The majority of studies on genetics of complex traits to date have been based on microsatellite marker (synonym, short tandem repeat polymorphisms [STRP]) analyses. These genetic markers (whose biological function is as yet unknown) typically contain a variable number of tandem repeats of dinucleotide, trinucleotide or tetranucleotide DNA sequences (e.g. the tetranucleotide [TATA]_n). The high degree of polymorphism results in great variation between individuals. Short tandem repeat polymorphisms of known location are found densely spaced throughout the genome and are used for genome-wide searches as well as for the analysis of candidate gene regions.

Most studies on the genetics of asthma are based on allele sharing methods, transmission disequilibrium test (TDT) analysis, or tests for associations. The allele sharing methods approach involves testing how often a genetic marker (or a chromosomal region) is shared by affected pedigree members. If allele sharing occurs significantly more often than expected by chance, linkage of the particular marker and disease can be assumed, indicating that the chromosomal region containing the genetic marker also contains a gene that contributes to disease expression.

The TDT approach is based on genotype analysis of affected subjects (no siblings are required) and their parents. The TDT tests whether genetic marker alleles from heterozygous parents are transmitted as frequently as expected by chance (by random, each parental allele is transmitted with a chance of 50%). Overtransmission of a particular marker allele indicates linkage of this allele with the respective 'disease' allele.

Association studies are usually applied once polymorphisms in candidate genes for asthma/atopy have been identified.

Results from linkage studies (genome-wide searches and candidate gene region analyses) are summarized in Supplementary Tables 1 and 2 (see also [10,11,12,13]). Multiple chromosomal regions were related to asthma and atopy. Few regions, however, have shown evidence for linkage in more than one population (Supplementary Table 2), which may be due to racial differences, to different definition of phenotypes, or (most probably) to insufficient numbers of affected sib-pairs in different study populations. The first successful attempts have been made to pool data from genetic studies of asthma and atopy in order to analyze major candidate gene regions [14,15].

Despite the high degree of inconsistent findings, it is intriguing that chromosomal regions linked to asthma have also shown evidence for linkage to other inflammatory and autoimmune diseases (such as psoriasis, inflammatory bowel disease, type I diabetes and multiple sclerosis). Becker et al. noted that susceptibility genes for various autoimmune and inflammatory diseases (including asthma) appear to cluster in 18 distinct chromosomal regions, implying common genetic elements in inflammatory disorders [16]. This speculation is further supported by two recent genome-wide searches for AD susceptibility genes. Regions linked to AD (Supplementary Table 1) have also been linked to psoriasis in other studies [17,18], suggesting that common genetic elements are involved in dermal inflammatory disorders.

Multiple genes are involved in the allergic inflammation (shown in Supplementary Figure 1). Multiple single nucleotide polymorphisms (SNPs) in candidate genes for asthma and atopy have been identified, and they are presented in Supplementary Table 3. The (often conflicting) results have to be interpreted with caution, since multiple genotypes are commonly tested for a large number of atopy-related (sub)phenotypes (using various statistical approaches) in often considerably small sample sizes. Therefore, type 1 errors (false-positive results) are likely to occur. In addition, publication favors positive results and, therefore, many negative studies have not been published.

Many SNPs listed in Supplementary Table 3 have been tested for functional differences in vitro. However, when several (potentially) functional SNPs are expressed in one (regulatory region of a) gene (e.g. IL-4Rα, IL-13, beta-2 adrenergic receptor [β₂AR]), they are likely to interact. The individual analysis of SNPs may therefore not reflect in vivo gene function, as a recent study on β₂AR haplotypes demonstrated (see 'β₂-agonists' subsection). (Note: a haplotype is a particular combination of alleles in a defined region of a chromosome. It is used to describe combinations of polymorphisms in a gene/chromosomal area.) In vitro differences in gene expression or function due to SNPs therefore have to be interpreted with caution when several other polymorphisms within the same gene may also alter functionality in vitro and in vivo. This notion may explain some of the controversial findings with regard to associations of individual SNPs in polymorphic genes (e.g. IL-4Rα).

The importance of haplotype analysis is further supported by the following studies. Seven SNPs in the IL-13 gene have been shown to be tightly linked [19], and therefore association studies of individual SNPs with the assumption of independent inheritance cannot easily be performed. Also, several SNPs within the IL-4Rα gene have been identified (see Supplementary Table 3). An association of two individual SNPs (S503P and Q576R) with decreased serum IgE levels was observed in a Caucasian population; however, most significant results with regard to low IgE levels were seen when both SNPs occurred together [20].

Similarly, Ober et al. performed TDT analysis for IL-4Rα SNPs and haplotypes in four populations. Again, the strongest evidence for linkage to asthma and/or atopy was observed with two-locus haplotype analysis [21].

A marked disparity in treatment response to pharmacotherapy is observed in asthma (as well as in many other diseases). Variations in genes encoding proteins that interact with specific drugs or drug metabolism are likely to contribute to variability in treatment response. The best examined gene with regard to pharmacogenetics is the gene encoding the enzyme cytochrome p450, for which various alterations that affect the metabolism of multiple drugs have been described. Gene chips for the determination of p450 alleles are commercially available in Sweden and North America (reviewed in [23]).

Pharmacotherapy of asthma and atopy comprises β-agonists, corticosteroids, anti-histamines (H1-receptor antagonists) and leukotriene (receptor) antagonists. The following pharmacogenetic studies have been performed.

Apart from pharmacogenetic studies, the analysis of gene–environment interactions to date is hypothesis driven. The difficulties in quantifying and characterizing environmental risk factors for atopy (including onset and length of period of exposure) make these studies a challenge. Very high numbers of affected and unaffected subjects carefully characterized (longitudinally) for both the environmental setting and disease expression may be required to test for interactions between genetic variants and non-genetic influences.

However, recent genetic studies support the 'hygiene hypothesis', which postulates that atopy may be the result of a misdirected immune response in the absence of infection.

First, resistance to Schistosoma mansoni [31] and Plasmodium falciparum blood levels [32] (two independent studies) were linked to chromosome 5q31-33, a region (containing the IL-4 cytokine gene cluster) that has shown strong evidence for linkage to atopy-associated traits. Furthermore, a major locus closely linked to the interferon-γ receptor gene appears to control the switch from a T helper 2 to a T helper 1 cytokine profile during S. mansoni infection [33,34].

Second, SNPs within the FcεRI-β gene have been related to increased total serum IgE levels in heavily parasitized Australian aborigines, indicating a protective role in parasitic infection [35]. These SNPs have also been related to asthma, bronchial hyperresponsiveness, AD and atopy (see Supplementary Table 3). FcεRI-β maps to 11q13, a region that showed evidence for linkage to asthma and associated traits in multiple studies (Supplementary Table 3).

Finally, a polymorphism in the β₂AR encoding gene (Arg16) that has been related to asthma (see Supplementary Table 3) was also associated with higher levels of parasitic infection [36].