91) has been suggestively associated
with allergic rhinitis
17
. The IL-2 and IL-21
cytokines are involved in the regulation of
multiple helper T cell types: IL-21 is upregu-
lated in T
H
2 and T
H
17 cells, and IL-2 is required for T
H
1 differentia-
tion and inhibits the differentiation of T
H
17 cells
42
.
In the 14q21.1 region, index SNP rs1998359 is upstream of
FOXA1, a member of the forkhead-box transcription factor family.
Table 2 Index SNPs from meta-analysis for shared effects
SNP Region Position Alleles RAF OR (95% CI) P Gene context
rs2101521 4p14 38811551 A/G 0.766 1.15 (1.11–1.18) 5.3 × 10
−21
TLR1-[]–TLR6
rs1438673 5q22.1 110467499 T/C 0.498 1.12 (1.09–1.14) 2.3 × 10
−20
WDR36-[]–CAMK4
rs2155219 11q13.5 76299194 G/T 0.511 1.11 (1.09–1.14) 1.6 × 10
−19
C11orf30–[]–LRRC32
rs10189629 2q12.1 102879464 A/C 0.857 1.16 (1.12–1.20) 1.8 × 10
−16
IL1RL2–[]–IL1RL1
rs6906021 6p21.32 32626311 T/C 0.475 1.10 (1.07–1.13) 7.1 × 10
−15
HLA-DQA1–[]-HLA-DQB1
rs9266772 6p21.33 31352113 T/C 0.193 1.11 (1.08–1.14) 3.2 × 10
−12
HLA-C—[]–MICA
rs7720838 5p13.1 40486896 G/T 0.580 1.08 (1.06–1.11) 8.2 × 10
−11
[]—PTGER4
rs10497813 2q33.1 198914072 T/G 0.483 1.08 (1.05–1.10) 6.1 × 10
−10
[PLCL1]
rs9860547 3q28 188128979 G/A 0.462 1.08 (1.05–1.10) 1.2 × 10
−9
[LPP]
rs7032572 9p24.1 6172380 A/G 0.167 1.12 (1.08–1.16) 1.7 × 10
−9
RANBP6—[]–IL33
rs6021270 20q13.2 50141264 C/T 0.939 1.16 (1.11–1.23) 6.9 × 10
−9
[NFATC2]
rs9303280 17q12 38074031 T/C 0.517 1.07 (1.05–1.10) 8.9 × 10
−9
[GSDMB]
rs17228058 15q22.33 67450305 A/G 0.240 1.08 (1.05–1.11) 1.2 × 10
−8
[SMAD3]
rs962993 10p14 9053132 T/C 0.576 1.07 (1.05–1.10) 1.5 × 10
−8
GATA3—[]
rs17388568 4q27 123329362 G/A 0.275 1.08 (1.05–1.10) 3.9 × 10
−8
[ADAD1]
rs1998359 14q21.1 38077148 C/G 0.246 1.08 (1.05–1.12) 4.8 × 10
−8
FOXA1–[]—TTC6
rs6473223 8q21.13 81268155 C/T 0.358 1.07 (1.04–1.10) 7.7 × 10
−8
TPD52—[]—ZBTB10
rs10174949 2p25.1 8442248 A/G 0.724 1.07 (1.05–1.10) 1.0 × 10
−7
[]—ID2
rs7203459 16p13.13 11230703 C/T 0.734 1.07 (1.04–1.10) 2.0 × 10
−7
[CLEC16A]
rs2107357 16p12.1 27410829 G/A 0.138 1.09 (1.06–1.13) 3.3 × 10
−7
IL4R–[]–IL21R
rs2056417 1p36.22 10581658 A/G 0.694 1.07 (1.04–1.10) 3.7 × 10
−7
[PEX14]
rs10893845 11q24.3 128186882 T/G 0.493 1.06 (1.04–1.09) 6.4 × 10
−7
[]—ETS1
Region, cytogenetic band; position, build 37 map position of the SNP; alleles, low-/high-risk alleles on genomic
reference strand; RAF, risk allele frequency across all study participants; OR, meta-analysis odds ratio for the high-risk
allele; CI, confidence interval; gene context, gene(s) spanning or flanking (<1 Mb away from) the index SNP: brackets
indicate the position of the SNP, and dashes indicate distance to a flanking gene (-, >1 kb; –, >10 kb; —, >100 kb).
