Genetic predisposition for atopy and allergic rhinitis in the Singapore Chinese population.

Abstract

The prevalence of allergic diseases is high globally, but especially in developed countries, with one in five to one in four individuals affected worldwide. The World Health Organization's "Allergic Rhinitis and its Impact on Asthma 2008 Update" guidelines stated explicitly that over 600 million patients from all countries, all ethnic groups and all ages suffer from allergic rhinitis (AR). There are clear evidences to support the concept that allergic diseases are influenced by genetic predisposition and environmental factors. The genetic basis of AR has been evaluated more intensively in the recent 10-20 years. Advances in technology and statistical methods, such as genome-wide association studies (GWAS) have enabled millions of single nucleotide polymorphisms (SNPs) to be genotyped at rapid pace and for less cost. However these studies have not yet answered the entire heritability profile of the disease. Additionally, environmental influences on these genetic variants cannot be discounted. Hence these allergic diseases must be evaluated as a complex interplay between genetic and environmental factors. This review focuses on the genetic basis of AR, with special emphasis on studies performed in Singapore. Candidate gene based studies and GWAS performed in Singapore cohorts have been discussed to suggest how these diseases could be understood better in a Singapore context which is still applicable to research in AR globally.

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Hypothesis & Experience
Asia Pacific
allergy
pISSN 2233-8276 · eISSN 2233-8268
http://dx.doi.org/10.5415/apallergy.2011.1.3.152
Asia Pac Allergy 2011;1:152-156
Genetic predisposition for atopy and allergic
rhinitis in the Singapore Chinese population
De Yun Wang
Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
The prevalence of allergic diseases is high globally, but especially in developed countries, with one in five to one in four individuals
affected worldwide. The World Health Organization’s “Allergic Rhinitis and its Impact on Asthma 2008 Update” guidelines stated
explicitly that over 600 million patients from all countries, all ethnic groups and all ages suffer from allergic rhinitis (AR). There are
clear evidences to support the concept that allergic diseases are influenced by genetic predisposition and environmental factors. The
genetic basis of AR has been evaluated more intensively in the recent 10-20 years. Advances in technology and statistical methods,
such as genome-wide association studies (GWAS) have enabled millions of single nucleotide polymorphisms (SNPs) to be genotyped
at rapid pace and for less cost. However these studies have not yet answered the entire heritability profile of the disease. Additionally,
environmental influences on these genetic variants cannot be discounted. Hence these allergic diseases must be evaluated as a
complex interplay between genetic and environmental factors. This review focuses on the genetic basis of AR, with special emphasis
on studies performed in Singapore. Candidate gene based studies and GWAS performed in Singapore cohorts have been discussed to
suggest how these diseases could be understood better in a Singapore context which is still applicable to research in AR globally.
Key words: Allergic rhinitis; Atopy; Genetic predisposition; Singapore Chinese
INTRODUCTION
Allergic diseases represent a major health problem in the
21st century accounting for nearly one-fourth of the world’s
population. Allergic Rhinitis (AR) individually affects nearly 10-
25% of the world population and the “Allergic rhinitis and its
impact on asthma (ARIA) 2008 update” document states that
over 600 million patients from all countries, all ethnic groups
and of all ages suffer from AR [1, 2]. The prevalence of AR in
Singapore is about 13.1%, but this is mostly represented by
perennial rhinitis, as the most common allergen found in our
city-state is the house dust mite - which is present throughout
the year [3, 4]. AR though classically not a life threatening disease
has significant influence on the quality of life of both children
and adults. Along with asthma, AR forms the two major diseases
affecting children worldwide. Nearly 40% of children having
Correspondence: De Yun Wang
Department of Otolaryngology, Yong Loo Lin School of
Medicine, National University of Singapore, Singapore
119228, Singapore
Tel: +65-6772-5373
Fax: +65-6775-3820
E-mail: entwdy@nus.edu.sg
Received: September 1, 2011
Accepted: September 8, 2011
The study was supported by grants from the Singapore Immunology
Network (SIgN-06-006 and SIgN-08-020); National Medical Research Council
(NMRC/1150/2008), Singapore; and National University of Singapore (NUS)
for the Graduate Research Scholarship for students involved in the study. The
funders had no role in study design, data collection and analysis, decision to
publish, or preparation of the manuscript.
This is an Open Access article distributed under the terms of the Creative
Commons Attribution. Non-Commercial License (http://creativecommons.
org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use,
distribution, and reproduction in any medium, provided the original work is
properly cited.
Copyright © 2011. Asia Pacific Association of Allergy, Asthma and Clinical Immunology.
http://apallergy.org

