A genomewide study of copy-number variation previously reported that copy-number at TCRγ
is associated with childhood allergic asthma.[23
] This study genotyped samples on the Illumina HumanHap550 BeadChip and intensity data from the 550,000 genotyped SNPs were used to infer copy-number at each position. Their data indicated that asthmatics had reduced copy-number at TCRγ
compared to healthy parents, and that detected CNVs appeared to be somatic events.[32
] In our study, individuals with childhood allergic asthma had significantly lower copy-number values at TCRγ
than controls, while values did not significantly differ between cases and controls at TCRα
. Our results support the association between childhood allergic asthma and reduced copy-number at the T-cell receptor gamma gene.
Two defining features of chronic asthma are airway hyperresponsiveness and airway inflammation.[34
] In humans, CD8+ T cells that bear the αβ T-cell receptor typically have pro-inflammatory effects, whereas CD8+ T cells bearing the γδ T-cell receptor can inhibit inflammation.[27
] This finding has led to the hypothesis that defective or altered γδ T-cell function may contribute to development of an allergic asthma phenotype.[25
] We did not seek to genotype the TCR delta gene (TCRδ
) because it is located within the telomeric end of the TCRα
locus and variation at this position could influence expression of either gene, making results difficult to interpret.
Our results indicate that children with allergic asthma do appear to have reduced copy-number at TCRγ
compared to non-asthmatic controls, reflecting somatic copy-number differences in a mosaic cell population. Interestingly, γδ T-cells are unique among T-cells in that they have anti-inflammatory effects.[35
] Because these are somatic mutations, we can not determine if these CNVs are a cause of allergic asthma, or if instead they represent an immunologic response to the disease. Our study of CNVs at TCR genes utilized DNA derived from buccal cells and demonstrates that these somatic events are not limited to blood-derived DNA. As the buccal mucosa contains leukocytes, including αβ and γδ T-cells [36
], it is not surprising that the somatic events observed in blood-derived DNA are also observed in DNA from buccal swabs.
Because this genomic region undergoes somatic rearrangement in T-cells,[37
] the association observed by Ionita-Laza, et al. may reflect inter-individual variation in the proportion of somatically rearranged cells among all white blood cells, rather than germline copy number variation. Although the DNA samples used in our study were obtained from buccal swabs and not from blood-derived DNA, genetic mosaicism can still exist in these cell populations. Therefore, calculated copy-number values were not classified into discrete copy-number classes in the primary analysis. Continuous copy-number values represent the average copy-number within a mosaic cell population.
The primary statistical test utilized in this study to compare copy-number values between cases and controls was the Mann-Whitney U test. This test statistic is most appropriate because it can identify significant differences in copy-number between two groups without imposing discrete copy-number values on the samples (e.g. 1 copy, 2 copies, 3 copies). In the presence of genetic mosaicism, discrete copy-number classes would not reflect the underlying biological phenomenon in which some cells are copy-number variable and others copy-neutral, resulting in an intermediate copy-number value. Because the copy-number values should vary around whole numbers, with increased variability reflecting greater levels of mosaicism, an assumption of normality cannot be made and a non-parametric test is appropriate.
The significant correlations observed between copy-number at various T-cell receptor genes may be the result of similar recombinogenic events occurring at these loci in a given individual. Another possibility is that this correlation reflects the level of genetic mosaicism in the cell population, regardless of the underlying copy-number. For instance, an individual with a mosaic deletion of one TCR gene and a mosaic duplication of another TCR gene may have correlated copy-number values at these two positions simply because their buccal cell population has remained largely wild-type, thus pushing the average copy-number of each gene closer to two. Thus, correlation could exist due to an individual’s underlying level of mosaicism, without two genes having undergone similar recombination events.
A recent study of somatic CNVs in peripheral-blood-derived DNA identified genomic regions which had discordant CNV profiles within monozygotic twin-pairs.[38
] Somatic mosaicism for pathogenic mutations may be more common than previously thought, and is currently not well-studied outside of cancer epidemiology. Our study joins studies of cancer, and a study phobic disorders,[39
] in implicating a role for somatically mosaic copy-number variants in disease etiology.
Further work is needed in order to resolve whether reduced copy-number at TCRγ predisposes individuals to asthma, or whether CNVs at this position arise as a result of the disease. If these somatic mutations do arise as a result of the disease, it will be valuable to determine if this is a coincidental marker of the asthma phenotype, or if deletion of this gene is a somatic response intended to alter disease progression or severity through establishment of a cell population which is mosaic for TCRγ copy-number.