Table 3 Summary of supporting evidence for allergy-associated loci
SNP Region Replication
a
Atopy
b
Autoimmune
disease
c
Nonsynonymous
SNP
d
eQTL
e
Gene context
f
rs2101521 4p14 *** * TLR6 TLR1-[]–TLR6
rs1438673 5q22.1 *** ** WDR36-[]—CAMK4
rs2155219 11q13.5 *** *** ** C11orf30–[]—LRRC32
rs10189629 2q12.1 ** * IL1RL2–[]–IL1RL1
rs6906021 6p21.32 *** HLA-DQA1–[]-HLA-DQB1
rs9266772 6p21.33 ** HLA-C—[]–MICA
rs7720838 5p13.1 * * []—PTGER4
rs2117339 2q33.1 * PLCL1 [PLCL1]
rs9860547 3q28 *** *** BCL6 [LPP]
rs7032572 9p24.1 ** RANBP6—[]–IL33
rs6021270 20q13.2 [NFATC2]
rs9303280 17q12 *** *** * IKZF3 [GSDMB]
rs17293632 15q22.33 * [SMAD3]
rs962993 10p14 * GATA3—[]
rs17388568 4q27 *** * *** [ADAD1]
rs9671863 14q21.1 FOXA1–[]—TTC6
rs2202749 8q21.13 *** TPD52—[]—ZBTB10
rs13416555 2p25.1 *** ID2 []—ID2
rs7203459 16p13.13 * * [CLEC16A]
rs2107357 16p12.1 IL4R–[]–IL21R
rs2056417 1p36.22 PEX14 [PEX14]
rs970924 11q24.3 []—ETS1
a
Strength of replication for allergic sensitization
20
: *P < 0.05, **P < 0.005, ***P < 0.0005 (Supplementary Table 4).
b
Nearby
(<500 kb away, r
2
> 0.5) GWAS findings for atopy phenotypes (Supplementary Table 7).
c
Nearby (<500 kb away, r
2
> 0.5)
GWAS findings for autoimmune disease phenotypes (
Supplementary Table 7).
d
Nonsynonymous SNP: *r
2
> 0.5 with
nonsynonymous SNP (
Supplementary Table 8).
e
Association with the expression of the gene listed (Supplementary Table 9).
f
Brackets indicate the position of the SNP, and dashes indicate distance to a flanking gene (-, >1 kb; –, >10 kb; —, >100 kb).
npg
© 2013 Nature America, Inc. All rights reserved.
910 VOLUME 45 | NUMBER 8 | AUGUST 2013 Nature GeNetics
L E T T E R S
In mice, the closely related Foxa1 and Foxa2
transcription factors have roles in the regu-
lation of T
H
2-mediated inflammation and
mucous production in allergic airway dis-
ease
43
; although a similar role for Foxa1 has
not been established, Foxa1 and Foxa2 are known to have overlapping
patterns of expression in the respiratory epithelium
44
.
In the 6p21.33 region, HLA-B and HLA-C encode major histocom-
patibility complex (MHC) class I molecules, which are expressed on
most cell types and are responsible for the presentation of intracellular
peptides to T cells. MICA encodes a protein that belongs to a family
of non-classical MHC molecules that resemble the class I molecules
and are thought to be involved in innate antitumor and antiviral
surveillance
45
. Alleles of HLA-B are associated with severe allergic
reactions, such as abacavir hypersensitivity and Stevens-Johnsons
syndrome
46,47
. SNPs in these three genes have been associated with a
number of immune system–related phenotypes, such as psoriasis and
HIV-1 control
48,49
.