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AR develop asthma, whereas close to 80% of asthmatic children
have AR [5]. Hence from an asthma management perspective,
concomitant AR should be assessed, evaluated, and managed as
well [6].
AR is defined as an IgE-mediated nasal allergic disorder caused
by exposure to allergens, both perennial and seasonal, which
exist in our indoor and outdoor environments. It is characterized
by symptoms such as rhinorrhea, sneezing, itching and nasal
blockage, which are experienced even when the individual is not
suffering from a cold or influenza-like diseases [1, 7]. AR, asthma
and other allergic diseases have been shown to be a result of
complex interactions between genetic- and environmental-factors
[8-10]. A series of genetic studies in the Singapore population has
identified possible candidate genes or loci associated with asthma
and AR along multiple chromosomes (Table 1). However many of
these candidate-gene based studies have resulted in no significant
association with AR. In this review we focus mainly on evaluating
the genetic basis of AR in the Singapore Chinese population.
Genetics of allergic rhinitis
Many candidate genes for AR have been identified over the past
decade as summarized by Dávila et al. [11], which describes the
various chromosomes and the corresponding genes which might
be implicated in AR. Another review by Vercelli [8], summarizes the
susceptibility genes for asthma and allergy, and in particular, those
that have been successfully replicated in multiple independent
populations. A striking observation from this review is that not
many candidates were successfully replicated when tested by
other research groups in different populations (and occasionally
even in similar populations). This observation could also be made
by surveying the literature for replicating genetic association
studies from different independent populations [8, 12-14].
Genome-wide association studies (GWAS) is a rapid way of
identifying candidate single nucleotide polymorphisms (SNPs)
and/or genes associated to complex diseases, and has seen some
success in identifying potential novel allergy-associated candidate
[15-19]. Nevertheless, the heritability accounted for by all these
genes put together clearly reveals a great amount of unaccounted
or ‘missing heritability’ [20, 21].
Applicability of the HapMap Chinese database for Singapore
Chinese
The HapMap project has been a great resource for genetic
association studies. In Phase I of the project (2004), SNP variations
of 270 samples from four reference populations with diverse
geographic ancestry were obtained: 30 trios (mother, father, and
adult child) from the Yoruba population in Ibadan, Nigeria; 30 trios
from the Centre d’Etude du Polymorphisme Humain collection
of Utah residents of Northern and Western European ancestry; 45
unrelated Han Chinese in Beijing (CHB); and 45 unrelated Japanese
in Tokyo. Our research group evaluated the applicability of this data
from the CHB population to our Singapore Chinese population. We
used two main approaches to evaluate this. (1) A genome-wide
comparison of SNPs genotypes from the Hapmap SNP database
for CHB population to the genotypes of the Singapore Chinese [22,
23], and (2) selected re-sequencing of 20 candidate genes on the
5q31-33 region in our Singapore Chinese population [24]. Although
we identified novel SNPs in our population, close to 75% of all
SNPs identified through resequencing could be tagged by SNPs
from the Hapmap CHB data [24]. Thus, both approaches clearly
demonstrated that we could generally use the Hapmap CHB as a
reference population for the Singapore Chinese population. The
Table 1. Candidate gene/region identified through genetic studies for allergies in Singapore
Type of studySingapore population studied
Candidate
gene/region
5q31-33
TLR4
CD14
IL4
IL18
Beta-2 adrenergic receptor
UGRP1
BDNF
19p13.2 and 10q24.2
Association
detected
Yes
No
No
Yes
No
No
Yes
Yes
Yes
Reference
Family based linkage
Case control association
Case control association
Case control association
Case control association
Case control association
Case control association
Case control association
Case control genome-wide association
Chinese
Chinese
Chinese
[27]
[28]
[29]
Chinese, Malays and Indians
Chinese, Malays and Indians
Chinese, Malays and Indians
Chinese
Chinese
Chinese
[unpublished data]
[30]
[unpublished data]
[25]
[26]
[19]

