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detected sequences have a biological function. Here, the main question is whether or not TEs within or in the vicinity of asthma susceptible genes modulate the gene expression of these genes. This can be performed using cap-analysis gene expression, a method that specifically and unequivocally identifies the exact transcription start sites of genes [6]. Once the regulated retrotransposon transcriptome of healthy tissue is known, it can be compared with that of asthma patients or additional complex diseases. This will provide unprecedented details about genes and gene expression patterns, and how they relate to the development and/or establishment of complex diseases. The impact of TEs on phenotype (variation) and disease are depicted in figure 1. With the advent of next generation sequencing and rapid genome and transcriptome analyses, the dynamic nature of TEs and their role in shaping intra-and inter-individual variation may soon be resolved. Because these developments will dissect TE-induced variation at ever increasing resolution, they will lead to a better understanding of TEs and their overall impact on gene expression, human health and the (epi)genetic constitution that underlies complex lung diseases, including asthma. We have already identified the number, position and type of TEs present in the 12 aforementioned asthma-associated genes and we are in the process of screening the same panel of genes in asthma patients. It may well be that some phenotypes of asthma are predominantly associated with TE-regulated genes of the immunological compartment, whereas other phenotypes of asthma are linked to a specific set of TE-regulated genes in lung tissue cells. Therefore, cell-and phenotype-specific understanding of the healthy and diseased transcriptomes may lead to better treatment and to personalised medicine. We would like to encourage pulmonary scientists to further examine the almost entirely unexplored TE field, which integrates clinics, the laboratory and bioinformatics. The development of entire novel strategies to treat complex lung diseases should be envisaged.

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