Previous studies have suggested associations between specific
allergen sensitivities and HLA class II alleles
50
. However, these
studies have been small and have reported inconsistent results
51
. Our
finding of a specific association with cat allergy is the first demonstra-
tion to our knowledge of allergen specificity in a GWAS context.
We assessed the directionality of effects in cases where our index
SNPs were in strong LD (r
2
> 0.5) with SNPs previously associated
with autoimmune disease (Supplementary Table 15). At some loci
(LRRC32, PTGER4, PLCL1, SMAD3, ADAD1 and CLEC16A
), auto-
immune disease and allergy were associated with the same risk alleles.
At others (GSDMB and LPP), the risk allele for autoimmune disease
seemed to be protective against allergy. Many autoimmune diseases
are associated with increased activation of T
H
1 responses, whereas
allergy has been associated with T
H
2 activity
52
. Our results may help
to identify elements that influence the balance between T
H
1 and T
H
2
activity, as well as elements that contribute to both responses.
Self-reported allergy status can be unreliable
53
, and the surveys we
used were not standardized or validated. In the 23andMe cohort, the
high proportion of allergy cases likely reflects responder bias in com-
pleting the allergy survey. The ALSPAC cohort was assessed during
pregnancy, which can alter allergic disease status
54
. These limitations
should not compromise the validity of our genetic associations, but
they make functional interpretation more challenging.
Our results demonstrate that self-reported allergy can be used to
identify disease susceptibility loci, with results consistent with studies
of more narrowly defined allergy manifestations and allergic sen-
sitization. Self-directed web-based data collection in the 23andMe
cohort yielded results largely consistent with those obtained with the
traditional survey methods used in the ALSPAC cohort. Our findings
reinforce and extend evidence of a shared genetic etiology of allergic
and autoimmune disease, with newly discovered susceptibility loci for
allergy identified near LPP-BCL6, HLA-C–MICA, PTGER4 and PLCL1,
all of which were previously associated with autoimmune disease. Our
findings also highlight the role of the T
H
2 lineage in the pathogenesis of
allergy, with associations identified in or near key T
H
2 genes, including
ID2, BCL6, GATA3, IL13, IL33, TSLP and IL1RL1. An important next
step will be to more carefully characterize the extent to which indi-
vidual associations lead to a global predisposition to allergy compared
to effects on specific target tissues, such as skin, lung or mucosa.
URLs.
BEAGLE, http://faculty.washington.edu/browning/beagle/
beagle.html; HapMap, http://hapmap.ncbi.nlm.nih.gov/; MaCH,
http://www.sph.umich.edu/csg/abecasis/MaCH/; Minimac, http://
genome.sph.umich.edu/wiki/Minimac; NCBI Gap Plus, http://www.
ncbi.nlm.nih.gov/projects/gapplus/sgap_plus.htm; 1000 Genomes
Project, http://www.1000genomes.org/; UCSC Genome Browser,
http://genome.ucsc.edu/.
METHODS
Methods and any associated references are available in the online
version of the paper.
Note: Supplementary information is available in the online version of the paper.
ACKNOWLEDGMENTS
We thank the customers of 23andMe who answered surveys, as well as the
employees of 23andMe, who together made this research possible. We also thank
K. Nadeau for assistance in survey development and S. Nelson and R. Altman
for reviewing surveys. This work was supported in part by the National Heart,
Lung, and Blood Institute of the US National Institutes of Health under grant
1R43HL115873-01.
We are extremely grateful to all the families who took part in ALSPAC, to the
midwives for their help in recruiting them and to the whole ALSPAC team, which
includes interviewers, computer and laboratory technicians, clerical workers,
research scientists, volunteers, managers, receptionists and nurses. The UK MRC
(grant 74882), the Wellcome Trust (grant 092731) and the University of Bristol
provide core support for ALSPAC.
This publication is the work of the authors, and D.A.H., N.J.T. and J.Y.T. will
serve as guarantors for the contents of this paper.
AUTHOR CONTRIBUTIONS
D.A.H. and G.M. analyzed the data. A.K.K. designed the survey for 23andMe.