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recent completion of Phase III of the Hapmap project contains
genotypes from 11 different populations for over 1.5 million
genetic variations in 1,115 individuals. This expanded dataset could
serve as a better reference than the 4 main HapMap populations
in Phase I when designing genetic association studies.
Genetics of allergic rhinitis in Singapore Chinese
After the completion of the Hapmap project, genetic
association studies could be designed using the Hapmap
reference populations to identify tagSNPs to represent all SNPs
in a particular gene. TagSNPs are generally marked or tagged
variants which are in strong linkage (usually r2 > 0.8) with other
variants in the gene. Hence to save cost, it is possible to genotype
only these tagSNPs in a gene which would help in identifying the
position of association in this particular gene, which can then be
biologically characterized to understand how it influences disease
predisposition.
Candidate gene studies
Many genetic association studies have been carried out in the
Singapore Chinese population to test the association of potential
candidate genes to AR (Table 1). Disappointingly, most of the early
results turned out not associated to AR. Replication of a locus
identified from a genome-wide linkage study for asthma and
allergies also yielded negative results (data not shown). However
these results might be due to the small sample sizes. Hence the
power of these genetic association studies is quite low which
suggests that these candidate genes might actually be involved
in the disease but that the studies were underpowered to detect
statistical significance.
Recently we have worked on validating the association of
known candidate genes for AR in a larger population. For example,
we evaluated the association of UGRP1 gene to AR in our cohort
with 795 AR cases and 717 healthy controls with no medical
history of allergy. We identified association of the 5’ upstream SNP
rs7726552 to AR with a protective odds ratio of 0.81 for the minor
T allele [25]. Similarly, we tested the association of SNPs in BDNF
gene for AR in the Singapore Chinese population. We identified
a SNP rs10767664 to be associated with AR with an odds ratio of
1.304 [26]. Interestingly, this SNP was in very strong LD (D’ = 1 and
r2 = 0.95) with rs6265 which a non-synonymous mutation which
results into an amino acid change from Val to Met and is referred
to as Val66Met. Our group is currently characterizing these along
with other significant SNPs to evaluate their role in conferring
genetic predisposition to allergic diseases and tease out the
potential mechanism and pathogenesis of AR.
GWAS
GWAS have been important in identifying many allergy
candidate genes for asthma and atopic dermatitis (AD). A
schematic of a typical genome wide association study design has
been briefly summarized in Fig. 1. We have recently published
the first GWAS on AR using the Singapore Chinese population.
Although GWAS performed for asthma and AD are important for
AR, we wanted to identify in a hypothesis-free manner the genetic
variants associated with AR in a Singapore Chinese population
consisting of 456 AR patients and 486 controls [19]. We then
replicated the top findings with the highest observed p values in
an independent population. The replication population consisted
of 676 AR patients and 511 controls from a Singapore Chinese
cohort collected in the same manner as the discovery cohort.
We had identified 2 SNPs (rs8111930, rs505010) which remained
significant in the replication population. Currently, our group
is working on characterizing these variants and identifying the
mechanism by which these genes predispose individuals to AR.
Sample collection
Sample ascertainment for disease status
GWAS
Identifcation of potential candidate SNPs
Targeted genotyping of the candidate SNPs
Validation of susceptibility genes
Functional studies
Role of gene(s) in disease mechanism(s)
Fig. 1. Flowchart for a genome-wide association study (GWAS) design.
SNPs: single nucleotide polymorphisms.

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Relevance of identifying genes predisposing to both AR and
asthma
Using our GWAS data we also replicated previously identified
SNPs through asthma GWAS in our population for both atopy and
AR phenotype [19]. SNPs from HLA-DQB1, HLA-DRB1, GRIN2B,
ACO1, HLA-DQA2, CA10, FAM82A, HIVEP3, SMAD2, PIP-3E and
NPSR1 were shown to be associated to atopy and AR albeit not
reaching the genome-wide threshold of 5 × 10-8. The previous
article mentioned which we identified association of BDNF SNPs
to AR and we have shown that the same tagSNP rs10767664 is also
associated with the atopic asthma at an OR = 1.3. Taken together
with other unpublished data from our group we are gaining more
evidence towards the hypothesis that asthma and AR could have
common SNPs/genes which might regulate their predisposition to
allergic disease.
CONCLUSION
Genetic studies in Singapore Chinese for AR and also to large
extent asthma show a similar trend in that a wide range of allergy
candidate genes were not found to be significantly associated to
disease even when tested on a larger population. There might be
two main reasons for these negative results: (1) gene-gene and (2)
gene-environment interactions.
Epistasis or gene-gene interaction is the masking effect of one
gene by another and hence when one considers a single gene/
SNP at a time, the association may not be observed statistically
[20, 21]. In other cases, it might be true that because complex
diseases are influenced by many SNPs - all with small effect
sizes individually, one may need to analyze them together using
models like Generalized Multifactor Dimensionality Reduction or
synergistic regression methods to identify significant associations
with disease phenotype. We have observed such interactions to
be significant for AR in our Singapore Chinese population. Gene-
environment interactions are another possible cause for the
negative association results in allergic disease research. Allergic
diseases result from a complex interplay between genes and the
environment as well as the age at which the exposure occurs [8,
9]. Future studies need to focus on using larger samples sizes to
detect the effect of gene-gene interactions and the role of the
environment in the expression of disease. As large sample sizes
are needed, it is imperative that research groups and consortiums
come together to help understand allergy better. Care, however,
should be taken to address the heterogeneity of such analysis;
such as controlling for ethnicity, environment, age and gender of
the volunteers used in the study.
ACKNOWLEDGEMENTS
The author would like to thank all the volunteers and their family
members who participated in this study and Dr. Chew Fook Tim
and Anand Kumar Andiappan for their suggestions in preparing
the manuscript.
The study was supported by grants from the Singapore
Immunology Network (SIgN-06-006 and SIgN-08-020); National
Medical Research Council (NMRC/1150/2008), Singapore; and
National University of Singapore (NUS) for the Graduate Research
Scholarship for students involved in the study. The funders had
no role in study design, data collection and analysis, decision to
publish, or preparation of the manuscript.
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