G.M., D.M.E. and B.S.P. were part of the ALSPAC GWAS preparation team.
1.5
Effect
1.4
1.3
1.2
1.1
1.0
0.9
Cat
23andMe
ALSPAC
Pollen Dust mite
Figure 3 Marginal effect sizes and 95% confidence intervals for
rs17533090 for cat, pollen and dust-mite allergy in the 23andMe and
ALSPAC cohorts. Effects are odds ratios for the high-risk G allele of
rs17533090.
Chromosome
0
5
10
1 2 3 4 5 6 7 8 9 10 11 12 14 16 18 20 22
HLA−DQA1
–log
10
(P value)
Figure 2 Manhattan plot of meta-analysis
results for interactions with allergen. The
gray line corresponds to P = 5 × 10
−8
, and
results above this threshold are shown in red.
Interaction tests were performed for markers
with P < 1 × 10
−4
for association with at least
one of cat, pollen or dust-mite allergy.
npg
© 2013 Nature America, Inc. All rights reserved.
Nature GeNetics VOLUME 45 | NUMBER 8 | AUGUST 2013 911
L E T T E R S
S.M.R. was responsible for ALSPAC sample collection and preparation. C.B.D. and
N.E. developed analytical tools. J.L.M., U.F. and G.D.-S. supervised the project.
D.A.H., G.M., N.J.T. and J.Y.T. designed the study and wrote the manuscript.
COMPETING FINANCIAL INTERESTS
The authors declare competing financial interests: details are available in the online
version of the paper.
Reprints and permissions information is available online at http://www.nature.com/
reprints/index.html.
1. Arbes, S.J. Jr., Gergen, P.J., Elliott, L. & Zeldin, D.C. Prevalences of positive skin
test responses to 10 common allergens in the US population: results from the third
National Health and Nutrition Examination Survey. J. Allergy Clin. Immunol. 116,
377–383 (2005).
2. Strachan, D.P. Family size, infection, and atopy: the first decade of the hygiene
hypthesis. Thorax 55 (suppl. 1), S2–S10 (2000).
3. Fagnani, C. et al. Heritability and shared genetic effects of asthma and hay fever:
an Italian study of young twins. Twin Res. Hum. Genet. 11, 121–131 (2008).
4. Willemsen, G., van Beijsterveldt, T.C.E.M., van Baal, C.G.C.M., Postma, D. &
Boomsma, D.I. Heritability of self-reported asthma and allergy: a study in adult
Dutch twins, siblings and parents. Twin Res. Hum. Genet. 11, 132–142 (2008).
5. Vercelli, D. Discovering susceptibility genes for asthma and allergy. Nat. Rev.
Immunol. 8, 169–182 (2008).
6. Himes, B.E. et al. Genome-wide association analysis identifies PDE4D as an asthma-
susceptibility gene. Am. J. Hum. Genet. 84, 581–593 (2009).
7. Sleiman, P.M.A. et al. Variants of DENND1B associated with asthma in children.
N. Engl. J. Med. 362, 36–44 (2010).
8. Moffatt, M.F. et al. A large-scale, consortium-based genomewide association study
of asthma. N. Engl. J. Med. 363, 1211–1221 (2010).
9. Hirota, T. et al. Genome-wide association study identifies three new susceptibility loci
for adult asthma in the Japanese population. Nat. Genet. 43, 893–896 (2011).
10. Torgerson, D.G. et al. Meta-analysis of genome-wide association studies of asthma in
ethnically diverse North American populations. Nat. Genet. 43, 887–892 (2011).
11. Ferreira, M.A.R. et al. Identification of IL6R and chromosome 11q13.5 as risk loci
for asthma. Lancet 378, 1006–1014 (2011).
12. Esparza-Gordillo, J. et al. A common variant on chromosome 11q13 is associated
with atopic dermatitis. Nat. Genet. 41, 596–601 (2009).
13. Sun, L.D. et al. Genome-wide association study identifies two new susceptibility
loci for atopic dermatitis in the Chinese Han population. Nat. Genet. 43, 690–694
(2011).
14. Paternoster, L. et al. Meta-analysis of genome-wide association studies identifies
three new risk loci for atopic dermatitis. Nat. Genet. 44, 187–192 (2012).
15. Andiappan, A.K. et al. Genome-wide association study for atopy and allergic rhinitis
in a Singapore Chinese population. PLoS ONE 6, e19719 (2011).
16. Wan, Y.I. et al. A genome-wide association study to identify genetic determinants
of atopy in subjects from the United Kingdom. J. Allergy Clin. Immunol. 127,
223–231 (2011).
17. Ramasamy, A. et al. A genome-wide meta-analysis of genetic variants associated
with allergic rhinitis and grass sensitization and their interaction with birth order.
J. Allergy Clin. Immunol. 128, 996–1005 (2011).
18. Eriksson, N. et al. Web-based, participant-driven studies yield novel genetic
associations for common traits. PLoS Genet. 6, e1000993 (2010).
19. Fraser, A. et al. Cohort profile: the Avon Longitudinal Study of Parents and Children:
ALSPAC mothers cohort. Int. J. Epidemiol. 42, 97–110 (2013).
20. Bønnelykke, K. et al. Meta-analysis of genome-wide association studies identifies
ten loci influencing allergic sensitization. Nat. Genet. published online; doi:10.1038/
ng.2694 (30 June 2013).
21. Zeller, T. et al. Genetics and beyond—the transcriptome of human monocytes and
disease susceptibility. PLoS ONE 5, e10693 (2010).
22. Eder, W. et al. Toll-like receptor 2 as a major gene for asthma in children of
European farmers. J. Allergy Clin. Immunol. 113, 482–488 (2004).
23. Tantisira, K. et al. Toll-like receptor 6 gene (TLR6): single-nucleotide polymorphism
frequencies and preliminary association with the diagnosis of asthma. Genes
Immun. 5, 343–346 (2004).
24. Kormann, M.S. et al. Toll-like receptor heterodimer variants protect from childhood
asthma. J. Allergy Clin. Immunol. 122, 86–92 (2008).
25. Kurz, T. et al. Fine mapping and positional candidate studies on chromosome 5p13
identify multiple asthma susceptibility loci. J. Allergy Clin. Immunol. 118, 396–402
(2006).
26. Evans, D.M. et al. Interaction between ERAP1 and HLA-B27 in ankylosing
spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease
susceptibility. Nat. Genet. 43, 761–767 (2011).
27. Libioulle, C. et al. Novel Crohn disease locus identified by genome-wide association
maps to a gene desert on 5p13.1 and modulates expression of PTGER4.
PLoS Genet. 3, e58 (2007).
28. Kabashima, K. et al. Prostaglandin E2–EP4 signaling initiates skin immune
responses by promoting migration and maturation of Langerhans cells. Nat. Med. 9,
744–749 (2003).
29. Yao, C. et al. Prostaglandin E2–EP4 signaling promotes immune inflammation
through Th1 cell differentiation and Th17 cell expansion. Nat. Med. 15, 633–640
(2009).
30. Lin, X. et al. Control of calcium signal propagation to the mitochondria by inositol
1,4,5-trisphosphate–binding proteins. J. Biol. Chem. 280, 12820–12832
(2005).
31. Franke, A. et al. Genome-wide meta-analysis increases to 71 the number of
confirmed Crohn’s disease susceptibility loci. Nat. Genet. 42, 1118–1125
(2010).
32. Hunt, K.A. et al. Newly identified genetic risk variants for celiac disease related to
the immune response. Nat. Genet. 40, 395–402 (2008).
33. Dubois, P.C. et al. Multiple common variants for celiac disease influencing immune
gene expression. Nat. Genet. 42, 295–302 (2010).
34. Jin, Y. et al. Variant of TYR and autoimmunity susceptibility loci in generalized
vitiligo. N. Engl. J. Med. 362, 1686–1697 (2010).
35. Harris, M.B. et al. Transcriptional repression of Stat6-dependent interleukin-4–
induced genes by BCL-6: specific regulation of Iε transcription and immunoglobulin
E switching. Mol. Cell Biol. 19, 7264–7275 (1999).
36. Kusam, S., Toney, L.M., Sato, H. & Dent, A.L. Inhibition of Th2 differentiation and
GATA-3 expression by BCL-6. J. Immunol. 170, 2435–2441 (2003).
37. Hermann-Kleiter, N. & Baier, G. NFAT pulls the strings during CD4
+
T helper cell
effector functions. Blood 115, 2989–2997 (2010).
38. Karwot, R. et al. Protective role of nuclear factor of activated T cells 2 in CD8
+
long-lived memory T cells in an allergy model. J. Allergy Clin. Immunol. 121,
992–999 (2008).
39. Karwot, R., Ubel, C., Bopp, T., Schmitt, E. & Finotto, S. Increased immunosuppressive
function of CD4
+
CD25
+
Foxp3
+
GITR
+
T regulatory cells from NFATc2
−/−
mice controls
allergen-induced experimental asthma. Immunobiology 217, 905–911 (2012).
40. Plagnol, V. et al. Genome-wide association analysis of autoantibody positivity in
type 1 diabetes cases. PLoS Genet. 7, e1002216 (2011).
41. Anderson, C.A. et al. Meta-analysis identifies 29 additional ulcerative colitis risk
loci, increasing the number of confirmed associations to 47. Nat. Genet. 43,
246–252 (2011).
42. Liao, W., Lin, J.-X., Wang, L., Li, P. & Leonard, W.J. Modulation of cytokine receptors
by IL-2 broadly regulates differentiation into helper T cell lineages. Nat. Immunol.
12, 551–559 (2011).
43. Park, S.-W. et al. Distinct roles of FOXA2 and FOXA3 in allergic airway disease
and asthma. Am. J. Respir. Crit. Care Med. 180, 603–610 (2009).
44. Wan, H. et al. Compensatory roles of Foxa1 and Foxa2 during lung morphogenesis.
J. Biol. Chem. 280, 13809–13816 (2005).
45. Bauer, S. et al. Activation of NK cells and T cells by NKG2D, a receptor for
stress-inducible MICA. Science 285, 727–729 (1999).
46. Martin, A.M. et al. Predisposition to abacavir hypersensitivity conferred by HLA-
B*5701 and a haplotypic Hsp70-Hom variant. Proc. Natl. Acad. Sci. USA 101,
4180–4185 (2004).
47. Ferrell, P.B. Jr. & McLeod, H.L. Carbamazepine, HLA-B*1502 and risk of Stevens-
Johnson syndrome and doxic epidermal necrolysis: US FDA recommendations.
Pharmacogenomics 9, 1543–1546 (2008).
48. Strange, A. et al. A genome-wide association study identifies new psoriasis
susceptibility loci and an interaction between HLA-C and ERAP1. Nat. Genet. 42,
985–990 (2010).
49. Pereyra, F. et al. The major genetic determinants of HIV-1 control affect HLA class I
peptide presentation. Science 330, 1551–1557 (2010).
50. Young, R.P. et al. HLA-DR and HLA-DP genotypes and immunoglobulin E responses
to common major allergens. Clin. Exp. Allergy 24, 431–439 (1994).
51. Howell, W.M. & Holgate, S.T. HLA genetics and allergic disease. Thorax 50,
815–818 (1995).
52. Romagnani, S. The Th1/Th2 paradigm. Immunol. Today 18, 263–266 (1997).
53. Smith, H.E. et al. Is structured allergy history sufficient when assessing patients
with asthma and rhinitis in general practice? J. Allergy Clin. Immunol. 123,
646–650 (2009).
54. Schatz, M. & Zeiger, R.S. Asthma and allergy in pregnancy. Clin. Perinatol. 24,
407–432 (1997).
npg
© 2013 Nature America, Inc. All rights reserved.